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llmeval-env/lib/python3.10/site-packages/accelerate/utils/dataclasses.py
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|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
"""
|
16 |
+
General namespace and dataclass related classes
|
17 |
+
"""
|
18 |
+
|
19 |
+
import argparse
|
20 |
+
import copy
|
21 |
+
import enum
|
22 |
+
import functools
|
23 |
+
import os
|
24 |
+
import typing
|
25 |
+
import warnings
|
26 |
+
from contextlib import contextmanager
|
27 |
+
from dataclasses import dataclass, field
|
28 |
+
from datetime import timedelta
|
29 |
+
from typing import Any, Callable, Dict, Iterable, List, Literal, Optional, Tuple, get_args
|
30 |
+
|
31 |
+
import torch
|
32 |
+
|
33 |
+
from .constants import FSDP_AUTO_WRAP_POLICY, FSDP_BACKWARD_PREFETCH, FSDP_SHARDING_STRATEGY, FSDP_STATE_DICT_TYPE
|
34 |
+
from .environment import str_to_bool
|
35 |
+
from .imports import is_cuda_available, is_npu_available, is_xpu_available
|
36 |
+
from .versions import compare_versions
|
37 |
+
|
38 |
+
|
39 |
+
class KwargsHandler:
|
40 |
+
"""
|
41 |
+
Internal mixin that implements a `to_kwargs()` method for a dataclass.
|
42 |
+
"""
|
43 |
+
|
44 |
+
def to_dict(self):
|
45 |
+
return copy.deepcopy(self.__dict__)
|
46 |
+
|
47 |
+
def to_kwargs(self):
|
48 |
+
"""
|
49 |
+
Returns a dictionary containing the attributes with values different from the default of this class.
|
50 |
+
"""
|
51 |
+
# import clear_environment here to avoid circular import problem
|
52 |
+
from .other import clear_environment
|
53 |
+
|
54 |
+
with clear_environment():
|
55 |
+
default_dict = self.__class__().to_dict()
|
56 |
+
this_dict = self.to_dict()
|
57 |
+
return {k: v for k, v in this_dict.items() if default_dict[k] != v}
|
58 |
+
|
59 |
+
|
60 |
+
@dataclass
|
61 |
+
class AutocastKwargs(KwargsHandler):
|
62 |
+
"""
|
63 |
+
Use this object in your [`Accelerator`] to customize how `torch.autocast` behaves. Please refer to the
|
64 |
+
documentation of this [context manager](https://pytorch.org/docs/stable/amp.html#torch.autocast) for more
|
65 |
+
information on each argument.
|
66 |
+
|
67 |
+
Example:
|
68 |
+
|
69 |
+
```python
|
70 |
+
from accelerate import Accelerator
|
71 |
+
from accelerate.utils import AutocastKwargs
|
72 |
+
|
73 |
+
kwargs = AutocastKwargs(cache_enabled=True)
|
74 |
+
accelerator = Accelerator(kwargs_handlers=[kwargs])
|
75 |
+
```
|
76 |
+
"""
|
77 |
+
|
78 |
+
enabled: bool = True
|
79 |
+
cache_enabled: bool = None
|
80 |
+
|
81 |
+
|
82 |
+
@dataclass
|
83 |
+
class DistributedDataParallelKwargs(KwargsHandler):
|
84 |
+
"""
|
85 |
+
Use this object in your [`Accelerator`] to customize how your model is wrapped in a
|
86 |
+
`torch.nn.parallel.DistributedDataParallel`. Please refer to the documentation of this
|
87 |
+
[wrapper](https://pytorch.org/docs/stable/generated/torch.nn.parallel.DistributedDataParallel.html) for more
|
88 |
+
information on each argument.
|
89 |
+
|
90 |
+
<Tip warning={true}>
|
91 |
+
|
92 |
+
`gradient_as_bucket_view` is only available in PyTorch 1.7.0 and later versions.
|
93 |
+
|
94 |
+
`static_graph` is only available in PyTorch 1.11.0 and later versions.
|
95 |
+
|
96 |
+
</Tip>
|
97 |
+
|
98 |
+
Example:
|
99 |
+
|
100 |
+
```python
|
101 |
+
from accelerate import Accelerator
|
102 |
+
from accelerate.utils import DistributedDataParallelKwargs
|
103 |
+
|
104 |
+
kwargs = DistributedDataParallelKwargs(find_unused_parameters=True)
|
105 |
+
accelerator = Accelerator(kwargs_handlers=[kwargs])
|
106 |
+
```
|
107 |
+
"""
|
108 |
+
|
109 |
+
dim: int = 0
|
110 |
+
broadcast_buffers: bool = True
|
111 |
+
bucket_cap_mb: int = 25
|
112 |
+
find_unused_parameters: bool = False
|
113 |
+
check_reduction: bool = False
|
114 |
+
gradient_as_bucket_view: bool = False
|
115 |
+
static_graph: bool = False
|
116 |
+
|
117 |
+
|
118 |
+
@dataclass
|
119 |
+
class GradScalerKwargs(KwargsHandler):
|
120 |
+
"""
|
121 |
+
Use this object in your [`Accelerator`] to customize the behavior of mixed precision, specifically how the
|
122 |
+
`torch.cuda.amp.GradScaler` used is created. Please refer to the documentation of this
|
123 |
+
[scaler](https://pytorch.org/docs/stable/amp.html?highlight=gradscaler) for more information on each argument.
|
124 |
+
|
125 |
+
<Tip warning={true}>
|
126 |
+
|
127 |
+
`GradScaler` is only available in PyTorch 1.5.0 and later versions.
|
128 |
+
|
129 |
+
</Tip>
|
130 |
+
|
131 |
+
Example:
|
132 |
+
|
133 |
+
```python
|
134 |
+
from accelerate import Accelerator
|
135 |
+
from accelerate.utils import GradScalerKwargs
|
136 |
+
|
137 |
+
kwargs = GradScalerKwargs(backoff_filter=0.25)
|
138 |
+
accelerator = Accelerator(kwargs_handlers=[kwargs])
|
139 |
+
```
|
140 |
+
"""
|
141 |
+
|
142 |
+
init_scale: float = 65536.0
|
143 |
+
growth_factor: float = 2.0
|
144 |
+
backoff_factor: float = 0.5
|
145 |
+
growth_interval: int = 2000
|
146 |
+
enabled: bool = True
|
147 |
+
|
148 |
+
|
149 |
+
@dataclass
|
150 |
+
class InitProcessGroupKwargs(KwargsHandler):
|
151 |
+
"""
|
152 |
+
Use this object in your [`Accelerator`] to customize the initialization of the distributed processes. Please refer
|
153 |
+
to the documentation of this
|
154 |
+
[method](https://pytorch.org/docs/stable/distributed.html#torch.distributed.init_process_group) for more
|
155 |
+
information on each argument.
|
156 |
+
|
157 |
+
```python
|
158 |
+
from datetime import timedelta
|
159 |
+
from accelerate import Accelerator
|
160 |
+
from accelerate.utils import InitProcessGroupKwargs
|
161 |
+
|
162 |
+
kwargs = InitProcessGroupKwargs(timeout=timedelta(seconds=800))
|
163 |
+
accelerator = Accelerator(kwargs_handlers=[kwargs])
|
164 |
+
```
|
165 |
+
"""
|
166 |
+
|
167 |
+
backend: Optional[str] = "nccl"
|
168 |
+
init_method: Optional[str] = None
|
169 |
+
timeout: timedelta = timedelta(seconds=1800)
|
170 |
+
|
171 |
+
|
172 |
+
# Literals
|
173 |
+
Backend = Literal["MSAMP", "TE"]
|
174 |
+
OptLevel = Literal["O1", "O2"]
|
175 |
+
FP8Format = Literal["E4M3", "HYBRID"]
|
176 |
+
AmaxComputeAlgorithm = Literal["max", "most_recent"]
|
177 |
+
|
178 |
+
|
179 |
+
@dataclass
|
180 |
+
class FP8RecipeKwargs(KwargsHandler):
|
181 |
+
"""
|
182 |
+
Use this object in your [`Accelerator`] to customize the initialization of the recipe for FP8 mixed precision
|
183 |
+
training with `transformer-engine` or `ms-amp`.
|
184 |
+
|
185 |
+
<Tip>
|
186 |
+
|
187 |
+
For more information on `transformer-engine` args, please refer to the API
|
188 |
+
[documentation](https://docs.nvidia.com/deeplearning/transformer-engine/user-guide/api/common.html).
|
189 |
+
|
190 |
+
For more information on the `ms-amp` args, please refer to the Optimization Level
|
191 |
+
[documentation](https://azure.github.io/MS-AMP/docs/user-tutorial/optimization-level).
|
192 |
+
|
193 |
+
</Tip>
|
194 |
+
|
195 |
+
```python
|
196 |
+
from accelerate import Accelerator
|
197 |
+
from accelerate.utils import FP8RecipeKwargs
|
198 |
+
|
199 |
+
kwargs = FP8RecipeKwargs(backend="te", fp8_format="HYBRID")
|
200 |
+
accelerator = Accelerator(mixed_precision="fp8", kwargs_handlers=[kwargs])
|
201 |
+
```
|
202 |
+
|
203 |
+
To use MS-AMP as an engine, pass `backend="msamp"` and the `optimization_level`:
|
204 |
+
|
205 |
+
```python
|
206 |
+
kwargs = FP8RecipeKwargs(backend="msamp", optimization_level="02")
|
207 |
+
```
|
208 |
+
|
209 |
+
Args:
|
210 |
+
backend (`str`, *optional*, defaults to "msamp"):
|
211 |
+
Which FP8 engine to use. Must be one of `"msamp"` (MS-AMP) or `"te"` (TransformerEngine).
|
212 |
+
margin (`int`, *optional*, default to 0):
|
213 |
+
The margin to use for the gradient scaling.
|
214 |
+
interval (`int`, *optional*, default to 1):
|
215 |
+
The interval to use for how often the scaling factor is recomputed.
|
216 |
+
fp8_format (`str`, *optional*, default to "E4M3"):
|
217 |
+
The format to use for the FP8 recipe. Must be one of `E4M3` or `HYBRID`.
|
218 |
+
amax_history_len (`int`, *optional*, default to 1024):
|
219 |
+
The length of the history to use for the scaling factor computation
|
220 |
+
amax_compute_algo (`str`, *optional*, default to "most_recent"):
|
221 |
+
The algorithm to use for the scaling factor computation. Must be one of `max` or `most_recent`.
|
222 |
+
override_linear_precision (`tuple` of three `bool`, *optional*, default to `(False, False, False)`):
|
223 |
+
Whether or not to execute `fprop`, `dgrad`, and `wgrad` GEMMS in higher precision.
|
224 |
+
optimization_level (`str`), one of `O1`, `O2`. (default is `O2`):
|
225 |
+
What level of 8-bit collective communication should be used with MS-AMP. In general:
|
226 |
+
* O1: Weight gradients and `all_reduce` communications are done in fp8, reducing GPU
|
227 |
+
memory usage and communication bandwidth
|
228 |
+
* O2: First-order optimizer states are in 8-bit, and second order states are in FP16.
|
229 |
+
Only available when using Adam or AdamW. This maintains accuracy and can potentially save the
|
230 |
+
highest memory.
|
231 |
+
* 03: Specifically for DeepSpeed, implements capabilities so weights and master weights of models
|
232 |
+
are stored in FP8. If `fp8` is selected and deepspeed is enabled, will be used by default. (Not
|
233 |
+
available currently).
|
234 |
+
"""
|
235 |
+
|
236 |
+
backend: Backend = "MSAMP"
|
237 |
+
opt_level: OptLevel = "O2"
|
238 |
+
margin: int = 0
|
239 |
+
interval: int = 1
|
240 |
+
fp8_format: FP8Format = "E4M3"
|
241 |
+
amax_history_len: int = 1
|
242 |
+
amax_compute_algo: AmaxComputeAlgorithm = "most_recent"
|
243 |
+
override_linear_precision: Tuple[bool, bool, bool] = (False, False, False)
|
244 |
+
|
245 |
+
def __post_init__(self):
|
246 |
+
if self.backend.upper() not in get_args(Backend):
|
247 |
+
raise ValueError("`backend` must be 'MSAMP' or 'TE' (TransformerEngine).")
|
248 |
+
|
249 |
+
self.backend = self.backend.upper()
|
250 |
+
# Check TE args
|
251 |
+
if self.backend == "TE":
|
252 |
+
self.fp8_format = self.fp8_format.upper()
|
253 |
+
if self.fp8_format not in get_args(FP8Format):
|
254 |
+
raise ValueError(f"`fp8_format` must be one of {' or '.join(get_args(FP8Format))}.")
|
255 |
+
if self.amax_compute_algo not in get_args(AmaxComputeAlgorithm):
|
256 |
+
raise ValueError(f"`amax_compute_algo` must be one of {' or '.join(get_args(AmaxComputeAlgorithm))}")
|
257 |
+
elif self.backend == "MSAMP":
|
258 |
+
if self.opt_level not in get_args(OptLevel):
|
259 |
+
raise ValueError(f"`optimization_level` must be one of {' or '.join(get_args(OptLevel))}")
|
260 |
+
|
261 |
+
|
262 |
+
class EnumWithContains(enum.EnumMeta):
|
263 |
+
"A metaclass that adds the ability to check if `self` contains an item with the `in` operator"
|
264 |
+
|
265 |
+
def __contains__(cls, item):
|
266 |
+
try:
|
267 |
+
cls(item)
|
268 |
+
except ValueError:
|
269 |
+
return False
|
270 |
+
return True
|
271 |
+
|
272 |
+
|
273 |
+
class BaseEnum(enum.Enum, metaclass=EnumWithContains):
|
274 |
+
"An enum class that can get the value of an item with `str(Enum.key)`"
|
275 |
+
|
276 |
+
def __str__(self):
|
277 |
+
return self.value
|
278 |
+
|
279 |
+
@classmethod
|
280 |
+
def list(cls):
|
281 |
+
"Method to list all the possible items in `cls`"
|
282 |
+
return list(map(str, cls))
|
283 |
+
|
284 |
+
|
285 |
+
class DeprecatedFieldDescriptor:
|
286 |
+
"""
|
287 |
+
Descriptor for deprecated fields in an enum class.
|
288 |
+
|
289 |
+
Args:
|
290 |
+
field_name (`str`):
|
291 |
+
The name of the deprecated field.
|
292 |
+
replaced_with (`str`):
|
293 |
+
The name of the field that replaces the deprecated one.
|
294 |
+
"""
|
295 |
+
|
296 |
+
def __init__(self, field_name, replaced_with):
|
297 |
+
self.field_name = field_name
|
298 |
+
self.replaced_with = replaced_with
|
299 |
+
|
300 |
+
def __get__(self, instance, owner):
|
301 |
+
warnings.warn(
|
302 |
+
f"The `{self.field_name}` of `{owner}` is deprecated and will be removed in v1.0.0. "
|
303 |
+
f"Please use the `{self.replaced_with}` instead.",
|
304 |
+
FutureWarning,
|
305 |
+
)
|
306 |
+
return getattr(owner, self.replaced_with)
|
307 |
+
|
308 |
+
|
309 |
+
class DistributedType(str, enum.Enum):
|
310 |
+
"""
|
311 |
+
Represents a type of distributed environment.
|
312 |
+
|
313 |
+
Values:
|
314 |
+
|
315 |
+
- **NO** -- Not a distributed environment, just a single process.
|
316 |
+
- **MULTI_CPU** -- Distributed on multiple CPU nodes.
|
317 |
+
- **MULTI_GPU** -- Distributed on multiple GPUs.
|
318 |
+
- **MULTI_MLU** -- Distributed on multiple MLUs.
|
319 |
+
- **MULTI_NPU** -- Distributed on multiple NPUs.
|
320 |
+
- **MULTI_XPU** -- Distributed on multiple XPUs.
|
321 |
+
- **DEEPSPEED** -- Using DeepSpeed.
|
322 |
+
- **XLA** -- Using TorchXLA.
|
323 |
+
- **TPU** -- This field will be deprecated in v0.27.0. Use XLA instead.
|
324 |
+
"""
|
325 |
+
|
326 |
+
# Subclassing str as well as Enum allows the `DistributedType` to be JSON-serializable out of the box.
|
327 |
+
NO = "NO"
|
328 |
+
MULTI_CPU = "MULTI_CPU"
|
329 |
+
MULTI_GPU = "MULTI_GPU"
|
330 |
+
MULTI_NPU = "MULTI_NPU"
|
331 |
+
MULTI_MLU = "MULTI_MLU"
|
332 |
+
MULTI_XPU = "MULTI_XPU"
|
333 |
+
DEEPSPEED = "DEEPSPEED"
|
334 |
+
FSDP = "FSDP"
|
335 |
+
XLA = "XLA"
|
336 |
+
MEGATRON_LM = "MEGATRON_LM"
|
337 |
+
TPU = DeprecatedFieldDescriptor("TPU", "XLA")
|
338 |
+
|
339 |
+
|
340 |
+
class SageMakerDistributedType(str, enum.Enum):
|
341 |
+
"""
|
342 |
+
Represents a type of distributed environment.
|
343 |
+
|
344 |
+
Values:
|
345 |
+
|
346 |
+
- **NO** -- Not a distributed environment, just a single process.
|
347 |
+
- **DATA_PARALLEL** -- using sagemaker distributed data parallelism.
|
348 |
+
- **MODEL_PARALLEL** -- using sagemaker distributed model parallelism.
|
349 |
+
"""
|
350 |
+
|
351 |
+
# Subclassing str as well as Enum allows the `SageMakerDistributedType` to be JSON-serializable out of the box.
|
352 |
+
NO = "NO"
|
353 |
+
DATA_PARALLEL = "DATA_PARALLEL"
|
354 |
+
MODEL_PARALLEL = "MODEL_PARALLEL"
|
355 |
+
|
356 |
+
|
357 |
+
class ComputeEnvironment(str, enum.Enum):
|
358 |
+
"""
|
359 |
+
Represents a type of the compute environment.
|
360 |
+
|
361 |
+
Values:
|
362 |
+
|
363 |
+
- **LOCAL_MACHINE** -- private/custom cluster hardware.
|
364 |
+
- **AMAZON_SAGEMAKER** -- Amazon SageMaker as compute environment.
|
365 |
+
"""
|
366 |
+
|
367 |
+
# Subclassing str as well as Enum allows the `ComputeEnvironment` to be JSON-serializable out of the box.
|
368 |
+
LOCAL_MACHINE = "LOCAL_MACHINE"
|
369 |
+
AMAZON_SAGEMAKER = "AMAZON_SAGEMAKER"
|
370 |
+
|
371 |
+
|
372 |
+
class DynamoBackend(str, BaseEnum):
|
373 |
+
"""
|
374 |
+
Represents a dynamo backend (see https://pytorch.org/docs/stable/torch.compiler.html).
|
375 |
+
|
376 |
+
Values:
|
377 |
+
|
378 |
+
- **NO** -- Do not use torch dynamo.
|
379 |
+
- **EAGER** -- Uses PyTorch to run the extracted GraphModule. This is quite useful in debugging TorchDynamo
|
380 |
+
issues.
|
381 |
+
- **AOT_EAGER** -- Uses AotAutograd with no compiler, i.e, just using PyTorch eager for the AotAutograd's
|
382 |
+
extracted forward and backward graphs. This is useful for debugging, and unlikely to give speedups.
|
383 |
+
- **INDUCTOR** -- Uses TorchInductor backend with AotAutograd and cudagraphs by leveraging codegened Triton
|
384 |
+
kernels. [Read
|
385 |
+
more](https://dev-discuss.pytorch.org/t/torchinductor-a-pytorch-native-compiler-with-define-by-run-ir-and-symbolic-shapes/747)
|
386 |
+
- **AOT_TS_NVFUSER** -- nvFuser with AotAutograd/TorchScript. [Read
|
387 |
+
more](https://dev-discuss.pytorch.org/t/tracing-with-primitives-update-1-nvfuser-and-its-primitives/593)
|
388 |
+
- **NVPRIMS_NVFUSER** -- nvFuser with PrimTorch. [Read
|
389 |
+
more](https://dev-discuss.pytorch.org/t/tracing-with-primitives-update-1-nvfuser-and-its-primitives/593)
|
390 |
+
- **CUDAGRAPHS** -- cudagraphs with AotAutograd. [Read more](https://github.com/pytorch/torchdynamo/pull/757)
|
391 |
+
- **OFI** -- Uses Torchscript optimize_for_inference. Inference only. [Read
|
392 |
+
more](https://pytorch.org/docs/stable/generated/torch.jit.optimize_for_inference.html)
|
393 |
+
- **FX2TRT** -- Uses Nvidia TensorRT for inference optimizations. Inference only. [Read
|
394 |
+
more](https://github.com/pytorch/TensorRT/blob/master/docsrc/tutorials/getting_started_with_fx_path.rst)
|
395 |
+
- **ONNXRT** -- Uses ONNXRT for inference on CPU/GPU. Inference only. [Read more](https://onnxruntime.ai/)
|
396 |
+
- **TENSORRT** -- Uses ONNXRT to run TensorRT for inference optimizations. [Read
|
397 |
+
more](https://github.com/onnx/onnx-tensorrt)
|
398 |
+
- **IPEX** -- Uses IPEX for inference on CPU. Inference only. [Read
|
399 |
+
more](https://github.com/intel/intel-extension-for-pytorch).
|
400 |
+
- **TVM** -- Uses Apach TVM for inference optimizations. [Read more](https://tvm.apache.org/)
|
401 |
+
|
402 |
+
"""
|
403 |
+
|
404 |
+
# Subclassing str as well as Enum allows the `SageMakerDistributedType` to be JSON-serializable out of the box.
|
405 |
+
NO = "NO"
|
406 |
+
EAGER = "EAGER"
|
407 |
+
AOT_EAGER = "AOT_EAGER"
|
408 |
+
INDUCTOR = "INDUCTOR"
|
409 |
+
AOT_TS_NVFUSER = "AOT_TS_NVFUSER"
|
410 |
+
NVPRIMS_NVFUSER = "NVPRIMS_NVFUSER"
|
411 |
+
CUDAGRAPHS = "CUDAGRAPHS"
|
412 |
+
OFI = "OFI"
|
413 |
+
FX2TRT = "FX2TRT"
|
414 |
+
ONNXRT = "ONNXRT"
|
415 |
+
TENSORRT = "TENSORRT"
|
416 |
+
IPEX = "IPEX"
|
417 |
+
TVM = "TVM"
|
418 |
+
|
419 |
+
|
420 |
+
class LoggerType(BaseEnum):
|
421 |
+
"""Represents a type of supported experiment tracker
|
422 |
+
|
423 |
+
Values:
|
424 |
+
|
425 |
+
- **ALL** -- all available trackers in the environment that are supported
|
426 |
+
- **TENSORBOARD** -- TensorBoard as an experiment tracker
|
427 |
+
- **WANDB** -- wandb as an experiment tracker
|
428 |
+
- **COMETML** -- comet_ml as an experiment tracker
|
429 |
+
- **DVCLIVE** -- dvclive as an experiment tracker
|
430 |
+
"""
|
431 |
+
|
432 |
+
ALL = "all"
|
433 |
+
AIM = "aim"
|
434 |
+
TENSORBOARD = "tensorboard"
|
435 |
+
WANDB = "wandb"
|
436 |
+
COMETML = "comet_ml"
|
437 |
+
MLFLOW = "mlflow"
|
438 |
+
CLEARML = "clearml"
|
439 |
+
DVCLIVE = "dvclive"
|
440 |
+
|
441 |
+
|
442 |
+
class PrecisionType(BaseEnum):
|
443 |
+
"""Represents a type of precision used on floating point values
|
444 |
+
|
445 |
+
Values:
|
446 |
+
|
447 |
+
- **NO** -- using full precision (FP32)
|
448 |
+
- **FP16** -- using half precision
|
449 |
+
- **BF16** -- using brain floating point precision
|
450 |
+
"""
|
451 |
+
|
452 |
+
NO = "no"
|
453 |
+
FP8 = "fp8"
|
454 |
+
FP16 = "fp16"
|
455 |
+
BF16 = "bf16"
|
456 |
+
|
457 |
+
|
458 |
+
class RNGType(BaseEnum):
|
459 |
+
TORCH = "torch"
|
460 |
+
CUDA = "cuda"
|
461 |
+
MLU = "mlu"
|
462 |
+
NPU = "npu"
|
463 |
+
XLA = "xla"
|
464 |
+
XPU = "xpu"
|
465 |
+
GENERATOR = "generator"
|
466 |
+
|
467 |
+
|
468 |
+
class CustomDtype(enum.Enum):
|
469 |
+
r"""
|
470 |
+
An enum that contains multiple custom dtypes that can be used for `infer_auto_device_map`.
|
471 |
+
"""
|
472 |
+
|
473 |
+
FP8 = "fp8"
|
474 |
+
INT4 = "int4"
|
475 |
+
INT2 = "int2"
|
476 |
+
|
477 |
+
|
478 |
+
# data classes
|
479 |
+
|
480 |
+
|
481 |
+
@dataclass
|
482 |
+
class TensorInformation:
|
483 |
+
shape: torch.Size
|
484 |
+
dtype: torch.dtype
|
485 |
+
|
486 |
+
|
487 |
+
@dataclass
|
488 |
+
class DataLoaderConfiguration:
|
489 |
+
"""
|
490 |
+
Configuration for dataloader-related items when calling `accelerator.prepare`.
|
491 |
+
"""
|
492 |
+
|
493 |
+
split_batches: bool = field(
|
494 |
+
default=False,
|
495 |
+
metadata={
|
496 |
+
"help": "Whether or not the accelerator should split the batches yielded by the dataloaders across the devices. If"
|
497 |
+
" `True` the actual batch size used will be the same on any kind of distributed processes, but it must be a"
|
498 |
+
" round multiple of the `num_processes` you are using. If `False`, actual batch size used will be the one set"
|
499 |
+
" in your script multiplied by the number of processes."
|
500 |
+
},
|
501 |
+
)
|
502 |
+
dispatch_batches: bool = field(
|
503 |
+
default=None,
|
504 |
+
metadata={
|
505 |
+
"help": "If set to `True`, the dataloader prepared by the Accelerator is only iterated through on the main process"
|
506 |
+
" and then the batches are split and broadcast to each process. Will default to `True` for `DataLoader` whose"
|
507 |
+
" underlying dataset is an `IterableDataslet`, `False` otherwise."
|
508 |
+
},
|
509 |
+
)
|
510 |
+
even_batches: bool = field(
|
511 |
+
default=True,
|
512 |
+
metadata={
|
513 |
+
"help": "If set to `True`, in cases where the total batch size across all processes does not exactly divide the"
|
514 |
+
" dataset, samples at the start of the dataset will be duplicated so the batch can be divided equally among"
|
515 |
+
" all workers."
|
516 |
+
},
|
517 |
+
)
|
518 |
+
use_seedable_sampler: bool = field(
|
519 |
+
default=False,
|
520 |
+
metadata={
|
521 |
+
"help": "Whether or not use a fully seedable random sampler ([`data_loader.SeedableRandomSampler`])."
|
522 |
+
"Ensures training results are fully reproducable using a different sampling technique. "
|
523 |
+
"While seed-to-seed results may differ, on average the differences are neglible when using"
|
524 |
+
"multiple different seeds to compare. Should also be ran with [`~utils.set_seed`] for the best results."
|
525 |
+
},
|
526 |
+
)
|
527 |
+
non_blocking: bool = field(
|
528 |
+
default=False,
|
529 |
+
metadata={
|
530 |
+
"help": "If set to `True`, the dataloader prepared by the Accelerator will utilize non-blocking host-to-device"
|
531 |
+
" transfers, allowing for better overlap between dataloader communication and computation. Recommended that the"
|
532 |
+
" prepared dataloader has `pin_memory` set to `True` to work properly."
|
533 |
+
},
|
534 |
+
)
|
535 |
+
|
536 |
+
|
537 |
+
@dataclass
|
538 |
+
class ProjectConfiguration:
|
539 |
+
"""
|
540 |
+
Configuration for the Accelerator object based on inner-project needs.
|
541 |
+
"""
|
542 |
+
|
543 |
+
project_dir: str = field(default=None, metadata={"help": "A path to a directory for storing data."})
|
544 |
+
logging_dir: str = field(
|
545 |
+
default=None,
|
546 |
+
metadata={
|
547 |
+
"help": "A path to a directory for storing logs of locally-compatible loggers. If None, defaults to `project_dir`."
|
548 |
+
},
|
549 |
+
)
|
550 |
+
automatic_checkpoint_naming: bool = field(
|
551 |
+
default=False,
|
552 |
+
metadata={"help": "Whether saved states should be automatically iteratively named."},
|
553 |
+
)
|
554 |
+
|
555 |
+
total_limit: int = field(
|
556 |
+
default=None,
|
557 |
+
metadata={"help": "The maximum number of total saved states to keep."},
|
558 |
+
)
|
559 |
+
|
560 |
+
iteration: int = field(
|
561 |
+
default=0,
|
562 |
+
metadata={"help": "The current save iteration."},
|
563 |
+
)
|
564 |
+
|
565 |
+
save_on_each_node: bool = field(
|
566 |
+
default=False,
|
567 |
+
metadata={
|
568 |
+
"help": (
|
569 |
+
"When doing multi-node distributed training, whether to save models and checkpoints on each node, or"
|
570 |
+
" only on the main one"
|
571 |
+
)
|
572 |
+
},
|
573 |
+
)
|
574 |
+
|
575 |
+
def set_directories(self, project_dir: str = None):
|
576 |
+
"Sets `self.project_dir` and `self.logging_dir` to the appropriate values."
|
577 |
+
self.project_dir = project_dir
|
578 |
+
if self.logging_dir is None:
|
579 |
+
self.logging_dir = project_dir
|
580 |
+
|
581 |
+
def __post_init__(self):
|
582 |
+
self.set_directories(self.project_dir)
|
583 |
+
|
584 |
+
|
585 |
+
@dataclass
|
586 |
+
class GradientAccumulationPlugin(KwargsHandler):
|
587 |
+
"""
|
588 |
+
A plugin to configure gradient accumulation behavior. You can only pass one of `gradient_accumulation_plugin` or
|
589 |
+
`gradient_accumulation_steps` to [`Accelerator`]. Passing both raises an error.
|
590 |
+
|
591 |
+
Parameters:
|
592 |
+
num_steps (`int`):
|
593 |
+
The number of steps to accumulate gradients for.
|
594 |
+
adjust_scheduler (`bool`, *optional*, defaults to `True`):
|
595 |
+
Whether to adjust the scheduler steps to account for the number of steps being accumulated. Should be
|
596 |
+
`True` if the used scheduler was not adjusted for gradient accumulation.
|
597 |
+
sync_with_dataloader (`bool`, *optional*, defaults to `True`):
|
598 |
+
Whether to synchronize setting the gradients when at the end of the dataloader.
|
599 |
+
sync_each_batch (`bool`, *optional*):
|
600 |
+
Whether to synchronize setting the gradients at each data batch. Seting to `True` may reduce memory
|
601 |
+
requirements when using gradient accumulation with distributed training, at expense of speed.
|
602 |
+
|
603 |
+
Example:
|
604 |
+
|
605 |
+
```python
|
606 |
+
from accelerate.utils import GradientAccumulationPlugin
|
607 |
+
|
608 |
+
gradient_accumulation_plugin = GradientAccumulationPlugin(num_steps=2)
|
609 |
+
accelerator = Accelerator(gradient_accumulation_plugin=gradient_accumulation_plugin)
|
610 |
+
```
|
611 |
+
"""
|
612 |
+
|
613 |
+
num_steps: int = field(default=None, metadata={"help": "The number of steps to accumulate gradients for."})
|
614 |
+
adjust_scheduler: bool = field(
|
615 |
+
default=True,
|
616 |
+
metadata={
|
617 |
+
"help": "Whether to adjust the scheduler steps to account for the number of steps being accumulated. Should be `True` if the used scheduler was not adjusted for gradient accumulation."
|
618 |
+
},
|
619 |
+
)
|
620 |
+
sync_with_dataloader: bool = field(
|
621 |
+
default=True,
|
622 |
+
metadata={
|
623 |
+
"help": "Whether to synchronize setting the gradients when at the end of the dataloader. Should only be set to `False` if you know what you're doing."
|
624 |
+
},
|
625 |
+
)
|
626 |
+
sync_each_batch: bool = field(
|
627 |
+
default=False,
|
628 |
+
metadata={
|
629 |
+
"help": "Whether to synchronize setting the gradients at each data batch. Setting to `True` may reduce memory requirements when using gradient accumulation with distributed training, at expense of speed."
|
630 |
+
},
|
631 |
+
)
|
632 |
+
|
633 |
+
|
634 |
+
@dataclass
|
635 |
+
class TorchDynamoPlugin(KwargsHandler):
|
636 |
+
"""
|
637 |
+
This plugin is used to compile a model with PyTorch 2.0
|
638 |
+
"""
|
639 |
+
|
640 |
+
backend: DynamoBackend = field(
|
641 |
+
default=None,
|
642 |
+
metadata={"help": f"Possible options are {[b.value.lower() for b in DynamoBackend]}"},
|
643 |
+
)
|
644 |
+
mode: str = field(
|
645 |
+
default=None, metadata={"help": "Possible options are 'default', 'reduce-overhead' or 'max-autotune'"}
|
646 |
+
)
|
647 |
+
fullgraph: bool = field(default=None, metadata={"help": "Whether it is ok to break model into several subgraphs"})
|
648 |
+
dynamic: bool = field(default=None, metadata={"help": "Whether to use dynamic shape for tracing"})
|
649 |
+
options: Any = field(default=None, metadata={"help": "A dictionary of options to pass to the backend."})
|
650 |
+
disable: bool = field(default=False, metadata={"help": "Turn torch.compile() into a no-op for testing"})
|
651 |
+
|
652 |
+
def __post_init__(self):
|
653 |
+
prefix = "ACCELERATE_DYNAMO_"
|
654 |
+
if self.backend is None:
|
655 |
+
self.backend = os.environ.get(prefix + "BACKEND", "no")
|
656 |
+
self.backend = DynamoBackend(self.backend.upper())
|
657 |
+
if self.mode is None:
|
658 |
+
self.mode = os.environ.get(prefix + "MODE", "default")
|
659 |
+
if self.fullgraph is None:
|
660 |
+
self.fullgraph = str_to_bool(os.environ.get(prefix + "USE_FULLGRAPH", "False")) == 1
|
661 |
+
if self.dynamic is None:
|
662 |
+
self.dynamic = str_to_bool(os.environ.get(prefix + "USE_DYNAMIC", "False")) == 1
|
663 |
+
|
664 |
+
def to_dict(self):
|
665 |
+
dynamo_config = copy.deepcopy(self.__dict__)
|
666 |
+
dynamo_config["backend"] = dynamo_config["backend"].value.lower()
|
667 |
+
return dynamo_config
|
668 |
+
|
669 |
+
|
670 |
+
@dataclass
|
671 |
+
class DeepSpeedPlugin:
|
672 |
+
"""
|
673 |
+
This plugin is used to integrate DeepSpeed.
|
674 |
+
"""
|
675 |
+
|
676 |
+
hf_ds_config: Any = field(
|
677 |
+
default=None,
|
678 |
+
metadata={
|
679 |
+
"help": "path to DeepSpeed config file or dict or an object of class `accelerate.utils.deepspeed.HfDeepSpeedConfig`."
|
680 |
+
},
|
681 |
+
)
|
682 |
+
gradient_accumulation_steps: int = field(
|
683 |
+
default=None,
|
684 |
+
metadata={
|
685 |
+
"help": "Number of steps to accumulate gradients before updating optimizer states. If not set, will use the value from the `Accelerator` directly."
|
686 |
+
},
|
687 |
+
)
|
688 |
+
gradient_clipping: float = field(default=None, metadata={"help": "Enable gradient clipping with value"})
|
689 |
+
zero_stage: int = field(
|
690 |
+
default=None,
|
691 |
+
metadata={"help": "Possible options are 0,1,2,3; Default will be taken from environment variable"},
|
692 |
+
)
|
693 |
+
is_train_batch_min: bool = field(
|
694 |
+
default=True,
|
695 |
+
metadata={"help": "If both train & eval dataloaders are specified, this will decide the train_batch_size"},
|
696 |
+
)
|
697 |
+
offload_optimizer_device: str = field(
|
698 |
+
default=None,
|
699 |
+
metadata={"help": "Possible options are none|cpu|nvme. Only applicable with ZeRO Stages 2 and 3."},
|
700 |
+
)
|
701 |
+
offload_param_device: str = field(
|
702 |
+
default=None,
|
703 |
+
metadata={"help": "Possible options are none|cpu|nvme. Only applicable with ZeRO Stage 3."},
|
704 |
+
)
|
705 |
+
offload_optimizer_nvme_path: str = field(
|
706 |
+
default=None,
|
707 |
+
metadata={"help": "Possible options are /nvme|/local_nvme. Only applicable with ZeRO Stage 3."},
|
708 |
+
)
|
709 |
+
offload_param_nvme_path: str = field(
|
710 |
+
default=None,
|
711 |
+
metadata={"help": "Possible options are /nvme|/local_nvme. Only applicable with ZeRO Stage 3."},
|
712 |
+
)
|
713 |
+
zero3_init_flag: bool = field(
|
714 |
+
default=None,
|
715 |
+
metadata={
|
716 |
+
"help": "Flag to indicate whether to enable `deepspeed.zero.Init` for constructing massive models."
|
717 |
+
"Only applicable with ZeRO Stage-3."
|
718 |
+
},
|
719 |
+
)
|
720 |
+
zero3_save_16bit_model: bool = field(
|
721 |
+
default=None,
|
722 |
+
metadata={"help": "Flag to indicate whether to save 16-bit model. Only applicable with ZeRO Stage-3."},
|
723 |
+
)
|
724 |
+
transformer_moe_cls_names: str = field(
|
725 |
+
default=None,
|
726 |
+
metadata={
|
727 |
+
"help": "comma-separated list of transformers MoE layer class names (case-sensitive), e.g : "
|
728 |
+
" `MixtralSparseMoeBlock`, `Qwen2MoeSparseMoeBlock`, `JetMoEAttention,JetMoEBlock` ..."
|
729 |
+
},
|
730 |
+
)
|
731 |
+
|
732 |
+
def __post_init__(self):
|
733 |
+
from .deepspeed import HfDeepSpeedConfig
|
734 |
+
|
735 |
+
if self.gradient_accumulation_steps is None:
|
736 |
+
gas = os.environ.get("ACCELERATE_GRADIENT_ACCUMULATION_STEPS", "auto")
|
737 |
+
self.gradient_accumulation_steps = int(gas) if gas.isdigit() else gas
|
738 |
+
|
739 |
+
if self.gradient_clipping is None:
|
740 |
+
gradient_clipping = os.environ.get("ACCELERATE_GRADIENT_CLIPPING", "auto")
|
741 |
+
self.gradient_clipping = gradient_clipping if gradient_clipping == "auto" else float(gradient_clipping)
|
742 |
+
|
743 |
+
if self.zero_stage is None:
|
744 |
+
self.zero_stage = int(os.environ.get("ACCELERATE_DEEPSPEED_ZERO_STAGE", 2))
|
745 |
+
|
746 |
+
if self.offload_optimizer_device is None:
|
747 |
+
self.offload_optimizer_device = os.environ.get("ACCELERATE_DEEPSPEED_OFFLOAD_OPTIMIZER_DEVICE", "none")
|
748 |
+
|
749 |
+
if self.offload_param_device is None:
|
750 |
+
self.offload_param_device = os.environ.get("ACCELERATE_DEEPSPEED_OFFLOAD_PARAM_DEVICE", "none")
|
751 |
+
|
752 |
+
if self.offload_optimizer_nvme_path is None:
|
753 |
+
self.offload_optimizer_nvme_path = os.environ.get(
|
754 |
+
"ACCELERATE_DEEPSPEED_OFFLOAD_OPTIMIZER_NVME_PATH", "none"
|
755 |
+
)
|
756 |
+
|
757 |
+
if self.offload_param_nvme_path is None:
|
758 |
+
self.offload_param_nvme_path = os.environ.get("ACCELERATE_DEEPSPEED_OFFLOAD_PARAM_NVME_PATH", "none")
|
759 |
+
|
760 |
+
if self.zero3_save_16bit_model is None:
|
761 |
+
self.zero3_save_16bit_model = (
|
762 |
+
os.environ.get("ACCELERATE_DEEPSPEED_ZERO3_SAVE_16BIT_MODEL", "false") == "true"
|
763 |
+
)
|
764 |
+
|
765 |
+
if self.hf_ds_config is None:
|
766 |
+
self.hf_ds_config = os.environ.get("ACCELERATE_DEEPSPEED_CONFIG_FILE", "none")
|
767 |
+
if (
|
768 |
+
isinstance(self.hf_ds_config, dict)
|
769 |
+
or (isinstance(self.hf_ds_config, str) and self.hf_ds_config != "none")
|
770 |
+
or isinstance(self.hf_ds_config, HfDeepSpeedConfig)
|
771 |
+
):
|
772 |
+
if not isinstance(self.hf_ds_config, HfDeepSpeedConfig):
|
773 |
+
self.hf_ds_config = HfDeepSpeedConfig(self.hf_ds_config)
|
774 |
+
if "gradient_accumulation_steps" not in self.hf_ds_config.config:
|
775 |
+
self.hf_ds_config.config["gradient_accumulation_steps"] = 1
|
776 |
+
if "zero_optimization" not in self.hf_ds_config.config:
|
777 |
+
raise ValueError("Please specify the ZeRO optimization config in the DeepSpeed config.")
|
778 |
+
|
779 |
+
self._deepspeed_config_checks()
|
780 |
+
plugin_to_config_mapping = {
|
781 |
+
"gradient_accumulation_steps": "gradient_accumulation_steps",
|
782 |
+
"gradient_clipping": "gradient_clipping",
|
783 |
+
"zero_stage": "zero_optimization.stage",
|
784 |
+
"offload_optimizer_device": "zero_optimization.offload_optimizer.device",
|
785 |
+
"offload_param_device": "zero_optimization.offload_param.device",
|
786 |
+
"offload_param_nvme_path": "zero_optimization.offload_param.nvme_path",
|
787 |
+
"offload_optimizer_nvme_path": "zero_optimization.offload_optimizer.nvme_path",
|
788 |
+
"zero3_save_16bit_model": "zero_optimization.stage3_gather_16bit_weights_on_model_save",
|
789 |
+
}
|
790 |
+
kwargs = {v: getattr(self, k) for k, v in plugin_to_config_mapping.items() if getattr(self, k) is not None}
|
791 |
+
for key in kwargs.keys():
|
792 |
+
self.fill_match(key, **kwargs, must_match=False)
|
793 |
+
self.hf_ds_config.set_stage_and_offload()
|
794 |
+
|
795 |
+
# filling the missing values in the class attributes from the DeepSpeed config
|
796 |
+
# when using the DeepSpeed config file.
|
797 |
+
for key, value in plugin_to_config_mapping.items():
|
798 |
+
config_value = self.hf_ds_config.get_value(value)
|
799 |
+
if config_value is not None and config_value != "auto":
|
800 |
+
setattr(self, key, config_value)
|
801 |
+
else:
|
802 |
+
config = {
|
803 |
+
"train_batch_size": "auto",
|
804 |
+
"train_micro_batch_size_per_gpu": "auto",
|
805 |
+
"gradient_accumulation_steps": self.gradient_accumulation_steps,
|
806 |
+
"zero_optimization": {
|
807 |
+
"stage": self.zero_stage,
|
808 |
+
"offload_optimizer": {
|
809 |
+
"device": self.offload_optimizer_device,
|
810 |
+
"nvme_path": self.offload_optimizer_nvme_path
|
811 |
+
if self.offload_optimizer_device == "nvme"
|
812 |
+
else None,
|
813 |
+
},
|
814 |
+
"offload_param": {
|
815 |
+
"device": self.offload_param_device,
|
816 |
+
"nvme_path": self.offload_param_nvme_path if self.offload_param_device == "nvme" else None,
|
817 |
+
},
|
818 |
+
"stage3_gather_16bit_weights_on_model_save": self.zero3_save_16bit_model,
|
819 |
+
},
|
820 |
+
}
|
821 |
+
if self.gradient_clipping:
|
822 |
+
config["gradient_clipping"] = self.gradient_clipping
|
823 |
+
self.hf_ds_config = HfDeepSpeedConfig(config)
|
824 |
+
|
825 |
+
self.deepspeed_config = self.hf_ds_config.config
|
826 |
+
self.deepspeed_config["steps_per_print"] = float("inf") # this will stop deepspeed from logging @ stdout
|
827 |
+
if self.zero3_init_flag is None:
|
828 |
+
self.zero3_init_flag = (
|
829 |
+
str_to_bool(os.environ.get("ACCELERATE_DEEPSPEED_ZERO3_INIT", str(self.hf_ds_config.is_zero3()))) == 1
|
830 |
+
)
|
831 |
+
if self.zero3_init_flag and not self.hf_ds_config.is_zero3():
|
832 |
+
warnings.warn("DeepSpeed Zero3 Init flag is only applicable for ZeRO Stage 3. Setting it to False.")
|
833 |
+
self.zero3_init_flag = False
|
834 |
+
|
835 |
+
def fill_match(self, ds_key_long, mismatches=None, must_match=True, **kwargs):
|
836 |
+
mismatches = [] if mismatches is None else mismatches
|
837 |
+
config, ds_key = self.hf_ds_config.find_config_node(ds_key_long)
|
838 |
+
if config is None:
|
839 |
+
return
|
840 |
+
|
841 |
+
if config.get(ds_key) == "auto":
|
842 |
+
if ds_key_long in kwargs:
|
843 |
+
config[ds_key] = kwargs[ds_key_long]
|
844 |
+
return
|
845 |
+
else:
|
846 |
+
raise ValueError(
|
847 |
+
f"`{ds_key_long}` not found in kwargs. "
|
848 |
+
f"Please specify `{ds_key_long}` without `auto` (set to correct value) in the DeepSpeed config file or "
|
849 |
+
"pass it in kwargs."
|
850 |
+
)
|
851 |
+
|
852 |
+
if not must_match:
|
853 |
+
return
|
854 |
+
|
855 |
+
ds_val = config.get(ds_key)
|
856 |
+
if ds_val is not None and ds_key_long in kwargs:
|
857 |
+
if ds_val != kwargs[ds_key_long]:
|
858 |
+
mismatches.append(f"- ds {ds_key_long}={ds_val} vs arg {ds_key_long}={kwargs[ds_key_long]}")
|
859 |
+
|
860 |
+
def is_auto(self, ds_key_long):
|
861 |
+
val = self.hf_ds_config.get_value(ds_key_long)
|
862 |
+
if val is None:
|
863 |
+
return False
|
864 |
+
else:
|
865 |
+
return val == "auto"
|
866 |
+
|
867 |
+
def get_value(self, ds_key_long, default=None):
|
868 |
+
return self.hf_ds_config.get_value(ds_key_long, default)
|
869 |
+
|
870 |
+
def deepspeed_config_process(self, prefix="", mismatches=None, config=None, must_match=True, **kwargs):
|
871 |
+
"""Process the DeepSpeed config with the values from the kwargs."""
|
872 |
+
mismatches = [] if mismatches is None else mismatches
|
873 |
+
if config is None:
|
874 |
+
config = self.deepspeed_config
|
875 |
+
for key, value in config.items():
|
876 |
+
if isinstance(value, dict):
|
877 |
+
self.deepspeed_config_process(
|
878 |
+
prefix=prefix + key + ".", mismatches=mismatches, config=value, must_match=must_match, **kwargs
|
879 |
+
)
|
880 |
+
else:
|
881 |
+
self.fill_match(prefix + key, mismatches, must_match=must_match, **kwargs)
|
882 |
+
if len(mismatches) > 0 and prefix == "":
|
883 |
+
mismatches_msg = "\n".join(mismatches)
|
884 |
+
raise ValueError(
|
885 |
+
"Please correct the following DeepSpeed config values that mismatch kwargs "
|
886 |
+
f" values:\n{mismatches_msg}\nThe easiest method is to set these DeepSpeed config values to 'auto'."
|
887 |
+
)
|
888 |
+
|
889 |
+
def set_mixed_precision(self, mixed_precision):
|
890 |
+
ds_config = self.deepspeed_config
|
891 |
+
kwargs = {
|
892 |
+
"fp16.enabled": mixed_precision == "fp16",
|
893 |
+
"bf16.enabled": mixed_precision == "bf16",
|
894 |
+
}
|
895 |
+
if mixed_precision == "fp16":
|
896 |
+
if "fp16" not in ds_config:
|
897 |
+
ds_config["fp16"] = {"enabled": True, "auto_cast": True}
|
898 |
+
elif mixed_precision == "bf16":
|
899 |
+
if "bf16" not in ds_config:
|
900 |
+
ds_config["bf16"] = {"enabled": True}
|
901 |
+
|
902 |
+
if mixed_precision != "no":
|
903 |
+
diff_dtype = "bf16" if mixed_precision == "fp16" else "fp16"
|
904 |
+
if str(ds_config.get(diff_dtype, {}).get("enabled", "False")).lower() == "true":
|
905 |
+
raise ValueError(
|
906 |
+
f"`--mixed_precision` arg cannot be set to `{mixed_precision}` when `{diff_dtype}` is set in the DeepSpeed config file."
|
907 |
+
)
|
908 |
+
for dtype in ["fp16", "bf16"]:
|
909 |
+
if dtype not in ds_config:
|
910 |
+
ds_config[dtype] = {"enabled": False}
|
911 |
+
self.fill_match("fp16.enabled", must_match=False, **kwargs)
|
912 |
+
self.fill_match("bf16.enabled", must_match=False, **kwargs)
|
913 |
+
|
914 |
+
def set_deepspeed_weakref(self):
|
915 |
+
from .imports import is_transformers_available
|
916 |
+
|
917 |
+
if self.zero3_init_flag:
|
918 |
+
if not is_transformers_available():
|
919 |
+
raise Exception(
|
920 |
+
"When `zero3_init_flag` is set, it requires Transformers to be installed. "
|
921 |
+
"Please run `pip install transformers`."
|
922 |
+
)
|
923 |
+
ds_config = copy.deepcopy(self.deepspeed_config)
|
924 |
+
if "gradient_accumulation_steps" not in ds_config or ds_config["gradient_accumulation_steps"] == "auto":
|
925 |
+
ds_config["gradient_accumulation_steps"] = 1
|
926 |
+
if (
|
927 |
+
"train_micro_batch_size_per_gpu" not in ds_config
|
928 |
+
or ds_config["train_micro_batch_size_per_gpu"] == "auto"
|
929 |
+
):
|
930 |
+
ds_config["train_micro_batch_size_per_gpu"] = 1
|
931 |
+
if ds_config.get("train_batch_size", None) == "auto":
|
932 |
+
del ds_config["train_batch_size"]
|
933 |
+
|
934 |
+
if compare_versions("transformers", "<", "4.33"):
|
935 |
+
from transformers.deepspeed import HfDeepSpeedConfig
|
936 |
+
else:
|
937 |
+
from transformers.integrations import HfDeepSpeedConfig
|
938 |
+
|
939 |
+
self.dschf = HfDeepSpeedConfig(ds_config) # keep this object alive # noqa
|
940 |
+
|
941 |
+
def is_zero3_init_enabled(self):
|
942 |
+
return self.zero3_init_flag
|
943 |
+
|
944 |
+
@contextmanager
|
945 |
+
def zero3_init_context_manager(self, enable=False):
|
946 |
+
old = self.zero3_init_flag
|
947 |
+
if old == enable:
|
948 |
+
yield
|
949 |
+
else:
|
950 |
+
self.zero3_init_flag = enable
|
951 |
+
self.dschf = None
|
952 |
+
self.set_deepspeed_weakref()
|
953 |
+
yield
|
954 |
+
self.zero3_init_flag = old
|
955 |
+
self.dschf = None
|
956 |
+
self.set_deepspeed_weakref()
|
957 |
+
|
958 |
+
def _deepspeed_config_checks(self):
|
959 |
+
env_variable_names_to_ignore = [
|
960 |
+
"ACCELERATE_GRADIENT_ACCUMULATION_STEPS",
|
961 |
+
"ACCELERATE_GRADIENT_CLIPPING",
|
962 |
+
"ACCELERATE_DEEPSPEED_ZERO_STAGE",
|
963 |
+
"ACCELERATE_DEEPSPEED_OFFLOAD_OPTIMIZER_DEVICE",
|
964 |
+
"ACCELERATE_DEEPSPEED_OFFLOAD_PARAM_DEVICE",
|
965 |
+
"ACCELERATE_DEEPSPEED_OFFLOAD_PARAM_NVME_PATH",
|
966 |
+
"ACCELERATE_DEEPSPEED_OFFLOAD_OPTIMIZER_NVME_PATH",
|
967 |
+
"ACCELERATE_DEEPSPEED_ZERO3_SAVE_16BIT_MODEL",
|
968 |
+
"ACCELERATE_MIXED_PRECISION",
|
969 |
+
]
|
970 |
+
env_variable_names_to_ignore = [
|
971 |
+
name.replace("ACCELERATE_", "").replace("DEEPSPEED_", "").lower() for name in env_variable_names_to_ignore
|
972 |
+
]
|
973 |
+
|
974 |
+
deepspeed_fields_from_accelerate_config = os.environ.get("ACCELERATE_CONFIG_DS_FIELDS", "").split(",")
|
975 |
+
|
976 |
+
if any(name in env_variable_names_to_ignore for name in deepspeed_fields_from_accelerate_config):
|
977 |
+
raise ValueError(
|
978 |
+
f"When using `deepspeed_config_file`, the following accelerate config variables will be ignored: {env_variable_names_to_ignore}.\n"
|
979 |
+
"Please specify them appropriately in the DeepSpeed config file.\n"
|
980 |
+
"If you are using an accelerate config file, remove others config variables mentioned in the above specified list.\n"
|
981 |
+
"The easiest method is to create a new config following the questionnaire via `accelerate config`.\n"
|
982 |
+
"It will only ask for the necessary config variables when using `deepspeed_config_file`."
|
983 |
+
)
|
984 |
+
|
985 |
+
def set_moe_leaf_modules(self, model):
|
986 |
+
if self.transformer_moe_cls_names is None:
|
987 |
+
self.transformer_moe_cls_names = os.environ.get("ACCELERATE_DEEPSPEED_MOE_LAYER_CLS_NAMES", None)
|
988 |
+
if self.transformer_moe_cls_names is not None:
|
989 |
+
if compare_versions("deepspeed", "<", "0.14.0"):
|
990 |
+
raise ImportError("DeepSpeed version must be >= 0.14.0 to use MOE support. Please update DeepSpeed.")
|
991 |
+
from deepspeed.utils import set_z3_leaf_modules
|
992 |
+
|
993 |
+
class_names = self.transformer_moe_cls_names.split(",")
|
994 |
+
transformer_moe_cls = []
|
995 |
+
for layer_class in class_names:
|
996 |
+
transformer_cls = get_module_class_from_name(model, layer_class)
|
997 |
+
if transformer_cls is None:
|
998 |
+
raise Exception(
|
999 |
+
f"Could not find a transformer layer class called '{layer_class}' to wrap in the model."
|
1000 |
+
)
|
1001 |
+
else:
|
1002 |
+
transformer_moe_cls.append(transformer_cls)
|
1003 |
+
set_z3_leaf_modules(model, transformer_moe_cls) # z3_leaf
|
1004 |
+
|
1005 |
+
|
1006 |
+
@dataclass
|
1007 |
+
class FullyShardedDataParallelPlugin:
|
1008 |
+
"""
|
1009 |
+
This plugin is used to enable fully sharded data parallelism.
|
1010 |
+
"""
|
1011 |
+
|
1012 |
+
sharding_strategy: "typing.Any" = field(
|
1013 |
+
default=None,
|
1014 |
+
metadata={
|
1015 |
+
"help": "FSDP Sharding Strategy of type `torch.distributed.fsdp.fully_sharded_data_parallel.ShardingStrategy`"
|
1016 |
+
},
|
1017 |
+
)
|
1018 |
+
backward_prefetch: "typing.Any" = field(
|
1019 |
+
default=None,
|
1020 |
+
metadata={
|
1021 |
+
"help": "FSDP Backward Prefetch of type `torch.distributed.fsdp.fully_sharded_data_parallel.BackwardPrefetch`"
|
1022 |
+
},
|
1023 |
+
)
|
1024 |
+
mixed_precision_policy: "typing.Any" = field(
|
1025 |
+
default=None,
|
1026 |
+
metadata={
|
1027 |
+
"help": "A config to enable mixed precision training with FullyShardedDataParallel. "
|
1028 |
+
"The 3 flags that are set are `param_dtype`, `reduce_dtype`, `buffer_dtype`. "
|
1029 |
+
"Each flag expects `torch.dtype` as the value. "
|
1030 |
+
"It is of type `torch.distributed.fsdp.fully_sharded_data_parallel.MixedPrecision`."
|
1031 |
+
},
|
1032 |
+
)
|
1033 |
+
auto_wrap_policy: Optional[Callable] = field(
|
1034 |
+
default=None,
|
1035 |
+
metadata={"help": "A callable specifying a policy to recursively wrap layers with FSDP"},
|
1036 |
+
)
|
1037 |
+
cpu_offload: "typing.Any" = field(
|
1038 |
+
default=None,
|
1039 |
+
metadata={
|
1040 |
+
"help": "Decides Whether to offload parameters and gradients to CPU. "
|
1041 |
+
"It is of type `torch.distributed.fsdp.fully_sharded_data_parallel.CPUOffload`."
|
1042 |
+
},
|
1043 |
+
)
|
1044 |
+
ignored_modules: Optional[Iterable[torch.nn.Module]] = field(
|
1045 |
+
default=None,
|
1046 |
+
metadata={"help": "A list of modules to ignore for FSDP."},
|
1047 |
+
)
|
1048 |
+
state_dict_type: "typing.Any" = field(
|
1049 |
+
default=None,
|
1050 |
+
metadata={
|
1051 |
+
"help": "FSDP State Dict Type of type `torch.distributed.fsdp.fully_sharded_data_parallel.StateDictType`"
|
1052 |
+
},
|
1053 |
+
)
|
1054 |
+
state_dict_config: "typing.Any" = field(
|
1055 |
+
default=None,
|
1056 |
+
metadata={
|
1057 |
+
"help": "FSDP State Dict Config of type `torch.distributed.fsdp.fully_sharded_data_parallel.StateDictConfig`"
|
1058 |
+
},
|
1059 |
+
)
|
1060 |
+
optim_state_dict_config: "typing.Any" = field(
|
1061 |
+
default=None,
|
1062 |
+
metadata={
|
1063 |
+
"help": "FSDP Optimizer State Dict Config of type `torch.distributed.fsdp.fully_sharded_data_parallel.OptimStateDictConfig`"
|
1064 |
+
},
|
1065 |
+
)
|
1066 |
+
limit_all_gathers: bool = field(
|
1067 |
+
default=True,
|
1068 |
+
metadata={
|
1069 |
+
"help": "If False, then FSDP allows the CPU thread to schedule all-gathers "
|
1070 |
+
"without any extra synchronization. If True, then FSDP explicitly synchronizes the CPU thread to prevent "
|
1071 |
+
"too many in-flight all-gathers. This bool only affects the sharded strategies that schedule all-gathers. "
|
1072 |
+
"Enabling this can help lower the number of CUDA malloc retries."
|
1073 |
+
},
|
1074 |
+
)
|
1075 |
+
use_orig_params: bool = field(
|
1076 |
+
default=True,
|
1077 |
+
metadata={
|
1078 |
+
"help": "If `True`, allows non-uniform `requires_grad` during init, which means support for interspersed frozen and trainable parameters. "
|
1079 |
+
"Useful in cases such as parameter-efficient fine-tuning. "
|
1080 |
+
"Please refer this [blog](https://dev-discuss.pytorch.org/t/rethinking-pytorch-fully-sharded-data-parallel-fsdp-from-first-principles/1019). "
|
1081 |
+
"This also enables multiple optimizer param groups. This should be `True` when creating an optimizer object before preparing/wrapping the model with FSDP."
|
1082 |
+
},
|
1083 |
+
)
|
1084 |
+
param_init_fn: Optional[Callable[[torch.nn.Module], None]] = field(
|
1085 |
+
default=None,
|
1086 |
+
metadata={
|
1087 |
+
"help": "A Callable[torch.nn.Module] -> None that specifies how modules "
|
1088 |
+
"that are currently on the meta device should be initialized onto an actual device."
|
1089 |
+
},
|
1090 |
+
)
|
1091 |
+
sync_module_states: bool = field(
|
1092 |
+
default=True,
|
1093 |
+
metadata={
|
1094 |
+
"help": "If True, each individually wrapped FSDP unit will broadcast module parameters from rank 0 "
|
1095 |
+
"to ensure they are the same across all ranks after initialization"
|
1096 |
+
},
|
1097 |
+
)
|
1098 |
+
forward_prefetch: bool = field(
|
1099 |
+
default=False,
|
1100 |
+
metadata={
|
1101 |
+
"help": "If True, then FSDP explicitly prefetches the next upcoming "
|
1102 |
+
"all-gather while executing in the forward pass. only use with Static graphs."
|
1103 |
+
},
|
1104 |
+
)
|
1105 |
+
activation_checkpointing: bool = field(
|
1106 |
+
default=False,
|
1107 |
+
metadata={
|
1108 |
+
"help": "If True, activation checkpointing is a technique to reduce memory usage by clearing activations of "
|
1109 |
+
"certain layers and recomputing them during a backward pass. Effectively, this trades extra computation time "
|
1110 |
+
"for reduced memory usage."
|
1111 |
+
},
|
1112 |
+
)
|
1113 |
+
|
1114 |
+
def __post_init__(self):
|
1115 |
+
from torch.distributed.fsdp.fully_sharded_data_parallel import BackwardPrefetch, CPUOffload, ShardingStrategy
|
1116 |
+
|
1117 |
+
prefix = "FSDP_"
|
1118 |
+
if self.sharding_strategy is None:
|
1119 |
+
sharding_strategy = os.environ.get(prefix + "SHARDING_STRATEGY", "FULL_SHARD")
|
1120 |
+
sharding_strategy = (
|
1121 |
+
FSDP_SHARDING_STRATEGY.index(sharding_strategy) + 1
|
1122 |
+
if not sharding_strategy.isdigit()
|
1123 |
+
else int(sharding_strategy)
|
1124 |
+
)
|
1125 |
+
self.sharding_strategy = ShardingStrategy(sharding_strategy)
|
1126 |
+
|
1127 |
+
if self.cpu_offload is None:
|
1128 |
+
if str_to_bool(os.environ.get(prefix + "OFFLOAD_PARAMS", "False")) == 1:
|
1129 |
+
self.cpu_offload = CPUOffload(offload_params=True)
|
1130 |
+
else:
|
1131 |
+
self.cpu_offload = CPUOffload(offload_params=False)
|
1132 |
+
|
1133 |
+
if self.backward_prefetch is None:
|
1134 |
+
prefetch_policy = os.environ.get(prefix + "BACKWARD_PREFETCH", "NO_PREFETCH")
|
1135 |
+
if prefetch_policy != FSDP_BACKWARD_PREFETCH[-1]:
|
1136 |
+
self.backward_prefetch = BackwardPrefetch(FSDP_BACKWARD_PREFETCH.index(prefetch_policy) + 1)
|
1137 |
+
|
1138 |
+
if self.state_dict_type is None:
|
1139 |
+
state_dict_type_policy = os.environ.get(prefix + "STATE_DICT_TYPE", "FULL_STATE_DICT")
|
1140 |
+
self.set_state_dict_type(state_dict_type_policy)
|
1141 |
+
self.use_orig_params = str_to_bool(os.environ.get(prefix + "USE_ORIG_PARAMS", "False")) == 1
|
1142 |
+
self.sync_module_states = str_to_bool(os.environ.get(prefix + "SYNC_MODULE_STATES", "True")) == 1
|
1143 |
+
self.forward_prefetch = str_to_bool(os.environ.get(prefix + "FORWARD_PREFETCH", "False")) == 1
|
1144 |
+
self.activation_checkpointing = str_to_bool(os.environ.get(prefix + "ACTIVATION_CHECKPOINTING", "False")) == 1
|
1145 |
+
|
1146 |
+
if str_to_bool(os.environ.get("FSDP_CPU_RAM_EFFICIENT_LOADING", "False")) == 1 and not self.sync_module_states:
|
1147 |
+
warnings.warn(
|
1148 |
+
"sync_module_states cannot be False since efficient cpu ram loading enabled. "
|
1149 |
+
"Setting sync_module_states to True."
|
1150 |
+
)
|
1151 |
+
self.sync_module_states = True
|
1152 |
+
|
1153 |
+
if self.sync_module_states:
|
1154 |
+
if is_npu_available():
|
1155 |
+
device = torch.npu.current_device()
|
1156 |
+
elif is_cuda_available():
|
1157 |
+
device = torch.cuda.current_device()
|
1158 |
+
elif is_xpu_available():
|
1159 |
+
device = torch.xpu.current_device()
|
1160 |
+
else:
|
1161 |
+
raise RuntimeError(
|
1162 |
+
"There are currently no available devices found, must be one of 'XPU', 'CUDA', or 'NPU'."
|
1163 |
+
)
|
1164 |
+
self.param_init_fn = lambda x: x.to_empty(device=device, recurse=False)
|
1165 |
+
|
1166 |
+
def set_auto_wrap_policy(self, model):
|
1167 |
+
from torch.distributed.fsdp.wrap import size_based_auto_wrap_policy, transformer_auto_wrap_policy
|
1168 |
+
|
1169 |
+
default_transformer_cls_names_to_wrap = (
|
1170 |
+
",".join(model._no_split_modules) if getattr(model, "_no_split_modules", None) is not None else ""
|
1171 |
+
)
|
1172 |
+
if self.auto_wrap_policy is None:
|
1173 |
+
auto_wrap_policy = os.environ.get("FSDP_AUTO_WRAP_POLICY", "NO_WRAP")
|
1174 |
+
if auto_wrap_policy == FSDP_AUTO_WRAP_POLICY[0]:
|
1175 |
+
transformer_cls_names_to_wrap = os.environ.get(
|
1176 |
+
"FSDP_TRANSFORMER_CLS_TO_WRAP", default_transformer_cls_names_to_wrap
|
1177 |
+
).split(",")
|
1178 |
+
transformer_cls_to_wrap = set()
|
1179 |
+
for layer_class in transformer_cls_names_to_wrap:
|
1180 |
+
transformer_cls = get_module_class_from_name(model, layer_class)
|
1181 |
+
if transformer_cls is None:
|
1182 |
+
raise Exception("Could not find the transformer layer class to wrap in the model.")
|
1183 |
+
else:
|
1184 |
+
transformer_cls_to_wrap.add(transformer_cls)
|
1185 |
+
|
1186 |
+
self.auto_wrap_policy = functools.partial(
|
1187 |
+
transformer_auto_wrap_policy,
|
1188 |
+
# Transformer layer class to wrap
|
1189 |
+
transformer_layer_cls=transformer_cls_to_wrap,
|
1190 |
+
)
|
1191 |
+
elif auto_wrap_policy == FSDP_AUTO_WRAP_POLICY[1]:
|
1192 |
+
min_num_params = int(os.environ.get("FSDP_MIN_NUM_PARAMS", 0))
|
1193 |
+
if min_num_params > 0:
|
1194 |
+
self.auto_wrap_policy = functools.partial(
|
1195 |
+
size_based_auto_wrap_policy, min_num_params=min_num_params
|
1196 |
+
)
|
1197 |
+
|
1198 |
+
def set_mixed_precision(self, mixed_precision, buffer_autocast=False, override=False):
|
1199 |
+
if isinstance(mixed_precision, str):
|
1200 |
+
if mixed_precision == "fp16":
|
1201 |
+
dtype = torch.float16
|
1202 |
+
elif mixed_precision == "bf16":
|
1203 |
+
dtype = torch.bfloat16
|
1204 |
+
elif mixed_precision == "fp32":
|
1205 |
+
dtype = torch.float32
|
1206 |
+
else:
|
1207 |
+
raise ValueError(f"Unknown mixed precision value: {mixed_precision}")
|
1208 |
+
else:
|
1209 |
+
dtype = mixed_precision
|
1210 |
+
|
1211 |
+
buffer_dtype = torch.float32 if buffer_autocast else dtype
|
1212 |
+
from torch.distributed.fsdp.fully_sharded_data_parallel import MixedPrecision
|
1213 |
+
|
1214 |
+
if self.mixed_precision_policy is None or override:
|
1215 |
+
self.mixed_precision_policy = MixedPrecision(
|
1216 |
+
param_dtype=dtype, reduce_dtype=dtype, buffer_dtype=buffer_dtype
|
1217 |
+
)
|
1218 |
+
|
1219 |
+
def set_state_dict_type(self, state_dict_type_policy):
|
1220 |
+
from torch.distributed.fsdp.fully_sharded_data_parallel import (
|
1221 |
+
FullOptimStateDictConfig,
|
1222 |
+
FullStateDictConfig,
|
1223 |
+
StateDictType,
|
1224 |
+
)
|
1225 |
+
|
1226 |
+
self.state_dict_type = StateDictType(FSDP_STATE_DICT_TYPE.index(state_dict_type_policy) + 1)
|
1227 |
+
|
1228 |
+
if self.state_dict_type == StateDictType.FULL_STATE_DICT:
|
1229 |
+
if self.state_dict_config is None:
|
1230 |
+
self.state_dict_config = FullStateDictConfig(offload_to_cpu=True, rank0_only=True)
|
1231 |
+
if self.optim_state_dict_config is None:
|
1232 |
+
self.optim_state_dict_config = FullOptimStateDictConfig(offload_to_cpu=True, rank0_only=True)
|
1233 |
+
|
1234 |
+
|
1235 |
+
@dataclass
|
1236 |
+
class MegatronLMPlugin:
|
1237 |
+
"""
|
1238 |
+
Plugin for Megatron-LM to enable tensor, pipeline, sequence and data parallelism. Also to enable selective
|
1239 |
+
activation recomputation and optimized fused kernels.
|
1240 |
+
"""
|
1241 |
+
|
1242 |
+
tp_degree: int = field(default=None, metadata={"help": "tensor parallelism degree."})
|
1243 |
+
pp_degree: int = field(default=None, metadata={"help": "pipeline parallelism degree."})
|
1244 |
+
num_micro_batches: int = field(default=None, metadata={"help": "number of micro-batches."})
|
1245 |
+
gradient_clipping: float = field(
|
1246 |
+
default=None, metadata={"help": "gradient clipping value based on global L2 Norm (0 to disable)"}
|
1247 |
+
)
|
1248 |
+
sequence_parallelism: bool = field(
|
1249 |
+
default=None,
|
1250 |
+
metadata={"help": "enable sequence parallelism"},
|
1251 |
+
)
|
1252 |
+
recompute_activations: bool = field(
|
1253 |
+
default=None,
|
1254 |
+
metadata={"help": "enable selective activation recomputation"},
|
1255 |
+
)
|
1256 |
+
use_distributed_optimizer: bool = field(
|
1257 |
+
default=None,
|
1258 |
+
metadata={"help": "enable distributed optimizer"},
|
1259 |
+
)
|
1260 |
+
pipeline_model_parallel_split_rank: int = field(
|
1261 |
+
default=None, metadata={"help": "Rank where encoder and decoder should be split."}
|
1262 |
+
)
|
1263 |
+
num_layers_per_virtual_pipeline_stage: int = field(
|
1264 |
+
default=None, metadata={"help": "Number of layers per virtual pipeline stage."}
|
1265 |
+
)
|
1266 |
+
is_train_batch_min: str = field(
|
1267 |
+
default=True,
|
1268 |
+
metadata={"help": "If both train & eval dataloaders are specified, this will decide the micro_batch_size"},
|
1269 |
+
)
|
1270 |
+
train_iters: int = field(
|
1271 |
+
default=None,
|
1272 |
+
metadata={
|
1273 |
+
"help": "Total number of iterations to train over all training runs. "
|
1274 |
+
"Note that either train-iters or train-samples should be provided when using `MegatronLMDummyScheduler`"
|
1275 |
+
},
|
1276 |
+
)
|
1277 |
+
train_samples: int = field(
|
1278 |
+
default=None,
|
1279 |
+
metadata={
|
1280 |
+
"help": "Total number of samples to train over all training runs. "
|
1281 |
+
"Note that either train-iters or train-samples should be provided when using `MegatronLMDummyScheduler`"
|
1282 |
+
},
|
1283 |
+
)
|
1284 |
+
weight_decay_incr_style: str = field(
|
1285 |
+
default="constant",
|
1286 |
+
metadata={"help": 'Weight decay increment function. choices=["constant", "linear", "cosine"]. '},
|
1287 |
+
)
|
1288 |
+
start_weight_decay: float = field(
|
1289 |
+
default=None,
|
1290 |
+
metadata={"help": "Initial weight decay coefficient for L2 regularization."},
|
1291 |
+
)
|
1292 |
+
end_weight_decay: float = field(
|
1293 |
+
default=None,
|
1294 |
+
metadata={"help": "End of run weight decay coefficient for L2 regularization."},
|
1295 |
+
)
|
1296 |
+
lr_decay_style: str = field(
|
1297 |
+
default="linear",
|
1298 |
+
metadata={"help": "Learning rate decay function. choices=['constant', 'linear', 'cosine']."},
|
1299 |
+
)
|
1300 |
+
lr_decay_iters: int = field(
|
1301 |
+
default=None,
|
1302 |
+
metadata={"help": "Number of iterations for learning rate decay. If None defaults to `train_iters`."},
|
1303 |
+
)
|
1304 |
+
lr_decay_samples: int = field(
|
1305 |
+
default=None,
|
1306 |
+
metadata={"help": "Number of samples for learning rate decay. If None defaults to `train_samples`."},
|
1307 |
+
)
|
1308 |
+
lr_warmup_iters: int = field(
|
1309 |
+
default=None,
|
1310 |
+
metadata={"help": "number of iterations to linearly warmup learning rate over."},
|
1311 |
+
)
|
1312 |
+
lr_warmup_samples: int = field(
|
1313 |
+
default=None,
|
1314 |
+
metadata={"help": "number of samples to linearly warmup learning rate over."},
|
1315 |
+
)
|
1316 |
+
lr_warmup_fraction: float = field(
|
1317 |
+
default=None,
|
1318 |
+
metadata={"help": "fraction of lr-warmup-(iters/samples) to linearly warmup learning rate over."},
|
1319 |
+
)
|
1320 |
+
min_lr: float = field(
|
1321 |
+
default=0,
|
1322 |
+
metadata={"help": "Minumum value for learning rate. The scheduler clip values below this threshold."},
|
1323 |
+
)
|
1324 |
+
consumed_samples: List[int] = field(
|
1325 |
+
default=None,
|
1326 |
+
metadata={
|
1327 |
+
"help": "Number of samples consumed in the same order as the dataloaders to `accelerator.prepare` call."
|
1328 |
+
},
|
1329 |
+
)
|
1330 |
+
no_wd_decay_cond: Optional[Callable] = field(default=None, metadata={"help": "Condition to disable weight decay."})
|
1331 |
+
scale_lr_cond: Optional[Callable] = field(default=None, metadata={"help": "Condition to scale learning rate."})
|
1332 |
+
lr_mult: float = field(default=1.0, metadata={"help": "Learning rate multiplier."})
|
1333 |
+
megatron_dataset_flag: bool = field(
|
1334 |
+
default=False,
|
1335 |
+
metadata={"help": "Whether the format of dataset follows Megatron-LM Indexed/Cached/MemoryMapped format."},
|
1336 |
+
)
|
1337 |
+
seq_length: int = field(
|
1338 |
+
default=None,
|
1339 |
+
metadata={"help": "Maximum sequence length to process."},
|
1340 |
+
)
|
1341 |
+
encoder_seq_length: int = field(
|
1342 |
+
default=None,
|
1343 |
+
metadata={"help": "Maximum sequence length to process for the encoder."},
|
1344 |
+
)
|
1345 |
+
decoder_seq_length: int = field(
|
1346 |
+
default=None,
|
1347 |
+
metadata={"help": "Maximum sequence length to process for the decoder."},
|
1348 |
+
)
|
1349 |
+
tensorboard_dir: str = field(
|
1350 |
+
default=None,
|
1351 |
+
metadata={"help": "Path to save tensorboard logs."},
|
1352 |
+
)
|
1353 |
+
set_all_logging_options: bool = field(
|
1354 |
+
default=False,
|
1355 |
+
metadata={"help": "Whether to set all logging options."},
|
1356 |
+
)
|
1357 |
+
eval_iters: int = field(
|
1358 |
+
default=100, metadata={"help": "Number of iterations to run for evaluation validation/test for."}
|
1359 |
+
)
|
1360 |
+
eval_interval: int = field(
|
1361 |
+
default=1000, metadata={"help": "Interval between running evaluation on validation set."}
|
1362 |
+
)
|
1363 |
+
return_logits: bool = field(
|
1364 |
+
default=False,
|
1365 |
+
metadata={"help": "Whether to return logits from the model."},
|
1366 |
+
)
|
1367 |
+
|
1368 |
+
# custom train step args
|
1369 |
+
custom_train_step_class: Optional[Any] = field(
|
1370 |
+
default=None,
|
1371 |
+
metadata={"help": "Custom train step class."},
|
1372 |
+
)
|
1373 |
+
custom_train_step_kwargs: Optional[Dict[str, Any]] = field(
|
1374 |
+
default=None,
|
1375 |
+
metadata={"help": "Custom train step kwargs."},
|
1376 |
+
)
|
1377 |
+
|
1378 |
+
# custom model args
|
1379 |
+
custom_model_provider_function: Optional[Callable] = field(
|
1380 |
+
default=None,
|
1381 |
+
metadata={"help": "Custom model provider function."},
|
1382 |
+
)
|
1383 |
+
custom_prepare_model_function: Optional[Callable] = field(
|
1384 |
+
default=None,
|
1385 |
+
metadata={"help": "Custom prepare model function."},
|
1386 |
+
)
|
1387 |
+
|
1388 |
+
# remaining args such as enabling Alibi/ROPE positional embeddings,
|
1389 |
+
# wandb logging, Multi-Query Attention, etc.
|
1390 |
+
other_megatron_args: Optional[Dict[str, Any]] = field(
|
1391 |
+
default=None,
|
1392 |
+
metadata={"help": "Other Megatron-LM arguments. Please refer Megatron-LM"},
|
1393 |
+
)
|
1394 |
+
|
1395 |
+
def __post_init__(self):
|
1396 |
+
prefix = "MEGATRON_LM_"
|
1397 |
+
if self.tp_degree is None:
|
1398 |
+
self.tp_degree = int(os.environ.get(prefix + "TP_DEGREE", 1))
|
1399 |
+
if self.pp_degree is None:
|
1400 |
+
self.pp_degree = int(os.environ.get(prefix + "PP_DEGREE", 1))
|
1401 |
+
if self.num_micro_batches is None:
|
1402 |
+
self.num_micro_batches = int(os.environ.get(prefix + "NUM_MICRO_BATCHES", 1))
|
1403 |
+
if self.gradient_clipping is None:
|
1404 |
+
self.gradient_clipping = float(os.environ.get(prefix + "GRADIENT_CLIPPING", 1.0))
|
1405 |
+
if self.recompute_activations is None:
|
1406 |
+
self.recompute_activations = str_to_bool(os.environ.get(prefix + "RECOMPUTE_ACTIVATIONS", "False")) == 1
|
1407 |
+
if self.use_distributed_optimizer is None:
|
1408 |
+
self.use_distributed_optimizer = (
|
1409 |
+
str_to_bool(os.environ.get(prefix + "USE_DISTRIBUTED_OPTIMIZER", "False")) == 1
|
1410 |
+
)
|
1411 |
+
if self.sequence_parallelism is None:
|
1412 |
+
self.sequence_parallelism = str_to_bool(os.environ.get(prefix + "SEQUENCE_PARALLELISM", "False")) == 1
|
1413 |
+
|
1414 |
+
if self.pp_degree > 1 or self.use_distributed_optimizer:
|
1415 |
+
self.DDP_impl = "local"
|
1416 |
+
else:
|
1417 |
+
self.DDP_impl = "torch"
|
1418 |
+
|
1419 |
+
if self.consumed_samples is not None:
|
1420 |
+
if len(self.consumed_samples) == 1:
|
1421 |
+
self.consumed_samples.extend([0, 0])
|
1422 |
+
elif len(self.consumed_samples) == 2:
|
1423 |
+
self.consumed_samples.append(0)
|
1424 |
+
|
1425 |
+
self.megatron_lm_default_args = {
|
1426 |
+
"tensor_model_parallel_size": self.tp_degree,
|
1427 |
+
"pipeline_model_parallel_size": self.pp_degree,
|
1428 |
+
"pipeline_model_parallel_split_rank": self.pipeline_model_parallel_split_rank,
|
1429 |
+
"num_layers_per_virtual_pipeline_stage": self.num_layers_per_virtual_pipeline_stage,
|
1430 |
+
"DDP_impl": self.DDP_impl,
|
1431 |
+
"use_distributed_optimizer": self.use_distributed_optimizer,
|
1432 |
+
"sequence_parallel": self.sequence_parallelism,
|
1433 |
+
"clip_grad": self.gradient_clipping,
|
1434 |
+
"num_micro_batches": self.num_micro_batches,
|
1435 |
+
"consumed_samples": self.consumed_samples,
|
1436 |
+
"no_wd_decay_cond": self.no_wd_decay_cond,
|
1437 |
+
"scale_lr_cond": self.scale_lr_cond,
|
1438 |
+
"lr_mult": self.lr_mult,
|
1439 |
+
"megatron_dataset_flag": self.megatron_dataset_flag,
|
1440 |
+
"eval_iters": self.eval_iters,
|
1441 |
+
"eval_interval": self.eval_interval,
|
1442 |
+
}
|
1443 |
+
if self.recompute_activations:
|
1444 |
+
self.megatron_lm_default_args["recompute_granularity"] = "selective"
|
1445 |
+
if self.tensorboard_dir is not None:
|
1446 |
+
self.megatron_lm_default_args["tensorboard_dir"] = self.tensorboard_dir
|
1447 |
+
if self.set_all_logging_options:
|
1448 |
+
self.set_tensorboard_logging_options()
|
1449 |
+
if self.other_megatron_args is not None:
|
1450 |
+
self.megatron_lm_default_args.update(self.other_megatron_args)
|
1451 |
+
|
1452 |
+
def set_network_size_args(self, model, batch_data=None):
|
1453 |
+
# Check if the model is either BERT, GPT or T5 else raise error
|
1454 |
+
# set 'num_layers', 'hidden_size', 'num_attention_heads', 'max_position_embeddings'
|
1455 |
+
if "megatron-bert" in model.config.model_type.lower():
|
1456 |
+
model_type_name = "bert"
|
1457 |
+
num_layers = model.config.num_hidden_layers
|
1458 |
+
hidden_size = model.config.hidden_size
|
1459 |
+
num_attention_heads = model.config.num_attention_heads
|
1460 |
+
max_position_embeddings = model.config.max_position_embeddings
|
1461 |
+
num_labels = model.config.num_labels
|
1462 |
+
orig_vocab_size = model.config.vocab_size
|
1463 |
+
if "maskedlm" in model.__class__.__name__.lower():
|
1464 |
+
pretraining_flag = True
|
1465 |
+
if self.seq_length is not None:
|
1466 |
+
if self.encoder_seq_length is not None:
|
1467 |
+
warnings.warn("Both `seq_length` and `encoder_seq_length` are set. Using `encoder_seq_length`.")
|
1468 |
+
self.seq_length = self.encoder_seq_length
|
1469 |
+
elif self.encoder_seq_length is not None:
|
1470 |
+
self.seq_length = self.encoder_seq_length
|
1471 |
+
elif batch_data is not None:
|
1472 |
+
self.seq_length = batch_data["input_ids"].shape[1]
|
1473 |
+
else:
|
1474 |
+
self.seq_length = max_position_embeddings
|
1475 |
+
self.megatron_lm_default_args["seq_length"] = self.seq_length
|
1476 |
+
elif "gpt2" in model.config.model_type.lower():
|
1477 |
+
model_type_name = "gpt"
|
1478 |
+
num_layers = model.config.n_layer
|
1479 |
+
hidden_size = model.config.n_embd
|
1480 |
+
num_attention_heads = model.config.n_head
|
1481 |
+
max_position_embeddings = model.config.n_positions
|
1482 |
+
orig_vocab_size = model.config.vocab_size
|
1483 |
+
pretraining_flag = True
|
1484 |
+
if self.seq_length is not None:
|
1485 |
+
if self.decoder_seq_length is not None:
|
1486 |
+
warnings.warn("Both `seq_length` and `decoder_seq_length` are set. Using `decoder_seq_length`.")
|
1487 |
+
self.seq_length = self.decoder_seq_length
|
1488 |
+
elif self.decoder_seq_length is not None:
|
1489 |
+
self.seq_length = self.decoder_seq_length
|
1490 |
+
elif batch_data is not None:
|
1491 |
+
self.seq_length = batch_data["input_ids"].shape[1]
|
1492 |
+
else:
|
1493 |
+
self.seq_length = max_position_embeddings
|
1494 |
+
self.megatron_lm_default_args["seq_length"] = self.seq_length
|
1495 |
+
self.megatron_lm_default_args["return_logits"] = self.return_logits
|
1496 |
+
self.megatron_lm_default_args["tokenizer_type"] = "GPT2BPETokenizer"
|
1497 |
+
elif "t5" in model.config.model_type.lower():
|
1498 |
+
model_type_name = "t5"
|
1499 |
+
num_layers = model.config.num_layers
|
1500 |
+
hidden_size = model.config.d_model
|
1501 |
+
num_attention_heads = model.config.num_heads
|
1502 |
+
max_position_embeddings = model.config.n_positions if hasattr(model.config, "n_positions") else 1024
|
1503 |
+
orig_vocab_size = model.config.vocab_size
|
1504 |
+
pretraining_flag = True
|
1505 |
+
if self.encoder_seq_length is None:
|
1506 |
+
if batch_data is not None:
|
1507 |
+
self.encoder_seq_length = batch_data["input_ids"].shape[1]
|
1508 |
+
else:
|
1509 |
+
self.encoder_seq_length = max_position_embeddings
|
1510 |
+
if self.decoder_seq_length is None:
|
1511 |
+
if batch_data is not None:
|
1512 |
+
self.decoder_seq_length = batch_data["labels"].shape[1]
|
1513 |
+
else:
|
1514 |
+
self.decoder_seq_length = max_position_embeddings
|
1515 |
+
|
1516 |
+
self.megatron_lm_default_args["encoder_seq_length"] = self.encoder_seq_length
|
1517 |
+
self.megatron_lm_default_args["decoder_seq_length"] = self.decoder_seq_length
|
1518 |
+
else:
|
1519 |
+
raise ValueError(
|
1520 |
+
"🤗 Accelerate Megatron-LM integration supports only BERT, GPT and T5 model. "
|
1521 |
+
"Please check the model you are using is one of those."
|
1522 |
+
)
|
1523 |
+
|
1524 |
+
self.megatron_lm_default_args["model_type_name"] = model_type_name
|
1525 |
+
self.megatron_lm_default_args["num_layers"] = num_layers
|
1526 |
+
self.megatron_lm_default_args["hidden_size"] = hidden_size
|
1527 |
+
self.megatron_lm_default_args["num_attention_heads"] = num_attention_heads
|
1528 |
+
self.megatron_lm_default_args["max_position_embeddings"] = max_position_embeddings
|
1529 |
+
self.megatron_lm_default_args["pretraining_flag"] = pretraining_flag
|
1530 |
+
self.megatron_lm_default_args["orig_vocab_size"] = orig_vocab_size
|
1531 |
+
self.megatron_lm_default_args["model_return_dict"] = model.config.return_dict
|
1532 |
+
if model_type_name == "bert":
|
1533 |
+
self.megatron_lm_default_args["num_labels"] = num_labels
|
1534 |
+
|
1535 |
+
def set_mixed_precision(self, mixed_precision):
|
1536 |
+
if mixed_precision == "fp16":
|
1537 |
+
self.megatron_lm_default_args["fp16"] = True
|
1538 |
+
elif mixed_precision == "bf16":
|
1539 |
+
self.megatron_lm_default_args["bf16"] = True
|
1540 |
+
self.DDP_impl = "local"
|
1541 |
+
self.megatron_lm_default_args["DDP_impl"] = self.DDP_impl
|
1542 |
+
|
1543 |
+
def set_training_args(self, micro_batch_size, dp_degree):
|
1544 |
+
self.data_parallel_size = dp_degree
|
1545 |
+
self.micro_batch_size = micro_batch_size
|
1546 |
+
self.global_batch_size = dp_degree * micro_batch_size * self.num_micro_batches
|
1547 |
+
self.megatron_lm_default_args["data_parallel_size"] = self.data_parallel_size
|
1548 |
+
self.megatron_lm_default_args["micro_batch_size"] = self.micro_batch_size
|
1549 |
+
self.megatron_lm_default_args["global_batch_size"] = self.global_batch_size
|
1550 |
+
|
1551 |
+
def set_optimizer_type(self, optimizer):
|
1552 |
+
optimizer_name = optimizer.__class__.__name__.lower()
|
1553 |
+
if "adam" in optimizer_name:
|
1554 |
+
self.megatron_lm_default_args["optimizer"] = "adam"
|
1555 |
+
self.megatron_lm_default_args["adam_beta1"] = optimizer.defaults["betas"][0]
|
1556 |
+
self.megatron_lm_default_args["adam_beta2"] = optimizer.defaults["betas"][1]
|
1557 |
+
self.megatron_lm_default_args["adam_eps"] = optimizer.defaults["eps"]
|
1558 |
+
elif "sgd" in optimizer_name:
|
1559 |
+
self.megatron_lm_default_args["optimizer"] = "sgd"
|
1560 |
+
self.megatron_lm_default_args["sgd_momentum"] = optimizer.defaults["momentum"]
|
1561 |
+
else:
|
1562 |
+
raise ValueError(f"Optimizer {optimizer_name} is not supported by Megatron-LM")
|
1563 |
+
|
1564 |
+
self.megatron_lm_default_args["lr"] = optimizer.defaults["lr"]
|
1565 |
+
self.megatron_lm_default_args["weight_decay"] = optimizer.defaults["weight_decay"]
|
1566 |
+
|
1567 |
+
def set_scheduler_args(self, scheduler):
|
1568 |
+
if self.train_iters is None:
|
1569 |
+
self.train_iters = scheduler.total_num_steps // self.megatron_lm_default_args["data_parallel_size"]
|
1570 |
+
if self.train_samples is not None:
|
1571 |
+
self.train_samples = None
|
1572 |
+
warnings.warn(
|
1573 |
+
"Ignoring `train_samples` as `train_iters` based on scheduler is being used for training."
|
1574 |
+
)
|
1575 |
+
if self.lr_warmup_iters is None:
|
1576 |
+
self.lr_warmup_iters = scheduler.warmup_num_steps // self.megatron_lm_default_args["data_parallel_size"]
|
1577 |
+
if self.lr_warmup_samples is not None:
|
1578 |
+
warnings.warn(
|
1579 |
+
"Ignoring `lr_warmup_samples` as `lr_warmup_iters` based on scheduler is being used for training."
|
1580 |
+
)
|
1581 |
+
self.lr_warmup_samples = 0
|
1582 |
+
|
1583 |
+
self.megatron_lm_default_args["train_iters"] = self.train_iters
|
1584 |
+
self.megatron_lm_default_args["lr_warmup_iters"] = self.lr_warmup_iters
|
1585 |
+
self.megatron_lm_default_args["train_samples"] = self.train_samples
|
1586 |
+
self.megatron_lm_default_args["lr_warmup_samples"] = self.lr_warmup_samples
|
1587 |
+
self.megatron_lm_default_args["lr_decay_iters"] = self.lr_decay_iters
|
1588 |
+
self.megatron_lm_default_args["lr_decay_samples"] = self.lr_decay_samples
|
1589 |
+
self.megatron_lm_default_args["lr_warmup_fraction"] = self.lr_warmup_fraction
|
1590 |
+
self.megatron_lm_default_args["lr_decay_style"] = self.lr_decay_style
|
1591 |
+
self.megatron_lm_default_args["weight_decay_incr_style"] = self.weight_decay_incr_style
|
1592 |
+
self.megatron_lm_default_args["start_weight_decay"] = self.start_weight_decay
|
1593 |
+
self.megatron_lm_default_args["end_weight_decay"] = self.end_weight_decay
|
1594 |
+
self.megatron_lm_default_args["min_lr"] = self.min_lr
|
1595 |
+
|
1596 |
+
def set_tensorboard_logging_options(self):
|
1597 |
+
from megatron.arguments import _add_logging_args
|
1598 |
+
|
1599 |
+
parser = argparse.ArgumentParser()
|
1600 |
+
parser = _add_logging_args(parser)
|
1601 |
+
logging_args = parser.parse_known_args()
|
1602 |
+
self.dataset_args = vars(logging_args[0])
|
1603 |
+
for key, value in self.dataset_args.items():
|
1604 |
+
if key.startswith("log_"):
|
1605 |
+
self.megatron_lm_default_args[key] = True
|
1606 |
+
elif key.startswith("no_log_"):
|
1607 |
+
self.megatron_lm_default_args[key.replace("no_", "")] = True
|
1608 |
+
|
1609 |
+
|
1610 |
+
@dataclass
|
1611 |
+
class BnbQuantizationConfig:
|
1612 |
+
"""
|
1613 |
+
A plugin to enable BitsAndBytes 4bit and 8bit quantization
|
1614 |
+
"""
|
1615 |
+
|
1616 |
+
load_in_8bit: bool = field(default=False, metadata={"help": "enable 8bit quantization."})
|
1617 |
+
|
1618 |
+
llm_int8_threshold: float = field(
|
1619 |
+
default=6.0, metadata={"help": "value of the outliner threshold. only relevant when load_in_8bit=True"}
|
1620 |
+
)
|
1621 |
+
|
1622 |
+
load_in_4bit: bool = field(default=False, metadata={"help": "enable 4bit quantization."})
|
1623 |
+
|
1624 |
+
bnb_4bit_quant_type: str = field(
|
1625 |
+
default="fp4",
|
1626 |
+
metadata={
|
1627 |
+
"help": "set the quantization data type in the `bnb.nn.Linear4Bit` layers. Options are {'fp4','np4'}."
|
1628 |
+
},
|
1629 |
+
)
|
1630 |
+
|
1631 |
+
bnb_4bit_use_double_quant: bool = field(
|
1632 |
+
default=False,
|
1633 |
+
metadata={
|
1634 |
+
"help": "enable nested quantization where the quantization constants from the first quantization are quantized again."
|
1635 |
+
},
|
1636 |
+
)
|
1637 |
+
|
1638 |
+
bnb_4bit_compute_dtype: bool = field(
|
1639 |
+
default="fp16",
|
1640 |
+
metadata={
|
1641 |
+
"help": "This sets the computational type which might be different than the input time. For example, inputs might be "
|
1642 |
+
"fp32, but computation can be set to bf16 for speedups. Options are {'fp32','fp16','bf16'}."
|
1643 |
+
},
|
1644 |
+
)
|
1645 |
+
|
1646 |
+
torch_dtype: torch.dtype = field(
|
1647 |
+
default=None,
|
1648 |
+
metadata={
|
1649 |
+
"help": "this sets the dtype of the remaining non quantized layers. `bitsandbytes` library suggests to set the value"
|
1650 |
+
"to `torch.float16` for 8 bit model and use the same dtype as the compute dtype for 4 bit model "
|
1651 |
+
},
|
1652 |
+
)
|
1653 |
+
|
1654 |
+
skip_modules: List[str] = field(
|
1655 |
+
default=None,
|
1656 |
+
metadata={
|
1657 |
+
"help": "an explicit list of the modules that we don't quantize. The dtype of these modules will be `torch_dtype`."
|
1658 |
+
},
|
1659 |
+
)
|
1660 |
+
|
1661 |
+
keep_in_fp32_modules: List[str] = field(
|
1662 |
+
default=None,
|
1663 |
+
metadata={"help": "an explicit list of the modules that we don't quantize. We keep them in `torch.float32`."},
|
1664 |
+
)
|
1665 |
+
|
1666 |
+
def __post_init__(self):
|
1667 |
+
"""
|
1668 |
+
Safety checker that arguments are correct - also replaces some NoneType arguments with their default values.
|
1669 |
+
"""
|
1670 |
+
if not isinstance(self.load_in_8bit, bool):
|
1671 |
+
raise ValueError("load_in_8bit must be a boolean")
|
1672 |
+
|
1673 |
+
if not isinstance(self.load_in_4bit, bool):
|
1674 |
+
raise ValueError("load_in_4bit must be a boolean")
|
1675 |
+
|
1676 |
+
if self.load_in_4bit and self.load_in_8bit:
|
1677 |
+
raise ValueError("load_in_4bit and load_in_8 can't be both True")
|
1678 |
+
|
1679 |
+
if not self.load_in_4bit and not self.load_in_8bit:
|
1680 |
+
raise ValueError("load_in_4bit and load_in_8 can't be both False")
|
1681 |
+
|
1682 |
+
if not isinstance(self.llm_int8_threshold, (int, float)):
|
1683 |
+
raise ValueError("llm_int8_threshold must be a float or an int")
|
1684 |
+
|
1685 |
+
if not isinstance(self.bnb_4bit_quant_type, str):
|
1686 |
+
raise ValueError("bnb_4bit_quant_type must be a string")
|
1687 |
+
elif self.bnb_4bit_quant_type not in ["fp4", "nf4"]:
|
1688 |
+
raise ValueError(f"bnb_4bit_quant_type must be in ['fp4','nf4'] but found {self.bnb_4bit_quant_type}")
|
1689 |
+
|
1690 |
+
if not isinstance(self.bnb_4bit_use_double_quant, bool):
|
1691 |
+
raise ValueError("bnb_4bit_use_double_quant must be a boolean")
|
1692 |
+
|
1693 |
+
if isinstance(self.bnb_4bit_compute_dtype, str):
|
1694 |
+
if self.bnb_4bit_compute_dtype == "fp32":
|
1695 |
+
self.bnb_4bit_compute_dtype = torch.float32
|
1696 |
+
elif self.bnb_4bit_compute_dtype == "fp16":
|
1697 |
+
self.bnb_4bit_compute_dtype = torch.float16
|
1698 |
+
elif self.bnb_4bit_compute_dtype == "bf16":
|
1699 |
+
self.bnb_4bit_compute_dtype = torch.bfloat16
|
1700 |
+
else:
|
1701 |
+
raise ValueError(
|
1702 |
+
f"bnb_4bit_compute_dtype must be in ['fp32','fp16','bf16'] but found {self.bnb_4bit_compute_dtype}"
|
1703 |
+
)
|
1704 |
+
elif not isinstance(self.bnb_4bit_compute_dtype, torch.dtype):
|
1705 |
+
raise ValueError("bnb_4bit_compute_dtype must be a string or a torch.dtype")
|
1706 |
+
|
1707 |
+
if self.skip_modules is not None and not isinstance(self.skip_modules, list):
|
1708 |
+
raise ValueError("skip_modules must be a list of strings")
|
1709 |
+
|
1710 |
+
if self.keep_in_fp32_modules is not None and not isinstance(self.keep_in_fp32_modules, list):
|
1711 |
+
raise ValueError("keep_in_fp_32_modules must be a list of strings")
|
1712 |
+
|
1713 |
+
if self.load_in_4bit:
|
1714 |
+
self.target_dtype = CustomDtype.INT4
|
1715 |
+
|
1716 |
+
if self.load_in_8bit:
|
1717 |
+
self.target_dtype = torch.int8
|
1718 |
+
|
1719 |
+
if self.load_in_4bit and self.llm_int8_threshold != 6.0:
|
1720 |
+
warnings.warn("llm_int8_threshold can only be used for model loaded in 8bit")
|
1721 |
+
|
1722 |
+
if isinstance(self.torch_dtype, str):
|
1723 |
+
if self.torch_dtype == "fp32":
|
1724 |
+
self.torch_dtype = torch.float32
|
1725 |
+
elif self.torch_dtype == "fp16":
|
1726 |
+
self.torch_dtype = torch.float16
|
1727 |
+
elif self.torch_dtype == "bf16":
|
1728 |
+
self.torch_dtype = torch.bfloat16
|
1729 |
+
else:
|
1730 |
+
raise ValueError(f"torch_dtype must be in ['fp32','fp16','bf16'] but found {self.torch_dtype}")
|
1731 |
+
if self.load_in_8bit and self.torch_dtype is None:
|
1732 |
+
self.torch_dtype = torch.float16
|
1733 |
+
|
1734 |
+
if self.load_in_4bit and self.torch_dtype is None:
|
1735 |
+
self.torch_dtype = self.bnb_4bit_compute_dtype
|
1736 |
+
|
1737 |
+
if not isinstance(self.torch_dtype, torch.dtype):
|
1738 |
+
raise ValueError("torch_dtype must be a torch.dtype")
|
1739 |
+
|
1740 |
+
|
1741 |
+
def get_module_class_from_name(module, name):
|
1742 |
+
"""
|
1743 |
+
Gets a class from a module by its name.
|
1744 |
+
|
1745 |
+
Args:
|
1746 |
+
module (`torch.nn.Module`): The module to get the class from.
|
1747 |
+
name (`str`): The name of the class.
|
1748 |
+
"""
|
1749 |
+
modules_children = list(module.children())
|
1750 |
+
if module.__class__.__name__ == name:
|
1751 |
+
return module.__class__
|
1752 |
+
elif len(modules_children) == 0:
|
1753 |
+
return
|
1754 |
+
else:
|
1755 |
+
for child_module in modules_children:
|
1756 |
+
module_class = get_module_class_from_name(child_module, name)
|
1757 |
+
if module_class is not None:
|
1758 |
+
return module_class
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/environment.py
ADDED
@@ -0,0 +1,274 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
import logging
|
16 |
+
import math
|
17 |
+
import os
|
18 |
+
import platform
|
19 |
+
import subprocess
|
20 |
+
import sys
|
21 |
+
from dataclasses import dataclass, field
|
22 |
+
from functools import lru_cache
|
23 |
+
from shutil import which
|
24 |
+
from typing import List, Optional
|
25 |
+
|
26 |
+
import torch
|
27 |
+
from packaging.version import parse
|
28 |
+
|
29 |
+
|
30 |
+
logger = logging.getLogger(__name__)
|
31 |
+
|
32 |
+
|
33 |
+
def convert_dict_to_env_variables(current_env: dict):
|
34 |
+
"""
|
35 |
+
Verifies that all keys and values in `current_env` do not contain illegal keys or values, and returns a list of
|
36 |
+
strings as the result.
|
37 |
+
|
38 |
+
Example:
|
39 |
+
```python
|
40 |
+
>>> from accelerate.utils.environment import verify_env
|
41 |
+
|
42 |
+
>>> env = {"ACCELERATE_DEBUG_MODE": "1", "BAD_ENV_NAME": "<mything", "OTHER_ENV": "2"}
|
43 |
+
>>> valid_env_items = verify_env(env)
|
44 |
+
>>> print(valid_env_items)
|
45 |
+
["ACCELERATE_DEBUG_MODE=1\n", "OTHER_ENV=2\n"]
|
46 |
+
```
|
47 |
+
"""
|
48 |
+
forbidden_chars = [";", "\n", "<", ">", " "]
|
49 |
+
valid_env_items = []
|
50 |
+
for key, value in current_env.items():
|
51 |
+
if all(char not in (key + value) for char in forbidden_chars) and len(key) >= 1 and len(value) >= 1:
|
52 |
+
valid_env_items.append(f"{key}={value}\n")
|
53 |
+
else:
|
54 |
+
logger.warning(f"WARNING: Skipping {key}={value} as it contains forbidden characters or missing values.")
|
55 |
+
return valid_env_items
|
56 |
+
|
57 |
+
|
58 |
+
def str_to_bool(value) -> int:
|
59 |
+
"""
|
60 |
+
Converts a string representation of truth to `True` (1) or `False` (0).
|
61 |
+
|
62 |
+
True values are `y`, `yes`, `t`, `true`, `on`, and `1`; False value are `n`, `no`, `f`, `false`, `off`, and `0`;
|
63 |
+
"""
|
64 |
+
value = value.lower()
|
65 |
+
if value in ("y", "yes", "t", "true", "on", "1"):
|
66 |
+
return 1
|
67 |
+
elif value in ("n", "no", "f", "false", "off", "0"):
|
68 |
+
return 0
|
69 |
+
else:
|
70 |
+
raise ValueError(f"invalid truth value {value}")
|
71 |
+
|
72 |
+
|
73 |
+
def get_int_from_env(env_keys, default):
|
74 |
+
"""Returns the first positive env value found in the `env_keys` list or the default."""
|
75 |
+
for e in env_keys:
|
76 |
+
val = int(os.environ.get(e, -1))
|
77 |
+
if val >= 0:
|
78 |
+
return val
|
79 |
+
return default
|
80 |
+
|
81 |
+
|
82 |
+
def parse_flag_from_env(key, default=False):
|
83 |
+
"""Returns truthy value for `key` from the env if available else the default."""
|
84 |
+
value = os.environ.get(key, str(default))
|
85 |
+
return str_to_bool(value) == 1 # As its name indicates `str_to_bool` actually returns an int...
|
86 |
+
|
87 |
+
|
88 |
+
def parse_choice_from_env(key, default="no"):
|
89 |
+
value = os.environ.get(key, str(default))
|
90 |
+
return value
|
91 |
+
|
92 |
+
|
93 |
+
def are_libraries_initialized(*library_names: str) -> List[str]:
|
94 |
+
"""
|
95 |
+
Checks if any of `library_names` are imported in the environment. Will return any names that are.
|
96 |
+
"""
|
97 |
+
return [lib_name for lib_name in library_names if lib_name in sys.modules.keys()]
|
98 |
+
|
99 |
+
|
100 |
+
def _nvidia_smi():
|
101 |
+
"""
|
102 |
+
Returns the right nvidia-smi command based on the system.
|
103 |
+
"""
|
104 |
+
if platform.system() == "Windows":
|
105 |
+
# If platform is Windows and nvidia-smi can't be found in path
|
106 |
+
# try from systemd drive with default installation path
|
107 |
+
command = which("nvidia-smi")
|
108 |
+
if command is None:
|
109 |
+
command = "%s\\Program Files\\NVIDIA Corporation\\NVSMI\\nvidia-smi.exe" % os.environ["systemdrive"]
|
110 |
+
else:
|
111 |
+
command = "nvidia-smi"
|
112 |
+
return command
|
113 |
+
|
114 |
+
|
115 |
+
def get_gpu_info():
|
116 |
+
"""
|
117 |
+
Gets GPU count and names using `nvidia-smi` instead of torch to not initialize CUDA.
|
118 |
+
|
119 |
+
Largely based on the `gputil` library.
|
120 |
+
"""
|
121 |
+
# Returns as list of `n` GPUs and their names
|
122 |
+
output = subprocess.check_output(
|
123 |
+
[_nvidia_smi(), "--query-gpu=count,name", "--format=csv,noheader"], universal_newlines=True
|
124 |
+
)
|
125 |
+
output = output.strip()
|
126 |
+
gpus = output.split(os.linesep)
|
127 |
+
# Get names from output
|
128 |
+
gpu_count = len(gpus)
|
129 |
+
gpu_names = [gpu.split(",")[1].strip() for gpu in gpus]
|
130 |
+
return gpu_names, gpu_count
|
131 |
+
|
132 |
+
|
133 |
+
def get_driver_version():
|
134 |
+
"""
|
135 |
+
Returns the driver version
|
136 |
+
|
137 |
+
In the case of multiple GPUs, will return the first.
|
138 |
+
"""
|
139 |
+
output = subprocess.check_output(
|
140 |
+
[_nvidia_smi(), "--query-gpu=driver_version", "--format=csv,noheader"], universal_newlines=True
|
141 |
+
)
|
142 |
+
output = output.strip()
|
143 |
+
return output.split(os.linesep)[0]
|
144 |
+
|
145 |
+
|
146 |
+
def check_cuda_p2p_ib_support():
|
147 |
+
"""
|
148 |
+
Checks if the devices being used have issues with P2P and IB communications, namely any consumer GPU hardware after
|
149 |
+
the 3090.
|
150 |
+
|
151 |
+
Noteably uses `nvidia-smi` instead of torch to not initialize CUDA.
|
152 |
+
"""
|
153 |
+
try:
|
154 |
+
device_names, device_count = get_gpu_info()
|
155 |
+
# As new consumer GPUs get released, add them to `unsupported_devices``
|
156 |
+
unsupported_devices = {"RTX 40"}
|
157 |
+
if device_count > 1:
|
158 |
+
if any(
|
159 |
+
unsupported_device in device_name
|
160 |
+
for device_name in device_names
|
161 |
+
for unsupported_device in unsupported_devices
|
162 |
+
):
|
163 |
+
# Check if they have the right driver version
|
164 |
+
acceptable_driver_version = "550.40.07"
|
165 |
+
current_driver_version = get_driver_version()
|
166 |
+
if parse(current_driver_version) < parse(acceptable_driver_version):
|
167 |
+
return False
|
168 |
+
return True
|
169 |
+
except Exception:
|
170 |
+
pass
|
171 |
+
return True
|
172 |
+
|
173 |
+
|
174 |
+
def check_fp8_capability():
|
175 |
+
"""
|
176 |
+
Checks if all the current GPUs available support FP8.
|
177 |
+
|
178 |
+
Notably must initialize `torch.cuda` to check.
|
179 |
+
"""
|
180 |
+
cuda_device_capacity = torch.cuda.get_device_capability()
|
181 |
+
return cuda_device_capacity >= (8, 9)
|
182 |
+
|
183 |
+
|
184 |
+
@dataclass
|
185 |
+
class CPUInformation:
|
186 |
+
"""
|
187 |
+
Stores information about the CPU in a distributed environment. It contains the following attributes:
|
188 |
+
- rank: The rank of the current process.
|
189 |
+
- world_size: The total number of processes in the world.
|
190 |
+
- local_rank: The rank of the current process on the local node.
|
191 |
+
- local_world_size: The total number of processes on the local node.
|
192 |
+
"""
|
193 |
+
|
194 |
+
rank: int = field(default=0, metadata={"help": "The rank of the current process."})
|
195 |
+
world_size: int = field(default=1, metadata={"help": "The total number of processes in the world."})
|
196 |
+
local_rank: int = field(default=0, metadata={"help": "The rank of the current process on the local node."})
|
197 |
+
local_world_size: int = field(default=1, metadata={"help": "The total number of processes on the local node."})
|
198 |
+
|
199 |
+
|
200 |
+
def get_cpu_distributed_information() -> CPUInformation:
|
201 |
+
"""
|
202 |
+
Returns various information about the environment in relation to CPU distributed training as a `CPUInformation`
|
203 |
+
dataclass.
|
204 |
+
"""
|
205 |
+
information = {}
|
206 |
+
information["rank"] = get_int_from_env(["RANK", "PMI_RANK", "OMPI_COMM_WORLD_RANK", "MV2_COMM_WORLD_RANK"], 0)
|
207 |
+
information["world_size"] = get_int_from_env(
|
208 |
+
["WORLD_SIZE", "PMI_SIZE", "OMPI_COMM_WORLD_SIZE", "MV2_COMM_WORLD_SIZE"], 1
|
209 |
+
)
|
210 |
+
information["local_rank"] = get_int_from_env(
|
211 |
+
["LOCAL_RANK", "MPI_LOCALRANKID", "OMPI_COMM_WORLD_LOCAL_RANK", "MV2_COMM_WORLD_LOCAL_RANK"], 0
|
212 |
+
)
|
213 |
+
information["local_world_size"] = get_int_from_env(
|
214 |
+
["LOCAL_WORLD_SIZE", "MPI_LOCALNRANKS", "OMPI_COMM_WORLD_LOCAL_SIZE", "MV2_COMM_WORLD_LOCAL_SIZE"],
|
215 |
+
1,
|
216 |
+
)
|
217 |
+
return CPUInformation(**information)
|
218 |
+
|
219 |
+
|
220 |
+
def override_numa_affinity(local_process_index: int, verbose: Optional[bool] = None) -> None:
|
221 |
+
"""
|
222 |
+
Overrides whatever NUMA affinity is set for the current process. This is very taxing and requires recalculating the
|
223 |
+
affinity to set, ideally you should use `utils.environment.set_numa_affinity` instead.
|
224 |
+
|
225 |
+
Args:
|
226 |
+
local_process_index (int):
|
227 |
+
The index of the current process on the current server.
|
228 |
+
verbose (bool, *optional*):
|
229 |
+
Whether to log out the assignment of each CPU. If `ACCELERATE_DEBUG_MODE` is enabled, will default to True.
|
230 |
+
"""
|
231 |
+
if verbose is None:
|
232 |
+
verbose = parse_flag_from_env("ACCELERATE_DEBUG_MODE", False)
|
233 |
+
if torch.cuda.is_available():
|
234 |
+
from accelerate.utils import is_pynvml_available
|
235 |
+
|
236 |
+
if not is_pynvml_available():
|
237 |
+
raise ImportError(
|
238 |
+
"To set CPU affinity on CUDA GPUs the `pynvml` package must be available. (`pip install pynvml`)"
|
239 |
+
)
|
240 |
+
import pynvml as nvml
|
241 |
+
|
242 |
+
# The below code is based on https://github.com/NVIDIA/DeepLearningExamples/blob/master/TensorFlow2/LanguageModeling/BERT/gpu_affinity.py
|
243 |
+
nvml.nvmlInit()
|
244 |
+
num_elements = math.ceil(os.cpu_count() / 64)
|
245 |
+
handle = nvml.nvmlDeviceGetHandleByIndex(local_process_index)
|
246 |
+
affinity_string = ""
|
247 |
+
for j in nvml.nvmlDeviceGetCpuAffinity(handle, num_elements):
|
248 |
+
# assume nvml returns list of 64 bit ints
|
249 |
+
affinity_string = f"{j:064b}{affinity_string}"
|
250 |
+
affinity_list = [int(x) for x in affinity_string]
|
251 |
+
affinity_list.reverse() # so core 0 is the 0th element
|
252 |
+
affinity_to_set = [i for i, e in enumerate(affinity_list) if e != 0]
|
253 |
+
os.sched_setaffinity(0, affinity_to_set)
|
254 |
+
if verbose:
|
255 |
+
cpu_cores = os.sched_getaffinity(0)
|
256 |
+
logger.info(f"Assigning {len(cpu_cores)} cpu cores to process {local_process_index}: {cpu_cores}")
|
257 |
+
|
258 |
+
|
259 |
+
@lru_cache
|
260 |
+
def set_numa_affinity(local_process_index: int, verbose: Optional[bool] = None) -> None:
|
261 |
+
"""
|
262 |
+
Assigns the current process to a specific NUMA node. Ideally most efficient when having at least 2 cpus per node.
|
263 |
+
|
264 |
+
This result is cached between calls. If you want to override it, please use
|
265 |
+
`accelerate.utils.environment.override_numa_afifnity`.
|
266 |
+
|
267 |
+
Args:
|
268 |
+
local_process_index (int):
|
269 |
+
The index of the current process on the current server.
|
270 |
+
verbose (bool, *optional*):
|
271 |
+
Whether to print the new cpu cores assignment for each process. If `ACCELERATE_DEBUG_MODE` is enabled, will
|
272 |
+
default to True.
|
273 |
+
"""
|
274 |
+
override_numa_affinity(local_process_index=local_process_index, verbose=verbose)
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/imports.py
ADDED
@@ -0,0 +1,403 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
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|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
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|
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|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
import importlib
|
16 |
+
import importlib.metadata
|
17 |
+
import os
|
18 |
+
import warnings
|
19 |
+
from functools import lru_cache
|
20 |
+
|
21 |
+
import torch
|
22 |
+
from packaging import version
|
23 |
+
from packaging.version import parse
|
24 |
+
|
25 |
+
from .environment import parse_flag_from_env, str_to_bool
|
26 |
+
from .versions import compare_versions, is_torch_version
|
27 |
+
|
28 |
+
|
29 |
+
# Try to run Torch native job in an environment with TorchXLA installed by setting this value to 0.
|
30 |
+
USE_TORCH_XLA = parse_flag_from_env("USE_TORCH_XLA", default=True)
|
31 |
+
|
32 |
+
_torch_xla_available = False
|
33 |
+
if USE_TORCH_XLA:
|
34 |
+
try:
|
35 |
+
import torch_xla.core.xla_model as xm # noqa: F401
|
36 |
+
import torch_xla.runtime
|
37 |
+
|
38 |
+
_torch_xla_available = True
|
39 |
+
except ImportError:
|
40 |
+
pass
|
41 |
+
|
42 |
+
# Keep it for is_tpu_available. It will be removed along with is_tpu_available.
|
43 |
+
_tpu_available = _torch_xla_available
|
44 |
+
|
45 |
+
# Cache this result has it's a C FFI call which can be pretty time-consuming
|
46 |
+
_torch_distributed_available = torch.distributed.is_available()
|
47 |
+
|
48 |
+
|
49 |
+
def _is_package_available(pkg_name, metadata_name=None):
|
50 |
+
# Check we're not importing a "pkg_name" directory somewhere but the actual library by trying to grab the version
|
51 |
+
package_exists = importlib.util.find_spec(pkg_name) is not None
|
52 |
+
if package_exists:
|
53 |
+
try:
|
54 |
+
# Some libraries have different names in the metadata
|
55 |
+
_ = importlib.metadata.metadata(pkg_name if metadata_name is None else metadata_name)
|
56 |
+
return True
|
57 |
+
except importlib.metadata.PackageNotFoundError:
|
58 |
+
return False
|
59 |
+
|
60 |
+
|
61 |
+
def is_torch_distributed_available() -> bool:
|
62 |
+
return _torch_distributed_available
|
63 |
+
|
64 |
+
|
65 |
+
def is_ccl_available():
|
66 |
+
try:
|
67 |
+
pass
|
68 |
+
except ImportError:
|
69 |
+
print(
|
70 |
+
"Intel(R) oneCCL Bindings for PyTorch* is required to run DDP on Intel(R) GPUs, but it is not"
|
71 |
+
" detected. If you see \"ValueError: Invalid backend: 'ccl'\" error, please install Intel(R) oneCCL"
|
72 |
+
" Bindings for PyTorch*."
|
73 |
+
)
|
74 |
+
return (
|
75 |
+
importlib.util.find_spec("torch_ccl") is not None
|
76 |
+
or importlib.util.find_spec("oneccl_bindings_for_pytorch") is not None
|
77 |
+
)
|
78 |
+
|
79 |
+
|
80 |
+
def get_ccl_version():
|
81 |
+
return importlib.metadata.version("oneccl_bind_pt")
|
82 |
+
|
83 |
+
|
84 |
+
def is_pynvml_available():
|
85 |
+
return _is_package_available("pynvml")
|
86 |
+
|
87 |
+
|
88 |
+
def is_pytest_available():
|
89 |
+
return _is_package_available("pytest")
|
90 |
+
|
91 |
+
|
92 |
+
def is_msamp_available():
|
93 |
+
return _is_package_available("msamp", "ms-amp")
|
94 |
+
|
95 |
+
|
96 |
+
def is_schedulefree_available():
|
97 |
+
return _is_package_available("schedulefree")
|
98 |
+
|
99 |
+
|
100 |
+
def is_transformer_engine_available():
|
101 |
+
return _is_package_available("transformer_engine")
|
102 |
+
|
103 |
+
|
104 |
+
def is_lomo_available():
|
105 |
+
return _is_package_available("lomo_optim")
|
106 |
+
|
107 |
+
|
108 |
+
def is_fp8_available():
|
109 |
+
return is_msamp_available() or is_transformer_engine_available()
|
110 |
+
|
111 |
+
|
112 |
+
def is_cuda_available():
|
113 |
+
"""
|
114 |
+
Checks if `cuda` is available via an `nvml-based` check which won't trigger the drivers and leave cuda
|
115 |
+
uninitialized.
|
116 |
+
"""
|
117 |
+
pytorch_nvml_based_cuda_check_previous_value = os.environ.get("PYTORCH_NVML_BASED_CUDA_CHECK")
|
118 |
+
try:
|
119 |
+
os.environ["PYTORCH_NVML_BASED_CUDA_CHECK"] = str(1)
|
120 |
+
available = torch.cuda.is_available()
|
121 |
+
finally:
|
122 |
+
if pytorch_nvml_based_cuda_check_previous_value:
|
123 |
+
os.environ["PYTORCH_NVML_BASED_CUDA_CHECK"] = pytorch_nvml_based_cuda_check_previous_value
|
124 |
+
else:
|
125 |
+
os.environ.pop("PYTORCH_NVML_BASED_CUDA_CHECK", None)
|
126 |
+
|
127 |
+
return available
|
128 |
+
|
129 |
+
|
130 |
+
@lru_cache
|
131 |
+
def is_tpu_available(check_device=True):
|
132 |
+
"Checks if `torch_xla` is installed and potentially if a TPU is in the environment"
|
133 |
+
warnings.warn(
|
134 |
+
"`is_tpu_available` is deprecated and will be removed in v0.27.0. "
|
135 |
+
"Please use the `is_torch_xla_available` instead.",
|
136 |
+
FutureWarning,
|
137 |
+
)
|
138 |
+
# Due to bugs on the amp series GPUs, we disable torch-xla on them
|
139 |
+
if is_cuda_available():
|
140 |
+
return False
|
141 |
+
if check_device:
|
142 |
+
if _tpu_available:
|
143 |
+
try:
|
144 |
+
# Will raise a RuntimeError if no XLA configuration is found
|
145 |
+
_ = xm.xla_device()
|
146 |
+
return True
|
147 |
+
except RuntimeError:
|
148 |
+
return False
|
149 |
+
return _tpu_available
|
150 |
+
|
151 |
+
|
152 |
+
@lru_cache
|
153 |
+
def is_torch_xla_available(check_is_tpu=False, check_is_gpu=False):
|
154 |
+
"""
|
155 |
+
Check if `torch_xla` is available. To train a native pytorch job in an environment with torch xla installed, set
|
156 |
+
the USE_TORCH_XLA to false.
|
157 |
+
"""
|
158 |
+
assert not (check_is_tpu and check_is_gpu), "The check_is_tpu and check_is_gpu cannot both be true."
|
159 |
+
|
160 |
+
if not _torch_xla_available:
|
161 |
+
return False
|
162 |
+
elif check_is_gpu:
|
163 |
+
return torch_xla.runtime.device_type() in ["GPU", "CUDA"]
|
164 |
+
elif check_is_tpu:
|
165 |
+
return torch_xla.runtime.device_type() == "TPU"
|
166 |
+
|
167 |
+
return True
|
168 |
+
|
169 |
+
|
170 |
+
def is_deepspeed_available():
|
171 |
+
if is_mlu_available():
|
172 |
+
return _is_package_available("deepspeed", metadata_name="deepspeed-mlu")
|
173 |
+
return _is_package_available("deepspeed")
|
174 |
+
|
175 |
+
|
176 |
+
def is_pippy_available():
|
177 |
+
package_exists = _is_package_available("pippy", "torchpippy")
|
178 |
+
if package_exists:
|
179 |
+
pippy_version = version.parse(importlib.metadata.version("torchpippy"))
|
180 |
+
return compare_versions(pippy_version, ">", "0.1.1")
|
181 |
+
return False
|
182 |
+
|
183 |
+
|
184 |
+
def is_bf16_available(ignore_tpu=False):
|
185 |
+
"Checks if bf16 is supported, optionally ignoring the TPU"
|
186 |
+
if is_torch_xla_available(check_is_tpu=True):
|
187 |
+
return not ignore_tpu
|
188 |
+
if is_cuda_available():
|
189 |
+
return torch.cuda.is_bf16_supported()
|
190 |
+
if is_mps_available():
|
191 |
+
return False
|
192 |
+
return True
|
193 |
+
|
194 |
+
|
195 |
+
def is_4bit_bnb_available():
|
196 |
+
package_exists = _is_package_available("bitsandbytes")
|
197 |
+
if package_exists:
|
198 |
+
bnb_version = version.parse(importlib.metadata.version("bitsandbytes"))
|
199 |
+
return compare_versions(bnb_version, ">=", "0.39.0")
|
200 |
+
return False
|
201 |
+
|
202 |
+
|
203 |
+
def is_8bit_bnb_available():
|
204 |
+
package_exists = _is_package_available("bitsandbytes")
|
205 |
+
if package_exists:
|
206 |
+
bnb_version = version.parse(importlib.metadata.version("bitsandbytes"))
|
207 |
+
return compare_versions(bnb_version, ">=", "0.37.2")
|
208 |
+
return False
|
209 |
+
|
210 |
+
|
211 |
+
def is_bnb_available():
|
212 |
+
return _is_package_available("bitsandbytes")
|
213 |
+
|
214 |
+
|
215 |
+
def is_torchvision_available():
|
216 |
+
return _is_package_available("torchvision")
|
217 |
+
|
218 |
+
|
219 |
+
def is_megatron_lm_available():
|
220 |
+
if str_to_bool(os.environ.get("ACCELERATE_USE_MEGATRON_LM", "False")) == 1:
|
221 |
+
package_exists = importlib.util.find_spec("megatron") is not None
|
222 |
+
if package_exists:
|
223 |
+
try:
|
224 |
+
megatron_version = parse(importlib.metadata.version("megatron-lm"))
|
225 |
+
return compare_versions(megatron_version, ">=", "2.2.0")
|
226 |
+
except Exception as e:
|
227 |
+
warnings.warn(f"Parse Megatron version failed. Exception:{e}")
|
228 |
+
return False
|
229 |
+
|
230 |
+
|
231 |
+
def is_transformers_available():
|
232 |
+
return _is_package_available("transformers")
|
233 |
+
|
234 |
+
|
235 |
+
def is_datasets_available():
|
236 |
+
return _is_package_available("datasets")
|
237 |
+
|
238 |
+
|
239 |
+
def is_peft_available():
|
240 |
+
return _is_package_available("peft")
|
241 |
+
|
242 |
+
|
243 |
+
def is_timm_available():
|
244 |
+
return _is_package_available("timm")
|
245 |
+
|
246 |
+
|
247 |
+
def is_aim_available():
|
248 |
+
package_exists = _is_package_available("aim")
|
249 |
+
if package_exists:
|
250 |
+
aim_version = version.parse(importlib.metadata.version("aim"))
|
251 |
+
return compare_versions(aim_version, "<", "4.0.0")
|
252 |
+
return False
|
253 |
+
|
254 |
+
|
255 |
+
def is_tensorboard_available():
|
256 |
+
return _is_package_available("tensorboard") or _is_package_available("tensorboardX")
|
257 |
+
|
258 |
+
|
259 |
+
def is_wandb_available():
|
260 |
+
return _is_package_available("wandb")
|
261 |
+
|
262 |
+
|
263 |
+
def is_comet_ml_available():
|
264 |
+
return _is_package_available("comet_ml")
|
265 |
+
|
266 |
+
|
267 |
+
def is_boto3_available():
|
268 |
+
return _is_package_available("boto3")
|
269 |
+
|
270 |
+
|
271 |
+
def is_rich_available():
|
272 |
+
if _is_package_available("rich"):
|
273 |
+
if "ACCELERATE_DISABLE_RICH" in os.environ:
|
274 |
+
warnings.warn(
|
275 |
+
"`ACCELERATE_DISABLE_RICH` is deprecated and will be removed in v0.22.0 and deactivated by default. Please use `ACCELERATE_ENABLE_RICH` if you wish to use `rich`."
|
276 |
+
)
|
277 |
+
return not parse_flag_from_env("ACCELERATE_DISABLE_RICH", False)
|
278 |
+
return parse_flag_from_env("ACCELERATE_ENABLE_RICH", False)
|
279 |
+
return False
|
280 |
+
|
281 |
+
|
282 |
+
def is_sagemaker_available():
|
283 |
+
return _is_package_available("sagemaker")
|
284 |
+
|
285 |
+
|
286 |
+
def is_tqdm_available():
|
287 |
+
return _is_package_available("tqdm")
|
288 |
+
|
289 |
+
|
290 |
+
def is_clearml_available():
|
291 |
+
return _is_package_available("clearml")
|
292 |
+
|
293 |
+
|
294 |
+
def is_pandas_available():
|
295 |
+
return _is_package_available("pandas")
|
296 |
+
|
297 |
+
|
298 |
+
def is_mlflow_available():
|
299 |
+
if _is_package_available("mlflow"):
|
300 |
+
return True
|
301 |
+
|
302 |
+
if importlib.util.find_spec("mlflow") is not None:
|
303 |
+
try:
|
304 |
+
_ = importlib.metadata.metadata("mlflow-skinny")
|
305 |
+
return True
|
306 |
+
except importlib.metadata.PackageNotFoundError:
|
307 |
+
return False
|
308 |
+
return False
|
309 |
+
|
310 |
+
|
311 |
+
def is_mps_available():
|
312 |
+
return is_torch_version(">=", "1.12") and torch.backends.mps.is_available() and torch.backends.mps.is_built()
|
313 |
+
|
314 |
+
|
315 |
+
def is_ipex_available():
|
316 |
+
def get_major_and_minor_from_version(full_version):
|
317 |
+
return str(version.parse(full_version).major) + "." + str(version.parse(full_version).minor)
|
318 |
+
|
319 |
+
_torch_version = importlib.metadata.version("torch")
|
320 |
+
if importlib.util.find_spec("intel_extension_for_pytorch") is None:
|
321 |
+
return False
|
322 |
+
_ipex_version = "N/A"
|
323 |
+
try:
|
324 |
+
_ipex_version = importlib.metadata.version("intel_extension_for_pytorch")
|
325 |
+
except importlib.metadata.PackageNotFoundError:
|
326 |
+
return False
|
327 |
+
torch_major_and_minor = get_major_and_minor_from_version(_torch_version)
|
328 |
+
ipex_major_and_minor = get_major_and_minor_from_version(_ipex_version)
|
329 |
+
if torch_major_and_minor != ipex_major_and_minor:
|
330 |
+
warnings.warn(
|
331 |
+
f"Intel Extension for PyTorch {ipex_major_and_minor} needs to work with PyTorch {ipex_major_and_minor}.*,"
|
332 |
+
f" but PyTorch {_torch_version} is found. Please switch to the matching version and run again."
|
333 |
+
)
|
334 |
+
return False
|
335 |
+
return True
|
336 |
+
|
337 |
+
|
338 |
+
@lru_cache
|
339 |
+
def is_mlu_available(check_device=False):
|
340 |
+
"Checks if `torch_mlu` is installed and potentially if a MLU is in the environment"
|
341 |
+
if importlib.util.find_spec("torch_mlu") is None:
|
342 |
+
return False
|
343 |
+
|
344 |
+
import torch
|
345 |
+
import torch_mlu # noqa: F401
|
346 |
+
|
347 |
+
if check_device:
|
348 |
+
try:
|
349 |
+
# Will raise a RuntimeError if no MLU is found
|
350 |
+
_ = torch.mlu.device_count()
|
351 |
+
return torch.mlu.is_available()
|
352 |
+
except RuntimeError:
|
353 |
+
return False
|
354 |
+
return hasattr(torch, "mlu") and torch.mlu.is_available()
|
355 |
+
|
356 |
+
|
357 |
+
@lru_cache
|
358 |
+
def is_npu_available(check_device=False):
|
359 |
+
"Checks if `torch_npu` is installed and potentially if a NPU is in the environment"
|
360 |
+
if importlib.util.find_spec("torch") is None or importlib.util.find_spec("torch_npu") is None:
|
361 |
+
return False
|
362 |
+
|
363 |
+
import torch
|
364 |
+
import torch_npu # noqa: F401
|
365 |
+
|
366 |
+
if check_device:
|
367 |
+
try:
|
368 |
+
# Will raise a RuntimeError if no NPU is found
|
369 |
+
_ = torch.npu.device_count()
|
370 |
+
return torch.npu.is_available()
|
371 |
+
except RuntimeError:
|
372 |
+
return False
|
373 |
+
return hasattr(torch, "npu") and torch.npu.is_available()
|
374 |
+
|
375 |
+
|
376 |
+
@lru_cache
|
377 |
+
def is_xpu_available(check_device=False):
|
378 |
+
"check if user disables it explicitly"
|
379 |
+
if not parse_flag_from_env("ACCELERATE_USE_XPU", default=True):
|
380 |
+
return False
|
381 |
+
"Checks if `intel_extension_for_pytorch` is installed and potentially if a XPU is in the environment"
|
382 |
+
if is_ipex_available():
|
383 |
+
import torch
|
384 |
+
|
385 |
+
if is_torch_version("<=", "1.12"):
|
386 |
+
return False
|
387 |
+
else:
|
388 |
+
return False
|
389 |
+
|
390 |
+
import intel_extension_for_pytorch # noqa: F401
|
391 |
+
|
392 |
+
if check_device:
|
393 |
+
try:
|
394 |
+
# Will raise a RuntimeError if no XPU is found
|
395 |
+
_ = torch.xpu.device_count()
|
396 |
+
return torch.xpu.is_available()
|
397 |
+
except RuntimeError:
|
398 |
+
return False
|
399 |
+
return hasattr(torch, "xpu") and torch.xpu.is_available()
|
400 |
+
|
401 |
+
|
402 |
+
def is_dvclive_available():
|
403 |
+
return _is_package_available("dvclive")
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/launch.py
ADDED
@@ -0,0 +1,626 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
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|
|
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|
|
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|
|
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
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|
|
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|
|
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|
|
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|
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|
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|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
import argparse
|
16 |
+
import os
|
17 |
+
import subprocess
|
18 |
+
import sys
|
19 |
+
import warnings
|
20 |
+
from ast import literal_eval
|
21 |
+
from shutil import which
|
22 |
+
from typing import Any, Dict, List, Tuple
|
23 |
+
|
24 |
+
import torch
|
25 |
+
|
26 |
+
from ..commands.config.config_args import SageMakerConfig
|
27 |
+
from ..utils import (
|
28 |
+
DynamoBackend,
|
29 |
+
PrecisionType,
|
30 |
+
is_ipex_available,
|
31 |
+
is_mlu_available,
|
32 |
+
is_npu_available,
|
33 |
+
is_torch_xla_available,
|
34 |
+
is_xpu_available,
|
35 |
+
)
|
36 |
+
from ..utils.constants import DEEPSPEED_MULTINODE_LAUNCHERS
|
37 |
+
from ..utils.other import is_port_in_use, merge_dicts
|
38 |
+
from .dataclasses import DistributedType, SageMakerDistributedType
|
39 |
+
|
40 |
+
|
41 |
+
def _filter_args(args, parser, default_args=[]):
|
42 |
+
"""
|
43 |
+
Filters out all `accelerate` specific args
|
44 |
+
"""
|
45 |
+
new_args, _ = parser.parse_known_args(default_args)
|
46 |
+
for key, value in vars(args).items():
|
47 |
+
if key in vars(new_args).keys():
|
48 |
+
setattr(new_args, key, value)
|
49 |
+
return new_args
|
50 |
+
|
51 |
+
|
52 |
+
def _get_mpirun_args():
|
53 |
+
"""
|
54 |
+
Determines the executable and argument names for mpirun, based on the type of install. The supported MPI programs
|
55 |
+
are: OpenMPI, Intel MPI, or MVAPICH.
|
56 |
+
|
57 |
+
Returns: Program name and arg names for hostfile, num processes, and processes per node
|
58 |
+
"""
|
59 |
+
# Find the MPI program name
|
60 |
+
mpi_apps = [x for x in ["mpirun", "mpiexec"] if which(x)]
|
61 |
+
|
62 |
+
if len(mpi_apps) == 0:
|
63 |
+
raise OSError("mpirun or mpiexec were not found. Ensure that Intel MPI, Open MPI, or MVAPICH are installed.")
|
64 |
+
|
65 |
+
# Call the app with the --version flag to determine which MPI app is installed
|
66 |
+
mpi_app = mpi_apps[0]
|
67 |
+
mpirun_version = subprocess.check_output([mpi_app, "--version"])
|
68 |
+
|
69 |
+
if b"Open MPI" in mpirun_version:
|
70 |
+
return mpi_app, "--hostfile", "-n", "--npernode"
|
71 |
+
else:
|
72 |
+
# Intel MPI and MVAPICH both use the same arg names
|
73 |
+
return mpi_app, "-f", "-n", "-ppn"
|
74 |
+
|
75 |
+
|
76 |
+
def prepare_simple_launcher_cmd_env(args: argparse.Namespace) -> Tuple[List[str], Dict[str, str]]:
|
77 |
+
"""
|
78 |
+
Prepares and returns the command list and an environment with the correct simple launcher environment variables.
|
79 |
+
"""
|
80 |
+
cmd = []
|
81 |
+
if args.no_python and args.module:
|
82 |
+
raise ValueError("--module and --no_python cannot be used together")
|
83 |
+
|
84 |
+
if args.mpirun_hostfile is not None:
|
85 |
+
mpi_app_name, hostfile_arg, num_proc_arg, proc_per_node_arg = _get_mpirun_args()
|
86 |
+
mpirun_ccl = getattr(args, "mpirun_ccl", None)
|
87 |
+
num_machines = args.num_machines
|
88 |
+
num_processes = getattr(args, "num_processes", None)
|
89 |
+
nproc_per_node = str(num_processes // num_machines) if num_processes and num_machines else "1"
|
90 |
+
cmd += [mpi_app_name, hostfile_arg, args.mpirun_hostfile, proc_per_node_arg, nproc_per_node]
|
91 |
+
if num_processes:
|
92 |
+
cmd += [num_proc_arg, str(num_processes)]
|
93 |
+
if not args.no_python:
|
94 |
+
cmd.append(sys.executable)
|
95 |
+
if args.module:
|
96 |
+
cmd.append("-m")
|
97 |
+
cmd.append(args.training_script)
|
98 |
+
cmd.extend(args.training_script_args)
|
99 |
+
|
100 |
+
current_env = os.environ.copy()
|
101 |
+
current_env["ACCELERATE_USE_CPU"] = str(args.cpu or args.use_cpu)
|
102 |
+
if args.debug:
|
103 |
+
current_env["ACCELERATE_DEBUG_MODE"] = "true"
|
104 |
+
if args.gpu_ids != "all" and args.gpu_ids is not None:
|
105 |
+
if is_xpu_available():
|
106 |
+
current_env["ZE_AFFINITY_MASK"] = args.gpu_ids
|
107 |
+
elif is_mlu_available():
|
108 |
+
current_env["MLU_VISIBLE_DEVICES"] = args.gpu_ids
|
109 |
+
elif is_npu_available():
|
110 |
+
current_env["ASCEND_RT_VISIBLE_DEVICES"] = args.gpu_ids
|
111 |
+
else:
|
112 |
+
current_env["CUDA_VISIBLE_DEVICES"] = args.gpu_ids
|
113 |
+
if args.num_machines > 1:
|
114 |
+
current_env["MASTER_ADDR"] = args.main_process_ip
|
115 |
+
current_env["MASTER_PORT"] = str(args.main_process_port)
|
116 |
+
|
117 |
+
if args.mpirun_hostfile is not None:
|
118 |
+
current_env["CCL_WORKER_COUNT"] = mpirun_ccl
|
119 |
+
elif args.num_processes > 1:
|
120 |
+
current_env["MASTER_ADDR"] = args.main_process_ip if args.main_process_ip is not None else "127.0.0.1"
|
121 |
+
current_env["MASTER_PORT"] = str(args.main_process_port) if args.main_process_port is not None else "29500"
|
122 |
+
|
123 |
+
try:
|
124 |
+
mixed_precision = PrecisionType(args.mixed_precision.lower())
|
125 |
+
except ValueError:
|
126 |
+
raise ValueError(
|
127 |
+
f"Unknown mixed_precision mode: {args.mixed_precision.lower()}. Choose between {PrecisionType.list()}."
|
128 |
+
)
|
129 |
+
|
130 |
+
current_env["ACCELERATE_MIXED_PRECISION"] = str(mixed_precision)
|
131 |
+
|
132 |
+
try:
|
133 |
+
dynamo_backend = DynamoBackend(args.dynamo_backend.upper())
|
134 |
+
except ValueError:
|
135 |
+
raise ValueError(
|
136 |
+
f"Unknown dynamo backend: {args.dynamo_backend.upper()}. Choose between {DynamoBackend.list()}."
|
137 |
+
)
|
138 |
+
current_env["ACCELERATE_DYNAMO_BACKEND"] = dynamo_backend.value
|
139 |
+
current_env["ACCELERATE_DYNAMO_MODE"] = args.dynamo_mode
|
140 |
+
current_env["ACCELERATE_DYNAMO_USE_FULLGRAPH"] = str(args.dynamo_use_fullgraph)
|
141 |
+
current_env["ACCELERATE_DYNAMO_USE_DYNAMIC"] = str(args.dynamo_use_dynamic)
|
142 |
+
|
143 |
+
current_env["OMP_NUM_THREADS"] = str(args.num_cpu_threads_per_process)
|
144 |
+
if is_ipex_available():
|
145 |
+
current_env["ACCELERATE_USE_IPEX"] = str(args.ipex).lower()
|
146 |
+
current_env["ACCELERATE_USE_XPU"] = str(args.use_xpu).lower()
|
147 |
+
if args.enable_cpu_affinity:
|
148 |
+
current_env["ACCELERATE_CPU_AFFINITY"] = "1"
|
149 |
+
return cmd, current_env
|
150 |
+
|
151 |
+
|
152 |
+
def prepare_multi_gpu_env(args: argparse.Namespace) -> Dict[str, str]:
|
153 |
+
"""
|
154 |
+
Prepares and returns an environment with the correct multi-GPU environment variables.
|
155 |
+
"""
|
156 |
+
num_processes = args.num_processes
|
157 |
+
num_machines = args.num_machines
|
158 |
+
main_process_ip = args.main_process_ip
|
159 |
+
main_process_port = args.main_process_port
|
160 |
+
if num_machines > 1:
|
161 |
+
args.nproc_per_node = str(num_processes // num_machines)
|
162 |
+
args.nnodes = str(num_machines)
|
163 |
+
args.node_rank = int(args.machine_rank)
|
164 |
+
if getattr(args, "same_network", False):
|
165 |
+
args.master_addr = str(main_process_ip)
|
166 |
+
args.master_port = str(main_process_port)
|
167 |
+
else:
|
168 |
+
args.rdzv_endpoint = f"{main_process_ip}:{main_process_port}"
|
169 |
+
else:
|
170 |
+
args.nproc_per_node = str(num_processes)
|
171 |
+
if main_process_port is not None:
|
172 |
+
args.master_port = str(main_process_port)
|
173 |
+
|
174 |
+
if main_process_port is None:
|
175 |
+
main_process_port = 29500
|
176 |
+
|
177 |
+
# only need to check port availability in main process, in case we have to start multiple launchers on the same machine
|
178 |
+
# for some reasons like splitting log files.
|
179 |
+
need_port_check = num_machines <= 1 or int(args.machine_rank) == 0
|
180 |
+
if need_port_check and is_port_in_use(main_process_port):
|
181 |
+
raise ConnectionError(
|
182 |
+
f"Tried to launch distributed communication on port `{main_process_port}`, but another process is utilizing it. "
|
183 |
+
"Please specify a different port (such as using the `--main_process_port` flag or specifying a different `main_process_port` in your config file)"
|
184 |
+
" and rerun your script. To automatically use the next open port (on a single node), you can set this to `0`."
|
185 |
+
)
|
186 |
+
|
187 |
+
if args.module and args.no_python:
|
188 |
+
raise ValueError("--module and --no_python cannot be used together")
|
189 |
+
elif args.module:
|
190 |
+
args.module = True
|
191 |
+
elif args.no_python:
|
192 |
+
args.no_python = True
|
193 |
+
|
194 |
+
current_env = os.environ.copy()
|
195 |
+
if args.debug:
|
196 |
+
current_env["ACCELERATE_DEBUG_MODE"] = "true"
|
197 |
+
gpu_ids = getattr(args, "gpu_ids", "all")
|
198 |
+
if gpu_ids != "all" and args.gpu_ids is not None:
|
199 |
+
if is_xpu_available():
|
200 |
+
current_env["ZE_AFFINITY_MASK"] = gpu_ids
|
201 |
+
elif is_mlu_available():
|
202 |
+
current_env["MLU_VISIBLE_DEVICES"] = gpu_ids
|
203 |
+
elif is_npu_available():
|
204 |
+
current_env["ASCEND_RT_VISIBLE_DEVICES"] = gpu_ids
|
205 |
+
else:
|
206 |
+
current_env["CUDA_VISIBLE_DEVICES"] = gpu_ids
|
207 |
+
mixed_precision = args.mixed_precision.lower()
|
208 |
+
try:
|
209 |
+
mixed_precision = PrecisionType(mixed_precision)
|
210 |
+
except ValueError:
|
211 |
+
raise ValueError(f"Unknown mixed_precision mode: {mixed_precision}. Choose between {PrecisionType.list()}.")
|
212 |
+
|
213 |
+
current_env["ACCELERATE_MIXED_PRECISION"] = str(mixed_precision)
|
214 |
+
|
215 |
+
try:
|
216 |
+
dynamo_backend = DynamoBackend(args.dynamo_backend.upper())
|
217 |
+
except ValueError:
|
218 |
+
raise ValueError(
|
219 |
+
f"Unknown dynamo backend: {args.dynamo_backend.upper()}. Choose between {DynamoBackend.list()}."
|
220 |
+
)
|
221 |
+
current_env["ACCELERATE_DYNAMO_BACKEND"] = dynamo_backend.value
|
222 |
+
current_env["ACCELERATE_DYNAMO_MODE"] = args.dynamo_mode
|
223 |
+
current_env["ACCELERATE_DYNAMO_USE_FULLGRAPH"] = str(args.dynamo_use_fullgraph)
|
224 |
+
current_env["ACCELERATE_DYNAMO_USE_DYNAMIC"] = str(args.dynamo_use_dynamic)
|
225 |
+
|
226 |
+
if args.use_fsdp:
|
227 |
+
current_env["ACCELERATE_USE_FSDP"] = "true"
|
228 |
+
if args.fsdp_cpu_ram_efficient_loading and not args.fsdp_sync_module_states:
|
229 |
+
raise ValueError("When using `--fsdp_cpu_ram_efficient_loading` set `--fsdp_sync_module_states` to `True`")
|
230 |
+
|
231 |
+
current_env["FSDP_SHARDING_STRATEGY"] = str(args.fsdp_sharding_strategy)
|
232 |
+
current_env["FSDP_OFFLOAD_PARAMS"] = str(args.fsdp_offload_params).lower()
|
233 |
+
current_env["FSDP_MIN_NUM_PARAMS"] = str(args.fsdp_min_num_params)
|
234 |
+
if args.fsdp_auto_wrap_policy is not None:
|
235 |
+
current_env["FSDP_AUTO_WRAP_POLICY"] = str(args.fsdp_auto_wrap_policy)
|
236 |
+
if args.fsdp_transformer_layer_cls_to_wrap is not None:
|
237 |
+
current_env["FSDP_TRANSFORMER_CLS_TO_WRAP"] = str(args.fsdp_transformer_layer_cls_to_wrap)
|
238 |
+
if args.fsdp_backward_prefetch_policy is not None:
|
239 |
+
warnings.warn(
|
240 |
+
"`fsdp_backward_prefetch_policy` is deprecated and will be removed in version 0.27.0 of 🤗 Accelerate. Use"
|
241 |
+
" `fsdp_backward_prefetch` instead",
|
242 |
+
FutureWarning,
|
243 |
+
)
|
244 |
+
args.fsdp_backward_prefetch = args.fsdp_backward_prefetch_policy
|
245 |
+
if args.fsdp_backward_prefetch is not None:
|
246 |
+
current_env["FSDP_BACKWARD_PREFETCH"] = str(args.fsdp_backward_prefetch)
|
247 |
+
if args.fsdp_state_dict_type is not None:
|
248 |
+
current_env["FSDP_STATE_DICT_TYPE"] = str(args.fsdp_state_dict_type)
|
249 |
+
current_env["FSDP_FORWARD_PREFETCH"] = str(args.fsdp_forward_prefetch).lower()
|
250 |
+
current_env["FSDP_USE_ORIG_PARAMS"] = str(args.fsdp_use_orig_params).lower()
|
251 |
+
current_env["FSDP_CPU_RAM_EFFICIENT_LOADING"] = str(args.fsdp_cpu_ram_efficient_loading).lower()
|
252 |
+
current_env["FSDP_SYNC_MODULE_STATES"] = str(args.fsdp_sync_module_states).lower()
|
253 |
+
|
254 |
+
if args.use_megatron_lm:
|
255 |
+
prefix = "MEGATRON_LM_"
|
256 |
+
current_env["ACCELERATE_USE_MEGATRON_LM"] = "true"
|
257 |
+
current_env[prefix + "TP_DEGREE"] = str(args.megatron_lm_tp_degree)
|
258 |
+
current_env[prefix + "PP_DEGREE"] = str(args.megatron_lm_pp_degree)
|
259 |
+
current_env[prefix + "GRADIENT_CLIPPING"] = str(args.megatron_lm_gradient_clipping)
|
260 |
+
if args.megatron_lm_num_micro_batches is not None:
|
261 |
+
current_env[prefix + "NUM_MICRO_BATCHES"] = str(args.megatron_lm_num_micro_batches)
|
262 |
+
if args.megatron_lm_sequence_parallelism is not None:
|
263 |
+
current_env[prefix + "SEQUENCE_PARALLELISM"] = str(args.megatron_lm_sequence_parallelism)
|
264 |
+
if args.megatron_lm_recompute_activations is not None:
|
265 |
+
current_env[prefix + "RECOMPUTE_ACTIVATIONS"] = str(args.megatron_lm_recompute_activations)
|
266 |
+
if args.megatron_lm_use_distributed_optimizer is not None:
|
267 |
+
current_env[prefix + "USE_DISTRIBUTED_OPTIMIZER"] = str(args.megatron_lm_use_distributed_optimizer)
|
268 |
+
|
269 |
+
current_env["OMP_NUM_THREADS"] = str(args.num_cpu_threads_per_process)
|
270 |
+
if args.enable_cpu_affinity:
|
271 |
+
current_env["ACCELERATE_CPU_AFFINITY"] = "1"
|
272 |
+
return current_env
|
273 |
+
|
274 |
+
|
275 |
+
def prepare_deepspeed_cmd_env(args: argparse.Namespace) -> Tuple[List[str], Dict[str, str]]:
|
276 |
+
"""
|
277 |
+
Prepares and returns the command list and an environment with the correct DeepSpeed environment variables.
|
278 |
+
"""
|
279 |
+
num_processes = args.num_processes
|
280 |
+
num_machines = args.num_machines
|
281 |
+
main_process_ip = args.main_process_ip
|
282 |
+
main_process_port = args.main_process_port
|
283 |
+
cmd = None
|
284 |
+
|
285 |
+
# make sure launcher is not None
|
286 |
+
if args.deepspeed_multinode_launcher is None:
|
287 |
+
# set to default pdsh
|
288 |
+
args.deepspeed_multinode_launcher = DEEPSPEED_MULTINODE_LAUNCHERS[0]
|
289 |
+
|
290 |
+
if num_machines > 1 and args.deepspeed_multinode_launcher != DEEPSPEED_MULTINODE_LAUNCHERS[1]:
|
291 |
+
cmd = ["deepspeed", "--no_local_rank"]
|
292 |
+
cmd.extend(["--hostfile", str(args.deepspeed_hostfile), "--launcher", str(args.deepspeed_multinode_launcher)])
|
293 |
+
if args.deepspeed_exclusion_filter is not None:
|
294 |
+
cmd.extend(
|
295 |
+
[
|
296 |
+
"--exclude",
|
297 |
+
str(args.deepspeed_exclusion_filter),
|
298 |
+
]
|
299 |
+
)
|
300 |
+
elif args.deepspeed_inclusion_filter is not None:
|
301 |
+
cmd.extend(
|
302 |
+
[
|
303 |
+
"--include",
|
304 |
+
str(args.deepspeed_inclusion_filter),
|
305 |
+
]
|
306 |
+
)
|
307 |
+
else:
|
308 |
+
cmd.extend(["--num_gpus", str(args.num_processes // args.num_machines)])
|
309 |
+
if main_process_ip:
|
310 |
+
cmd.extend(["--master_addr", str(main_process_ip)])
|
311 |
+
cmd.extend(["--master_port", str(main_process_port)])
|
312 |
+
if args.module and args.no_python:
|
313 |
+
raise ValueError("--module and --no_python cannot be used together")
|
314 |
+
elif args.module:
|
315 |
+
cmd.append("--module")
|
316 |
+
elif args.no_python:
|
317 |
+
cmd.append("--no_python")
|
318 |
+
cmd.append(args.training_script)
|
319 |
+
cmd.extend(args.training_script_args)
|
320 |
+
elif num_machines > 1 and args.deepspeed_multinode_launcher == DEEPSPEED_MULTINODE_LAUNCHERS[1]:
|
321 |
+
args.nproc_per_node = str(num_processes // num_machines)
|
322 |
+
args.nnodes = str(num_machines)
|
323 |
+
args.node_rank = int(args.machine_rank)
|
324 |
+
if getattr(args, "same_network", False):
|
325 |
+
args.master_addr = str(main_process_ip)
|
326 |
+
args.master_port = str(main_process_port)
|
327 |
+
else:
|
328 |
+
args.rdzv_endpoint = f"{main_process_ip}:{main_process_port}"
|
329 |
+
else:
|
330 |
+
args.nproc_per_node = str(num_processes)
|
331 |
+
if main_process_port is not None:
|
332 |
+
args.master_port = str(main_process_port)
|
333 |
+
|
334 |
+
if main_process_port is None:
|
335 |
+
main_process_port = 29500
|
336 |
+
|
337 |
+
# only need to check port availability in main process, in case we have to start multiple launchers on the same machine
|
338 |
+
# for some reasons like splitting log files.
|
339 |
+
need_port_check = num_machines <= 1 or int(args.machine_rank) == 0
|
340 |
+
if need_port_check and is_port_in_use(main_process_port):
|
341 |
+
raise ConnectionError(
|
342 |
+
f"Tried to launch distributed communication on port `{main_process_port}`, but another process is utilizing it. "
|
343 |
+
"Please specify a different port (such as using the `--main_process_port` flag or specifying a different `main_process_port` in your config file)"
|
344 |
+
" and rerun your script. To automatically use the next open port (on a single node), you can set this to `0`."
|
345 |
+
)
|
346 |
+
|
347 |
+
if args.module and args.no_python:
|
348 |
+
raise ValueError("--module and --no_python cannot be used together")
|
349 |
+
elif args.module:
|
350 |
+
args.module = True
|
351 |
+
elif args.no_python:
|
352 |
+
args.no_python = True
|
353 |
+
|
354 |
+
current_env = os.environ.copy()
|
355 |
+
if args.debug:
|
356 |
+
current_env["ACCELERATE_DEBUG_MODE"] = "true"
|
357 |
+
gpu_ids = getattr(args, "gpu_ids", "all")
|
358 |
+
if gpu_ids != "all" and args.gpu_ids is not None:
|
359 |
+
if is_xpu_available():
|
360 |
+
current_env["ZE_AFFINITY_MASK"] = gpu_ids
|
361 |
+
elif is_mlu_available():
|
362 |
+
current_env["MLU_VISIBLE_DEVICES"] = gpu_ids
|
363 |
+
elif is_npu_available():
|
364 |
+
current_env["ASCEND_RT_VISIBLE_DEVICES"] = gpu_ids
|
365 |
+
else:
|
366 |
+
current_env["CUDA_VISIBLE_DEVICES"] = gpu_ids
|
367 |
+
try:
|
368 |
+
mixed_precision = PrecisionType(args.mixed_precision.lower())
|
369 |
+
except ValueError:
|
370 |
+
raise ValueError(
|
371 |
+
f"Unknown mixed_precision mode: {args.mixed_precision.lower()}. Choose between {PrecisionType.list()}."
|
372 |
+
)
|
373 |
+
|
374 |
+
current_env["PYTHONPATH"] = env_var_path_add("PYTHONPATH", os.path.abspath("."))
|
375 |
+
current_env["ACCELERATE_MIXED_PRECISION"] = str(mixed_precision)
|
376 |
+
current_env["ACCELERATE_CONFIG_DS_FIELDS"] = str(args.deepspeed_fields_from_accelerate_config).lower()
|
377 |
+
current_env["ACCELERATE_USE_DEEPSPEED"] = "true"
|
378 |
+
if args.zero_stage is not None:
|
379 |
+
current_env["ACCELERATE_DEEPSPEED_ZERO_STAGE"] = str(args.zero_stage)
|
380 |
+
if args.gradient_accumulation_steps is not None:
|
381 |
+
current_env["ACCELERATE_GRADIENT_ACCUMULATION_STEPS"] = str(args.gradient_accumulation_steps)
|
382 |
+
if args.gradient_clipping is not None:
|
383 |
+
current_env["ACCELERATE_GRADIENT_CLIPPING"] = str(args.gradient_clipping).lower()
|
384 |
+
if args.offload_optimizer_device is not None:
|
385 |
+
current_env["ACCELERATE_DEEPSPEED_OFFLOAD_OPTIMIZER_DEVICE"] = str(args.offload_optimizer_device).lower()
|
386 |
+
if args.offload_param_device is not None:
|
387 |
+
current_env["ACCELERATE_DEEPSPEED_OFFLOAD_PARAM_DEVICE"] = str(args.offload_param_device).lower()
|
388 |
+
if args.zero3_init_flag is not None:
|
389 |
+
current_env["ACCELERATE_DEEPSPEED_ZERO3_INIT"] = str(args.zero3_init_flag).lower()
|
390 |
+
if args.zero3_save_16bit_model is not None:
|
391 |
+
current_env["ACCELERATE_DEEPSPEED_ZERO3_SAVE_16BIT_MODEL"] = str(args.zero3_save_16bit_model).lower()
|
392 |
+
if args.deepspeed_config_file is not None:
|
393 |
+
current_env["ACCELERATE_DEEPSPEED_CONFIG_FILE"] = str(args.deepspeed_config_file)
|
394 |
+
if args.enable_cpu_affinity:
|
395 |
+
current_env["ACCELERATE_CPU_AFFINITY"] = "1"
|
396 |
+
if args.deepspeed_moe_layer_cls_names is not None:
|
397 |
+
current_env["ACCELERATE_DEEPSPEED_MOE_LAYER_CLS_NAMES"] = str(args.deepspeed_moe_layer_cls_names)
|
398 |
+
return cmd, current_env
|
399 |
+
|
400 |
+
|
401 |
+
def prepare_tpu(
|
402 |
+
args: argparse.Namespace, current_env: Dict[str, str], pod: bool = False
|
403 |
+
) -> Tuple[argparse.Namespace, Dict[str, str]]:
|
404 |
+
"""
|
405 |
+
Prepares and returns an environment with the correct TPU environment variables.
|
406 |
+
"""
|
407 |
+
if args.mixed_precision == "bf16" and is_torch_xla_available(check_is_tpu=True):
|
408 |
+
if args.downcast_bf16:
|
409 |
+
current_env["XLA_DOWNCAST_BF16"] = "1"
|
410 |
+
else:
|
411 |
+
current_env["XLA_USE_BF16"] = "1"
|
412 |
+
if args.debug:
|
413 |
+
current_env["ACCELERATE_DEBUG_MODE"] = "true"
|
414 |
+
if pod:
|
415 |
+
# Take explicit args and set them up for XLA
|
416 |
+
args.vm = args.tpu_vm
|
417 |
+
args.tpu = args.tpu_name
|
418 |
+
return args, current_env
|
419 |
+
|
420 |
+
|
421 |
+
def _convert_nargs_to_dict(nargs: List[str]) -> Dict[str, str]:
|
422 |
+
if len(nargs) < 0:
|
423 |
+
return {}
|
424 |
+
# helper function to infer type for argsparser
|
425 |
+
|
426 |
+
def _infer_type(s):
|
427 |
+
try:
|
428 |
+
s = float(s)
|
429 |
+
|
430 |
+
if s // 1 == s:
|
431 |
+
return int(s)
|
432 |
+
return s
|
433 |
+
except ValueError:
|
434 |
+
return s
|
435 |
+
|
436 |
+
parser = argparse.ArgumentParser()
|
437 |
+
_, unknown = parser.parse_known_args(nargs)
|
438 |
+
for index, argument in enumerate(unknown):
|
439 |
+
if argument.startswith(("-", "--")):
|
440 |
+
action = None
|
441 |
+
if index + 1 < len(unknown): # checks if next index would be in list
|
442 |
+
if unknown[index + 1].startswith(("-", "--")): # checks if next element is an key
|
443 |
+
# raise an error if element is store_true or store_false
|
444 |
+
raise ValueError(
|
445 |
+
"SageMaker doesn’t support argparse actions for `store_true` or `store_false`. Please define explicit types"
|
446 |
+
)
|
447 |
+
else: # raise an error if last element is store_true or store_false
|
448 |
+
raise ValueError(
|
449 |
+
"SageMaker doesn’t support argparse actions for `store_true` or `store_false`. Please define explicit types"
|
450 |
+
)
|
451 |
+
# adds argument to parser based on action_store true
|
452 |
+
if action is None:
|
453 |
+
parser.add_argument(argument, type=_infer_type)
|
454 |
+
else:
|
455 |
+
parser.add_argument(argument, action=action)
|
456 |
+
|
457 |
+
return {
|
458 |
+
key: (literal_eval(value) if value in ("True", "False") else value)
|
459 |
+
for key, value in parser.parse_args(nargs).__dict__.items()
|
460 |
+
}
|
461 |
+
|
462 |
+
|
463 |
+
def prepare_sagemager_args_inputs(
|
464 |
+
sagemaker_config: SageMakerConfig, args: argparse.Namespace
|
465 |
+
) -> Tuple[argparse.Namespace, Dict[str, Any]]:
|
466 |
+
# configure environment
|
467 |
+
print("Configuring Amazon SageMaker environment")
|
468 |
+
os.environ["AWS_DEFAULT_REGION"] = sagemaker_config.region
|
469 |
+
|
470 |
+
# configure credentials
|
471 |
+
if sagemaker_config.profile is not None:
|
472 |
+
os.environ["AWS_PROFILE"] = sagemaker_config.profile
|
473 |
+
elif args.aws_access_key_id is not None and args.aws_secret_access_key is not None:
|
474 |
+
os.environ["AWS_ACCESS_KEY_ID"] = args.aws_access_key_id
|
475 |
+
os.environ["AWS_SECRET_ACCESS_KEY"] = args.aws_secret_access_key
|
476 |
+
else:
|
477 |
+
raise OSError("You need to provide an aws_access_key_id and aws_secret_access_key when not using aws_profile")
|
478 |
+
|
479 |
+
# extract needed arguments
|
480 |
+
source_dir = os.path.dirname(args.training_script)
|
481 |
+
if not source_dir: # checks if string is empty
|
482 |
+
source_dir = "."
|
483 |
+
entry_point = os.path.basename(args.training_script)
|
484 |
+
if not entry_point.endswith(".py"):
|
485 |
+
raise ValueError(f'Your training script should be a python script and not "{entry_point}"')
|
486 |
+
|
487 |
+
print("Converting Arguments to Hyperparameters")
|
488 |
+
hyperparameters = _convert_nargs_to_dict(args.training_script_args)
|
489 |
+
|
490 |
+
try:
|
491 |
+
mixed_precision = PrecisionType(args.mixed_precision.lower())
|
492 |
+
except ValueError:
|
493 |
+
raise ValueError(
|
494 |
+
f"Unknown mixed_precision mode: {args.mixed_precision.lower()}. Choose between {PrecisionType.list()}."
|
495 |
+
)
|
496 |
+
|
497 |
+
try:
|
498 |
+
dynamo_backend = DynamoBackend(args.dynamo_backend.upper())
|
499 |
+
except ValueError:
|
500 |
+
raise ValueError(
|
501 |
+
f"Unknown dynamo backend: {args.dynamo_backend.upper()}. Choose between {DynamoBackend.list()}."
|
502 |
+
)
|
503 |
+
|
504 |
+
# Environment variables to be set for use during training job
|
505 |
+
environment = {
|
506 |
+
"ACCELERATE_USE_SAGEMAKER": "true",
|
507 |
+
"ACCELERATE_MIXED_PRECISION": str(mixed_precision),
|
508 |
+
"ACCELERATE_DYNAMO_BACKEND": dynamo_backend.value,
|
509 |
+
"ACCELERATE_DYNAMO_MODE": args.dynamo_mode,
|
510 |
+
"ACCELERATE_DYNAMO_USE_FULLGRAPH": str(args.dynamo_use_fullgraph),
|
511 |
+
"ACCELERATE_DYNAMO_USE_DYNAMIC": str(args.dynamo_use_dynamic),
|
512 |
+
"ACCELERATE_SAGEMAKER_DISTRIBUTED_TYPE": sagemaker_config.distributed_type.value,
|
513 |
+
}
|
514 |
+
# configure distribution set up
|
515 |
+
distribution = None
|
516 |
+
if sagemaker_config.distributed_type == SageMakerDistributedType.DATA_PARALLEL:
|
517 |
+
distribution = {"smdistributed": {"dataparallel": {"enabled": True}}}
|
518 |
+
|
519 |
+
# configure sagemaker inputs
|
520 |
+
sagemaker_inputs = None
|
521 |
+
if sagemaker_config.sagemaker_inputs_file is not None:
|
522 |
+
print(f"Loading SageMaker Inputs from {sagemaker_config.sagemaker_inputs_file} file")
|
523 |
+
sagemaker_inputs = {}
|
524 |
+
with open(sagemaker_config.sagemaker_inputs_file) as file:
|
525 |
+
for i, line in enumerate(file):
|
526 |
+
if i == 0:
|
527 |
+
continue
|
528 |
+
l = line.split("\t")
|
529 |
+
sagemaker_inputs[l[0]] = l[1].strip()
|
530 |
+
print(f"Loaded SageMaker Inputs: {sagemaker_inputs}")
|
531 |
+
|
532 |
+
# configure sagemaker metrics
|
533 |
+
sagemaker_metrics = None
|
534 |
+
if sagemaker_config.sagemaker_metrics_file is not None:
|
535 |
+
print(f"Loading SageMaker Metrics from {sagemaker_config.sagemaker_metrics_file} file")
|
536 |
+
sagemaker_metrics = []
|
537 |
+
with open(sagemaker_config.sagemaker_metrics_file) as file:
|
538 |
+
for i, line in enumerate(file):
|
539 |
+
if i == 0:
|
540 |
+
continue
|
541 |
+
l = line.split("\t")
|
542 |
+
metric_dict = {
|
543 |
+
"Name": l[0],
|
544 |
+
"Regex": l[1].strip(),
|
545 |
+
}
|
546 |
+
sagemaker_metrics.append(metric_dict)
|
547 |
+
print(f"Loaded SageMaker Metrics: {sagemaker_metrics}")
|
548 |
+
|
549 |
+
# configure session
|
550 |
+
print("Creating Estimator")
|
551 |
+
args = {
|
552 |
+
"image_uri": sagemaker_config.image_uri,
|
553 |
+
"entry_point": entry_point,
|
554 |
+
"source_dir": source_dir,
|
555 |
+
"role": sagemaker_config.iam_role_name,
|
556 |
+
"transformers_version": sagemaker_config.transformers_version,
|
557 |
+
"pytorch_version": sagemaker_config.pytorch_version,
|
558 |
+
"py_version": sagemaker_config.py_version,
|
559 |
+
"base_job_name": sagemaker_config.base_job_name,
|
560 |
+
"instance_count": sagemaker_config.num_machines,
|
561 |
+
"instance_type": sagemaker_config.ec2_instance_type,
|
562 |
+
"debugger_hook_config": False,
|
563 |
+
"distribution": distribution,
|
564 |
+
"hyperparameters": hyperparameters,
|
565 |
+
"environment": environment,
|
566 |
+
"metric_definitions": sagemaker_metrics,
|
567 |
+
}
|
568 |
+
|
569 |
+
if sagemaker_config.additional_args is not None:
|
570 |
+
args = merge_dicts(sagemaker_config.additional_args, args)
|
571 |
+
return args, sagemaker_inputs
|
572 |
+
|
573 |
+
|
574 |
+
def env_var_path_add(env_var_name, path_to_add):
|
575 |
+
"""
|
576 |
+
Extends a path-based environment variable's value with a new path and returns the updated value. It's up to the
|
577 |
+
caller to set it in os.environ.
|
578 |
+
"""
|
579 |
+
paths = [p for p in os.environ.get(env_var_name, "").split(":") if len(p) > 0]
|
580 |
+
paths.append(str(path_to_add))
|
581 |
+
return ":".join(paths)
|
582 |
+
|
583 |
+
|
584 |
+
class PrepareForLaunch:
|
585 |
+
"""
|
586 |
+
Prepare a function that will launched in a distributed setup.
|
587 |
+
|
588 |
+
Args:
|
589 |
+
launcher (`Callable`):
|
590 |
+
The function to launch.
|
591 |
+
distributed_type ([`~state.DistributedType`]):
|
592 |
+
The distributed type to prepare for.
|
593 |
+
debug (`bool`, *optional*, defaults to `False`):
|
594 |
+
Whether or not this is a debug launch.
|
595 |
+
"""
|
596 |
+
|
597 |
+
def __init__(self, launcher, distributed_type="NO", debug=False):
|
598 |
+
self.launcher = launcher
|
599 |
+
self.distributed_type = DistributedType(distributed_type)
|
600 |
+
self.debug = debug
|
601 |
+
|
602 |
+
def __call__(self, index, *args):
|
603 |
+
if self.debug:
|
604 |
+
world_size = int(os.environ.get("WORLD_SIZE"))
|
605 |
+
rdv_file = os.environ.get("ACCELERATE_DEBUG_RDV_FILE")
|
606 |
+
torch.distributed.init_process_group(
|
607 |
+
"gloo",
|
608 |
+
rank=index,
|
609 |
+
store=torch.distributed.FileStore(rdv_file, world_size),
|
610 |
+
world_size=world_size,
|
611 |
+
)
|
612 |
+
elif self.distributed_type in (
|
613 |
+
DistributedType.MULTI_GPU,
|
614 |
+
DistributedType.MULTI_MLU,
|
615 |
+
DistributedType.MULTI_NPU,
|
616 |
+
DistributedType.MULTI_XPU,
|
617 |
+
DistributedType.MULTI_CPU,
|
618 |
+
):
|
619 |
+
# Prepare the environment for torch.distributed
|
620 |
+
os.environ["LOCAL_RANK"] = str(index)
|
621 |
+
nproc = int(os.environ.get("NPROC", 1))
|
622 |
+
node_rank = int(os.environ.get("NODE_RANK", 0))
|
623 |
+
os.environ["RANK"] = str(nproc * node_rank + index)
|
624 |
+
|
625 |
+
os.environ["FORK_LAUNCHED"] = str(1)
|
626 |
+
self.launcher(*args)
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/megatron_lm.py
ADDED
@@ -0,0 +1,1435 @@
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1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
import argparse
|
16 |
+
import math
|
17 |
+
from abc import ABC
|
18 |
+
from functools import partial
|
19 |
+
|
20 |
+
import torch
|
21 |
+
import torch.nn.functional as F
|
22 |
+
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
|
23 |
+
from torch.nn.parallel.distributed import DistributedDataParallel as torchDDP
|
24 |
+
|
25 |
+
from ..optimizer import AcceleratedOptimizer
|
26 |
+
from ..scheduler import AcceleratedScheduler
|
27 |
+
from .imports import is_megatron_lm_available, is_transformers_available
|
28 |
+
from .operations import recursively_apply, send_to_device
|
29 |
+
|
30 |
+
|
31 |
+
if is_transformers_available():
|
32 |
+
from transformers.modeling_outputs import (
|
33 |
+
CausalLMOutputWithCrossAttentions,
|
34 |
+
Seq2SeqLMOutput,
|
35 |
+
SequenceClassifierOutput,
|
36 |
+
)
|
37 |
+
|
38 |
+
|
39 |
+
if is_megatron_lm_available():
|
40 |
+
from megatron import (
|
41 |
+
get_args,
|
42 |
+
get_num_microbatches,
|
43 |
+
get_tensorboard_writer,
|
44 |
+
get_timers,
|
45 |
+
get_tokenizer,
|
46 |
+
mpu,
|
47 |
+
print_rank_0,
|
48 |
+
print_rank_last,
|
49 |
+
)
|
50 |
+
from megatron.arguments import _add_data_args, _add_validation_args, parse_args, validate_args
|
51 |
+
from megatron.checkpointing import load_args_from_checkpoint, load_checkpoint, save_checkpoint
|
52 |
+
from megatron.data.data_samplers import MegatronPretrainingRandomSampler, MegatronPretrainingSampler
|
53 |
+
from megatron.global_vars import set_global_variables
|
54 |
+
from megatron.initialize import (
|
55 |
+
_compile_dependencies,
|
56 |
+
_init_autoresume,
|
57 |
+
_set_random_seed,
|
58 |
+
set_jit_fusion_options,
|
59 |
+
write_args_to_tensorboard,
|
60 |
+
)
|
61 |
+
from megatron.model import BertModel, Float16Module, GPTModel, ModelType, T5Model
|
62 |
+
from megatron.model import DistributedDataParallel as LocalDDP
|
63 |
+
from megatron.model.classification import Classification
|
64 |
+
from megatron.optimizer import get_megatron_optimizer
|
65 |
+
from megatron.schedules import get_forward_backward_func
|
66 |
+
from megatron.text_generation.communication import broadcast_int_list, broadcast_tensor
|
67 |
+
from megatron.text_generation.generation import (
|
68 |
+
beam_search_and_return_on_first_stage,
|
69 |
+
generate_tokens_probs_and_return_on_first_stage,
|
70 |
+
)
|
71 |
+
from megatron.tokenizer.tokenizer import _vocab_size_with_padding
|
72 |
+
from megatron.training import get_model, get_optimizer_param_scheduler, training_log
|
73 |
+
from megatron.utils import (
|
74 |
+
average_losses_across_data_parallel_group,
|
75 |
+
calc_params_l2_norm,
|
76 |
+
get_ltor_masks_and_position_ids,
|
77 |
+
unwrap_model,
|
78 |
+
)
|
79 |
+
|
80 |
+
|
81 |
+
# model utilities
|
82 |
+
def model_provider_func(pre_process=True, post_process=True, add_encoder=True, add_decoder=True):
|
83 |
+
"""Build the model."""
|
84 |
+
args = get_args()
|
85 |
+
mode = "pre-training" if args.pretraining_flag else "fine-tuning"
|
86 |
+
if args.rank == 0:
|
87 |
+
print(f"Building {args.model_type_name} model in the {mode} mode.")
|
88 |
+
print(
|
89 |
+
"The Megatron LM model weights are initialized at random in `accelerator.prepare`. "
|
90 |
+
"Please use `accelerator.load_checkpoint` to load a pre-trained checkpoint matching the distributed setup."
|
91 |
+
)
|
92 |
+
if args.model_type_name == "bert":
|
93 |
+
if args.pretraining_flag:
|
94 |
+
num_tokentypes = 2 if args.bert_binary_head else 0
|
95 |
+
model = BertModel(
|
96 |
+
num_tokentypes=num_tokentypes,
|
97 |
+
add_binary_head=args.bert_binary_head,
|
98 |
+
parallel_output=True,
|
99 |
+
pre_process=pre_process,
|
100 |
+
post_process=post_process,
|
101 |
+
)
|
102 |
+
else:
|
103 |
+
model = Classification(
|
104 |
+
num_classes=args.num_labels, num_tokentypes=2, pre_process=pre_process, post_process=post_process
|
105 |
+
)
|
106 |
+
elif args.model_type_name == "gpt":
|
107 |
+
model = GPTModel(num_tokentypes=0, parallel_output=True, pre_process=pre_process, post_process=post_process)
|
108 |
+
elif args.model_type_name == "t5":
|
109 |
+
model = T5Model(
|
110 |
+
num_tokentypes=0,
|
111 |
+
parallel_output=True,
|
112 |
+
pre_process=pre_process,
|
113 |
+
post_process=post_process,
|
114 |
+
add_encoder=add_encoder,
|
115 |
+
add_decoder=add_decoder,
|
116 |
+
)
|
117 |
+
else:
|
118 |
+
raise ValueError(f"Unsupported model type: {args.model_type_name}")
|
119 |
+
return model
|
120 |
+
|
121 |
+
|
122 |
+
def prepare_model(accelerator):
|
123 |
+
accelerator.print("Preparing model")
|
124 |
+
args = get_args()
|
125 |
+
if accelerator.state.megatron_lm_plugin.custom_prepare_model_function is not None:
|
126 |
+
if accelerator.state.megatron_lm_plugin.custom_model_provider_function is None:
|
127 |
+
raise ValueError(
|
128 |
+
"You must provide a `custom_model_provider_function` when using a `custom_prepare_model_function`."
|
129 |
+
)
|
130 |
+
custom_model_provider_func = accelerator.state.megatron_lm_plugin.custom_model_provider_function
|
131 |
+
model = accelerator.state.megatron_lm_plugin.custom_prepare_model_function(custom_model_provider_func)
|
132 |
+
else:
|
133 |
+
if args.model_type_name in ("bert", "gpt"):
|
134 |
+
model_type = ModelType.encoder_or_decoder
|
135 |
+
elif args.model_type_name == "t5":
|
136 |
+
model_type = ModelType.encoder_and_decoder
|
137 |
+
if args.pipeline_model_parallel_split_rank is None and args.pipeline_model_parallel_size > 1:
|
138 |
+
args.pipeline_model_parallel_split_rank = args.pipeline_model_parallel_size // 2
|
139 |
+
model = get_model(model_provider_func, model_type)
|
140 |
+
return model
|
141 |
+
|
142 |
+
|
143 |
+
# dataloader utilities
|
144 |
+
class MegatronLMDummyDataLoader:
|
145 |
+
"""
|
146 |
+
Dummy dataloader presents model parameters or param groups, this is primarily used to follow conventional training
|
147 |
+
|
148 |
+
Args:
|
149 |
+
**dataset_kwargs: Megatron data arguments.
|
150 |
+
"""
|
151 |
+
|
152 |
+
def __init__(self, **dataset_kwargs):
|
153 |
+
parser = argparse.ArgumentParser()
|
154 |
+
parser = _add_data_args(parser)
|
155 |
+
parser = _add_validation_args(parser)
|
156 |
+
data_args = parser.parse_known_args()
|
157 |
+
self.dataset_args = vars(data_args[0])
|
158 |
+
self.dataset_args.update(dataset_kwargs)
|
159 |
+
self.dataset_args["megatron_dataset_flag"] = True
|
160 |
+
|
161 |
+
def set_megatron_data_args(self):
|
162 |
+
args = get_args()
|
163 |
+
for key, value in self.dataset_args.items():
|
164 |
+
setattr(args, key, value)
|
165 |
+
|
166 |
+
def get_train_valid_test_datasets_provider(self):
|
167 |
+
def train_valid_test_datasets_provider(train_val_test_num_samples):
|
168 |
+
"""Build train, valid, and test datasets."""
|
169 |
+
args = get_args()
|
170 |
+
dataset_args = {
|
171 |
+
"data_prefix": args.data_path,
|
172 |
+
"data_impl": args.data_impl,
|
173 |
+
"splits_string": args.split,
|
174 |
+
"train_valid_test_num_samples": train_val_test_num_samples,
|
175 |
+
"skip_warmup": (not args.mmap_warmup),
|
176 |
+
"seed": args.seed,
|
177 |
+
}
|
178 |
+
if args.model_type_name == "bert":
|
179 |
+
dataset_args.update(
|
180 |
+
{
|
181 |
+
"max_seq_length": args.seq_length,
|
182 |
+
"masked_lm_prob": args.mask_prob,
|
183 |
+
"short_seq_prob": args.short_seq_prob,
|
184 |
+
"binary_head": args.bert_binary_head,
|
185 |
+
}
|
186 |
+
)
|
187 |
+
elif args.model_type_name == "gpt":
|
188 |
+
dataset_args.update(
|
189 |
+
{
|
190 |
+
"seq_length": args.seq_length,
|
191 |
+
}
|
192 |
+
)
|
193 |
+
elif args.model_type_name == "t5":
|
194 |
+
dataset_args.update(
|
195 |
+
{
|
196 |
+
"max_seq_length": args.encoder_seq_length,
|
197 |
+
"max_seq_length_dec": args.decoder_seq_length,
|
198 |
+
"masked_lm_prob": args.mask_prob,
|
199 |
+
"short_seq_prob": args.short_seq_prob,
|
200 |
+
"dataset_type": "t5",
|
201 |
+
}
|
202 |
+
)
|
203 |
+
else:
|
204 |
+
raise ValueError(f"Unsupported model type: {args.model_type_name}")
|
205 |
+
if args.model_type_name == "gpt":
|
206 |
+
from megatron.data.gpt_dataset import build_train_valid_test_datasets
|
207 |
+
else:
|
208 |
+
from megatron.data.dataset_utils import build_train_valid_test_datasets
|
209 |
+
train_ds, valid_ds, test_ds = build_train_valid_test_datasets(**dataset_args)
|
210 |
+
return train_ds, valid_ds, test_ds
|
211 |
+
|
212 |
+
return train_valid_test_datasets_provider
|
213 |
+
|
214 |
+
def build_pretraining_data_loader(self, dataset, consumed_samples):
|
215 |
+
if dataset is None:
|
216 |
+
return None
|
217 |
+
args = get_args()
|
218 |
+
micro_batch_size = args.micro_batch_size * args.num_micro_batches
|
219 |
+
|
220 |
+
# Megatron sampler
|
221 |
+
if args.dataloader_type == "single":
|
222 |
+
batch_sampler = MegatronPretrainingSampler(
|
223 |
+
total_samples=len(dataset),
|
224 |
+
consumed_samples=consumed_samples,
|
225 |
+
micro_batch_size=micro_batch_size,
|
226 |
+
data_parallel_rank=mpu.get_data_parallel_rank(),
|
227 |
+
data_parallel_size=mpu.get_data_parallel_world_size(),
|
228 |
+
)
|
229 |
+
elif args.dataloader_type == "cyclic":
|
230 |
+
batch_sampler = MegatronPretrainingRandomSampler(
|
231 |
+
dataset,
|
232 |
+
total_samples=len(dataset),
|
233 |
+
consumed_samples=consumed_samples,
|
234 |
+
micro_batch_size=micro_batch_size,
|
235 |
+
data_parallel_rank=mpu.get_data_parallel_rank(),
|
236 |
+
data_parallel_size=mpu.get_data_parallel_world_size(),
|
237 |
+
data_sharding=args.data_sharding,
|
238 |
+
)
|
239 |
+
else:
|
240 |
+
raise Exception(f"{args.dataloader_type} dataloader type is not supported.")
|
241 |
+
|
242 |
+
# Torch dataloader.
|
243 |
+
return torch.utils.data.DataLoader(
|
244 |
+
dataset, batch_sampler=batch_sampler, num_workers=args.num_workers, pin_memory=True
|
245 |
+
)
|
246 |
+
|
247 |
+
def build_train_valid_test_data_iterators(self):
|
248 |
+
def cyclic_iter(iter):
|
249 |
+
while True:
|
250 |
+
yield from iter
|
251 |
+
|
252 |
+
args = get_args()
|
253 |
+
|
254 |
+
(train_dataloader, valid_dataloader, test_dataloader) = (None, None, None)
|
255 |
+
|
256 |
+
print_rank_0("> building train, validation, and test datasets ...")
|
257 |
+
|
258 |
+
# Backward compatibility, assume fixed batch size.
|
259 |
+
if args.iteration > 0 and args.consumed_train_samples == 0:
|
260 |
+
assert args.train_samples is None, "only backward compatiblity support for iteration-based training"
|
261 |
+
args.consumed_train_samples = args.iteration * args.global_batch_size
|
262 |
+
if args.iteration > 0 and args.consumed_valid_samples == 0:
|
263 |
+
if args.train_samples is None:
|
264 |
+
args.consumed_valid_samples = (
|
265 |
+
(args.iteration // args.eval_interval) * args.eval_iters * args.global_batch_size
|
266 |
+
)
|
267 |
+
|
268 |
+
# Data loader only on rank 0 of each model parallel group.
|
269 |
+
if mpu.get_tensor_model_parallel_rank() == 0:
|
270 |
+
# Number of train/valid/test samples.
|
271 |
+
if args.train_samples:
|
272 |
+
train_samples = args.train_samples
|
273 |
+
else:
|
274 |
+
train_samples = args.train_iters * args.global_batch_size
|
275 |
+
eval_iters = (args.train_iters // args.eval_interval + 1) * args.eval_iters
|
276 |
+
test_iters = args.eval_iters
|
277 |
+
train_val_test_num_samples = [
|
278 |
+
train_samples,
|
279 |
+
eval_iters * args.global_batch_size,
|
280 |
+
test_iters * args.global_batch_size,
|
281 |
+
]
|
282 |
+
print_rank_0(" > datasets target sizes (minimum size):")
|
283 |
+
print_rank_0(f" train: {train_val_test_num_samples[0]}")
|
284 |
+
print_rank_0(f" validation: {train_val_test_num_samples[1]}")
|
285 |
+
print_rank_0(f" test: {train_val_test_num_samples[2]}")
|
286 |
+
|
287 |
+
# Build the datasets.
|
288 |
+
train_valid_test_datasets_provider = self.get_train_valid_test_datasets_provider()
|
289 |
+
train_ds, valid_ds, test_ds = train_valid_test_datasets_provider(train_val_test_num_samples)
|
290 |
+
|
291 |
+
# Build dataloders.
|
292 |
+
train_dataloader = self.build_pretraining_data_loader(train_ds, args.consumed_train_samples)
|
293 |
+
valid_dataloader = self.build_pretraining_data_loader(valid_ds, args.consumed_valid_samples)
|
294 |
+
test_dataloader = self.build_pretraining_data_loader(test_ds, 0)
|
295 |
+
|
296 |
+
# Flags to know if we need to do training/validation/testing.
|
297 |
+
do_train = train_dataloader is not None and args.train_iters > 0
|
298 |
+
do_valid = valid_dataloader is not None and args.eval_iters > 0
|
299 |
+
do_test = test_dataloader is not None and args.eval_iters > 0
|
300 |
+
# Need to broadcast num_tokens and num_type_tokens.
|
301 |
+
flags = torch.cuda.LongTensor([int(do_train), int(do_valid), int(do_test)])
|
302 |
+
else:
|
303 |
+
flags = torch.cuda.LongTensor([0, 0, 0])
|
304 |
+
|
305 |
+
# Broadcast num tokens.
|
306 |
+
torch.distributed.broadcast(
|
307 |
+
flags, mpu.get_tensor_model_parallel_src_rank(), group=mpu.get_tensor_model_parallel_group()
|
308 |
+
)
|
309 |
+
args.do_train = flags[0].item()
|
310 |
+
args.do_valid = flags[1].item()
|
311 |
+
args.do_test = flags[2].item()
|
312 |
+
|
313 |
+
# Build iterators.
|
314 |
+
dl_type = args.dataloader_type
|
315 |
+
assert dl_type in ["single", "cyclic"]
|
316 |
+
|
317 |
+
if train_dataloader is not None:
|
318 |
+
train_data_iterator = (
|
319 |
+
iter(train_dataloader) if dl_type == "single" else iter(cyclic_iter(train_dataloader))
|
320 |
+
)
|
321 |
+
else:
|
322 |
+
train_data_iterator = None
|
323 |
+
|
324 |
+
if valid_dataloader is not None:
|
325 |
+
valid_data_iterator = (
|
326 |
+
iter(valid_dataloader) if dl_type == "single" else iter(cyclic_iter(valid_dataloader))
|
327 |
+
)
|
328 |
+
else:
|
329 |
+
valid_data_iterator = None
|
330 |
+
|
331 |
+
if test_dataloader is not None:
|
332 |
+
test_data_iterator = iter(test_dataloader) if dl_type == "single" else iter(cyclic_iter(test_dataloader))
|
333 |
+
else:
|
334 |
+
test_data_iterator = None
|
335 |
+
|
336 |
+
return train_data_iterator, valid_data_iterator, test_data_iterator
|
337 |
+
|
338 |
+
|
339 |
+
def prepare_data_loader(accelerator, dataloader):
|
340 |
+
accelerator.print("Preparing dataloader")
|
341 |
+
args = get_args()
|
342 |
+
if not args.megatron_dataset_flag:
|
343 |
+
from ..data_loader import _PYTORCH_DATALOADER_KWARGS, prepare_data_loader
|
344 |
+
|
345 |
+
args = get_args()
|
346 |
+
micro_batch_size = args.micro_batch_size * args.num_micro_batches
|
347 |
+
kwargs = {k: getattr(dataloader, k, _PYTORCH_DATALOADER_KWARGS[k]) for k in _PYTORCH_DATALOADER_KWARGS}
|
348 |
+
if kwargs["batch_size"] is None:
|
349 |
+
if isinstance(kwargs["sampler"], torch.utils.data.BatchSampler):
|
350 |
+
kwargs["sampler"].batch_size = micro_batch_size
|
351 |
+
else:
|
352 |
+
del kwargs["sampler"]
|
353 |
+
del kwargs["shuffle"]
|
354 |
+
del kwargs["batch_size"]
|
355 |
+
kwargs["batch_sampler"].batch_size = micro_batch_size
|
356 |
+
else:
|
357 |
+
del kwargs["batch_sampler"]
|
358 |
+
kwargs["batch_size"] = micro_batch_size
|
359 |
+
|
360 |
+
dataloader = torch.utils.data.DataLoader(dataloader.dataset, **kwargs)
|
361 |
+
return prepare_data_loader(
|
362 |
+
dataloader,
|
363 |
+
accelerator.device,
|
364 |
+
num_processes=mpu.get_data_parallel_world_size(),
|
365 |
+
process_index=mpu.get_data_parallel_rank(),
|
366 |
+
split_batches=accelerator.split_batches,
|
367 |
+
put_on_device=True,
|
368 |
+
rng_types=accelerator.rng_types.copy(),
|
369 |
+
dispatch_batches=accelerator.dispatch_batches,
|
370 |
+
)
|
371 |
+
else:
|
372 |
+
if args.consumed_samples is not None:
|
373 |
+
(
|
374 |
+
args.consumed_train_samples,
|
375 |
+
args.consumed_valid_samples,
|
376 |
+
args.consumed_test_samples,
|
377 |
+
) = args.consumed_samples
|
378 |
+
else:
|
379 |
+
args.consumed_train_samples, args.consumed_valid_samples, args.consumed_test_samples = 0, 0, 0
|
380 |
+
(
|
381 |
+
train_data_iterator,
|
382 |
+
valid_data_iterator,
|
383 |
+
test_data_iterator,
|
384 |
+
) = dataloader.build_train_valid_test_data_iterators()
|
385 |
+
return train_data_iterator, valid_data_iterator, test_data_iterator
|
386 |
+
|
387 |
+
|
388 |
+
# optimizer utilities
|
389 |
+
class MegatronLMOptimizerWrapper(AcceleratedOptimizer):
|
390 |
+
def __init__(self, optimizer):
|
391 |
+
super().__init__(optimizer, device_placement=False, scaler=None)
|
392 |
+
|
393 |
+
def zero_grad(self, set_to_none=None):
|
394 |
+
pass # `model(**batch)` is doing that automatically. Therefore, it's implementation is not needed
|
395 |
+
|
396 |
+
def step(self):
|
397 |
+
pass # `model(**batch)` is doing that automatically. Therefore, it's implementation is not needed
|
398 |
+
|
399 |
+
@property
|
400 |
+
def step_was_skipped(self):
|
401 |
+
"""Whether or not the optimizer step was done, or skipped because of gradient overflow."""
|
402 |
+
return self.optimizer.skipped_iter
|
403 |
+
|
404 |
+
|
405 |
+
def prepare_optimizer(accelerator, model):
|
406 |
+
accelerator.print("Preparing optimizer")
|
407 |
+
args = get_args()
|
408 |
+
optimizer = get_megatron_optimizer(model, args.no_wd_decay_cond, args.scale_lr_cond, args.lr_mult)
|
409 |
+
return optimizer
|
410 |
+
|
411 |
+
|
412 |
+
# scheduler utilities
|
413 |
+
class MegatronLMDummyScheduler:
|
414 |
+
"""
|
415 |
+
Dummy scheduler presents model parameters or param groups, this is primarily used to follow conventional training
|
416 |
+
loop when scheduler config is specified in the deepspeed config file.
|
417 |
+
|
418 |
+
Args:
|
419 |
+
optimizer (`torch.optim.optimizer.Optimizer`):
|
420 |
+
The optimizer to wrap.
|
421 |
+
total_num_steps (int):
|
422 |
+
Total number of steps.
|
423 |
+
warmup_num_steps (int):
|
424 |
+
Number of steps for warmup.
|
425 |
+
**kwargs (additional keyword arguments, *optional*):
|
426 |
+
Other arguments.
|
427 |
+
"""
|
428 |
+
|
429 |
+
def __init__(self, optimizer, total_num_steps=None, warmup_num_steps=0, **kwargs):
|
430 |
+
self.optimizer = optimizer
|
431 |
+
self.total_num_steps = total_num_steps
|
432 |
+
self.warmup_num_steps = warmup_num_steps
|
433 |
+
self.kwargs = kwargs
|
434 |
+
|
435 |
+
|
436 |
+
class MegatronLMSchedulerWrapper(AcceleratedScheduler):
|
437 |
+
def __init__(self, scheduler, optimizers):
|
438 |
+
super().__init__(scheduler, optimizers)
|
439 |
+
|
440 |
+
def step(self, *args, **kwargs):
|
441 |
+
return # `model(**batch)` is doing that automatically. Therefore, it's implementation is not needed
|
442 |
+
|
443 |
+
|
444 |
+
def prepare_scheduler(accelerator, optimizer, scheduler):
|
445 |
+
accelerator.print("Preparing scheduler")
|
446 |
+
scheduler = get_optimizer_param_scheduler(optimizer)
|
447 |
+
return scheduler
|
448 |
+
|
449 |
+
|
450 |
+
class AbstractTrainStep(ABC):
|
451 |
+
"""Abstract class for batching, forward pass and loss handler."""
|
452 |
+
|
453 |
+
def __init__(self, name):
|
454 |
+
super().__init__()
|
455 |
+
self.name = name
|
456 |
+
|
457 |
+
def get_batch_func(self):
|
458 |
+
pass
|
459 |
+
|
460 |
+
def get_forward_step_func(self):
|
461 |
+
pass
|
462 |
+
|
463 |
+
def get_loss_func(self):
|
464 |
+
pass
|
465 |
+
|
466 |
+
|
467 |
+
class BertTrainStep(AbstractTrainStep):
|
468 |
+
"""
|
469 |
+
Bert train step class.
|
470 |
+
|
471 |
+
Args:
|
472 |
+
args (`argparse.Namespace`): Megatron-LM arguments.
|
473 |
+
"""
|
474 |
+
|
475 |
+
def __init__(self, args):
|
476 |
+
super().__init__("BertTrainStep")
|
477 |
+
self.get_batch = self.get_batch_func(args.megatron_dataset_flag)
|
478 |
+
self.loss_func = self.get_loss_func(args.pretraining_flag, args.num_labels)
|
479 |
+
self.forward_step = self.get_forward_step_func(args.pretraining_flag, args.bert_binary_head)
|
480 |
+
if not args.model_return_dict:
|
481 |
+
self.model_output_class = None
|
482 |
+
else:
|
483 |
+
self.model_output_class = SequenceClassifierOutput
|
484 |
+
|
485 |
+
def get_batch_func(self, megatron_dataset_flag):
|
486 |
+
def get_batch_megatron(data_iterator):
|
487 |
+
"""Build the batch."""
|
488 |
+
|
489 |
+
# Items and their type.
|
490 |
+
keys = ["text", "types", "labels", "is_random", "loss_mask", "padding_mask"]
|
491 |
+
datatype = torch.int64
|
492 |
+
|
493 |
+
# Broadcast data.
|
494 |
+
if data_iterator is not None:
|
495 |
+
data = next(data_iterator)
|
496 |
+
else:
|
497 |
+
data = None
|
498 |
+
data_b = mpu.broadcast_data(keys, data, datatype)
|
499 |
+
|
500 |
+
# Unpack.
|
501 |
+
tokens = data_b["text"].long()
|
502 |
+
types = data_b["types"].long()
|
503 |
+
sentence_order = data_b["is_random"].long()
|
504 |
+
loss_mask = data_b["loss_mask"].float()
|
505 |
+
lm_labels = data_b["labels"].long()
|
506 |
+
padding_mask = data_b["padding_mask"].long()
|
507 |
+
|
508 |
+
return tokens, types, sentence_order, loss_mask, lm_labels, padding_mask
|
509 |
+
|
510 |
+
def get_batch_transformer(data_iterator):
|
511 |
+
"""Build the batch."""
|
512 |
+
data = next(data_iterator)
|
513 |
+
data = send_to_device(data, torch.cuda.current_device())
|
514 |
+
|
515 |
+
# Unpack.
|
516 |
+
tokens = data["input_ids"].long()
|
517 |
+
padding_mask = data["attention_mask"].long()
|
518 |
+
if "token_type_ids" in data:
|
519 |
+
types = data["token_type_ids"].long()
|
520 |
+
else:
|
521 |
+
types = None
|
522 |
+
if "labels" in data:
|
523 |
+
lm_labels = data["labels"].long()
|
524 |
+
loss_mask = (data["labels"] != -100).to(torch.float)
|
525 |
+
else:
|
526 |
+
lm_labels = None
|
527 |
+
loss_mask = None
|
528 |
+
if "next_sentence_label" in data:
|
529 |
+
sentence_order = data["next_sentence_label"].long()
|
530 |
+
else:
|
531 |
+
sentence_order = None
|
532 |
+
|
533 |
+
return tokens, types, sentence_order, loss_mask, lm_labels, padding_mask
|
534 |
+
|
535 |
+
if megatron_dataset_flag:
|
536 |
+
return get_batch_megatron
|
537 |
+
else:
|
538 |
+
return get_batch_transformer
|
539 |
+
|
540 |
+
def get_loss_func(self, pretraining_flag, num_labels):
|
541 |
+
def loss_func_pretrain(loss_mask, sentence_order, output_tensor):
|
542 |
+
lm_loss_, sop_logits = output_tensor
|
543 |
+
|
544 |
+
lm_loss_ = lm_loss_.float()
|
545 |
+
loss_mask = loss_mask.float()
|
546 |
+
lm_loss = torch.sum(lm_loss_.view(-1) * loss_mask.reshape(-1)) / loss_mask.sum()
|
547 |
+
|
548 |
+
if sop_logits is not None:
|
549 |
+
sop_loss = F.cross_entropy(sop_logits.view(-1, 2).float(), sentence_order.view(-1), ignore_index=-1)
|
550 |
+
sop_loss = sop_loss.float()
|
551 |
+
loss = lm_loss + sop_loss
|
552 |
+
averaged_losses = average_losses_across_data_parallel_group([lm_loss, sop_loss])
|
553 |
+
return loss, {"lm loss": averaged_losses[0], "sop loss": averaged_losses[1]}
|
554 |
+
|
555 |
+
else:
|
556 |
+
loss = lm_loss
|
557 |
+
averaged_losses = average_losses_across_data_parallel_group([lm_loss])
|
558 |
+
return loss, {"lm loss": averaged_losses[0]}
|
559 |
+
|
560 |
+
def loss_func_finetune(labels, logits):
|
561 |
+
if num_labels == 1:
|
562 |
+
# We are doing regression
|
563 |
+
loss_fct = MSELoss()
|
564 |
+
loss = loss_fct(logits.view(-1), labels.view(-1))
|
565 |
+
elif self.num_labels > 1 and (labels.dtype in (torch.long, torch.int)):
|
566 |
+
loss_fct = CrossEntropyLoss()
|
567 |
+
loss = loss_fct(logits.view(-1, num_labels), labels.view(-1))
|
568 |
+
else:
|
569 |
+
loss_fct = BCEWithLogitsLoss()
|
570 |
+
loss = loss_fct(logits, labels)
|
571 |
+
averaged_losses = average_losses_across_data_parallel_group([loss])
|
572 |
+
return loss, {"loss": averaged_losses[0]}
|
573 |
+
|
574 |
+
if pretraining_flag:
|
575 |
+
return loss_func_pretrain
|
576 |
+
else:
|
577 |
+
return loss_func_finetune
|
578 |
+
|
579 |
+
def get_forward_step_func(self, pretraining_flag, bert_binary_head):
|
580 |
+
def forward_step(data_iterator, model):
|
581 |
+
"""Forward step."""
|
582 |
+
tokens, types, sentence_order, loss_mask, labels, padding_mask = self.get_batch(data_iterator)
|
583 |
+
if not bert_binary_head:
|
584 |
+
types = None
|
585 |
+
# Forward pass through the model.
|
586 |
+
if pretraining_flag:
|
587 |
+
output_tensor = model(tokens, padding_mask, tokentype_ids=types, lm_labels=labels)
|
588 |
+
return output_tensor, partial(self.loss_func, loss_mask, sentence_order)
|
589 |
+
else:
|
590 |
+
logits = model(tokens, padding_mask, tokentype_ids=types)
|
591 |
+
return logits, partial(self.loss_func, labels)
|
592 |
+
|
593 |
+
return forward_step
|
594 |
+
|
595 |
+
|
596 |
+
class GPTTrainStep(AbstractTrainStep):
|
597 |
+
"""
|
598 |
+
GPT train step class.
|
599 |
+
|
600 |
+
Args:
|
601 |
+
args (`argparse.Namespace`): Megatron-LM arguments.
|
602 |
+
"""
|
603 |
+
|
604 |
+
def __init__(self, args):
|
605 |
+
super().__init__("GPTTrainStep")
|
606 |
+
self.get_batch = self.get_batch_func(args.megatron_dataset_flag)
|
607 |
+
self.loss_func = self.get_loss_func()
|
608 |
+
self.forward_step = self.get_forward_step_func()
|
609 |
+
self.eod_token = args.padded_vocab_size - 1
|
610 |
+
if args.vocab_file is not None:
|
611 |
+
tokenizer = get_tokenizer()
|
612 |
+
self.eod_token = tokenizer.eod
|
613 |
+
self.reset_position_ids = args.reset_position_ids
|
614 |
+
self.reset_attention_mask = args.reset_attention_mask
|
615 |
+
self.eod_mask_loss = args.eod_mask_loss
|
616 |
+
if not args.model_return_dict:
|
617 |
+
self.model_output_class = None
|
618 |
+
else:
|
619 |
+
self.model_output_class = CausalLMOutputWithCrossAttentions
|
620 |
+
|
621 |
+
def get_batch_func(self, megatron_dataset_flag):
|
622 |
+
def get_batch_megatron(data_iterator):
|
623 |
+
"""Generate a batch"""
|
624 |
+
# Items and their type.
|
625 |
+
keys = ["text"]
|
626 |
+
datatype = torch.int64
|
627 |
+
|
628 |
+
# Broadcast data.
|
629 |
+
if data_iterator is not None:
|
630 |
+
data = next(data_iterator)
|
631 |
+
else:
|
632 |
+
data = None
|
633 |
+
data_b = mpu.broadcast_data(keys, data, datatype)
|
634 |
+
|
635 |
+
# Unpack.
|
636 |
+
tokens_ = data_b["text"].long()
|
637 |
+
labels = tokens_[:, 1:].contiguous()
|
638 |
+
tokens = tokens_[:, :-1].contiguous()
|
639 |
+
|
640 |
+
# Get the masks and postition ids.
|
641 |
+
attention_mask, loss_mask, position_ids = get_ltor_masks_and_position_ids(
|
642 |
+
tokens, self.eod_token, self.reset_position_ids, self.reset_attention_mask, self.eod_mask_loss
|
643 |
+
)
|
644 |
+
|
645 |
+
return tokens, labels, loss_mask, attention_mask, position_ids
|
646 |
+
|
647 |
+
def get_batch_transformer(data_iterator):
|
648 |
+
data = next(data_iterator)
|
649 |
+
data = {"input_ids": data["input_ids"]}
|
650 |
+
data = send_to_device(data, torch.cuda.current_device())
|
651 |
+
|
652 |
+
tokens_ = data["input_ids"].long()
|
653 |
+
padding = torch.zeros((tokens_.shape[0], 1), dtype=tokens_.dtype, device=tokens_.device) + self.eod_token
|
654 |
+
tokens_ = torch.concat([tokens_, padding], dim=1)
|
655 |
+
labels = tokens_[:, 1:].contiguous()
|
656 |
+
tokens = tokens_[:, :-1].contiguous()
|
657 |
+
# Get the masks and postition ids.
|
658 |
+
attention_mask, loss_mask, position_ids = get_ltor_masks_and_position_ids(
|
659 |
+
tokens, self.eod_token, self.reset_position_ids, self.reset_attention_mask, True
|
660 |
+
)
|
661 |
+
return tokens, labels, loss_mask, attention_mask, position_ids
|
662 |
+
|
663 |
+
if megatron_dataset_flag:
|
664 |
+
return get_batch_megatron
|
665 |
+
else:
|
666 |
+
return get_batch_transformer
|
667 |
+
|
668 |
+
def get_loss_func(self):
|
669 |
+
args = get_args()
|
670 |
+
|
671 |
+
def loss_func(loss_mask, output_tensor):
|
672 |
+
if args.return_logits:
|
673 |
+
losses, logits = output_tensor
|
674 |
+
else:
|
675 |
+
losses = output_tensor
|
676 |
+
losses = losses.float()
|
677 |
+
loss_mask = loss_mask.view(-1).float()
|
678 |
+
loss = torch.sum(losses.view(-1) * loss_mask) / loss_mask.sum()
|
679 |
+
|
680 |
+
# Reduce loss for logging.
|
681 |
+
averaged_loss = average_losses_across_data_parallel_group([loss])
|
682 |
+
|
683 |
+
output_dict = {"lm loss": averaged_loss[0]}
|
684 |
+
if args.return_logits:
|
685 |
+
output_dict.update({"logits": logits})
|
686 |
+
return loss, output_dict
|
687 |
+
|
688 |
+
return loss_func
|
689 |
+
|
690 |
+
def get_forward_step_func(self):
|
691 |
+
def forward_step(data_iterator, model):
|
692 |
+
"""Forward step."""
|
693 |
+
# Get the batch.
|
694 |
+
tokens, labels, loss_mask, attention_mask, position_ids = self.get_batch(data_iterator)
|
695 |
+
output_tensor = model(tokens, position_ids, attention_mask, labels=labels)
|
696 |
+
|
697 |
+
return output_tensor, partial(self.loss_func, loss_mask)
|
698 |
+
|
699 |
+
return forward_step
|
700 |
+
|
701 |
+
|
702 |
+
class T5TrainStep(AbstractTrainStep):
|
703 |
+
"""
|
704 |
+
T5 train step class.
|
705 |
+
|
706 |
+
Args:
|
707 |
+
args (`argparse.Namespace`): Megatron-LM arguments.
|
708 |
+
"""
|
709 |
+
|
710 |
+
def __init__(self, args):
|
711 |
+
super().__init__("T5TrainStep")
|
712 |
+
self.get_batch = self.get_batch_func(args.megatron_dataset_flag)
|
713 |
+
self.loss_func = self.get_loss_func()
|
714 |
+
self.forward_step = self.get_forward_step_func()
|
715 |
+
if not args.model_return_dict:
|
716 |
+
self.model_output_class = None
|
717 |
+
else:
|
718 |
+
self.model_output_class = Seq2SeqLMOutput
|
719 |
+
|
720 |
+
@staticmethod
|
721 |
+
def attn_mask_postprocess(attention_mask):
|
722 |
+
# We create a 3D attention mask from a 2D tensor mask.
|
723 |
+
# [b, 1, s]
|
724 |
+
attention_mask_b1s = attention_mask.unsqueeze(1)
|
725 |
+
# [b, s, 1]
|
726 |
+
attention_mask_bs1 = attention_mask.unsqueeze(2)
|
727 |
+
# [b, s, s]
|
728 |
+
attention_mask_bss = attention_mask_b1s * attention_mask_bs1
|
729 |
+
# Convert attention mask to binary:
|
730 |
+
extended_attention_mask = attention_mask_bss < 0.5
|
731 |
+
return extended_attention_mask
|
732 |
+
|
733 |
+
@staticmethod
|
734 |
+
def get_decoder_mask(seq_length, device):
|
735 |
+
attention_mask = torch.tril(torch.ones((1, seq_length, seq_length), device=device))
|
736 |
+
attention_mask = attention_mask < 0.5
|
737 |
+
return attention_mask
|
738 |
+
|
739 |
+
@staticmethod
|
740 |
+
def get_enc_dec_mask(attention_mask, dec_seq_length, device):
|
741 |
+
batch_size, _ = attention_mask.shape
|
742 |
+
# We create a 3D attention mask from a 2D tensor mask.
|
743 |
+
# [b, 1, s]
|
744 |
+
attention_mask_b1s = attention_mask.unsqueeze(1)
|
745 |
+
# [b, s, 1]
|
746 |
+
attention_mask_bs1 = torch.ones((batch_size, dec_seq_length, 1), device=device)
|
747 |
+
attention_mask_bss = attention_mask_bs1 * attention_mask_b1s
|
748 |
+
extended_attention_mask = attention_mask_bss < 0.5
|
749 |
+
return extended_attention_mask
|
750 |
+
|
751 |
+
def get_batch_func(self, megatron_dataset_flag):
|
752 |
+
def get_batch_megatron(data_iterator):
|
753 |
+
"""Build the batch."""
|
754 |
+
|
755 |
+
keys = ["text_enc", "text_dec", "labels", "loss_mask", "enc_mask", "dec_mask", "enc_dec_mask"]
|
756 |
+
datatype = torch.int64
|
757 |
+
|
758 |
+
# Broadcast data.
|
759 |
+
if data_iterator is not None:
|
760 |
+
data = next(data_iterator)
|
761 |
+
else:
|
762 |
+
data = None
|
763 |
+
data_b = mpu.broadcast_data(keys, data, datatype)
|
764 |
+
|
765 |
+
# Unpack.
|
766 |
+
tokens_enc = data_b["text_enc"].long()
|
767 |
+
tokens_dec = data_b["text_dec"].long()
|
768 |
+
labels = data_b["labels"].long()
|
769 |
+
loss_mask = data_b["loss_mask"].float()
|
770 |
+
|
771 |
+
enc_mask = data_b["enc_mask"] < 0.5
|
772 |
+
dec_mask = data_b["dec_mask"] < 0.5
|
773 |
+
enc_dec_mask = data_b["enc_dec_mask"] < 0.5
|
774 |
+
|
775 |
+
return tokens_enc, tokens_dec, loss_mask, labels, enc_mask, dec_mask, enc_dec_mask
|
776 |
+
|
777 |
+
def get_batch_transformer(data_iterator):
|
778 |
+
"""Build the batch."""
|
779 |
+
data = next(data_iterator)
|
780 |
+
data = send_to_device(data, torch.cuda.current_device())
|
781 |
+
|
782 |
+
tokens_enc = data["input_ids"].long()
|
783 |
+
labels = data["labels"].long()
|
784 |
+
loss_mask = (labels != -100).to(torch.float)
|
785 |
+
if "decoder_input_ids" in data:
|
786 |
+
tokens_dec = data["decoder_input_ids"].long()
|
787 |
+
else:
|
788 |
+
tokens_dec = labels.new_zeros(labels.shape, device=labels.device, dtype=torch.long)
|
789 |
+
tokens_dec[..., 1:] = labels[..., :-1].clone()
|
790 |
+
tokens_dec[..., 0] = 0
|
791 |
+
tokens_dec.masked_fill_(tokens_dec == -100, 0)
|
792 |
+
enc_mask = T5TrainStep.attn_mask_postprocess(data["attention_mask"].long())
|
793 |
+
dec_mask = T5TrainStep.get_decoder_mask(tokens_dec.shape[1], tokens_dec.device)
|
794 |
+
enc_dec_mask = T5TrainStep.get_enc_dec_mask(
|
795 |
+
data["attention_mask"].long(), tokens_dec.shape[1], tokens_dec.device
|
796 |
+
)
|
797 |
+
|
798 |
+
return tokens_enc, tokens_dec, loss_mask, labels, enc_mask, dec_mask, enc_dec_mask
|
799 |
+
|
800 |
+
if megatron_dataset_flag:
|
801 |
+
return get_batch_megatron
|
802 |
+
else:
|
803 |
+
return get_batch_transformer
|
804 |
+
|
805 |
+
def get_loss_func(self):
|
806 |
+
def loss_func(loss_mask, output_tensor):
|
807 |
+
lm_loss_ = output_tensor.float()
|
808 |
+
lm_loss = torch.sum(lm_loss_.view(-1) * loss_mask.reshape(-1)) / loss_mask.sum()
|
809 |
+
|
810 |
+
loss = lm_loss
|
811 |
+
averaged_losses = average_losses_across_data_parallel_group([lm_loss])
|
812 |
+
|
813 |
+
return loss, {"lm loss": averaged_losses[0]}
|
814 |
+
|
815 |
+
return loss_func
|
816 |
+
|
817 |
+
def get_forward_step_func(self):
|
818 |
+
def forward_step(data_iterator, model):
|
819 |
+
"""Forward step."""
|
820 |
+
# Get the batch.
|
821 |
+
tokens_enc, tokens_dec, loss_mask, lm_labels, enc_mask, dec_mask, enc_dec_mask = self.get_batch(
|
822 |
+
data_iterator
|
823 |
+
)
|
824 |
+
# Forward model lm_labels
|
825 |
+
output_tensor = model(
|
826 |
+
tokens_enc, tokens_dec, enc_mask, dec_mask, enc_dec_mask, tokentype_ids=None, lm_labels=lm_labels
|
827 |
+
)
|
828 |
+
|
829 |
+
return output_tensor, partial(self.loss_func, loss_mask)
|
830 |
+
|
831 |
+
return forward_step
|
832 |
+
|
833 |
+
|
834 |
+
# intialize megatron setup
|
835 |
+
def initialize(accelerator, extra_args_provider=None, args_defaults={}):
|
836 |
+
accelerator.print("Initializing Megatron-LM")
|
837 |
+
assert torch.cuda.is_available(), "Megatron requires CUDA."
|
838 |
+
|
839 |
+
# Parse arguments
|
840 |
+
args = parse_args(extra_args_provider, ignore_unknown_args=True)
|
841 |
+
|
842 |
+
# Set defaults
|
843 |
+
for key, value in args_defaults.items():
|
844 |
+
if getattr(args, key, None) is not None:
|
845 |
+
if args.rank == 0:
|
846 |
+
print(
|
847 |
+
f"WARNING: overriding default arguments for " f"{key}:{getattr(args, key)} with {key}:{value}",
|
848 |
+
flush=True,
|
849 |
+
)
|
850 |
+
setattr(args, key, value)
|
851 |
+
|
852 |
+
if args.use_checkpoint_args or args_defaults.get("use_checkpoint_args", False):
|
853 |
+
assert args.load is not None, "--use-checkpoints-args requires --load argument"
|
854 |
+
load_args_from_checkpoint(args)
|
855 |
+
|
856 |
+
validate_args(args)
|
857 |
+
|
858 |
+
# set global args, build tokenizer, and set adlr-autoresume,
|
859 |
+
# tensorboard-writer, and timers.
|
860 |
+
set_global_variables(args)
|
861 |
+
|
862 |
+
# torch.distributed initialization
|
863 |
+
def finish_mpu_init():
|
864 |
+
args = get_args()
|
865 |
+
# Pytorch distributed.
|
866 |
+
device_count = torch.cuda.device_count()
|
867 |
+
args.rank = torch.distributed.get_rank()
|
868 |
+
args.world_size = torch.distributed.get_world_size()
|
869 |
+
if device_count > 0:
|
870 |
+
device = args.rank % device_count
|
871 |
+
if args.local_rank is not None:
|
872 |
+
assert args.local_rank == device, "expected local-rank to be the same as rank % device-count."
|
873 |
+
else:
|
874 |
+
args.local_rank = device
|
875 |
+
|
876 |
+
# Set the tensor model-parallel, pipeline model-parallel, and
|
877 |
+
# data-parallel communicators.
|
878 |
+
if mpu.model_parallel_is_initialized():
|
879 |
+
print("model parallel is already initialized")
|
880 |
+
else:
|
881 |
+
mpu.initialize_model_parallel(
|
882 |
+
args.tensor_model_parallel_size,
|
883 |
+
args.pipeline_model_parallel_size,
|
884 |
+
args.virtual_pipeline_model_parallel_size,
|
885 |
+
args.pipeline_model_parallel_split_rank,
|
886 |
+
)
|
887 |
+
|
888 |
+
# Random seeds for reproducibility.
|
889 |
+
if args.rank == 0:
|
890 |
+
print(f"> setting random seeds to {args.seed} ...")
|
891 |
+
_set_random_seed(args.seed, args.data_parallel_random_init)
|
892 |
+
|
893 |
+
args = get_args()
|
894 |
+
|
895 |
+
# Megatron's MPU is the master. Complete initialization right away.
|
896 |
+
finish_mpu_init()
|
897 |
+
|
898 |
+
# Autoresume.
|
899 |
+
_init_autoresume()
|
900 |
+
|
901 |
+
# Compile dependencies.
|
902 |
+
_compile_dependencies()
|
903 |
+
|
904 |
+
# Set pytorch JIT layer fusion options and warmup JIT functions.
|
905 |
+
set_jit_fusion_options()
|
906 |
+
args = get_args()
|
907 |
+
args.padded_vocab_size = _vocab_size_with_padding(args.orig_vocab_size, args)
|
908 |
+
if args.model_type_name == "bert" and args.pretraining_flag and args.num_labels == 2:
|
909 |
+
args.bert_binary_head = True
|
910 |
+
else:
|
911 |
+
args.bert_binary_head = False
|
912 |
+
args.iteration = 0
|
913 |
+
|
914 |
+
|
915 |
+
class MegatronEngine(torch.nn.Module):
|
916 |
+
"""
|
917 |
+
Megatron-LM model wrapper
|
918 |
+
|
919 |
+
Args:
|
920 |
+
accelerator (:class:`~accelerate.Accelerator`): The accelerator object to use.
|
921 |
+
model: Megatron-LM model
|
922 |
+
optimizer: Megatron-LM optimizer
|
923 |
+
lr_scheduler: Megatron-LM lr scheduler
|
924 |
+
"""
|
925 |
+
|
926 |
+
def __init__(self, accelerator, model, optimizer, scheduler):
|
927 |
+
super().__init__()
|
928 |
+
self.module = model
|
929 |
+
self.base_model = model[0]
|
930 |
+
self.optimizer = optimizer
|
931 |
+
self.scheduler = scheduler
|
932 |
+
args = get_args()
|
933 |
+
if accelerator.state.megatron_lm_plugin.custom_train_step_class is not None:
|
934 |
+
self.train_step_handler = accelerator.state.megatron_lm_plugin.custom_train_step_class(
|
935 |
+
args, **accelerator.state.megatron_lm_plugin.custom_train_step_kwargs
|
936 |
+
)
|
937 |
+
elif args.model_type_name == "bert":
|
938 |
+
self.train_step_handler = BertTrainStep(args)
|
939 |
+
elif args.model_type_name == "gpt":
|
940 |
+
self.train_step_handler = GPTTrainStep(args)
|
941 |
+
elif args.model_type_name == "t5":
|
942 |
+
self.train_step_handler = T5TrainStep(args)
|
943 |
+
else:
|
944 |
+
raise ValueError(f"Unsupported model type: {args.model_type_name}")
|
945 |
+
self.optimizer.skipped_iter = False
|
946 |
+
|
947 |
+
# Tracking loss.
|
948 |
+
self.total_loss_dict = {}
|
949 |
+
self.eval_total_loss_dict = {}
|
950 |
+
self.iteration = 0
|
951 |
+
self.report_memory_flag = True
|
952 |
+
if args.tensorboard_dir is not None:
|
953 |
+
write_args_to_tensorboard()
|
954 |
+
|
955 |
+
def train(self):
|
956 |
+
for model_module in self.module:
|
957 |
+
model_module.train()
|
958 |
+
self.log_eval_results()
|
959 |
+
|
960 |
+
def eval(self):
|
961 |
+
for model_module in self.module:
|
962 |
+
model_module.eval()
|
963 |
+
|
964 |
+
def train_step(self, **batch_data):
|
965 |
+
"""
|
966 |
+
Training step for Megatron-LM
|
967 |
+
|
968 |
+
Args:
|
969 |
+
batch_data (:obj:`dict`): The batch data to train on.
|
970 |
+
"""
|
971 |
+
|
972 |
+
args = get_args()
|
973 |
+
timers = get_timers()
|
974 |
+
|
975 |
+
if len(batch_data) > 0:
|
976 |
+
data_chunks = []
|
977 |
+
if args.num_micro_batches > 1:
|
978 |
+
for i in range(0, args.num_micro_batches):
|
979 |
+
data_chunks.append(
|
980 |
+
{
|
981 |
+
k: v[i * args.micro_batch_size : (i + 1) * args.micro_batch_size]
|
982 |
+
for k, v in batch_data.items()
|
983 |
+
}
|
984 |
+
)
|
985 |
+
else:
|
986 |
+
data_chunks = [batch_data]
|
987 |
+
|
988 |
+
if len(self.module) > 1:
|
989 |
+
batch_data_iterator = (
|
990 |
+
[iter(data_chunks) for _ in range(len(self.module))]
|
991 |
+
if len(batch_data) > 0
|
992 |
+
else [None] * len(self.module)
|
993 |
+
)
|
994 |
+
else:
|
995 |
+
batch_data_iterator = iter(data_chunks) if len(batch_data) > 0 else None
|
996 |
+
|
997 |
+
# Set grad to zero.
|
998 |
+
if args.DDP_impl == "local" and args.use_contiguous_buffers_in_local_ddp:
|
999 |
+
for partition in self.module:
|
1000 |
+
partition.zero_grad_buffer()
|
1001 |
+
self.optimizer.zero_grad()
|
1002 |
+
|
1003 |
+
# Forward pass.
|
1004 |
+
forward_backward_func = get_forward_backward_func()
|
1005 |
+
losses_reduced = forward_backward_func(
|
1006 |
+
self.train_step_handler.forward_step,
|
1007 |
+
batch_data_iterator,
|
1008 |
+
self.module,
|
1009 |
+
self.optimizer,
|
1010 |
+
None,
|
1011 |
+
forward_only=False,
|
1012 |
+
)
|
1013 |
+
|
1014 |
+
# Empty unused memory.
|
1015 |
+
if args.empty_unused_memory_level >= 1:
|
1016 |
+
torch.cuda.empty_cache()
|
1017 |
+
|
1018 |
+
# Reduce gradients.
|
1019 |
+
timers("backward-reduce-model-grads").start()
|
1020 |
+
self.optimizer.reduce_model_grads(args, timers)
|
1021 |
+
timers("backward-reduce-model-grads").stop()
|
1022 |
+
|
1023 |
+
# Update parameters.
|
1024 |
+
timers("optimizer").start()
|
1025 |
+
update_successful, grad_norm, num_zeros_in_grad = self.optimizer.step(args, timers)
|
1026 |
+
timers("optimizer").stop()
|
1027 |
+
|
1028 |
+
# Gather params.
|
1029 |
+
if update_successful:
|
1030 |
+
timers("backward-gather-model-params").start()
|
1031 |
+
self.optimizer.gather_model_params(args, timers)
|
1032 |
+
timers("backward-gather-model-params").stop()
|
1033 |
+
|
1034 |
+
# Update learning rate.
|
1035 |
+
if update_successful:
|
1036 |
+
if self.scheduler is not None:
|
1037 |
+
increment = get_num_microbatches() * args.micro_batch_size * args.data_parallel_size
|
1038 |
+
self.scheduler.step(increment=increment)
|
1039 |
+
skipped_iter = 0
|
1040 |
+
else:
|
1041 |
+
skipped_iter = 1
|
1042 |
+
|
1043 |
+
self.optimizer.skipped_iter = not update_successful
|
1044 |
+
|
1045 |
+
# Empty unused memory.
|
1046 |
+
if args.empty_unused_memory_level >= 2:
|
1047 |
+
torch.cuda.empty_cache()
|
1048 |
+
|
1049 |
+
args.consumed_train_samples += (
|
1050 |
+
mpu.get_data_parallel_world_size() * args.micro_batch_size * get_num_microbatches()
|
1051 |
+
)
|
1052 |
+
|
1053 |
+
if mpu.is_pipeline_last_stage(ignore_virtual=True):
|
1054 |
+
# Average loss across microbatches.
|
1055 |
+
loss_reduced = {}
|
1056 |
+
for key in losses_reduced[0]:
|
1057 |
+
losses_reduced_for_key = [x[key] for x in losses_reduced]
|
1058 |
+
if len(losses_reduced_for_key[0].shape) == 0:
|
1059 |
+
loss_reduced[key] = sum(losses_reduced_for_key) / len(losses_reduced_for_key)
|
1060 |
+
else:
|
1061 |
+
loss_reduced[key] = torch.concat(losses_reduced_for_key)
|
1062 |
+
return loss_reduced, skipped_iter, grad_norm, num_zeros_in_grad
|
1063 |
+
return {}, skipped_iter, grad_norm, num_zeros_in_grad
|
1064 |
+
|
1065 |
+
def eval_step(self, **batch_data):
|
1066 |
+
"""
|
1067 |
+
Evaluation step for Megatron-LM
|
1068 |
+
|
1069 |
+
Args:
|
1070 |
+
batch_data (:obj:`dict`): The batch data to evaluate on.
|
1071 |
+
"""
|
1072 |
+
|
1073 |
+
args = get_args()
|
1074 |
+
data_chunks = []
|
1075 |
+
if args.num_micro_batches > 1:
|
1076 |
+
for i in range(0, args.num_micro_batches):
|
1077 |
+
data_chunks.append(
|
1078 |
+
{k: v[i * args.micro_batch_size : (i + 1) * args.micro_batch_size] for k, v in batch_data.items()}
|
1079 |
+
)
|
1080 |
+
else:
|
1081 |
+
data_chunks = [batch_data]
|
1082 |
+
|
1083 |
+
if len(self.module) > 1:
|
1084 |
+
batch_data_iterator = [iter(data_chunks) for _ in range(len(self.module))]
|
1085 |
+
else:
|
1086 |
+
batch_data_iterator = iter(data_chunks)
|
1087 |
+
forward_backward_func = get_forward_backward_func()
|
1088 |
+
loss_dicts = forward_backward_func(
|
1089 |
+
self.train_step_handler.forward_step,
|
1090 |
+
batch_data_iterator,
|
1091 |
+
self.module,
|
1092 |
+
optimizer=None,
|
1093 |
+
timers=None,
|
1094 |
+
forward_only=True,
|
1095 |
+
)
|
1096 |
+
# Empty unused memory
|
1097 |
+
if args.empty_unused_memory_level >= 1:
|
1098 |
+
torch.cuda.empty_cache()
|
1099 |
+
|
1100 |
+
args.consumed_valid_samples += (
|
1101 |
+
mpu.get_data_parallel_world_size() * args.micro_batch_size * get_num_microbatches()
|
1102 |
+
)
|
1103 |
+
|
1104 |
+
if mpu.is_pipeline_last_stage(ignore_virtual=True):
|
1105 |
+
# Average loss across microbatches.
|
1106 |
+
loss_reduced = {}
|
1107 |
+
for key in loss_dicts[0]:
|
1108 |
+
losses_reduced_for_key = [x[key] for x in loss_dicts]
|
1109 |
+
if len(losses_reduced_for_key[0].shape) == 0:
|
1110 |
+
loss_reduced[key] = sum(losses_reduced_for_key) / len(losses_reduced_for_key)
|
1111 |
+
else:
|
1112 |
+
loss_reduced[key] = torch.concat(losses_reduced_for_key)
|
1113 |
+
return loss_reduced
|
1114 |
+
else:
|
1115 |
+
return {}
|
1116 |
+
|
1117 |
+
def forward(self, **batch_data):
|
1118 |
+
# During training, we use train_step()
|
1119 |
+
# model(**batch_data) performs following operations by delegating it to `self.train_step`:
|
1120 |
+
# 1. Prepare **batch_data for Tendor, Pipeline and Model Parallelism
|
1121 |
+
# 2. Set grad to zero.
|
1122 |
+
# 3. forward pass and backward pass using Pipeline Parallelism
|
1123 |
+
# 4. Empty unused memory.
|
1124 |
+
# 5. Reduce gradients.
|
1125 |
+
# 6. Update parameters.
|
1126 |
+
# 7. Gather params when using Distributed Optimizer (Data Parallelism).
|
1127 |
+
# 8. Update learning rate if scheduler is specified.
|
1128 |
+
# 9. Empty unused memory.
|
1129 |
+
# 10. Average loss across microbatches and across DP ranks.
|
1130 |
+
#
|
1131 |
+
# During evaluation, we use eval_step()
|
1132 |
+
args = get_args()
|
1133 |
+
if self.module[0].training:
|
1134 |
+
loss_dict, skipped_iter, grad_norm, num_zeros_in_grad = self.train_step(**batch_data)
|
1135 |
+
self.iteration += 1
|
1136 |
+
if args.tensorboard_dir is not None:
|
1137 |
+
# Logging.
|
1138 |
+
loss_scale = self.optimizer.get_loss_scale().item()
|
1139 |
+
params_norm = None
|
1140 |
+
if args.log_params_norm:
|
1141 |
+
params_norm = calc_params_l2_norm(self.model)
|
1142 |
+
self.report_memory_flag = training_log(
|
1143 |
+
loss_dict,
|
1144 |
+
self.total_loss_dict,
|
1145 |
+
self.optimizer.param_groups[0]["lr"],
|
1146 |
+
self.iteration,
|
1147 |
+
loss_scale,
|
1148 |
+
self.report_memory_flag,
|
1149 |
+
skipped_iter,
|
1150 |
+
grad_norm,
|
1151 |
+
params_norm,
|
1152 |
+
num_zeros_in_grad,
|
1153 |
+
)
|
1154 |
+
else:
|
1155 |
+
loss_dict = self.eval_step(**batch_data)
|
1156 |
+
if args.tensorboard_dir is not None:
|
1157 |
+
for key in loss_dict:
|
1158 |
+
self.eval_total_loss_dict[key] = (
|
1159 |
+
self.eval_total_loss_dict.get(key, torch.cuda.FloatTensor([0.0])) + loss_dict[key]
|
1160 |
+
)
|
1161 |
+
self.eval_total_loss_dict[key + "_num_iters"] = self.eval_total_loss_dict.get(
|
1162 |
+
key + "_num_iters", torch.cuda.FloatTensor([0.0])
|
1163 |
+
) + torch.cuda.FloatTensor([1.0])
|
1164 |
+
|
1165 |
+
loss = torch.tensor(0.0, device=args.local_rank)
|
1166 |
+
for key in loss_dict:
|
1167 |
+
if len(loss_dict[key].shape) == 0:
|
1168 |
+
loss += loss_dict[key]
|
1169 |
+
|
1170 |
+
logits = None
|
1171 |
+
if "logits" in loss_dict:
|
1172 |
+
logits = loss_dict["logits"]
|
1173 |
+
# loss = reduce(loss)
|
1174 |
+
if self.train_step_handler.model_output_class is not None:
|
1175 |
+
return self.train_step_handler.model_output_class(loss=loss, logits=logits)
|
1176 |
+
return loss
|
1177 |
+
|
1178 |
+
def log_eval_results(self):
|
1179 |
+
args = get_args()
|
1180 |
+
if args.tensorboard_dir is None or self.iteration == 0:
|
1181 |
+
return
|
1182 |
+
args = get_args()
|
1183 |
+
writer = get_tensorboard_writer()
|
1184 |
+
string = f"validation loss at iteration {self.iteration} | "
|
1185 |
+
for key in self.eval_total_loss_dict:
|
1186 |
+
if key.endswith("_num_iters"):
|
1187 |
+
continue
|
1188 |
+
value = self.eval_total_loss_dict[key] / self.eval_total_loss_dict[key + "_num_iters"]
|
1189 |
+
string += f"{key} value: {value} | "
|
1190 |
+
ppl = math.exp(min(20, value.item()))
|
1191 |
+
if args.pretraining_flag:
|
1192 |
+
string += f"{key} PPL: {ppl} | "
|
1193 |
+
if writer:
|
1194 |
+
writer.add_scalar(f"{key} validation", value.item(), self.iteration)
|
1195 |
+
if args.pretraining_flag:
|
1196 |
+
writer.add_scalar(f"{key} validation ppl", ppl, self.iteration)
|
1197 |
+
|
1198 |
+
length = len(string) + 1
|
1199 |
+
print_rank_last("-" * length)
|
1200 |
+
print_rank_last(string)
|
1201 |
+
print_rank_last("-" * length)
|
1202 |
+
self.eval_total_loss_dict = {}
|
1203 |
+
|
1204 |
+
def save_checkpoint(self, output_dir):
|
1205 |
+
self.log_eval_results()
|
1206 |
+
args = get_args()
|
1207 |
+
args.save = output_dir
|
1208 |
+
torch.distributed.barrier()
|
1209 |
+
save_checkpoint(self.iteration, self.module, self.optimizer, self.scheduler)
|
1210 |
+
torch.distributed.barrier()
|
1211 |
+
|
1212 |
+
def load_checkpoint(self, input_dir):
|
1213 |
+
args = get_args()
|
1214 |
+
args.load = input_dir
|
1215 |
+
args.consumed_train_samples = 0
|
1216 |
+
args.consumed_valid_samples = 0
|
1217 |
+
torch.distributed.barrier()
|
1218 |
+
iteration = load_checkpoint(self.module, self.optimizer, self.scheduler)
|
1219 |
+
torch.distributed.barrier()
|
1220 |
+
self.iteration = iteration
|
1221 |
+
if args.fp16 and self.iteration == 0:
|
1222 |
+
self.optimizer.reload_model_params()
|
1223 |
+
|
1224 |
+
def megatron_generate(
|
1225 |
+
self,
|
1226 |
+
inputs,
|
1227 |
+
attention_mask=None,
|
1228 |
+
max_length=None,
|
1229 |
+
max_new_tokens=None,
|
1230 |
+
num_beams=None,
|
1231 |
+
temperature=None,
|
1232 |
+
top_k=None,
|
1233 |
+
top_p=None,
|
1234 |
+
length_penalty=None,
|
1235 |
+
**kwargs,
|
1236 |
+
):
|
1237 |
+
"""
|
1238 |
+
Generate method for GPT2 model. This method is used for inference. Supports both greedy and beam search along
|
1239 |
+
with sampling. Refer the Megatron-LM repo for more details
|
1240 |
+
|
1241 |
+
Args:
|
1242 |
+
inputs (torch.Tensor): input ids
|
1243 |
+
attention_mask (torch.Tensor, optional): attention mask. Defaults to None.
|
1244 |
+
max_length (int, optional): max length of the generated sequence. Defaults to None.
|
1245 |
+
Either this or max_new_tokens should be provided.
|
1246 |
+
max_new_tokens (int, optional): max number of tokens to be generated. Defaults to None.
|
1247 |
+
Either this or max_length should be provided.
|
1248 |
+
num_beams (int, optional): number of beams to use for beam search. Defaults to None.
|
1249 |
+
temperature (float, optional): temperature for sampling. Defaults to 1.0.
|
1250 |
+
top_k (int, optional): top k tokens to consider for sampling. Defaults to 0.0.
|
1251 |
+
top_p (float, optional): tokens in top p probability are considered for sampling. Defaults to 0.0.
|
1252 |
+
length_penalty (float, optional): length penalty for beam search. Defaults to None.
|
1253 |
+
kwargs: additional key-value arguments
|
1254 |
+
"""
|
1255 |
+
|
1256 |
+
# checking if required arguments are passed
|
1257 |
+
args = get_args()
|
1258 |
+
if args.model_type_name != "gpt":
|
1259 |
+
raise NotImplementedError("Generate method is not implemented for this model")
|
1260 |
+
|
1261 |
+
if args.data_parallel_size > 1:
|
1262 |
+
raise ValueError("Generate method requires data parallelism to be 1")
|
1263 |
+
|
1264 |
+
if args.sequence_parallel:
|
1265 |
+
raise ValueError("Generate method requires sequence parallelism to be False")
|
1266 |
+
|
1267 |
+
if args.recompute_granularity is not None:
|
1268 |
+
raise ValueError("Checkpoint activations cannot be set for inference")
|
1269 |
+
|
1270 |
+
if args.vocab_file is None:
|
1271 |
+
raise ValueError("Vocab file is required for inference")
|
1272 |
+
|
1273 |
+
# Prepare inputs
|
1274 |
+
if max_length is None and max_new_tokens is None:
|
1275 |
+
raise ValueError("`max_length` or `max_new_tokens` are required for inference")
|
1276 |
+
|
1277 |
+
if temperature is None:
|
1278 |
+
temperature = 1.0
|
1279 |
+
elif not (0.0 < temperature <= 100.0):
|
1280 |
+
raise ValueError("temperature must be a positive number less than or equal to 100.0")
|
1281 |
+
|
1282 |
+
if top_k is None:
|
1283 |
+
top_k = 0
|
1284 |
+
elif not (0 <= top_k <= 1000):
|
1285 |
+
raise ValueError("top_k must be a positive number less than or equal to 1000")
|
1286 |
+
|
1287 |
+
if top_p is None:
|
1288 |
+
top_p = 0.0
|
1289 |
+
elif top_p > 0.0 and top_k > 0.0:
|
1290 |
+
raise ValueError("top_p and top_k sampling cannot be set together")
|
1291 |
+
else:
|
1292 |
+
if not (0.0 <= top_p <= 1.0):
|
1293 |
+
raise ValueError("top_p must be less than or equal to 1.0")
|
1294 |
+
|
1295 |
+
top_p_decay = kwargs.get("top_p_decay", 0.0)
|
1296 |
+
if not (0.0 <= top_p_decay <= 1.0):
|
1297 |
+
raise ValueError("top_p_decay must be less than or equal to 1.0")
|
1298 |
+
|
1299 |
+
top_p_bound = kwargs.get("top_p_bound", 0.0)
|
1300 |
+
if not (0.0 <= top_p_bound <= 1.0):
|
1301 |
+
raise ValueError("top_p_bound must be less than or equal to 1.0")
|
1302 |
+
|
1303 |
+
add_BOS = kwargs.get("add_BOS", False)
|
1304 |
+
if not (isinstance(add_BOS, bool)):
|
1305 |
+
raise ValueError("add_BOS must be a boolean")
|
1306 |
+
|
1307 |
+
beam_width = num_beams
|
1308 |
+
if beam_width is not None:
|
1309 |
+
if not isinstance(beam_width, int):
|
1310 |
+
raise ValueError("beam_width must be an integer")
|
1311 |
+
if beam_width < 1:
|
1312 |
+
raise ValueError("beam_width must be greater than 0")
|
1313 |
+
if inputs.shape[0] > 1:
|
1314 |
+
return "When doing beam_search, batch size must be 1"
|
1315 |
+
|
1316 |
+
tokenizer = get_tokenizer()
|
1317 |
+
|
1318 |
+
stop_token = kwargs.get("stop_token", tokenizer.eod)
|
1319 |
+
if stop_token is not None:
|
1320 |
+
if not isinstance(stop_token, int):
|
1321 |
+
raise ValueError("stop_token must be an integer")
|
1322 |
+
|
1323 |
+
if length_penalty is None:
|
1324 |
+
length_penalty = 1.0
|
1325 |
+
|
1326 |
+
sizes_list = None
|
1327 |
+
prompts_tokens_tensor = None
|
1328 |
+
prompts_length_tensor = None
|
1329 |
+
if torch.distributed.get_rank() == 0:
|
1330 |
+
# Get the prompts length.
|
1331 |
+
if attention_mask is None:
|
1332 |
+
prompts_length_tensor = torch.cuda.LongTensor([inputs.shape[1]] * inputs.shape[0])
|
1333 |
+
else:
|
1334 |
+
prompts_length_tensor = attention_mask.sum(axis=-1).cuda()
|
1335 |
+
|
1336 |
+
if max_new_tokens is None:
|
1337 |
+
max_new_tokens = max_length - inputs.shape[1]
|
1338 |
+
if max_new_tokens <= 0:
|
1339 |
+
raise ValueError("max_new_tokens must be greater than 0")
|
1340 |
+
|
1341 |
+
if add_BOS:
|
1342 |
+
max_length = max_new_tokens + inputs.shape[1] + 1
|
1343 |
+
# making sure that `max_length` is a multiple of 4 to leverage fused kernels
|
1344 |
+
max_length = 4 * math.ceil(max_length / 4)
|
1345 |
+
max_new_tokens = max_length - (inputs.shape[1] + 1)
|
1346 |
+
padding = torch.cuda.LongTensor([[tokenizer.eod] * max_new_tokens] * inputs.shape[0])
|
1347 |
+
prompts_tokens_tensor = torch.concat(
|
1348 |
+
[torch.unsqueeze(padding[:, 0], axis=-1), inputs.cuda(), padding], axis=-1
|
1349 |
+
)
|
1350 |
+
else:
|
1351 |
+
# making sure that `max_length` is a multiple of 4 to leverage fused kernels
|
1352 |
+
max_length = max_new_tokens + inputs.shape[1]
|
1353 |
+
max_length = 4 * math.ceil(max_length / 4)
|
1354 |
+
max_new_tokens = max_length - inputs.shape[1]
|
1355 |
+
padding = torch.cuda.LongTensor([[tokenizer.eod] * max_new_tokens] * inputs.shape[0])
|
1356 |
+
prompts_tokens_tensor = torch.concat([inputs.cuda(), padding], axis=-1)
|
1357 |
+
|
1358 |
+
# We need the sizes of these tensors for the boradcast
|
1359 |
+
sizes_list = [
|
1360 |
+
prompts_tokens_tensor.size(0), # Batch size
|
1361 |
+
prompts_tokens_tensor.size(1),
|
1362 |
+
] # Sequence lenght
|
1363 |
+
|
1364 |
+
# First, broadcast the sizes.
|
1365 |
+
sizes_tensor = broadcast_int_list(2, int_list=sizes_list, rank=0)
|
1366 |
+
|
1367 |
+
# Now that we have the sizes, we can boradcast the tokens
|
1368 |
+
# and length tensors.
|
1369 |
+
sizes = sizes_tensor.tolist()
|
1370 |
+
context_tokens_tensor = broadcast_tensor(sizes, torch.int64, tensor=prompts_tokens_tensor, rank=0)
|
1371 |
+
context_length_tensor = broadcast_tensor(sizes[0], torch.int64, tensor=prompts_length_tensor, rank=0)
|
1372 |
+
|
1373 |
+
# Run the inference
|
1374 |
+
random_seed = kwargs.get("random_seed", 0)
|
1375 |
+
torch.random.manual_seed(random_seed)
|
1376 |
+
unwrapped_model = unwrap_model(self.base_model, (torchDDP, LocalDDP, Float16Module))
|
1377 |
+
if beam_width is not None:
|
1378 |
+
tokens, _ = beam_search_and_return_on_first_stage(
|
1379 |
+
unwrapped_model,
|
1380 |
+
context_tokens_tensor,
|
1381 |
+
context_length_tensor,
|
1382 |
+
beam_width,
|
1383 |
+
stop_token=stop_token,
|
1384 |
+
num_return_gen=1,
|
1385 |
+
length_penalty=length_penalty,
|
1386 |
+
)
|
1387 |
+
else:
|
1388 |
+
tokens, _, _ = generate_tokens_probs_and_return_on_first_stage(
|
1389 |
+
unwrapped_model,
|
1390 |
+
context_tokens_tensor,
|
1391 |
+
context_length_tensor,
|
1392 |
+
return_output_log_probs=False,
|
1393 |
+
top_k=top_k,
|
1394 |
+
top_p=top_p,
|
1395 |
+
top_p_decay=top_p_decay,
|
1396 |
+
top_p_bound=top_p_bound,
|
1397 |
+
temperature=temperature,
|
1398 |
+
use_eod_token_for_early_termination=True,
|
1399 |
+
)
|
1400 |
+
return tokens
|
1401 |
+
|
1402 |
+
|
1403 |
+
# other utilities
|
1404 |
+
def avg_losses_across_data_parallel_group(losses):
|
1405 |
+
"""
|
1406 |
+
Average losses across data parallel group.
|
1407 |
+
|
1408 |
+
Args:
|
1409 |
+
losses (List[Tensor]): List of losses to average across data parallel group.
|
1410 |
+
"""
|
1411 |
+
|
1412 |
+
return average_losses_across_data_parallel_group(losses)
|
1413 |
+
|
1414 |
+
|
1415 |
+
def gather_across_data_parallel_groups(tensor):
|
1416 |
+
"""
|
1417 |
+
Recursively gather tensor in a nested list/tuple/dictionary of tensors from data parallel ranks.
|
1418 |
+
|
1419 |
+
Args:
|
1420 |
+
tensor (nested list/tuple/dictionary of `torch.Tensor`):
|
1421 |
+
The data to gather across data parallel ranks.
|
1422 |
+
|
1423 |
+
"""
|
1424 |
+
|
1425 |
+
def _gpu_gather_one(tensor):
|
1426 |
+
if tensor.ndim == 0:
|
1427 |
+
tensor = tensor.clone()[None]
|
1428 |
+
output_tensors = [
|
1429 |
+
torch.empty_like(tensor)
|
1430 |
+
for _ in range(torch.distributed.get_world_size(group=mpu.get_data_parallel_group()))
|
1431 |
+
]
|
1432 |
+
torch.distributed.all_gather(output_tensors, tensor, group=mpu.get_data_parallel_group())
|
1433 |
+
return torch.cat(output_tensors, dim=0)
|
1434 |
+
|
1435 |
+
return recursively_apply(_gpu_gather_one, tensor, error_on_other_type=True)
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/modeling.py
ADDED
@@ -0,0 +1,1802 @@
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|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
import contextlib
|
16 |
+
import gc
|
17 |
+
import importlib
|
18 |
+
import inspect
|
19 |
+
import json
|
20 |
+
import logging
|
21 |
+
import os
|
22 |
+
import re
|
23 |
+
import shutil
|
24 |
+
import tempfile
|
25 |
+
import warnings
|
26 |
+
from collections import OrderedDict, defaultdict
|
27 |
+
from typing import Dict, List, Optional, Tuple, Union
|
28 |
+
|
29 |
+
import packaging
|
30 |
+
import torch
|
31 |
+
import torch.nn as nn
|
32 |
+
|
33 |
+
from ..state import AcceleratorState
|
34 |
+
from .constants import SAFE_WEIGHTS_NAME, WEIGHTS_NAME
|
35 |
+
from .dataclasses import AutocastKwargs, CustomDtype, DistributedType
|
36 |
+
from .imports import (
|
37 |
+
is_mlu_available,
|
38 |
+
is_mps_available,
|
39 |
+
is_npu_available,
|
40 |
+
is_peft_available,
|
41 |
+
is_torch_xla_available,
|
42 |
+
is_xpu_available,
|
43 |
+
)
|
44 |
+
from .offload import load_offloaded_weight, offload_weight, save_offload_index
|
45 |
+
from .tqdm import is_tqdm_available, tqdm
|
46 |
+
from .versions import compare_versions
|
47 |
+
|
48 |
+
|
49 |
+
if is_npu_available(check_device=False):
|
50 |
+
import torch_npu # noqa: F401
|
51 |
+
|
52 |
+
if is_mlu_available(check_device=False):
|
53 |
+
import torch_mlu # noqa: F401
|
54 |
+
|
55 |
+
from safetensors import safe_open
|
56 |
+
from safetensors.torch import load_file as safe_load_file
|
57 |
+
|
58 |
+
|
59 |
+
WEIGHTS_INDEX_NAME = "pytorch_model.bin.index.json"
|
60 |
+
|
61 |
+
logger = logging.getLogger(__name__)
|
62 |
+
|
63 |
+
|
64 |
+
def is_peft_model(model):
|
65 |
+
from .other import extract_model_from_parallel
|
66 |
+
|
67 |
+
if is_peft_available():
|
68 |
+
from peft import PeftModel
|
69 |
+
|
70 |
+
return is_peft_available() and isinstance(extract_model_from_parallel(model), PeftModel)
|
71 |
+
|
72 |
+
|
73 |
+
def check_device_same(first_device, second_device):
|
74 |
+
"""
|
75 |
+
Utility method to check if two `torch` devices are similar. When dealing with CUDA devices, torch throws `False`
|
76 |
+
for `torch.device("cuda") == torch.device("cuda:0")` whereas they should be the same
|
77 |
+
|
78 |
+
Args:
|
79 |
+
first_device (`torch.device`):
|
80 |
+
First device to check
|
81 |
+
second_device (`torch.device`):
|
82 |
+
Second device to check
|
83 |
+
"""
|
84 |
+
if first_device.type != second_device.type:
|
85 |
+
return False
|
86 |
+
|
87 |
+
if first_device.type == "cuda" and first_device.index is None:
|
88 |
+
# In case the first_device is a cuda device and have
|
89 |
+
# the index attribute set to `None`, default it to `0`
|
90 |
+
first_device = torch.device("cuda", index=0)
|
91 |
+
|
92 |
+
if second_device.type == "cuda" and second_device.index is None:
|
93 |
+
# In case the second_device is a cuda device and have
|
94 |
+
# the index attribute set to `None`, default it to `0`
|
95 |
+
second_device = torch.device("cuda", index=0)
|
96 |
+
|
97 |
+
return first_device == second_device
|
98 |
+
|
99 |
+
|
100 |
+
def convert_file_size_to_int(size: Union[int, str]):
|
101 |
+
"""
|
102 |
+
Converts a size expressed as a string with digits an unit (like `"5MB"`) to an integer (in bytes).
|
103 |
+
|
104 |
+
Args:
|
105 |
+
size (`int` or `str`): The size to convert. Will be directly returned if an `int`.
|
106 |
+
|
107 |
+
Example:
|
108 |
+
|
109 |
+
```py
|
110 |
+
>>> convert_file_size_to_int("1MiB")
|
111 |
+
1048576
|
112 |
+
```
|
113 |
+
"""
|
114 |
+
mem_size = -1
|
115 |
+
err_msg = (
|
116 |
+
f"`size` {size} is not in a valid format. Use an integer for bytes, or a string with an unit (like '5.0GB')."
|
117 |
+
)
|
118 |
+
try:
|
119 |
+
if isinstance(size, int):
|
120 |
+
mem_size = size
|
121 |
+
elif size.upper().endswith("GIB"):
|
122 |
+
mem_size = int(float(size[:-3]) * (2**30))
|
123 |
+
elif size.upper().endswith("MIB"):
|
124 |
+
mem_size = int(float(size[:-3]) * (2**20))
|
125 |
+
elif size.upper().endswith("KIB"):
|
126 |
+
mem_size = int(float(size[:-3]) * (2**10))
|
127 |
+
elif size.upper().endswith("GB"):
|
128 |
+
int_size = int(float(size[:-2]) * (10**9))
|
129 |
+
mem_size = int_size // 8 if size.endswith("b") else int_size
|
130 |
+
elif size.upper().endswith("MB"):
|
131 |
+
int_size = int(float(size[:-2]) * (10**6))
|
132 |
+
mem_size = int_size // 8 if size.endswith("b") else int_size
|
133 |
+
elif size.upper().endswith("KB"):
|
134 |
+
int_size = int(float(size[:-2]) * (10**3))
|
135 |
+
mem_size = int_size // 8 if size.endswith("b") else int_size
|
136 |
+
except ValueError:
|
137 |
+
raise ValueError(err_msg)
|
138 |
+
|
139 |
+
if mem_size < 0:
|
140 |
+
raise ValueError(err_msg)
|
141 |
+
return mem_size
|
142 |
+
|
143 |
+
|
144 |
+
def dtype_byte_size(dtype: torch.dtype):
|
145 |
+
"""
|
146 |
+
Returns the size (in bytes) occupied by one parameter of type `dtype`.
|
147 |
+
|
148 |
+
Example:
|
149 |
+
|
150 |
+
```py
|
151 |
+
>>> dtype_byte_size(torch.float32)
|
152 |
+
4
|
153 |
+
```
|
154 |
+
"""
|
155 |
+
if dtype == torch.bool:
|
156 |
+
return 1 / 8
|
157 |
+
elif dtype == CustomDtype.INT2:
|
158 |
+
return 1 / 4
|
159 |
+
elif dtype == CustomDtype.INT4:
|
160 |
+
return 1 / 2
|
161 |
+
elif dtype == CustomDtype.FP8:
|
162 |
+
return 1
|
163 |
+
bit_search = re.search(r"[^\d](\d+)$", str(dtype))
|
164 |
+
if bit_search is None:
|
165 |
+
raise ValueError(f"`dtype` is not a valid dtype: {dtype}.")
|
166 |
+
bit_size = int(bit_search.groups()[0])
|
167 |
+
return bit_size // 8
|
168 |
+
|
169 |
+
|
170 |
+
def id_tensor_storage(tensor: torch.Tensor) -> Tuple[torch.device, int, int]:
|
171 |
+
"""
|
172 |
+
Unique identifier to a tensor storage. Multiple different tensors can share the same underlying storage. For
|
173 |
+
example, "meta" tensors all share the same storage, and thus their identifier will all be equal. This identifier is
|
174 |
+
guaranteed to be unique and constant for this tensor's storage during its lifetime. Two tensor storages with
|
175 |
+
non-overlapping lifetimes may have the same id.
|
176 |
+
"""
|
177 |
+
_SIZE = {
|
178 |
+
torch.int64: 8,
|
179 |
+
torch.float32: 4,
|
180 |
+
torch.int32: 4,
|
181 |
+
torch.bfloat16: 2,
|
182 |
+
torch.float16: 2,
|
183 |
+
torch.int16: 2,
|
184 |
+
torch.uint8: 1,
|
185 |
+
torch.int8: 1,
|
186 |
+
torch.bool: 1,
|
187 |
+
torch.float64: 8,
|
188 |
+
}
|
189 |
+
try:
|
190 |
+
storage_ptr = tensor.untyped_storage().data_ptr()
|
191 |
+
storage_size = tensor.untyped_storage().nbytes()
|
192 |
+
except Exception:
|
193 |
+
# Fallback for torch==1.10
|
194 |
+
try:
|
195 |
+
storage_ptr = tensor.storage().data_ptr()
|
196 |
+
storage_size = tensor.storage().size() * _SIZE[tensor.dtype]
|
197 |
+
except NotImplementedError:
|
198 |
+
# Fallback for meta storage
|
199 |
+
storage_ptr = 0
|
200 |
+
# On torch >=2.0 this is the tensor size
|
201 |
+
storage_size = tensor.nelement() * _SIZE[tensor.dtype]
|
202 |
+
|
203 |
+
return tensor.device, storage_ptr, storage_size
|
204 |
+
|
205 |
+
|
206 |
+
def shard_checkpoint(
|
207 |
+
state_dict: Dict[str, torch.Tensor], max_shard_size: Union[int, str] = "10GB", weights_name: str = WEIGHTS_NAME
|
208 |
+
):
|
209 |
+
"""
|
210 |
+
Splits a model state dictionary in sub-checkpoints so that the final size of each sub-checkpoint does not exceed a
|
211 |
+
given size.
|
212 |
+
|
213 |
+
The sub-checkpoints are determined by iterating through the `state_dict` in the order of its keys, so there is no
|
214 |
+
optimization made to make each sub-checkpoint as close as possible to the maximum size passed. For example, if the
|
215 |
+
limit is 10GB and we have weights of sizes [6GB, 6GB, 2GB, 6GB, 2GB, 2GB] they will get sharded as [6GB], [6+2GB],
|
216 |
+
[6+2+2GB] and not [6+2+2GB], [6+2GB], [6GB].
|
217 |
+
|
218 |
+
<Tip warning={true}>
|
219 |
+
|
220 |
+
If one of the model's weight is bigger that `max_sahrd_size`, it will end up in its own sub-checkpoint which will
|
221 |
+
have a size greater than `max_shard_size`.
|
222 |
+
|
223 |
+
</Tip>
|
224 |
+
|
225 |
+
Args:
|
226 |
+
state_dict (`Dict[str, torch.Tensor]`): The state dictionary of a model to save.
|
227 |
+
max_shard_size (`int` or `str`, *optional*, defaults to `"10GB"`):
|
228 |
+
The maximum size of each sub-checkpoint. If expressed as a string, needs to be digits followed by a unit
|
229 |
+
(like `"5MB"`).
|
230 |
+
weights_name (`str`, *optional*, defaults to `"pytorch_model.bin"`):
|
231 |
+
The name of the model save file.
|
232 |
+
"""
|
233 |
+
max_shard_size = convert_file_size_to_int(max_shard_size)
|
234 |
+
|
235 |
+
sharded_state_dicts = [{}]
|
236 |
+
last_block_size = 0
|
237 |
+
total_size = 0
|
238 |
+
storage_id_to_block = {}
|
239 |
+
|
240 |
+
for key, weight in state_dict.items():
|
241 |
+
# when bnb serialization is used the weights in the state dict can be strings
|
242 |
+
# check: https://github.com/huggingface/transformers/pull/24416 for more details
|
243 |
+
if isinstance(weight, str):
|
244 |
+
continue
|
245 |
+
else:
|
246 |
+
storage_id = id_tensor_storage(weight)
|
247 |
+
|
248 |
+
# If a `weight` shares the same underlying storage as another tensor, we put `weight` in the same `block`
|
249 |
+
if storage_id in storage_id_to_block:
|
250 |
+
block_id = storage_id_to_block[storage_id]
|
251 |
+
sharded_state_dicts[block_id][key] = weight
|
252 |
+
continue
|
253 |
+
|
254 |
+
weight_size = weight.numel() * dtype_byte_size(weight.dtype)
|
255 |
+
|
256 |
+
# If this weight is going to tip up over the maximal size, we split.
|
257 |
+
if last_block_size + weight_size > max_shard_size:
|
258 |
+
sharded_state_dicts.append({})
|
259 |
+
last_block_size = 0
|
260 |
+
|
261 |
+
sharded_state_dicts[-1][key] = weight
|
262 |
+
last_block_size += weight_size
|
263 |
+
total_size += weight_size
|
264 |
+
storage_id_to_block[storage_id] = len(sharded_state_dicts) - 1
|
265 |
+
|
266 |
+
# If we only have one shard, we return it
|
267 |
+
if len(sharded_state_dicts) == 1:
|
268 |
+
return {weights_name: sharded_state_dicts[0]}, None
|
269 |
+
|
270 |
+
# Otherwise, let's build the index
|
271 |
+
weight_map = {}
|
272 |
+
shards = {}
|
273 |
+
for idx, shard in enumerate(sharded_state_dicts):
|
274 |
+
shard_file = weights_name.replace(".bin", f"-{idx + 1:05d}-of-{len(sharded_state_dicts):05d}.bin")
|
275 |
+
shard_file = shard_file.replace(
|
276 |
+
".safetensors", f"-{idx + 1:05d}-of-{len(sharded_state_dicts):05d}.safetensors"
|
277 |
+
)
|
278 |
+
shards[shard_file] = shard
|
279 |
+
for key in shard.keys():
|
280 |
+
weight_map[key] = shard_file
|
281 |
+
|
282 |
+
# Add the metadata
|
283 |
+
metadata = {"total_size": total_size}
|
284 |
+
index = {"metadata": metadata, "weight_map": weight_map}
|
285 |
+
return shards, index
|
286 |
+
|
287 |
+
|
288 |
+
def set_module_tensor_to_device(
|
289 |
+
module: nn.Module,
|
290 |
+
tensor_name: str,
|
291 |
+
device: Union[int, str, torch.device],
|
292 |
+
value: Optional[torch.Tensor] = None,
|
293 |
+
dtype: Optional[Union[str, torch.dtype]] = None,
|
294 |
+
fp16_statistics: Optional[torch.HalfTensor] = None,
|
295 |
+
tied_params_map: Optional[Dict[int, Dict[torch.device, torch.Tensor]]] = None,
|
296 |
+
):
|
297 |
+
"""
|
298 |
+
A helper function to set a given tensor (parameter of buffer) of a module on a specific device (note that doing
|
299 |
+
`param.to(device)` creates a new tensor not linked to the parameter, which is why we need this function).
|
300 |
+
|
301 |
+
Args:
|
302 |
+
module (`torch.nn.Module`):
|
303 |
+
The module in which the tensor we want to move lives.
|
304 |
+
tensor_name (`str`):
|
305 |
+
The full name of the parameter/buffer.
|
306 |
+
device (`int`, `str` or `torch.device`):
|
307 |
+
The device on which to set the tensor.
|
308 |
+
value (`torch.Tensor`, *optional*):
|
309 |
+
The value of the tensor (useful when going from the meta device to any other device).
|
310 |
+
dtype (`torch.dtype`, *optional*):
|
311 |
+
If passed along the value of the parameter will be cast to this `dtype`. Otherwise, `value` will be cast to
|
312 |
+
the dtype of the existing parameter in the model.
|
313 |
+
fp16_statistics (`torch.HalfTensor`, *optional*):
|
314 |
+
The list of fp16 statistics to set on the module, used for 8 bit model serialization.
|
315 |
+
tied_params_map (Dict[int, Dict[torch.device, torch.Tensor]], *optional*, defaults to `None`):
|
316 |
+
A map of current data pointers to dictionaries of devices to already dispatched tied weights. For a given
|
317 |
+
execution device, this parameter is useful to reuse the first available pointer of a shared weight on the
|
318 |
+
device for all others, instead of duplicating memory.
|
319 |
+
"""
|
320 |
+
# Recurse if needed
|
321 |
+
if "." in tensor_name:
|
322 |
+
splits = tensor_name.split(".")
|
323 |
+
for split in splits[:-1]:
|
324 |
+
new_module = getattr(module, split)
|
325 |
+
if new_module is None:
|
326 |
+
raise ValueError(f"{module} has no attribute {split}.")
|
327 |
+
module = new_module
|
328 |
+
tensor_name = splits[-1]
|
329 |
+
|
330 |
+
if tensor_name not in module._parameters and tensor_name not in module._buffers:
|
331 |
+
raise ValueError(f"{module} does not have a parameter or a buffer named {tensor_name}.")
|
332 |
+
is_buffer = tensor_name in module._buffers
|
333 |
+
old_value = getattr(module, tensor_name)
|
334 |
+
|
335 |
+
# Treat the case where old_value (or a custom `value`, typically offloaded to RAM/disk) belongs to a tied group, and one of the weight
|
336 |
+
# in the tied group has already been dispatched to the device, by avoiding reallocating memory on the device and just copying the pointer.
|
337 |
+
if (
|
338 |
+
value is not None
|
339 |
+
and tied_params_map is not None
|
340 |
+
and value.data_ptr() in tied_params_map
|
341 |
+
and device in tied_params_map[value.data_ptr()]
|
342 |
+
):
|
343 |
+
module._parameters[tensor_name] = tied_params_map[value.data_ptr()][device]
|
344 |
+
return
|
345 |
+
elif (
|
346 |
+
tied_params_map is not None
|
347 |
+
and old_value.data_ptr() in tied_params_map
|
348 |
+
and device in tied_params_map[old_value.data_ptr()]
|
349 |
+
):
|
350 |
+
module._parameters[tensor_name] = tied_params_map[old_value.data_ptr()][device]
|
351 |
+
return
|
352 |
+
|
353 |
+
if old_value.device == torch.device("meta") and device not in ["meta", torch.device("meta")] and value is None:
|
354 |
+
raise ValueError(f"{tensor_name} is on the meta device, we need a `value` to put in on {device}.")
|
355 |
+
|
356 |
+
if value is not None:
|
357 |
+
if old_value.shape != value.shape:
|
358 |
+
raise ValueError(
|
359 |
+
f'Trying to set a tensor of shape {value.shape} in "{tensor_name}" (which has shape {old_value.shape}), this look incorrect.'
|
360 |
+
)
|
361 |
+
|
362 |
+
if dtype is None:
|
363 |
+
# For compatibility with PyTorch load_state_dict which converts state dict dtype to existing dtype in model
|
364 |
+
value = value.to(old_value.dtype)
|
365 |
+
elif not str(value.dtype).startswith(("torch.uint", "torch.int", "torch.bool")):
|
366 |
+
value = value.to(dtype)
|
367 |
+
|
368 |
+
param = module._parameters[tensor_name] if tensor_name in module._parameters else None
|
369 |
+
param_cls = type(param)
|
370 |
+
|
371 |
+
device_quantization = None
|
372 |
+
with torch.no_grad():
|
373 |
+
# leave it on cpu first before moving them to cuda
|
374 |
+
# # fix the case where the device is meta, we don't want to put it on cpu because there is no data =0
|
375 |
+
if (
|
376 |
+
param is not None
|
377 |
+
and param.device.type != "cuda"
|
378 |
+
and torch.device(device).type == "cuda"
|
379 |
+
and param_cls.__name__ in ["Int8Params", "FP4Params", "Params4bit"]
|
380 |
+
):
|
381 |
+
device_quantization = device
|
382 |
+
device = "cpu"
|
383 |
+
# `torch.Tensor.to(<int num>)` is not supported by `torch_npu` (see this [issue](https://github.com/Ascend/pytorch/issues/16)).
|
384 |
+
if isinstance(device, int):
|
385 |
+
if is_npu_available():
|
386 |
+
device = f"npu:{device}"
|
387 |
+
elif is_mlu_available():
|
388 |
+
device = f"mlu:{device}"
|
389 |
+
elif is_xpu_available():
|
390 |
+
device = f"xpu:{device}"
|
391 |
+
if value is None:
|
392 |
+
new_value = old_value.to(device)
|
393 |
+
if dtype is not None and device in ["meta", torch.device("meta")]:
|
394 |
+
if not str(old_value.dtype).startswith(("torch.uint", "torch.int", "torch.bool")):
|
395 |
+
new_value = new_value.to(dtype)
|
396 |
+
|
397 |
+
if not is_buffer:
|
398 |
+
module._parameters[tensor_name] = param_cls(new_value, requires_grad=old_value.requires_grad)
|
399 |
+
elif isinstance(value, torch.Tensor):
|
400 |
+
new_value = value.to(device)
|
401 |
+
else:
|
402 |
+
new_value = torch.tensor(value, device=device)
|
403 |
+
if device_quantization is not None:
|
404 |
+
device = device_quantization
|
405 |
+
if is_buffer:
|
406 |
+
module._buffers[tensor_name] = new_value
|
407 |
+
elif value is not None or not check_device_same(torch.device(device), module._parameters[tensor_name].device):
|
408 |
+
param_cls = type(module._parameters[tensor_name])
|
409 |
+
kwargs = module._parameters[tensor_name].__dict__
|
410 |
+
if param_cls.__name__ in ["Int8Params", "FP4Params"]:
|
411 |
+
if param_cls.__name__ == "Int8Params" and new_value.dtype == torch.float32:
|
412 |
+
# downcast to fp16 if any - needed for 8bit serialization
|
413 |
+
new_value = new_value.to(torch.float16)
|
414 |
+
# quantize module that are going to stay on the cpu so that we offload quantized weights
|
415 |
+
if device == "cpu" and param_cls.__name__ == "Int8Params":
|
416 |
+
new_value = param_cls(new_value, requires_grad=old_value.requires_grad, **kwargs).to(0).to("cpu")
|
417 |
+
new_value.CB = new_value.CB.to("cpu")
|
418 |
+
new_value.SCB = new_value.SCB.to("cpu")
|
419 |
+
else:
|
420 |
+
new_value = param_cls(new_value, requires_grad=old_value.requires_grad, **kwargs).to(device)
|
421 |
+
elif param_cls.__name__ in ["QTensor", "QBitsTensor"]:
|
422 |
+
new_value = torch.nn.Parameter(new_value, requires_grad=old_value.requires_grad).to(device)
|
423 |
+
else:
|
424 |
+
new_value = param_cls(new_value, requires_grad=old_value.requires_grad).to(device)
|
425 |
+
|
426 |
+
module._parameters[tensor_name] = new_value
|
427 |
+
if fp16_statistics is not None:
|
428 |
+
module._parameters[tensor_name].SCB = fp16_statistics.to(device)
|
429 |
+
del fp16_statistics
|
430 |
+
# as we put the weight to meta, it doesn't have SCB attr anymore. make sure that it is not a meta weight
|
431 |
+
if (
|
432 |
+
module.__class__.__name__ == "Linear8bitLt"
|
433 |
+
and getattr(module.weight, "SCB", None) is None
|
434 |
+
and str(module.weight.device) != "meta"
|
435 |
+
):
|
436 |
+
# quantize only if necessary
|
437 |
+
device_index = torch.device(device).index if torch.device(device).type == "cuda" else None
|
438 |
+
if not getattr(module.weight, "SCB", None) and device_index is not None:
|
439 |
+
if module.bias is not None and module.bias.device.type != "meta":
|
440 |
+
# if a bias exists, we need to wait until the bias is set on the correct device
|
441 |
+
module = module.cuda(device_index)
|
442 |
+
elif module.bias is None:
|
443 |
+
# if no bias exists, we can quantize right away
|
444 |
+
module = module.cuda(device_index)
|
445 |
+
elif module.__class__.__name__ == "Linear4bit" and getattr(module.weight, "quant_state", None) is None:
|
446 |
+
# quantize only if necessary
|
447 |
+
device_index = torch.device(device).index if torch.device(device).type == "cuda" else None
|
448 |
+
if not getattr(module.weight, "quant_state", None) and device_index is not None:
|
449 |
+
module.weight = module.weight.cuda(device_index)
|
450 |
+
# clean pre and post foward hook
|
451 |
+
if device != "cpu":
|
452 |
+
if is_npu_available():
|
453 |
+
torch.npu.empty_cache()
|
454 |
+
elif is_mlu_available():
|
455 |
+
torch.mlu.empty_cache()
|
456 |
+
elif is_xpu_available():
|
457 |
+
torch.xpu.empty_cache()
|
458 |
+
else:
|
459 |
+
torch.cuda.empty_cache()
|
460 |
+
|
461 |
+
# When handling tied weights, we update tied_params_map to keep track of the tied weights that have already been allocated on the device in
|
462 |
+
# order to avoid duplicating memory, see above.
|
463 |
+
if (
|
464 |
+
tied_params_map is not None
|
465 |
+
and old_value.data_ptr() in tied_params_map
|
466 |
+
and device not in tied_params_map[old_value.data_ptr()]
|
467 |
+
):
|
468 |
+
tied_params_map[old_value.data_ptr()][device] = new_value
|
469 |
+
elif (
|
470 |
+
value is not None
|
471 |
+
and tied_params_map is not None
|
472 |
+
and value.data_ptr() in tied_params_map
|
473 |
+
and device not in tied_params_map[value.data_ptr()]
|
474 |
+
):
|
475 |
+
tied_params_map[value.data_ptr()][device] = new_value
|
476 |
+
|
477 |
+
|
478 |
+
def named_module_tensors(
|
479 |
+
module: nn.Module, include_buffers: bool = True, recurse: bool = False, remove_non_persistent: bool = False
|
480 |
+
):
|
481 |
+
"""
|
482 |
+
A helper function that gathers all the tensors (parameters + buffers) of a given module. If `include_buffers=True`
|
483 |
+
it's the same as doing `module.named_parameters(recurse=recurse) + module.named_buffers(recurse=recurse)`.
|
484 |
+
|
485 |
+
Args:
|
486 |
+
module (`torch.nn.Module`):
|
487 |
+
The module we want the tensors on.
|
488 |
+
include_buffer (`bool`, *optional*, defaults to `True`):
|
489 |
+
Whether or not to include the buffers in the result.
|
490 |
+
recurse (`bool`, *optional`, defaults to `False`):
|
491 |
+
Whether or not to go look in every submodule or just return the direct parameters and buffers.
|
492 |
+
remove_non_persistent (`bool`, *optional*, defaults to `False`):
|
493 |
+
Whether or not to remove the non persistent buffer from the buffers. Useful only when include_buffers =
|
494 |
+
True
|
495 |
+
"""
|
496 |
+
yield from module.named_parameters(recurse=recurse)
|
497 |
+
|
498 |
+
if include_buffers:
|
499 |
+
non_persistent_buffers = set()
|
500 |
+
if remove_non_persistent:
|
501 |
+
non_persistent_buffers = get_non_persistent_buffers(module, recurse=recurse)
|
502 |
+
for named_buffer in module.named_buffers(recurse=recurse):
|
503 |
+
name, _ = named_buffer
|
504 |
+
if name not in non_persistent_buffers:
|
505 |
+
yield named_buffer
|
506 |
+
|
507 |
+
|
508 |
+
def get_non_persistent_buffers(module: nn.Module, recurse: bool = False):
|
509 |
+
"""
|
510 |
+
Gather all non persistent buffers of a given modules into a set
|
511 |
+
|
512 |
+
Args:
|
513 |
+
module (`nn.Module`):
|
514 |
+
The module we want the non persistent buffers on.
|
515 |
+
recurse (`bool`, *optional*, defaults to `False`):
|
516 |
+
Whether or not to go look in every submodule or just return the direct non persistent buffers.
|
517 |
+
"""
|
518 |
+
|
519 |
+
non_persistent_buffers_set = module._non_persistent_buffers_set
|
520 |
+
if recurse:
|
521 |
+
for _, m in module.named_modules():
|
522 |
+
non_persistent_buffers_set |= m._non_persistent_buffers_set
|
523 |
+
|
524 |
+
return non_persistent_buffers_set
|
525 |
+
|
526 |
+
|
527 |
+
class FindTiedParametersResult(list):
|
528 |
+
"""
|
529 |
+
This is a subclass of a list to handle backward compatibility for Transformers. Do not rely on the fact this is not
|
530 |
+
a list or on the `values` method as in the future this will be removed.
|
531 |
+
"""
|
532 |
+
|
533 |
+
def __init__(self, *args, **kwargs):
|
534 |
+
super().__init__(*args, **kwargs)
|
535 |
+
|
536 |
+
def values(self):
|
537 |
+
# TODO: at the next Transformers release (4.28.0) issue a deprecation warning here.
|
538 |
+
return sum([x[1:] for x in self], [])
|
539 |
+
|
540 |
+
|
541 |
+
def check_tied_parameters_in_config(model: nn.Module):
|
542 |
+
"""
|
543 |
+
Check if there is any indication in the given model that some weights should be tied.
|
544 |
+
|
545 |
+
Args:
|
546 |
+
model (`torch.nn.Module`): The model to inspect
|
547 |
+
|
548 |
+
Returns:
|
549 |
+
bool: True if the model needs to have tied weights
|
550 |
+
"""
|
551 |
+
|
552 |
+
# based on model.tie_weights() method
|
553 |
+
has_tied_word_embedding = False
|
554 |
+
has_tied_encoder_decoder = False
|
555 |
+
has_tied_module = False
|
556 |
+
|
557 |
+
if "PreTrainedModel" in [c.__name__ for c in inspect.getmro(model.__class__)]:
|
558 |
+
has_tied_word_embedding = (
|
559 |
+
hasattr(model, "config")
|
560 |
+
and getattr(model.config, "tie_word_embeddings", False)
|
561 |
+
and model.get_output_embeddings()
|
562 |
+
)
|
563 |
+
has_tied_encoder_decoder = (
|
564 |
+
hasattr(model, "config")
|
565 |
+
and getattr(model.config, "is_encoder_decoder", False)
|
566 |
+
and getattr(model.config, "tie_encoder_decoder", False)
|
567 |
+
)
|
568 |
+
has_tied_module = any(hasattr(module, "_tie_weights") for module in model.modules())
|
569 |
+
|
570 |
+
return any([has_tied_word_embedding, has_tied_encoder_decoder, has_tied_module])
|
571 |
+
|
572 |
+
|
573 |
+
def _get_param_device(param, device_map):
|
574 |
+
if param in device_map:
|
575 |
+
return device_map[param]
|
576 |
+
parent_param = ".".join(param.split(".")[:-1])
|
577 |
+
if parent_param == param:
|
578 |
+
raise ValueError(f"The `device_map` does not contain the module {param}.")
|
579 |
+
else:
|
580 |
+
return _get_param_device(parent_param, device_map)
|
581 |
+
|
582 |
+
|
583 |
+
def check_tied_parameters_on_same_device(tied_params, device_map):
|
584 |
+
"""
|
585 |
+
Check if tied parameters are on the same device
|
586 |
+
|
587 |
+
Args:
|
588 |
+
tied_params (`List[List[str]]`):
|
589 |
+
A list of lists of parameter names being all tied together.
|
590 |
+
|
591 |
+
device_map (`Dict[str, Union[int, str, torch.device]]`):
|
592 |
+
A map that specifies where each submodule should go.
|
593 |
+
|
594 |
+
"""
|
595 |
+
for tie_param in tied_params:
|
596 |
+
tie_param_devices = {}
|
597 |
+
for param in tie_param:
|
598 |
+
tie_param_devices[param] = _get_param_device(param, device_map)
|
599 |
+
if len(set(tie_param_devices.values())) > 1:
|
600 |
+
logger.warn(
|
601 |
+
f"Tied parameters are on different devices: {tie_param_devices}. "
|
602 |
+
"Please modify your custom device map or set `device_map='auto'`. "
|
603 |
+
)
|
604 |
+
|
605 |
+
|
606 |
+
def find_tied_parameters(model: nn.Module, **kwargs):
|
607 |
+
"""
|
608 |
+
Find the tied parameters in a given model.
|
609 |
+
|
610 |
+
<Tip warning={true}>
|
611 |
+
|
612 |
+
The signature accepts keyword arguments, but they are for the recursive part of this function and you should ignore
|
613 |
+
them.
|
614 |
+
|
615 |
+
</Tip>
|
616 |
+
|
617 |
+
Args:
|
618 |
+
model (`torch.nn.Module`): The model to inspect.
|
619 |
+
|
620 |
+
Returns:
|
621 |
+
List[List[str]]: A list of lists of parameter names being all tied together.
|
622 |
+
|
623 |
+
Example:
|
624 |
+
|
625 |
+
```py
|
626 |
+
>>> from collections import OrderedDict
|
627 |
+
>>> import torch.nn as nn
|
628 |
+
|
629 |
+
>>> model = nn.Sequential(OrderedDict([("linear1", nn.Linear(4, 4)), ("linear2", nn.Linear(4, 4))]))
|
630 |
+
>>> model.linear2.weight = model.linear1.weight
|
631 |
+
>>> find_tied_parameters(model)
|
632 |
+
[['linear1.weight', 'linear2.weight']]
|
633 |
+
```
|
634 |
+
"""
|
635 |
+
# Initialize result and named_parameters before recursing.
|
636 |
+
named_parameters = kwargs.get("named_parameters", None)
|
637 |
+
prefix = kwargs.get("prefix", "")
|
638 |
+
result = kwargs.get("result", {})
|
639 |
+
|
640 |
+
if named_parameters is None:
|
641 |
+
named_parameters = {n: p for n, p in model.named_parameters()}
|
642 |
+
else:
|
643 |
+
# A tied parameter will not be in the full `named_parameters` seen above but will be in the `named_parameters`
|
644 |
+
# of the submodule it belongs to. So while recursing we track the names that are not in the initial
|
645 |
+
# `named_parameters`.
|
646 |
+
for name, parameter in model.named_parameters():
|
647 |
+
full_name = name if prefix == "" else f"{prefix}.{name}"
|
648 |
+
if full_name not in named_parameters:
|
649 |
+
# When we find one, it has to be one of the existing parameters.
|
650 |
+
for new_name, new_param in named_parameters.items():
|
651 |
+
if new_param is parameter:
|
652 |
+
if new_name not in result:
|
653 |
+
result[new_name] = []
|
654 |
+
result[new_name].append(full_name)
|
655 |
+
|
656 |
+
# Once we have treated direct parameters, we move to the child modules.
|
657 |
+
for name, child in model.named_children():
|
658 |
+
child_name = name if prefix == "" else f"{prefix}.{name}"
|
659 |
+
find_tied_parameters(child, named_parameters=named_parameters, prefix=child_name, result=result)
|
660 |
+
|
661 |
+
return FindTiedParametersResult([sorted([weight] + list(set(tied))) for weight, tied in result.items()])
|
662 |
+
|
663 |
+
|
664 |
+
def retie_parameters(model, tied_params):
|
665 |
+
"""
|
666 |
+
Reties tied parameters in a given model if the link was broken (for instance when adding hooks).
|
667 |
+
|
668 |
+
Args:
|
669 |
+
model (`torch.nn.Module`):
|
670 |
+
The model in which to retie parameters.
|
671 |
+
tied_params (`List[List[str]]`):
|
672 |
+
A mapping parameter name to tied parameter name as obtained by `find_tied_parameters`.
|
673 |
+
"""
|
674 |
+
for tied_group in tied_params:
|
675 |
+
param_to_tie = None
|
676 |
+
# two loops : the first one to set param_to_tie , the second one to change the values of tied_group
|
677 |
+
for param_name in tied_group:
|
678 |
+
module = model
|
679 |
+
splits = param_name.split(".")
|
680 |
+
for split in splits[:-1]:
|
681 |
+
module = getattr(module, split)
|
682 |
+
param = getattr(module, splits[-1])
|
683 |
+
if param_to_tie is None and param.device != torch.device("meta"):
|
684 |
+
param_to_tie = param
|
685 |
+
break
|
686 |
+
if param_to_tie is not None:
|
687 |
+
for param_name in tied_group:
|
688 |
+
module = model
|
689 |
+
splits = param_name.split(".")
|
690 |
+
for split in splits[:-1]:
|
691 |
+
module = getattr(module, split)
|
692 |
+
setattr(module, splits[-1], param_to_tie)
|
693 |
+
|
694 |
+
|
695 |
+
def _get_proper_dtype(dtype: Union[str, torch.device]) -> torch.dtype:
|
696 |
+
"""
|
697 |
+
Just does torch.dtype(dtype) if necessary.
|
698 |
+
"""
|
699 |
+
if isinstance(dtype, str):
|
700 |
+
# We accept "torch.float16" or just "float16"
|
701 |
+
dtype = dtype.replace("torch.", "")
|
702 |
+
dtype = getattr(torch, dtype)
|
703 |
+
return dtype
|
704 |
+
|
705 |
+
|
706 |
+
def compute_module_sizes(
|
707 |
+
model: nn.Module,
|
708 |
+
dtype: Optional[Union[str, torch.device]] = None,
|
709 |
+
special_dtypes: Optional[Dict[str, Union[str, torch.device]]] = None,
|
710 |
+
buffers_only: bool = False,
|
711 |
+
):
|
712 |
+
"""
|
713 |
+
Compute the size of each submodule of a given model.
|
714 |
+
"""
|
715 |
+
if dtype is not None:
|
716 |
+
dtype = _get_proper_dtype(dtype)
|
717 |
+
dtype_size = dtype_byte_size(dtype)
|
718 |
+
if special_dtypes is not None:
|
719 |
+
special_dtypes = {key: _get_proper_dtype(dtyp) for key, dtyp in special_dtypes.items()}
|
720 |
+
special_dtypes_size = {key: dtype_byte_size(dtyp) for key, dtyp in special_dtypes.items()}
|
721 |
+
module_sizes = defaultdict(int)
|
722 |
+
|
723 |
+
module_list = []
|
724 |
+
|
725 |
+
if not buffers_only:
|
726 |
+
module_list = named_module_tensors(model, recurse=True)
|
727 |
+
else:
|
728 |
+
module_list = model.named_buffers(recurse=True)
|
729 |
+
|
730 |
+
for name, tensor in module_list:
|
731 |
+
if special_dtypes is not None and name in special_dtypes:
|
732 |
+
size = tensor.numel() * special_dtypes_size[name]
|
733 |
+
elif dtype is None:
|
734 |
+
size = tensor.numel() * dtype_byte_size(tensor.dtype)
|
735 |
+
elif str(tensor.dtype).startswith(("torch.uint", "torch.int", "torch.bool")):
|
736 |
+
# According to the code in set_module_tensor_to_device, these types won't be converted
|
737 |
+
# so use their original size here
|
738 |
+
size = tensor.numel() * dtype_byte_size(tensor.dtype)
|
739 |
+
else:
|
740 |
+
size = tensor.numel() * min(dtype_size, dtype_byte_size(tensor.dtype))
|
741 |
+
name_parts = name.split(".")
|
742 |
+
for idx in range(len(name_parts) + 1):
|
743 |
+
module_sizes[".".join(name_parts[:idx])] += size
|
744 |
+
|
745 |
+
return module_sizes
|
746 |
+
|
747 |
+
|
748 |
+
def compute_module_total_buffer_size(
|
749 |
+
model: nn.Module,
|
750 |
+
dtype: Optional[Union[str, torch.device]] = None,
|
751 |
+
special_dtypes: Optional[Dict[str, Union[str, torch.device]]] = None,
|
752 |
+
):
|
753 |
+
"""
|
754 |
+
Compute the total size of buffers in each submodule of a given model.
|
755 |
+
"""
|
756 |
+
module_sizes = compute_module_sizes(model, dtype=dtype, special_dtypes=special_dtypes, buffers_only=True)
|
757 |
+
return module_sizes.get("", 0)
|
758 |
+
|
759 |
+
|
760 |
+
def get_max_layer_size(
|
761 |
+
modules: List[Tuple[str, torch.nn.Module]], module_sizes: Dict[str, int], no_split_module_classes: List[str]
|
762 |
+
):
|
763 |
+
"""
|
764 |
+
Utility function that will scan a list of named modules and return the maximum size used by one full layer. The
|
765 |
+
definition of a layer being:
|
766 |
+
- a module with no direct children (just parameters and buffers)
|
767 |
+
- a module whose class name is in the list `no_split_module_classes`
|
768 |
+
|
769 |
+
Args:
|
770 |
+
modules (`List[Tuple[str, torch.nn.Module]]`):
|
771 |
+
The list of named modules where we want to determine the maximum layer size.
|
772 |
+
module_sizes (`Dict[str, int]`):
|
773 |
+
A dictionary mapping each layer name to its size (as generated by `compute_module_sizes`).
|
774 |
+
no_split_module_classes (`List[str]`):
|
775 |
+
A list of class names for layers we don't want to be split.
|
776 |
+
|
777 |
+
Returns:
|
778 |
+
`Tuple[int, List[str]]`: The maximum size of a layer with the list of layer names realizing that maximum size.
|
779 |
+
"""
|
780 |
+
max_size = 0
|
781 |
+
layer_names = []
|
782 |
+
modules_to_treat = modules.copy()
|
783 |
+
while len(modules_to_treat) > 0:
|
784 |
+
module_name, module = modules_to_treat.pop(0)
|
785 |
+
modules_children = list(module.named_children()) if isinstance(module, torch.nn.Module) else []
|
786 |
+
if len(modules_children) == 0 or module.__class__.__name__ in no_split_module_classes:
|
787 |
+
# No splitting this one so we compare to the max_size
|
788 |
+
size = module_sizes[module_name]
|
789 |
+
if size > max_size:
|
790 |
+
max_size = size
|
791 |
+
layer_names = [module_name]
|
792 |
+
elif size == max_size:
|
793 |
+
layer_names.append(module_name)
|
794 |
+
else:
|
795 |
+
modules_to_treat = [(f"{module_name}.{n}", v) for n, v in modules_children] + modules_to_treat
|
796 |
+
return max_size, layer_names
|
797 |
+
|
798 |
+
|
799 |
+
def get_max_memory(max_memory: Optional[Dict[Union[int, str], Union[int, str]]] = None):
|
800 |
+
"""
|
801 |
+
Get the maximum memory available if nothing is passed, converts string to int otherwise.
|
802 |
+
"""
|
803 |
+
import psutil
|
804 |
+
|
805 |
+
if max_memory is None:
|
806 |
+
if not (torch.cuda.is_available() or is_npu_available() or is_mlu_available() or is_xpu_available()):
|
807 |
+
max_memory = {}
|
808 |
+
|
809 |
+
else:
|
810 |
+
# Make sure CUDA is initialized on each GPU to have the right memory info.
|
811 |
+
if is_npu_available():
|
812 |
+
for i in range(torch.npu.device_count()):
|
813 |
+
_ = torch.tensor(0, device=torch.device("npu", i))
|
814 |
+
max_memory = {i: torch.npu.mem_get_info(i)[0] for i in range(torch.npu.device_count())}
|
815 |
+
elif is_mlu_available():
|
816 |
+
for i in range(torch.mlu.device_count()):
|
817 |
+
_ = torch.tensor(0, device=torch.device("mlu", i))
|
818 |
+
max_memory = {i: torch.mlu.mem_get_info(i)[0] for i in range(torch.mlu.device_count())}
|
819 |
+
elif is_xpu_available():
|
820 |
+
for i in range(torch.xpu.device_count()):
|
821 |
+
_ = torch.tensor(0, device=torch.device("xpu", i))
|
822 |
+
max_memory = {i: torch.xpu.max_memory_allocated(i) for i in range(torch.xpu.device_count())}
|
823 |
+
else:
|
824 |
+
for i in range(torch.cuda.device_count()):
|
825 |
+
_ = torch.tensor([0], device=i)
|
826 |
+
max_memory = {i: torch.cuda.mem_get_info(i)[0] for i in range(torch.cuda.device_count())}
|
827 |
+
# allocate everything in the mps device as the RAM is shared
|
828 |
+
if is_mps_available():
|
829 |
+
max_memory["mps"] = psutil.virtual_memory().available
|
830 |
+
else:
|
831 |
+
max_memory["cpu"] = psutil.virtual_memory().available
|
832 |
+
return max_memory
|
833 |
+
|
834 |
+
for key in max_memory:
|
835 |
+
if isinstance(max_memory[key], str):
|
836 |
+
max_memory[key] = convert_file_size_to_int(max_memory[key])
|
837 |
+
|
838 |
+
# Need to sort the device by type to make sure that we allocate the gpu first.
|
839 |
+
# As gpu/npu/xpu are represented by int, we need to sort them first.
|
840 |
+
gpu_devices = [k for k in max_memory.keys() if isinstance(k, int)]
|
841 |
+
gpu_devices.sort()
|
842 |
+
# check if gpu/npu/xpu devices are available and if not, throw a warning
|
843 |
+
if is_npu_available():
|
844 |
+
num_devices = torch.npu.device_count()
|
845 |
+
elif is_mlu_available():
|
846 |
+
num_devices = torch.mlu.device_count()
|
847 |
+
elif is_xpu_available():
|
848 |
+
num_devices = torch.xpu.device_count()
|
849 |
+
else:
|
850 |
+
num_devices = torch.cuda.device_count()
|
851 |
+
for device in gpu_devices:
|
852 |
+
if device >= num_devices or device < 0:
|
853 |
+
logger.warning(f"Device {device} is not available, available devices are {list(range(num_devices))}")
|
854 |
+
# Add the other devices in the preset order if they are available
|
855 |
+
all_devices = gpu_devices + [k for k in ["mps", "cpu", "disk"] if k in max_memory.keys()]
|
856 |
+
# Raise an error if a device is not recognized
|
857 |
+
for k in max_memory.keys():
|
858 |
+
if k not in all_devices:
|
859 |
+
raise ValueError(
|
860 |
+
f"Device {k} is not recognized, available devices are integers(for GPU/XPU), 'mps', 'cpu' and 'disk'"
|
861 |
+
)
|
862 |
+
max_memory = {k: max_memory[k] for k in all_devices}
|
863 |
+
|
864 |
+
return max_memory
|
865 |
+
|
866 |
+
|
867 |
+
def clean_device_map(device_map: Dict[str, Union[int, str, torch.device]], module_name: str = ""):
|
868 |
+
"""
|
869 |
+
Cleans a device_map by grouping all submodules that go on the same device together.
|
870 |
+
"""
|
871 |
+
# Get the value of the current module and if there is only one split across several keys, regroup it.
|
872 |
+
prefix = "" if module_name == "" else f"{module_name}."
|
873 |
+
values = [v for k, v in device_map.items() if k.startswith(prefix)]
|
874 |
+
if len(set(values)) == 1 and len(values) > 1:
|
875 |
+
for k in [k for k in device_map if k.startswith(prefix)]:
|
876 |
+
del device_map[k]
|
877 |
+
device_map[module_name] = values[0]
|
878 |
+
|
879 |
+
# Recurse over the children
|
880 |
+
children_modules = [k for k in device_map.keys() if k.startswith(prefix) and len(k) > len(module_name)]
|
881 |
+
idx = len(module_name.split(".")) + 1 if len(module_name) > 0 else 1
|
882 |
+
children_modules = set(".".join(k.split(".")[:idx]) for k in children_modules)
|
883 |
+
for child in children_modules:
|
884 |
+
clean_device_map(device_map, module_name=child)
|
885 |
+
|
886 |
+
return device_map
|
887 |
+
|
888 |
+
|
889 |
+
def load_offloaded_weights(model, index, offload_folder):
|
890 |
+
"""
|
891 |
+
Loads the weights from the offload folder into the model.
|
892 |
+
|
893 |
+
Args:
|
894 |
+
model (`torch.nn.Module`):
|
895 |
+
The model to load the weights into.
|
896 |
+
index (`dict`):
|
897 |
+
A dictionary containing the parameter name and its metadata for each parameter that was offloaded from the
|
898 |
+
model.
|
899 |
+
offload_folder (`str`):
|
900 |
+
The folder where the offloaded weights are stored.
|
901 |
+
"""
|
902 |
+
if index is None or len(index) == 0:
|
903 |
+
# Nothing to do
|
904 |
+
return
|
905 |
+
for param_name, metadata in index.items():
|
906 |
+
if "SCB" in param_name:
|
907 |
+
continue
|
908 |
+
fp16_statistics = None
|
909 |
+
if "weight" in param_name and param_name.replace("weight", "SCB") in index.keys():
|
910 |
+
weight_name = param_name.replace("weight", "SCB")
|
911 |
+
fp16_statistics = load_offloaded_weight(
|
912 |
+
os.path.join(offload_folder, f"{weight_name}.dat"), index[weight_name]
|
913 |
+
)
|
914 |
+
tensor_file = os.path.join(offload_folder, f"{param_name}.dat")
|
915 |
+
weight = load_offloaded_weight(tensor_file, metadata)
|
916 |
+
set_module_tensor_to_device(model, param_name, "cpu", value=weight, fp16_statistics=fp16_statistics)
|
917 |
+
|
918 |
+
|
919 |
+
def get_balanced_memory(
|
920 |
+
model: nn.Module,
|
921 |
+
max_memory: Optional[Dict[Union[int, str], Union[int, str]]] = None,
|
922 |
+
no_split_module_classes: Optional[List[str]] = None,
|
923 |
+
dtype: Optional[Union[str, torch.dtype]] = None,
|
924 |
+
special_dtypes: Optional[Dict[str, Union[str, torch.device]]] = None,
|
925 |
+
low_zero: bool = False,
|
926 |
+
):
|
927 |
+
"""
|
928 |
+
Compute a `max_memory` dictionary for [`infer_auto_device_map`] that will balance the use of each available GPU.
|
929 |
+
|
930 |
+
<Tip>
|
931 |
+
|
932 |
+
All computation is done analyzing sizes and dtypes of the model parameters. As a result, the model can be on the
|
933 |
+
meta device (as it would if initialized within the `init_empty_weights` context manager).
|
934 |
+
|
935 |
+
</Tip>
|
936 |
+
|
937 |
+
Args:
|
938 |
+
model (`torch.nn.Module`):
|
939 |
+
The model to analyze.
|
940 |
+
max_memory (`Dict`, *optional*):
|
941 |
+
A dictionary device identifier to maximum memory. Will default to the maximum memory available if unset.
|
942 |
+
Example: `max_memory={0: "1GB"}`.
|
943 |
+
no_split_module_classes (`List[str]`, *optional*):
|
944 |
+
A list of layer class names that should never be split across device (for instance any layer that has a
|
945 |
+
residual connection).
|
946 |
+
dtype (`str` or `torch.dtype`, *optional*):
|
947 |
+
If provided, the weights will be converted to that type when loaded.
|
948 |
+
special_dtypes (`Dict[str, Union[str, torch.device]]`, *optional*):
|
949 |
+
If provided, special dtypes to consider for some specific weights (will override dtype used as default for
|
950 |
+
all weights).
|
951 |
+
low_zero (`bool`, *optional*):
|
952 |
+
Minimizes the number of weights on GPU 0, which is convenient when it's used for other operations (like the
|
953 |
+
Transformers generate function).
|
954 |
+
"""
|
955 |
+
# Get default / clean up max_memory
|
956 |
+
user_not_set_max_memory = max_memory is None
|
957 |
+
max_memory = get_max_memory(max_memory)
|
958 |
+
|
959 |
+
if is_npu_available():
|
960 |
+
num_devices = len([d for d in max_memory if torch.device(d).type == "npu" and max_memory[d] > 0])
|
961 |
+
elif is_mlu_available():
|
962 |
+
num_devices = len([d for d in max_memory if torch.device(d).type == "mlu" and max_memory[d] > 0])
|
963 |
+
elif is_xpu_available():
|
964 |
+
num_devices = len(
|
965 |
+
[
|
966 |
+
d
|
967 |
+
for d in max_memory
|
968 |
+
if (
|
969 |
+
d != "cpu"
|
970 |
+
and (torch.device(d).type == "xpu" or torch.xpu.get_device_properties(d).dev_type == "gpu")
|
971 |
+
)
|
972 |
+
and max_memory[d] > 0
|
973 |
+
]
|
974 |
+
)
|
975 |
+
else:
|
976 |
+
num_devices = len([d for d in max_memory if torch.device(d).type == "cuda" and max_memory[d] > 0])
|
977 |
+
|
978 |
+
if num_devices == 0:
|
979 |
+
return max_memory
|
980 |
+
|
981 |
+
if num_devices == 1:
|
982 |
+
# We cannot do low_zero on just one GPU, but we will still reserve some memory for the buffer
|
983 |
+
low_zero = False
|
984 |
+
# If user just asked us to handle memory usage, we should avoid OOM
|
985 |
+
if user_not_set_max_memory:
|
986 |
+
for key in max_memory.keys():
|
987 |
+
if isinstance(key, int):
|
988 |
+
max_memory[key] *= 0.9 # 90% is a good compromise
|
989 |
+
logger.info(
|
990 |
+
f"We will use 90% of the memory on device {key} for storing the model, and 10% for the buffer to avoid OOM. "
|
991 |
+
"You can set `max_memory` in to a higher value to use more memory (at your own risk)."
|
992 |
+
)
|
993 |
+
break # only one device
|
994 |
+
|
995 |
+
module_sizes = compute_module_sizes(model, dtype=dtype, special_dtypes=special_dtypes)
|
996 |
+
per_gpu = module_sizes[""] // (num_devices - 1 if low_zero else num_devices)
|
997 |
+
|
998 |
+
# We can't just set the memory to model_size // num_devices as it will end being too small: each GPU will get
|
999 |
+
# slightly less layers and some layers will end up offload at the end. So this function computes a buffer size to
|
1000 |
+
# add which is the biggest of:
|
1001 |
+
# - the size of no split block (if applicable)
|
1002 |
+
# - the mean of the layer sizes
|
1003 |
+
if no_split_module_classes is None:
|
1004 |
+
no_split_module_classes = []
|
1005 |
+
elif not isinstance(no_split_module_classes, (list, tuple)):
|
1006 |
+
no_split_module_classes = [no_split_module_classes]
|
1007 |
+
|
1008 |
+
# Identify the size of the no_split_block modules
|
1009 |
+
if len(no_split_module_classes) > 0:
|
1010 |
+
no_split_children = {}
|
1011 |
+
for name, size in module_sizes.items():
|
1012 |
+
if name == "":
|
1013 |
+
continue
|
1014 |
+
submodule = model
|
1015 |
+
for submodule_name in name.split("."):
|
1016 |
+
submodule = getattr(submodule, submodule_name)
|
1017 |
+
class_name = submodule.__class__.__name__
|
1018 |
+
if class_name in no_split_module_classes and class_name not in no_split_children:
|
1019 |
+
no_split_children[class_name] = size
|
1020 |
+
|
1021 |
+
if set(no_split_children.keys()) == set(no_split_module_classes):
|
1022 |
+
break
|
1023 |
+
buffer = max(no_split_children.values()) if len(no_split_children) > 0 else 0
|
1024 |
+
else:
|
1025 |
+
buffer = 0
|
1026 |
+
|
1027 |
+
# Compute mean of final modules. In the first dict of module sizes, leaves are the parameters
|
1028 |
+
leaves = [n for n in module_sizes if len([p for p in module_sizes if n == "" or p.startswith(n + ".")]) == 0]
|
1029 |
+
module_sizes = {n: v for n, v in module_sizes.items() if n not in leaves}
|
1030 |
+
# Once removed, leaves are the final modules.
|
1031 |
+
leaves = [n for n in module_sizes if len([p for p in module_sizes if n == "" or p.startswith(n + ".")]) == 0]
|
1032 |
+
mean_leaves = int(sum([module_sizes[n] for n in leaves]) / max(len(leaves), 1))
|
1033 |
+
buffer = int(1.25 * max(buffer, mean_leaves))
|
1034 |
+
per_gpu += buffer
|
1035 |
+
|
1036 |
+
# Sorted list of GPUs id (we may have some gpu ids not included in the our max_memory list - let's ignore them)
|
1037 |
+
gpus_idx_list = list(
|
1038 |
+
sorted(
|
1039 |
+
device_id for device_id, device_mem in max_memory.items() if isinstance(device_id, int) and device_mem > 0
|
1040 |
+
)
|
1041 |
+
)
|
1042 |
+
# The last device is left with max_memory just in case the buffer is not enough.
|
1043 |
+
for idx in gpus_idx_list[:-1]:
|
1044 |
+
max_memory[idx] = min(max_memory[0] if low_zero and idx == 0 else per_gpu, max_memory[idx])
|
1045 |
+
|
1046 |
+
if low_zero:
|
1047 |
+
min_zero = max(0, module_sizes[""] - sum([max_memory[i] for i in range(1, num_devices)]))
|
1048 |
+
max_memory[0] = min(min_zero, max_memory[0])
|
1049 |
+
|
1050 |
+
return max_memory
|
1051 |
+
|
1052 |
+
|
1053 |
+
def calculate_maximum_sizes(model: torch.nn.Module):
|
1054 |
+
"Computes the total size of the model and its largest layer"
|
1055 |
+
sizes = compute_module_sizes(model)
|
1056 |
+
# `transformers` models store this information for us
|
1057 |
+
no_split_modules = getattr(model, "_no_split_modules", None)
|
1058 |
+
if no_split_modules is None:
|
1059 |
+
no_split_modules = []
|
1060 |
+
|
1061 |
+
modules_to_treat = (
|
1062 |
+
list(model.named_parameters(recurse=False))
|
1063 |
+
+ list(model.named_children())
|
1064 |
+
+ list(model.named_buffers(recurse=False))
|
1065 |
+
)
|
1066 |
+
largest_layer = get_max_layer_size(modules_to_treat, sizes, no_split_modules)
|
1067 |
+
total_size = sizes[""]
|
1068 |
+
return total_size, largest_layer
|
1069 |
+
|
1070 |
+
|
1071 |
+
def infer_auto_device_map(
|
1072 |
+
model: nn.Module,
|
1073 |
+
max_memory: Optional[Dict[Union[int, str], Union[int, str]]] = None,
|
1074 |
+
no_split_module_classes: Optional[List[str]] = None,
|
1075 |
+
dtype: Optional[Union[str, torch.dtype]] = None,
|
1076 |
+
special_dtypes: Optional[Dict[str, Union[str, torch.dtype]]] = None,
|
1077 |
+
verbose: bool = False,
|
1078 |
+
clean_result: bool = True,
|
1079 |
+
offload_buffers: bool = False,
|
1080 |
+
):
|
1081 |
+
"""
|
1082 |
+
Compute a device map for a given model giving priority to GPUs, then offload on CPU and finally offload to disk,
|
1083 |
+
such that:
|
1084 |
+
- we don't exceed the memory available of any of the GPU.
|
1085 |
+
- if offload to the CPU is needed, there is always room left on GPU 0 to put back the layer offloaded on CPU that
|
1086 |
+
has the largest size.
|
1087 |
+
- if offload to the CPU is needed,we don't exceed the RAM available on the CPU.
|
1088 |
+
- if offload to the disk is needed, there is always room left on the CPU to put back the layer offloaded on disk
|
1089 |
+
that has the largest size.
|
1090 |
+
|
1091 |
+
<Tip>
|
1092 |
+
|
1093 |
+
All computation is done analyzing sizes and dtypes of the model parameters. As a result, the model can be on the
|
1094 |
+
meta device (as it would if initialized within the `init_empty_weights` context manager).
|
1095 |
+
|
1096 |
+
</Tip>
|
1097 |
+
|
1098 |
+
Args:
|
1099 |
+
model (`torch.nn.Module`):
|
1100 |
+
The model to analyze.
|
1101 |
+
max_memory (`Dict`, *optional*):
|
1102 |
+
A dictionary device identifier to maximum memory. Will default to the maximum memory available if unset.
|
1103 |
+
Example: `max_memory={0: "1GB"}`.
|
1104 |
+
no_split_module_classes (`List[str]`, *optional*):
|
1105 |
+
A list of layer class names that should never be split across device (for instance any layer that has a
|
1106 |
+
residual connection).
|
1107 |
+
dtype (`str` or `torch.dtype`, *optional*):
|
1108 |
+
If provided, the weights will be converted to that type when loaded.
|
1109 |
+
special_dtypes (`Dict[str, Union[str, torch.device]]`, *optional*):
|
1110 |
+
If provided, special dtypes to consider for some specific weights (will override dtype used as default for
|
1111 |
+
all weights).
|
1112 |
+
verbose (`bool`, *optional*, defaults to `False`):
|
1113 |
+
Whether or not to provide debugging statements as the function builds the device_map.
|
1114 |
+
clean_result (`bool`, *optional*, defaults to `True`):
|
1115 |
+
Clean the resulting device_map by grouping all submodules that go on the same device together.
|
1116 |
+
offload_buffers (`bool`, *optional*, defaults to `False`):
|
1117 |
+
In the layers that are offloaded on the CPU or the hard drive, whether or not to offload the buffers as
|
1118 |
+
well as the parameters.
|
1119 |
+
"""
|
1120 |
+
# Get default / clean up max_memory
|
1121 |
+
max_memory = get_max_memory(max_memory)
|
1122 |
+
if no_split_module_classes is None:
|
1123 |
+
no_split_module_classes = []
|
1124 |
+
elif not isinstance(no_split_module_classes, (list, tuple)):
|
1125 |
+
no_split_module_classes = [no_split_module_classes]
|
1126 |
+
|
1127 |
+
devices = list(max_memory.keys())
|
1128 |
+
if "disk" not in devices:
|
1129 |
+
devices.append("disk")
|
1130 |
+
gpus = [device for device in devices if device not in ["cpu", "disk"]]
|
1131 |
+
|
1132 |
+
# Devices that need to keep space for a potential offloaded layer.
|
1133 |
+
if "mps" in gpus:
|
1134 |
+
main_devices = ["mps"]
|
1135 |
+
elif len(gpus) > 0:
|
1136 |
+
main_devices = [gpus[0], "cpu"]
|
1137 |
+
else:
|
1138 |
+
main_devices = ["cpu"]
|
1139 |
+
|
1140 |
+
module_sizes = compute_module_sizes(model, dtype=dtype, special_dtypes=special_dtypes)
|
1141 |
+
tied_parameters = find_tied_parameters(model)
|
1142 |
+
|
1143 |
+
if check_tied_parameters_in_config(model) and len(tied_parameters) == 0:
|
1144 |
+
logger.warn(
|
1145 |
+
"The model weights are not tied. Please use the `tie_weights` method before using the `infer_auto_device` function."
|
1146 |
+
)
|
1147 |
+
|
1148 |
+
device_map = OrderedDict()
|
1149 |
+
current_device = 0
|
1150 |
+
current_memory_used = 0
|
1151 |
+
device_memory_used = {}
|
1152 |
+
device_buffer_sizes = {}
|
1153 |
+
|
1154 |
+
# Direct submodules and parameters
|
1155 |
+
modules_to_treat = (
|
1156 |
+
list(model.named_parameters(recurse=False))
|
1157 |
+
+ list(model.named_children())
|
1158 |
+
+ list(model.named_buffers(recurse=False))
|
1159 |
+
)
|
1160 |
+
# Initialize maximum largest layer, to know which space to keep in memory
|
1161 |
+
max_layer_size, max_layer_names = get_max_layer_size(modules_to_treat, module_sizes, no_split_module_classes)
|
1162 |
+
|
1163 |
+
# Ready ? This is going to be a bit messy.
|
1164 |
+
while len(modules_to_treat) > 0:
|
1165 |
+
name, module = modules_to_treat.pop(0)
|
1166 |
+
if verbose:
|
1167 |
+
print(f"\nTreating module {name}.")
|
1168 |
+
# Max size in the remaining layers may have changed since we took one, so we maybe update it.
|
1169 |
+
max_layer_names = [n for n in max_layer_names if n != name and not n.startswith(name + ".")]
|
1170 |
+
if len(max_layer_names) == 0:
|
1171 |
+
max_layer_size, max_layer_names = get_max_layer_size(
|
1172 |
+
[(n, m) for n, m in modules_to_treat if isinstance(m, torch.nn.Module)],
|
1173 |
+
module_sizes,
|
1174 |
+
no_split_module_classes,
|
1175 |
+
)
|
1176 |
+
# Assess size needed
|
1177 |
+
module_size = module_sizes[name]
|
1178 |
+
|
1179 |
+
# We keep relevant tied parameters only: one of the tied parameters in the group is inside the current module
|
1180 |
+
# and the other is not.
|
1181 |
+
# Note: If we are currently processing the name `compute.weight`, an other parameter named e.g. `compute.weight_submodule.parameter`
|
1182 |
+
# needs to be considered outside the current module, hence the check with additional dots.
|
1183 |
+
tied_param_goups = [
|
1184 |
+
tied_group
|
1185 |
+
for tied_group in tied_parameters
|
1186 |
+
if any(name + "." in k + "." for k in tied_group) and not all(name + "." in k + "." for k in tied_group)
|
1187 |
+
]
|
1188 |
+
|
1189 |
+
if verbose and len(tied_param_goups) > 0:
|
1190 |
+
print(f" Found the relevant tied param groups {tied_param_goups}")
|
1191 |
+
|
1192 |
+
# Then we keep track of all the parameters that are tied to the current module, but not in the current module
|
1193 |
+
tied_params = sum(
|
1194 |
+
[[p for p in tied_group if name + "." not in p + "."] for tied_group in tied_param_goups], []
|
1195 |
+
)
|
1196 |
+
|
1197 |
+
if verbose and len(tied_params) > 0:
|
1198 |
+
print(f" So those parameters need to be taken into account {tied_params}")
|
1199 |
+
|
1200 |
+
device = devices[current_device]
|
1201 |
+
current_max_size = max_memory[device] if device != "disk" else None
|
1202 |
+
current_memory_reserved = 0
|
1203 |
+
# Reduce max size available by the largest layer.
|
1204 |
+
if devices[current_device] in main_devices:
|
1205 |
+
current_max_size = current_max_size - max_layer_size
|
1206 |
+
current_memory_reserved = max_layer_size
|
1207 |
+
# Case 1 -> We're too big!
|
1208 |
+
if current_max_size is not None and current_memory_used + module_size > current_max_size:
|
1209 |
+
# Split or not split?
|
1210 |
+
modules_children = (
|
1211 |
+
[]
|
1212 |
+
if isinstance(module, nn.Parameter) or isinstance(module, torch.Tensor)
|
1213 |
+
else list(module.named_children())
|
1214 |
+
)
|
1215 |
+
if verbose:
|
1216 |
+
print(
|
1217 |
+
f"Not enough space on {devices[current_device]} to put {name} (space available "
|
1218 |
+
f"{current_max_size - current_memory_used}, module size {module_size})."
|
1219 |
+
)
|
1220 |
+
if len(modules_children) == 0 or module.__class__.__name__ in no_split_module_classes:
|
1221 |
+
# -> no split, we go to the next device
|
1222 |
+
if verbose:
|
1223 |
+
print("This module cannot be split, going to the next device.")
|
1224 |
+
|
1225 |
+
device_memory_used[device] = current_memory_used + current_memory_reserved
|
1226 |
+
current_device += 1
|
1227 |
+
modules_to_treat = [(name, module)] + modules_to_treat
|
1228 |
+
current_memory_used = 0
|
1229 |
+
else:
|
1230 |
+
# -> split, we replace the module studied by its children + parameters
|
1231 |
+
if verbose:
|
1232 |
+
print(f"Splitting {name}.")
|
1233 |
+
modules_children = list(module.named_parameters(recurse=False)) + modules_children
|
1234 |
+
modules_to_treat = [(f"{name}.{n}", v) for n, v in modules_children] + modules_to_treat
|
1235 |
+
# Update the max layer size.
|
1236 |
+
max_layer_size, max_layer_names = get_max_layer_size(
|
1237 |
+
[(n, m) for n, m in modules_to_treat if isinstance(m, torch.nn.Module)],
|
1238 |
+
module_sizes,
|
1239 |
+
no_split_module_classes,
|
1240 |
+
)
|
1241 |
+
|
1242 |
+
# Case 2, it fits! We're not entirely out of the wood though, because we may have some tied parameters.
|
1243 |
+
elif len(tied_params) > 0:
|
1244 |
+
# First locate all tied modules
|
1245 |
+
tied_module_names = []
|
1246 |
+
tied_modules = []
|
1247 |
+
for tied_param in tied_params:
|
1248 |
+
tied_module_index = [i for i, (n, _) in enumerate(modules_to_treat) if n in tied_param][0]
|
1249 |
+
tied_module_names.append(modules_to_treat[tied_module_index][0])
|
1250 |
+
tied_modules.append(modules_to_treat[tied_module_index][1])
|
1251 |
+
if verbose:
|
1252 |
+
print(
|
1253 |
+
f" It looks like {name} is going to fit on {devices[current_device]} but we have tied "
|
1254 |
+
f"parameters to account for.\n - Names {tied_params}\n - Module names {tied_module_names}"
|
1255 |
+
)
|
1256 |
+
|
1257 |
+
# Let's see if it all fits first
|
1258 |
+
module_size_with_ties = module_size
|
1259 |
+
for tied_param, tied_module_name in zip(tied_params, tied_module_names):
|
1260 |
+
module_size_with_ties += module_sizes[tied_module_name] - module_sizes[tied_param]
|
1261 |
+
|
1262 |
+
if current_max_size is None or current_memory_used + module_size_with_ties <= current_max_size:
|
1263 |
+
# We really really fit!
|
1264 |
+
if verbose:
|
1265 |
+
print(f"Putting {name} and {tied_module_names} on {devices[current_device]}.")
|
1266 |
+
current_memory_used += module_size_with_ties
|
1267 |
+
device_map[name] = devices[current_device]
|
1268 |
+
for tied_module_name in tied_module_names:
|
1269 |
+
if tied_module_name in [m[0] for m in modules_to_treat]:
|
1270 |
+
# The module may have been removed by a previous iteration of this loop.
|
1271 |
+
tied_module_index = [i for i, (n, _) in enumerate(modules_to_treat) if n == tied_module_name][
|
1272 |
+
0
|
1273 |
+
]
|
1274 |
+
modules_to_treat.pop(tied_module_index)
|
1275 |
+
device_map[tied_module_name] = devices[current_device]
|
1276 |
+
|
1277 |
+
if not offload_buffers and isinstance(module, nn.Module):
|
1278 |
+
current_buffer_size = compute_module_total_buffer_size(
|
1279 |
+
module, dtype=dtype, special_dtypes=special_dtypes
|
1280 |
+
)
|
1281 |
+
device_buffer_sizes[device] = device_buffer_sizes.get(device, 0) + current_buffer_size
|
1282 |
+
|
1283 |
+
else:
|
1284 |
+
# We don't fit with the tied modules. Next question is: can we split one of the tied modules to make it
|
1285 |
+
# smaller or do we need to go on the next device?
|
1286 |
+
if verbose:
|
1287 |
+
print(
|
1288 |
+
f"Not enough space on {devices[current_device]} to put {name} and {tied_module_names} (space "
|
1289 |
+
f"available {current_max_size - current_memory_used}, needed size {module_size_with_ties})."
|
1290 |
+
)
|
1291 |
+
split_happened = False
|
1292 |
+
for tied_module_name, tied_module in zip(tied_module_names, tied_modules):
|
1293 |
+
tied_module_children = list(tied_module.named_children())
|
1294 |
+
if len(tied_module_children) == 0 or tied_module.__class__.__name__ in no_split_module_classes:
|
1295 |
+
# can't break this one.
|
1296 |
+
continue
|
1297 |
+
|
1298 |
+
if verbose:
|
1299 |
+
print(f"Splitting {tied_module_name}.")
|
1300 |
+
tied_module_children = list(tied_module.named_parameters(recurse=False)) + tied_module_children
|
1301 |
+
tied_module_children = [(f"{tied_module_name}.{n}", v) for n, v in tied_module_children]
|
1302 |
+
tied_module_index = [i for i, (n, _) in enumerate(modules_to_treat) if n == tied_module_name][0]
|
1303 |
+
|
1304 |
+
modules_to_treat = (
|
1305 |
+
[(name, module)]
|
1306 |
+
+ modules_to_treat[:tied_module_index]
|
1307 |
+
+ tied_module_children
|
1308 |
+
+ modules_to_treat[tied_module_index + 1 :]
|
1309 |
+
)
|
1310 |
+
# Update the max layer size.
|
1311 |
+
max_layer_size, max_layer_names = get_max_layer_size(
|
1312 |
+
[(n, m) for n, m in modules_to_treat if isinstance(m, torch.nn.Module)],
|
1313 |
+
module_sizes,
|
1314 |
+
no_split_module_classes,
|
1315 |
+
)
|
1316 |
+
split_happened = True
|
1317 |
+
break
|
1318 |
+
|
1319 |
+
if not split_happened:
|
1320 |
+
# If the tied module is not split, we go to the next device
|
1321 |
+
if verbose:
|
1322 |
+
print("None of the tied module can be split, going to the next device.")
|
1323 |
+
|
1324 |
+
device_memory_used[device] = current_memory_used + current_memory_reserved
|
1325 |
+
current_device += 1
|
1326 |
+
modules_to_treat = [(name, module)] + modules_to_treat
|
1327 |
+
current_memory_used = 0
|
1328 |
+
|
1329 |
+
else:
|
1330 |
+
if verbose:
|
1331 |
+
if current_max_size is None:
|
1332 |
+
print(f"Putting {name} (size={module_size}) on {devices[current_device]}.")
|
1333 |
+
else:
|
1334 |
+
print(
|
1335 |
+
f"Putting {name} (size={module_size}) on {devices[current_device]} "
|
1336 |
+
f"(available={current_max_size - current_memory_used})."
|
1337 |
+
)
|
1338 |
+
current_memory_used += module_size
|
1339 |
+
device_memory_used[device] = current_memory_used + current_memory_reserved
|
1340 |
+
device_map[name] = devices[current_device]
|
1341 |
+
|
1342 |
+
if not offload_buffers and isinstance(module, nn.Module):
|
1343 |
+
current_buffer_size = compute_module_total_buffer_size(
|
1344 |
+
module, dtype=dtype, special_dtypes=special_dtypes
|
1345 |
+
)
|
1346 |
+
device_buffer_sizes[device] = device_buffer_sizes.get(device, 0) + current_buffer_size
|
1347 |
+
|
1348 |
+
if clean_result:
|
1349 |
+
device_map = clean_device_map(device_map)
|
1350 |
+
|
1351 |
+
non_gpu_buffer_size = device_buffer_sizes.get("cpu", 0) + device_buffer_sizes.get("disk", 0)
|
1352 |
+
if non_gpu_buffer_size > 0 and not offload_buffers:
|
1353 |
+
is_buffer_fit_any_gpu = False
|
1354 |
+
for gpu_device, gpu_max_memory in max_memory.items():
|
1355 |
+
if gpu_device == "cpu" or gpu_device == "disk":
|
1356 |
+
continue
|
1357 |
+
|
1358 |
+
if not is_buffer_fit_any_gpu:
|
1359 |
+
gpu_memory_used = device_memory_used.get(gpu_device, 0)
|
1360 |
+
|
1361 |
+
if gpu_max_memory >= non_gpu_buffer_size + gpu_memory_used:
|
1362 |
+
is_buffer_fit_any_gpu = True
|
1363 |
+
|
1364 |
+
if len(gpus) > 0 and not is_buffer_fit_any_gpu:
|
1365 |
+
warnings.warn(
|
1366 |
+
f"Current model requires {non_gpu_buffer_size} bytes of buffer for offloaded layers, which seems does "
|
1367 |
+
f"not fit any GPU's remaining memory. If you are experiencing a OOM later, please consider using "
|
1368 |
+
f"offload_buffers=True."
|
1369 |
+
)
|
1370 |
+
|
1371 |
+
return device_map
|
1372 |
+
|
1373 |
+
|
1374 |
+
def check_device_map(model: nn.Module, device_map: Dict[str, Union[int, str, torch.device]]):
|
1375 |
+
"""
|
1376 |
+
Checks a device map covers everything in a given model.
|
1377 |
+
|
1378 |
+
Args:
|
1379 |
+
model (`torch.nn.Module`): The model to check the device map against.
|
1380 |
+
device_map (`Dict[str, Union[int, str, torch.device]]`): The device map to check.
|
1381 |
+
"""
|
1382 |
+
all_model_tensors = [name for name, _ in model.state_dict().items()]
|
1383 |
+
for module_name in device_map.keys():
|
1384 |
+
if module_name == "":
|
1385 |
+
all_model_tensors.clear()
|
1386 |
+
break
|
1387 |
+
else:
|
1388 |
+
all_model_tensors = [
|
1389 |
+
name
|
1390 |
+
for name in all_model_tensors
|
1391 |
+
if not name == module_name and not name.startswith(module_name + ".")
|
1392 |
+
]
|
1393 |
+
if len(all_model_tensors) > 0:
|
1394 |
+
non_covered_params = ", ".join(all_model_tensors)
|
1395 |
+
raise ValueError(
|
1396 |
+
f"The device_map provided does not give any device for the following parameters: {non_covered_params}"
|
1397 |
+
)
|
1398 |
+
|
1399 |
+
|
1400 |
+
def load_state_dict(checkpoint_file, device_map=None):
|
1401 |
+
"""
|
1402 |
+
Load a checkpoint from a given file. If the checkpoint is in the safetensors format and a device map is passed, the
|
1403 |
+
weights can be fast-loaded directly on the GPU.
|
1404 |
+
|
1405 |
+
Args:
|
1406 |
+
checkpoint_file (`str`): The path to the checkpoint to load.
|
1407 |
+
device_map (`Dict[str, Union[int, str, torch.device]]`, *optional*):
|
1408 |
+
A map that specifies where each submodule should go. It doesn't need to be refined to each parameter/buffer
|
1409 |
+
name, once a given module name is inside, every submodule of it will be sent to the same device.
|
1410 |
+
"""
|
1411 |
+
if checkpoint_file.endswith(".safetensors"):
|
1412 |
+
with safe_open(checkpoint_file, framework="pt") as f:
|
1413 |
+
metadata = f.metadata()
|
1414 |
+
weight_names = f.keys()
|
1415 |
+
|
1416 |
+
if metadata is None:
|
1417 |
+
logger.warn(
|
1418 |
+
f"The safetensors archive passed at {checkpoint_file} does not contain metadata. "
|
1419 |
+
"Make sure to save your model with the `save_pretrained` method. Defaulting to 'pt' metadata."
|
1420 |
+
)
|
1421 |
+
metadata = {"format": "pt"}
|
1422 |
+
|
1423 |
+
if metadata.get("format") not in ["pt", "tf", "flax"]:
|
1424 |
+
raise OSError(
|
1425 |
+
f"The safetensors archive passed at {checkpoint_file} does not contain the valid metadata. Make sure "
|
1426 |
+
"you save your model with the `save_pretrained` method."
|
1427 |
+
)
|
1428 |
+
elif metadata["format"] != "pt":
|
1429 |
+
raise ValueError(f"The checkpoint passed was saved with {metadata['format']}, we need a the pt format.")
|
1430 |
+
if device_map is None:
|
1431 |
+
return safe_load_file(checkpoint_file)
|
1432 |
+
else:
|
1433 |
+
# if we only have one device we can load everything directly
|
1434 |
+
if len(set(device_map.values())) == 1:
|
1435 |
+
return safe_load_file(checkpoint_file, device=list(device_map.values())[0])
|
1436 |
+
|
1437 |
+
devices = list(set(device_map.values()) - {"disk"})
|
1438 |
+
# cpu device should always exist as fallback option
|
1439 |
+
if "cpu" not in devices:
|
1440 |
+
devices.append("cpu")
|
1441 |
+
|
1442 |
+
# For each device, get the weights that go there
|
1443 |
+
device_weights = {device: [] for device in devices}
|
1444 |
+
for module_name, device in device_map.items():
|
1445 |
+
if device in devices:
|
1446 |
+
device_weights[device].extend(
|
1447 |
+
[k for k in weight_names if k == module_name or k.startswith(module_name + ".")]
|
1448 |
+
)
|
1449 |
+
|
1450 |
+
# all weights that haven't defined a device should be loaded on CPU
|
1451 |
+
device_weights["cpu"].extend([k for k in weight_names if k not in sum(device_weights.values(), [])])
|
1452 |
+
tensors = {}
|
1453 |
+
if is_tqdm_available():
|
1454 |
+
progress_bar = tqdm(
|
1455 |
+
main_process_only=False,
|
1456 |
+
total=sum([len(device_weights[device]) for device in devices]),
|
1457 |
+
unit="w",
|
1458 |
+
smoothing=0,
|
1459 |
+
leave=False,
|
1460 |
+
)
|
1461 |
+
else:
|
1462 |
+
progress_bar = None
|
1463 |
+
for device in devices:
|
1464 |
+
target_device = device
|
1465 |
+
|
1466 |
+
if is_xpu_available():
|
1467 |
+
current_safetensors_version = packaging.version.parse(importlib.metadata.version("safetensors"))
|
1468 |
+
|
1469 |
+
if compare_versions(current_safetensors_version, "<", "0.4.2"):
|
1470 |
+
raise ModuleNotFoundError(
|
1471 |
+
f"You need at least safetensors 0.4.2 for Intel GPU, while you have {current_safetensors_version}"
|
1472 |
+
)
|
1473 |
+
|
1474 |
+
if isinstance(device, int):
|
1475 |
+
target_device = f"xpu:{device}"
|
1476 |
+
|
1477 |
+
with safe_open(checkpoint_file, framework="pt", device=target_device) as f:
|
1478 |
+
for key in device_weights[device]:
|
1479 |
+
if progress_bar is not None:
|
1480 |
+
progress_bar.set_postfix(dev=device, refresh=False)
|
1481 |
+
progress_bar.set_description(key)
|
1482 |
+
tensors[key] = f.get_tensor(key)
|
1483 |
+
if progress_bar is not None:
|
1484 |
+
progress_bar.update()
|
1485 |
+
if progress_bar is not None:
|
1486 |
+
progress_bar.close()
|
1487 |
+
|
1488 |
+
return tensors
|
1489 |
+
else:
|
1490 |
+
return torch.load(checkpoint_file, map_location=torch.device("cpu"))
|
1491 |
+
|
1492 |
+
|
1493 |
+
def get_state_dict_offloaded_model(model: nn.Module):
|
1494 |
+
"""
|
1495 |
+
Returns the state dictionary for an offloaded model via iterative onloading
|
1496 |
+
|
1497 |
+
Args:
|
1498 |
+
model (`torch.nn.Module`):
|
1499 |
+
The offloaded model we want to save
|
1500 |
+
"""
|
1501 |
+
from ..hooks import AlignDevicesHook
|
1502 |
+
|
1503 |
+
state_dict = {}
|
1504 |
+
placeholders = set()
|
1505 |
+
for name, module in model.named_modules():
|
1506 |
+
if name == "":
|
1507 |
+
continue
|
1508 |
+
if hasattr(module, "_hf_hook") and isinstance(module._hf_hook, AlignDevicesHook) and module._hf_hook.offload:
|
1509 |
+
original_device = module._hf_hook.execution_device
|
1510 |
+
# assign hook execution device to cpu
|
1511 |
+
module._hf_hook.execution_device = "cpu"
|
1512 |
+
# onload meta tensors to execution device
|
1513 |
+
try:
|
1514 |
+
module._hf_hook.pre_forward(module)
|
1515 |
+
except MemoryError:
|
1516 |
+
raise MemoryError("Offloaded module must fit in CPU memory to call save_model!") from None
|
1517 |
+
module_state_dict = module.state_dict()
|
1518 |
+
# offload meta tensors from cpu
|
1519 |
+
module._hf_hook.post_forward(module, torch.tensor([]))
|
1520 |
+
# re-assign hook to original execution device
|
1521 |
+
module._hf_hook.execution_device = original_device
|
1522 |
+
else:
|
1523 |
+
module_state_dict = module.state_dict()
|
1524 |
+
|
1525 |
+
for key in module_state_dict:
|
1526 |
+
# ignore placeholder parameters that are still on the meta device
|
1527 |
+
if module_state_dict[key].device == torch.device("meta"):
|
1528 |
+
placeholders.add(name + f".{key}")
|
1529 |
+
continue
|
1530 |
+
params = module_state_dict[key]
|
1531 |
+
state_dict[name + f".{key}"] = params
|
1532 |
+
for key in placeholders.copy():
|
1533 |
+
if key in state_dict:
|
1534 |
+
placeholders.remove(key)
|
1535 |
+
if placeholders:
|
1536 |
+
logger.warning(f"The following tensors were not saved because they were still on meta device: {placeholders}")
|
1537 |
+
|
1538 |
+
return state_dict
|
1539 |
+
|
1540 |
+
|
1541 |
+
def load_checkpoint_in_model(
|
1542 |
+
model: nn.Module,
|
1543 |
+
checkpoint: Union[str, os.PathLike],
|
1544 |
+
device_map: Optional[Dict[str, Union[int, str, torch.device]]] = None,
|
1545 |
+
offload_folder: Optional[Union[str, os.PathLike]] = None,
|
1546 |
+
dtype: Optional[Union[str, torch.dtype]] = None,
|
1547 |
+
offload_state_dict: bool = False,
|
1548 |
+
offload_buffers: bool = False,
|
1549 |
+
keep_in_fp32_modules: List[str] = None,
|
1550 |
+
offload_8bit_bnb: bool = False,
|
1551 |
+
strict: bool = False,
|
1552 |
+
):
|
1553 |
+
"""
|
1554 |
+
Loads a (potentially sharded) checkpoint inside a model, potentially sending weights to a given device as they are
|
1555 |
+
loaded.
|
1556 |
+
|
1557 |
+
<Tip warning={true}>
|
1558 |
+
|
1559 |
+
Once loaded across devices, you still need to call [`dispatch_model`] on your model to make it able to run. To
|
1560 |
+
group the checkpoint loading and dispatch in one single call, use [`load_checkpoint_and_dispatch`].
|
1561 |
+
|
1562 |
+
</Tip>
|
1563 |
+
|
1564 |
+
Args:
|
1565 |
+
model (`torch.nn.Module`):
|
1566 |
+
The model in which we want to load a checkpoint.
|
1567 |
+
checkpoint (`str` or `os.PathLike`):
|
1568 |
+
The folder checkpoint to load. It can be:
|
1569 |
+
- a path to a file containing a whole model state dict
|
1570 |
+
- a path to a `.json` file containing the index to a sharded checkpoint
|
1571 |
+
- a path to a folder containing a unique `.index.json` file and the shards of a checkpoint.
|
1572 |
+
- a path to a folder containing a unique pytorch_model.bin or a model.safetensors file.
|
1573 |
+
device_map (`Dict[str, Union[int, str, torch.device]]`, *optional*):
|
1574 |
+
A map that specifies where each submodule should go. It doesn't need to be refined to each parameter/buffer
|
1575 |
+
name, once a given module name is inside, every submodule of it will be sent to the same device.
|
1576 |
+
offload_folder (`str` or `os.PathLike`, *optional*):
|
1577 |
+
If the `device_map` contains any value `"disk"`, the folder where we will offload weights.
|
1578 |
+
dtype (`str` or `torch.dtype`, *optional*):
|
1579 |
+
If provided, the weights will be converted to that type when loaded.
|
1580 |
+
offload_state_dict (`bool`, *optional*, defaults to `False`):
|
1581 |
+
If `True`, will temporarily offload the CPU state dict on the hard drive to avoid getting out of CPU RAM if
|
1582 |
+
the weight of the CPU state dict + the biggest shard does not fit.
|
1583 |
+
offload_buffers (`bool`, *optional*, defaults to `False`):
|
1584 |
+
Whether or not to include the buffers in the weights offloaded to disk.
|
1585 |
+
keep_in_fp32_modules(`List[str]`, *optional*):
|
1586 |
+
A list of the modules that we keep in `torch.float32` dtype.
|
1587 |
+
offload_8bit_bnb (`bool`, *optional*):
|
1588 |
+
Whether or not to enable offload of 8-bit modules on cpu/disk.
|
1589 |
+
strict (`bool`, *optional*, defaults to `False`):
|
1590 |
+
Whether to strictly enforce that the keys in the checkpoint state_dict match the keys of the model's
|
1591 |
+
state_dict.
|
1592 |
+
|
1593 |
+
"""
|
1594 |
+
if offload_8bit_bnb:
|
1595 |
+
from .bnb import quantize_and_offload_8bit
|
1596 |
+
|
1597 |
+
tied_params = find_tied_parameters(model)
|
1598 |
+
|
1599 |
+
if check_tied_parameters_in_config(model) and len(tied_params) == 0:
|
1600 |
+
logger.warn(
|
1601 |
+
"The model weights are not tied. Please use the `tie_weights` method before using the `infer_auto_device` function."
|
1602 |
+
)
|
1603 |
+
if device_map is not None:
|
1604 |
+
check_tied_parameters_on_same_device(tied_params, device_map)
|
1605 |
+
|
1606 |
+
if offload_folder is None and device_map is not None and "disk" in device_map.values():
|
1607 |
+
raise ValueError(
|
1608 |
+
"At least one of the model submodule will be offloaded to disk, please pass along an `offload_folder`."
|
1609 |
+
)
|
1610 |
+
elif offload_folder is not None and device_map is not None and "disk" in device_map.values():
|
1611 |
+
os.makedirs(offload_folder, exist_ok=True)
|
1612 |
+
|
1613 |
+
if isinstance(dtype, str):
|
1614 |
+
# We accept "torch.float16" or just "float16"
|
1615 |
+
dtype = dtype.replace("torch.", "")
|
1616 |
+
dtype = getattr(torch, dtype)
|
1617 |
+
|
1618 |
+
checkpoint_files = None
|
1619 |
+
index_filename = None
|
1620 |
+
if os.path.isfile(checkpoint):
|
1621 |
+
if str(checkpoint).endswith(".json"):
|
1622 |
+
index_filename = checkpoint
|
1623 |
+
else:
|
1624 |
+
checkpoint_files = [checkpoint]
|
1625 |
+
elif os.path.isdir(checkpoint):
|
1626 |
+
# check if the whole state dict is present
|
1627 |
+
potential_state_bin = [f for f in os.listdir(checkpoint) if f == WEIGHTS_NAME]
|
1628 |
+
potential_state_safetensor = [f for f in os.listdir(checkpoint) if f == SAFE_WEIGHTS_NAME]
|
1629 |
+
if len(potential_state_bin) == 1:
|
1630 |
+
checkpoint_files = [os.path.join(checkpoint, potential_state_bin[0])]
|
1631 |
+
elif len(potential_state_safetensor) == 1:
|
1632 |
+
checkpoint_files = [os.path.join(checkpoint, potential_state_safetensor[0])]
|
1633 |
+
else:
|
1634 |
+
# otherwise check for sharded checkpoints
|
1635 |
+
potential_index = [f for f in os.listdir(checkpoint) if f.endswith(".index.json")]
|
1636 |
+
if len(potential_index) == 0:
|
1637 |
+
raise ValueError(
|
1638 |
+
f"{checkpoint} is not a folder containing a `.index.json` file or a {WEIGHTS_NAME} or a {SAFE_WEIGHTS_NAME} file"
|
1639 |
+
)
|
1640 |
+
elif len(potential_index) == 1:
|
1641 |
+
index_filename = os.path.join(checkpoint, potential_index[0])
|
1642 |
+
else:
|
1643 |
+
raise ValueError(
|
1644 |
+
f"{checkpoint} containing more than one `.index.json` file, delete the irrelevant ones."
|
1645 |
+
)
|
1646 |
+
else:
|
1647 |
+
raise ValueError(
|
1648 |
+
"`checkpoint` should be the path to a file containing a whole state dict, or the index of a sharded "
|
1649 |
+
f"checkpoint, or a folder containing a sharded checkpoint or the whole state dict, but got {checkpoint}."
|
1650 |
+
)
|
1651 |
+
|
1652 |
+
if index_filename is not None:
|
1653 |
+
checkpoint_folder = os.path.split(index_filename)[0]
|
1654 |
+
with open(index_filename) as f:
|
1655 |
+
index = json.loads(f.read())
|
1656 |
+
|
1657 |
+
if "weight_map" in index:
|
1658 |
+
index = index["weight_map"]
|
1659 |
+
checkpoint_files = sorted(list(set(index.values())))
|
1660 |
+
checkpoint_files = [os.path.join(checkpoint_folder, f) for f in checkpoint_files]
|
1661 |
+
|
1662 |
+
# Logic for missing/unexepected keys goes here.
|
1663 |
+
|
1664 |
+
offload_index = {}
|
1665 |
+
if offload_state_dict:
|
1666 |
+
state_dict_folder = tempfile.mkdtemp()
|
1667 |
+
state_dict_index = {}
|
1668 |
+
|
1669 |
+
unexpected_keys = set()
|
1670 |
+
model_keys = set(model.state_dict().keys())
|
1671 |
+
buffer_names = [name for name, _ in model.named_buffers()]
|
1672 |
+
for checkpoint_file in checkpoint_files:
|
1673 |
+
loaded_checkpoint = load_state_dict(checkpoint_file, device_map=device_map)
|
1674 |
+
if device_map is None:
|
1675 |
+
model.load_state_dict(loaded_checkpoint, strict=strict)
|
1676 |
+
unexpected_keys.update(set(loaded_checkpoint.keys()) - model_keys)
|
1677 |
+
else:
|
1678 |
+
for param_name, param in loaded_checkpoint.items():
|
1679 |
+
# skip SCB parameter (for 8-bit serialization)
|
1680 |
+
if "SCB" in param_name:
|
1681 |
+
continue
|
1682 |
+
|
1683 |
+
if param_name not in model_keys:
|
1684 |
+
unexpected_keys.add(param_name)
|
1685 |
+
if not strict:
|
1686 |
+
continue # Skip loading this parameter.
|
1687 |
+
|
1688 |
+
module_name = param_name
|
1689 |
+
|
1690 |
+
while len(module_name) > 0 and module_name not in device_map:
|
1691 |
+
module_name = ".".join(module_name.split(".")[:-1])
|
1692 |
+
if module_name == "" and "" not in device_map:
|
1693 |
+
# TODO: group all errors and raise at the end.
|
1694 |
+
raise ValueError(f"{param_name} doesn't have any device set.")
|
1695 |
+
param_device = device_map[module_name]
|
1696 |
+
new_dtype = dtype
|
1697 |
+
if dtype is not None and torch.is_floating_point(param):
|
1698 |
+
if keep_in_fp32_modules is not None and dtype == torch.float16:
|
1699 |
+
proceed = False
|
1700 |
+
for key in keep_in_fp32_modules:
|
1701 |
+
if ((key in param_name) and (key + "." in param_name)) or key == param_name:
|
1702 |
+
proceed = True
|
1703 |
+
break
|
1704 |
+
if proceed:
|
1705 |
+
new_dtype = torch.float32
|
1706 |
+
|
1707 |
+
if "weight" in param_name and param_name.replace("weight", "SCB") in loaded_checkpoint.keys():
|
1708 |
+
if param.dtype == torch.int8:
|
1709 |
+
fp16_statistics = loaded_checkpoint[param_name.replace("weight", "SCB")]
|
1710 |
+
else:
|
1711 |
+
fp16_statistics = None
|
1712 |
+
|
1713 |
+
if param_device == "disk":
|
1714 |
+
if offload_buffers or param_name not in buffer_names:
|
1715 |
+
if new_dtype is None:
|
1716 |
+
new_dtype = param.dtype
|
1717 |
+
if offload_8bit_bnb:
|
1718 |
+
quantize_and_offload_8bit(
|
1719 |
+
model, param, param_name, new_dtype, offload_folder, offload_index, fp16_statistics
|
1720 |
+
)
|
1721 |
+
continue
|
1722 |
+
else:
|
1723 |
+
set_module_tensor_to_device(model, param_name, "meta", dtype=new_dtype)
|
1724 |
+
offload_weight(param, param_name, offload_folder, index=offload_index)
|
1725 |
+
elif param_device == "cpu" and offload_state_dict:
|
1726 |
+
if new_dtype is None:
|
1727 |
+
new_dtype = param.dtype
|
1728 |
+
if offload_8bit_bnb:
|
1729 |
+
quantize_and_offload_8bit(
|
1730 |
+
model, param, param_name, new_dtype, state_dict_folder, state_dict_index, fp16_statistics
|
1731 |
+
)
|
1732 |
+
else:
|
1733 |
+
set_module_tensor_to_device(model, param_name, "meta", dtype=new_dtype)
|
1734 |
+
offload_weight(param, param_name, state_dict_folder, index=state_dict_index)
|
1735 |
+
else:
|
1736 |
+
set_module_tensor_to_device(
|
1737 |
+
model,
|
1738 |
+
param_name,
|
1739 |
+
param_device,
|
1740 |
+
value=param,
|
1741 |
+
dtype=new_dtype,
|
1742 |
+
fp16_statistics=fp16_statistics,
|
1743 |
+
)
|
1744 |
+
|
1745 |
+
# Force Python to clean up.
|
1746 |
+
del loaded_checkpoint
|
1747 |
+
gc.collect()
|
1748 |
+
|
1749 |
+
if not strict and len(unexpected_keys) > 0:
|
1750 |
+
logger.warning(
|
1751 |
+
f"Some weights of the model checkpoint at {checkpoint} were not used when"
|
1752 |
+
f" initializing {model.__class__.__name__}: {unexpected_keys}. This may or may not be an issue - make sure that the checkpoint does not have unnecessary parameters, or that the model definition correctly corresponds to the checkpoint."
|
1753 |
+
)
|
1754 |
+
|
1755 |
+
save_offload_index(offload_index, offload_folder)
|
1756 |
+
|
1757 |
+
# Load back offloaded state dict on CPU
|
1758 |
+
if offload_state_dict:
|
1759 |
+
load_offloaded_weights(model, state_dict_index, state_dict_folder)
|
1760 |
+
shutil.rmtree(state_dict_folder)
|
1761 |
+
|
1762 |
+
retie_parameters(model, tied_params)
|
1763 |
+
|
1764 |
+
|
1765 |
+
def get_mixed_precision_context_manager(native_amp: bool = False, autocast_kwargs: AutocastKwargs = None):
|
1766 |
+
"""
|
1767 |
+
Return a context manager for autocasting mixed precision
|
1768 |
+
|
1769 |
+
Args:
|
1770 |
+
native_amp (`bool`, *optional*, defaults to False):
|
1771 |
+
Whether mixed precision is actually enabled.
|
1772 |
+
cache_enabled (`bool`, *optional*, defaults to True):
|
1773 |
+
Whether the weight cache inside autocast should be enabled.
|
1774 |
+
"""
|
1775 |
+
state = AcceleratorState()
|
1776 |
+
if autocast_kwargs is None:
|
1777 |
+
autocast_kwargs = {}
|
1778 |
+
else:
|
1779 |
+
autocast_kwargs = autocast_kwargs.to_kwargs()
|
1780 |
+
if native_amp:
|
1781 |
+
device_type = (
|
1782 |
+
"cuda"
|
1783 |
+
if (state.distributed_type == DistributedType.XLA and is_torch_xla_available(check_is_gpu=True))
|
1784 |
+
else state.device.type
|
1785 |
+
)
|
1786 |
+
if state.mixed_precision == "fp16":
|
1787 |
+
return torch.autocast(device_type=device_type, dtype=torch.float16, **autocast_kwargs)
|
1788 |
+
elif state.mixed_precision in ["bf16", "fp8"] and state.distributed_type in [
|
1789 |
+
DistributedType.NO,
|
1790 |
+
DistributedType.MULTI_CPU,
|
1791 |
+
DistributedType.MULTI_GPU,
|
1792 |
+
DistributedType.MULTI_MLU,
|
1793 |
+
DistributedType.MULTI_NPU,
|
1794 |
+
DistributedType.MULTI_XPU,
|
1795 |
+
DistributedType.FSDP,
|
1796 |
+
DistributedType.XLA,
|
1797 |
+
]:
|
1798 |
+
return torch.autocast(device_type=device_type, dtype=torch.bfloat16, **autocast_kwargs)
|
1799 |
+
else:
|
1800 |
+
return torch.autocast(device_type=device_type, **autocast_kwargs)
|
1801 |
+
else:
|
1802 |
+
return contextlib.nullcontext()
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/offload.py
ADDED
@@ -0,0 +1,213 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
import json
|
16 |
+
import os
|
17 |
+
from collections.abc import Mapping
|
18 |
+
from typing import Dict, List, Optional, Union
|
19 |
+
|
20 |
+
import numpy as np
|
21 |
+
import torch
|
22 |
+
from safetensors import safe_open
|
23 |
+
|
24 |
+
|
25 |
+
def offload_weight(weight, weight_name, offload_folder, index=None):
|
26 |
+
dtype = None
|
27 |
+
# Check the string instead of the dtype to be compatible with versions of PyTorch that don't have bfloat16.
|
28 |
+
if str(weight.dtype) == "torch.bfloat16":
|
29 |
+
# Need to reinterpret the underlined data as int16 since NumPy does not handle bfloat16s.
|
30 |
+
weight = weight.view(torch.int16)
|
31 |
+
dtype = "bfloat16"
|
32 |
+
array = weight.cpu().numpy()
|
33 |
+
tensor_file = os.path.join(offload_folder, f"{weight_name}.dat")
|
34 |
+
if index is not None:
|
35 |
+
if dtype is None:
|
36 |
+
dtype = str(array.dtype)
|
37 |
+
index[weight_name] = {"dtype": dtype, "shape": list(array.shape)}
|
38 |
+
if array.ndim == 0:
|
39 |
+
array = array[None]
|
40 |
+
file_array = np.memmap(tensor_file, dtype=array.dtype, mode="w+", shape=array.shape)
|
41 |
+
file_array[:] = array[:]
|
42 |
+
file_array.flush()
|
43 |
+
return index
|
44 |
+
|
45 |
+
|
46 |
+
def load_offloaded_weight(weight_file, weight_info):
|
47 |
+
shape = tuple(weight_info["shape"])
|
48 |
+
if shape == ():
|
49 |
+
# NumPy memory-mapped arrays can't have 0 dims so it was saved as 1d tensor
|
50 |
+
shape = (1,)
|
51 |
+
|
52 |
+
dtype = weight_info["dtype"]
|
53 |
+
if dtype == "bfloat16":
|
54 |
+
# NumPy does not support bfloat16 so this was saved as a int16
|
55 |
+
dtype = "int16"
|
56 |
+
|
57 |
+
weight = np.memmap(weight_file, dtype=dtype, shape=shape, mode="r")
|
58 |
+
|
59 |
+
if len(weight_info["shape"]) == 0:
|
60 |
+
weight = weight[0]
|
61 |
+
weight = torch.tensor(weight)
|
62 |
+
if weight_info["dtype"] == "bfloat16":
|
63 |
+
weight = weight.view(torch.bfloat16)
|
64 |
+
|
65 |
+
return weight
|
66 |
+
|
67 |
+
|
68 |
+
def save_offload_index(index, offload_folder):
|
69 |
+
if index is None or len(index) == 0:
|
70 |
+
# Nothing to save
|
71 |
+
return
|
72 |
+
|
73 |
+
offload_index_file = os.path.join(offload_folder, "index.json")
|
74 |
+
if os.path.isfile(offload_index_file):
|
75 |
+
with open(offload_index_file, encoding="utf-8") as f:
|
76 |
+
current_index = json.load(f)
|
77 |
+
else:
|
78 |
+
current_index = {}
|
79 |
+
current_index.update(index)
|
80 |
+
|
81 |
+
with open(offload_index_file, "w", encoding="utf-8") as f:
|
82 |
+
json.dump(current_index, f, indent=2)
|
83 |
+
|
84 |
+
|
85 |
+
def offload_state_dict(save_dir: Union[str, os.PathLike], state_dict: Dict[str, torch.Tensor]):
|
86 |
+
"""
|
87 |
+
Offload a state dict in a given folder.
|
88 |
+
|
89 |
+
Args:
|
90 |
+
save_dir (`str` or `os.PathLike`):
|
91 |
+
The directory in which to offload the state dict.
|
92 |
+
state_dict (`Dict[str, torch.Tensor]`):
|
93 |
+
The dictionary of tensors to offload.
|
94 |
+
"""
|
95 |
+
os.makedirs(save_dir, exist_ok=True)
|
96 |
+
index = {}
|
97 |
+
for name, parameter in state_dict.items():
|
98 |
+
index = offload_weight(parameter, name, save_dir, index=index)
|
99 |
+
|
100 |
+
# Update index
|
101 |
+
save_offload_index(index, save_dir)
|
102 |
+
|
103 |
+
|
104 |
+
class PrefixedDataset(Mapping):
|
105 |
+
"""
|
106 |
+
Will access keys in a given dataset by adding a prefix.
|
107 |
+
|
108 |
+
Args:
|
109 |
+
dataset (`Mapping`): Any map with string keys.
|
110 |
+
prefix (`str`): A prefix to add when trying to access any element in the underlying dataset.
|
111 |
+
"""
|
112 |
+
|
113 |
+
def __init__(self, dataset: Mapping, prefix: str):
|
114 |
+
self.dataset = dataset
|
115 |
+
self.prefix = prefix
|
116 |
+
|
117 |
+
def __getitem__(self, key):
|
118 |
+
return self.dataset[f"{self.prefix}{key}"]
|
119 |
+
|
120 |
+
def __iter__(self):
|
121 |
+
return iter([key for key in self.dataset if key.startswith(self.prefix)])
|
122 |
+
|
123 |
+
def __len__(self):
|
124 |
+
return len(self.dataset)
|
125 |
+
|
126 |
+
|
127 |
+
class OffloadedWeightsLoader(Mapping):
|
128 |
+
"""
|
129 |
+
A collection that loads weights stored in a given state dict or memory-mapped on disk.
|
130 |
+
|
131 |
+
Args:
|
132 |
+
state_dict (`Dict[str, torch.Tensor]`, *optional*):
|
133 |
+
A dictionary parameter name to tensor.
|
134 |
+
save_folder (`str` or `os.PathLike`, *optional*):
|
135 |
+
The directory in which the weights are stored (by `offload_state_dict` for instance).
|
136 |
+
index (`Dict`, *optional*):
|
137 |
+
A dictionary from weight name to their information (`dtype`/ `shape` or safetensors filename). Will default
|
138 |
+
to the index saved in `save_folder`.
|
139 |
+
"""
|
140 |
+
|
141 |
+
def __init__(
|
142 |
+
self,
|
143 |
+
state_dict: Dict[str, torch.Tensor] = None,
|
144 |
+
save_folder: Optional[Union[str, os.PathLike]] = None,
|
145 |
+
index: Mapping = None,
|
146 |
+
device=None,
|
147 |
+
):
|
148 |
+
if state_dict is None and save_folder is None and index is None:
|
149 |
+
raise ValueError("Need either a `state_dict`, a `save_folder` or an `index` containing offloaded weights.")
|
150 |
+
|
151 |
+
self.state_dict = {} if state_dict is None else state_dict
|
152 |
+
self.save_folder = save_folder
|
153 |
+
if index is None and save_folder is not None:
|
154 |
+
with open(os.path.join(save_folder, "index.json")) as f:
|
155 |
+
index = json.load(f)
|
156 |
+
self.index = {} if index is None else index
|
157 |
+
self.all_keys = list(self.state_dict.keys())
|
158 |
+
self.all_keys.extend([key for key in self.index if key not in self.all_keys])
|
159 |
+
self.device = device
|
160 |
+
|
161 |
+
def __getitem__(self, key: str):
|
162 |
+
# State dict gets priority
|
163 |
+
if key in self.state_dict:
|
164 |
+
return self.state_dict[key]
|
165 |
+
weight_info = self.index[key]
|
166 |
+
if weight_info.get("safetensors_file") is not None:
|
167 |
+
device = "cpu" if self.device is None else self.device
|
168 |
+
tensor = None
|
169 |
+
try:
|
170 |
+
with safe_open(weight_info["safetensors_file"], framework="pt", device=device) as f:
|
171 |
+
tensor = f.get_tensor(weight_info.get("weight_name", key))
|
172 |
+
except TypeError:
|
173 |
+
# if failed to get_tensor on the device, such as bf16 on mps, try to load it on CPU first
|
174 |
+
with safe_open(weight_info["safetensors_file"], framework="pt", device="cpu") as f:
|
175 |
+
tensor = f.get_tensor(weight_info.get("weight_name", key))
|
176 |
+
|
177 |
+
if "dtype" in weight_info:
|
178 |
+
tensor = tensor.to(getattr(torch, weight_info["dtype"]))
|
179 |
+
|
180 |
+
if tensor.device != torch.device(device):
|
181 |
+
tensor = tensor.to(device)
|
182 |
+
return tensor
|
183 |
+
|
184 |
+
weight_file = os.path.join(self.save_folder, f"{key}.dat")
|
185 |
+
return load_offloaded_weight(weight_file, weight_info)
|
186 |
+
|
187 |
+
def __iter__(self):
|
188 |
+
return iter(self.all_keys)
|
189 |
+
|
190 |
+
def __len__(self):
|
191 |
+
return len(self.all_keys)
|
192 |
+
|
193 |
+
|
194 |
+
def extract_submodules_state_dict(state_dict: Dict[str, torch.Tensor], submodule_names: List[str]):
|
195 |
+
"""
|
196 |
+
Extract the sub state-dict corresponding to a list of given submodules.
|
197 |
+
|
198 |
+
Args:
|
199 |
+
state_dict (`Dict[str, torch.Tensor]`): The state dict to extract from.
|
200 |
+
submodule_names (`List[str]`): The list of submodule names we want to extract.
|
201 |
+
"""
|
202 |
+
result = {}
|
203 |
+
for module_name in submodule_names:
|
204 |
+
# We want to catch module_name parameter (module_name.xxx) or potentially module_name, but not any of the
|
205 |
+
# submodules that could being like module_name (transformers.h.1 and transformers.h.10 for instance)
|
206 |
+
result.update(
|
207 |
+
{
|
208 |
+
key: param
|
209 |
+
for key, param in state_dict.items()
|
210 |
+
if key == module_name or key.startswith(module_name + ".")
|
211 |
+
}
|
212 |
+
)
|
213 |
+
return result
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/operations.py
ADDED
@@ -0,0 +1,848 @@
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
"""
|
15 |
+
A set of basic tensor ops compatible with tpu, gpu, and multigpu
|
16 |
+
"""
|
17 |
+
|
18 |
+
import pickle
|
19 |
+
import warnings
|
20 |
+
from functools import update_wrapper, wraps
|
21 |
+
from typing import Any, Mapping
|
22 |
+
|
23 |
+
import torch
|
24 |
+
|
25 |
+
from ..state import PartialState
|
26 |
+
from .constants import TORCH_DISTRIBUTED_OPERATION_TYPES
|
27 |
+
from .dataclasses import DistributedType, TensorInformation
|
28 |
+
from .imports import (
|
29 |
+
is_npu_available,
|
30 |
+
is_torch_distributed_available,
|
31 |
+
is_torch_version,
|
32 |
+
is_torch_xla_available,
|
33 |
+
is_xpu_available,
|
34 |
+
)
|
35 |
+
|
36 |
+
|
37 |
+
if is_torch_xla_available():
|
38 |
+
import torch_xla.core.xla_model as xm
|
39 |
+
|
40 |
+
if is_torch_distributed_available():
|
41 |
+
from torch.distributed import ReduceOp
|
42 |
+
|
43 |
+
|
44 |
+
def is_torch_tensor(tensor):
|
45 |
+
return isinstance(tensor, torch.Tensor)
|
46 |
+
|
47 |
+
|
48 |
+
def is_torch_xpu_tensor(tensor):
|
49 |
+
return isinstance(
|
50 |
+
tensor,
|
51 |
+
torch.xpu.FloatTensor,
|
52 |
+
torch.xpu.ByteTensor,
|
53 |
+
torch.xpu.IntTensor,
|
54 |
+
torch.xpu.LongTensor,
|
55 |
+
torch.xpu.HalfTensor,
|
56 |
+
torch.xpu.DoubleTensor,
|
57 |
+
torch.xpu.BFloat16Tensor,
|
58 |
+
)
|
59 |
+
|
60 |
+
|
61 |
+
def is_tensor_information(tensor_info):
|
62 |
+
return isinstance(tensor_info, TensorInformation)
|
63 |
+
|
64 |
+
|
65 |
+
def is_namedtuple(data):
|
66 |
+
"""
|
67 |
+
Checks if `data` is a `namedtuple` or not. Can have false positives, but only if a user is trying to mimic a
|
68 |
+
`namedtuple` perfectly.
|
69 |
+
"""
|
70 |
+
return isinstance(data, tuple) and hasattr(data, "_asdict") and hasattr(data, "_fields")
|
71 |
+
|
72 |
+
|
73 |
+
def honor_type(obj, generator):
|
74 |
+
"""
|
75 |
+
Cast a generator to the same type as obj (list, tuple, or namedtuple)
|
76 |
+
"""
|
77 |
+
# Some objects may not be able to instantiate from a generator directly
|
78 |
+
if is_namedtuple(obj):
|
79 |
+
return type(obj)(*list(generator))
|
80 |
+
else:
|
81 |
+
return type(obj)(generator)
|
82 |
+
|
83 |
+
|
84 |
+
def recursively_apply(func, data, *args, test_type=is_torch_tensor, error_on_other_type=False, **kwargs):
|
85 |
+
"""
|
86 |
+
Recursively apply a function on a data structure that is a nested list/tuple/dictionary of a given base type.
|
87 |
+
|
88 |
+
Args:
|
89 |
+
func (`callable`):
|
90 |
+
The function to recursively apply.
|
91 |
+
data (nested list/tuple/dictionary of `main_type`):
|
92 |
+
The data on which to apply `func`
|
93 |
+
*args:
|
94 |
+
Positional arguments that will be passed to `func` when applied on the unpacked data.
|
95 |
+
main_type (`type`, *optional*, defaults to `torch.Tensor`):
|
96 |
+
The base type of the objects to which apply `func`.
|
97 |
+
error_on_other_type (`bool`, *optional*, defaults to `False`):
|
98 |
+
Whether to return an error or not if after unpacking `data`, we get on an object that is not of type
|
99 |
+
`main_type`. If `False`, the function will leave objects of types different than `main_type` unchanged.
|
100 |
+
**kwargs (additional keyword arguments, *optional*):
|
101 |
+
Keyword arguments that will be passed to `func` when applied on the unpacked data.
|
102 |
+
|
103 |
+
Returns:
|
104 |
+
The same data structure as `data` with `func` applied to every object of type `main_type`.
|
105 |
+
"""
|
106 |
+
if isinstance(data, (tuple, list)):
|
107 |
+
return honor_type(
|
108 |
+
data,
|
109 |
+
(
|
110 |
+
recursively_apply(
|
111 |
+
func, o, *args, test_type=test_type, error_on_other_type=error_on_other_type, **kwargs
|
112 |
+
)
|
113 |
+
for o in data
|
114 |
+
),
|
115 |
+
)
|
116 |
+
elif isinstance(data, Mapping):
|
117 |
+
return type(data)(
|
118 |
+
{
|
119 |
+
k: recursively_apply(
|
120 |
+
func, v, *args, test_type=test_type, error_on_other_type=error_on_other_type, **kwargs
|
121 |
+
)
|
122 |
+
for k, v in data.items()
|
123 |
+
}
|
124 |
+
)
|
125 |
+
elif test_type(data):
|
126 |
+
return func(data, *args, **kwargs)
|
127 |
+
elif error_on_other_type:
|
128 |
+
raise TypeError(
|
129 |
+
f"Unsupported types ({type(data)}) passed to `{func.__name__}`. Only nested list/tuple/dicts of "
|
130 |
+
f"objects that are valid for `{test_type.__name__}` should be passed."
|
131 |
+
)
|
132 |
+
return data
|
133 |
+
|
134 |
+
|
135 |
+
def send_to_device(tensor, device, non_blocking=False, skip_keys=None):
|
136 |
+
"""
|
137 |
+
Recursively sends the elements in a nested list/tuple/dictionary of tensors to a given device.
|
138 |
+
|
139 |
+
Args:
|
140 |
+
tensor (nested list/tuple/dictionary of `torch.Tensor`):
|
141 |
+
The data to send to a given device.
|
142 |
+
device (`torch.device`):
|
143 |
+
The device to send the data to.
|
144 |
+
|
145 |
+
Returns:
|
146 |
+
The same data structure as `tensor` with all tensors sent to the proper device.
|
147 |
+
"""
|
148 |
+
if is_torch_tensor(tensor) or hasattr(tensor, "to"):
|
149 |
+
# `torch.Tensor.to("npu")` could not find context when called for the first time (see this [issue](https://gitee.com/ascend/pytorch/issues/I8KECW?from=project-issue)).
|
150 |
+
if device == "npu":
|
151 |
+
device = "npu:0"
|
152 |
+
if device == "xpu":
|
153 |
+
device = "xpu:0"
|
154 |
+
# TODO: torch_mlu LongTensor.to(<int num>) has bugs, we will fix this later.
|
155 |
+
if is_torch_tensor(tensor) and tensor.device.type in ["mlu"] and tensor.dtype in [torch.int64]:
|
156 |
+
tensor = tensor.cpu()
|
157 |
+
try:
|
158 |
+
return tensor.to(device, non_blocking=non_blocking)
|
159 |
+
except TypeError: # .to() doesn't accept non_blocking as kwarg
|
160 |
+
return tensor.to(device)
|
161 |
+
except AssertionError as error:
|
162 |
+
# `torch.Tensor.to(<int num>)` is not supported by `torch_npu` (see this [issue](https://github.com/Ascend/pytorch/issues/16)).
|
163 |
+
# This call is inside the try-block since is_npu_available is not supported by torch.compile.
|
164 |
+
if is_npu_available():
|
165 |
+
if isinstance(device, int):
|
166 |
+
device = f"npu:{device}"
|
167 |
+
elif is_xpu_available():
|
168 |
+
if isinstance(device, int):
|
169 |
+
device = f"xpu:{device}"
|
170 |
+
else:
|
171 |
+
raise error
|
172 |
+
try:
|
173 |
+
return tensor.to(device, non_blocking=non_blocking)
|
174 |
+
except TypeError: # .to() doesn't accept non_blocking as kwarg
|
175 |
+
return tensor.to(device)
|
176 |
+
elif isinstance(tensor, (tuple, list)):
|
177 |
+
return honor_type(
|
178 |
+
tensor, (send_to_device(t, device, non_blocking=non_blocking, skip_keys=skip_keys) for t in tensor)
|
179 |
+
)
|
180 |
+
elif isinstance(tensor, Mapping):
|
181 |
+
if isinstance(skip_keys, str):
|
182 |
+
skip_keys = [skip_keys]
|
183 |
+
elif skip_keys is None:
|
184 |
+
skip_keys = []
|
185 |
+
return type(tensor)(
|
186 |
+
{
|
187 |
+
k: t if k in skip_keys else send_to_device(t, device, non_blocking=non_blocking, skip_keys=skip_keys)
|
188 |
+
for k, t in tensor.items()
|
189 |
+
}
|
190 |
+
)
|
191 |
+
else:
|
192 |
+
return tensor
|
193 |
+
|
194 |
+
|
195 |
+
def get_data_structure(data):
|
196 |
+
"""
|
197 |
+
Recursively gathers the information needed to rebuild a nested list/tuple/dictionary of tensors.
|
198 |
+
|
199 |
+
Args:
|
200 |
+
data (nested list/tuple/dictionary of `torch.Tensor`):
|
201 |
+
The data to send to analyze.
|
202 |
+
|
203 |
+
Returns:
|
204 |
+
The same data structure as `data` with [`~utils.TensorInformation`] instead of tensors.
|
205 |
+
"""
|
206 |
+
|
207 |
+
def _get_data_structure(tensor):
|
208 |
+
return TensorInformation(shape=tensor.shape, dtype=tensor.dtype)
|
209 |
+
|
210 |
+
return recursively_apply(_get_data_structure, data)
|
211 |
+
|
212 |
+
|
213 |
+
def get_shape(data):
|
214 |
+
"""
|
215 |
+
Recursively gathers the shape of a nested list/tuple/dictionary of tensors as a list.
|
216 |
+
|
217 |
+
Args:
|
218 |
+
data (nested list/tuple/dictionary of `torch.Tensor`):
|
219 |
+
The data to send to analyze.
|
220 |
+
|
221 |
+
Returns:
|
222 |
+
The same data structure as `data` with lists of tensor shapes instead of tensors.
|
223 |
+
"""
|
224 |
+
|
225 |
+
def _get_shape(tensor):
|
226 |
+
return list(tensor.shape)
|
227 |
+
|
228 |
+
return recursively_apply(_get_shape, data)
|
229 |
+
|
230 |
+
|
231 |
+
def initialize_tensors(data_structure):
|
232 |
+
"""
|
233 |
+
Recursively initializes tensors from a nested list/tuple/dictionary of [`~utils.TensorInformation`].
|
234 |
+
|
235 |
+
Returns:
|
236 |
+
The same data structure as `data` with tensors instead of [`~utils.TensorInformation`].
|
237 |
+
"""
|
238 |
+
|
239 |
+
def _initialize_tensor(tensor_info):
|
240 |
+
return torch.empty(*tensor_info.shape, dtype=tensor_info.dtype)
|
241 |
+
|
242 |
+
return recursively_apply(_initialize_tensor, data_structure, test_type=is_tensor_information)
|
243 |
+
|
244 |
+
|
245 |
+
def find_batch_size(data):
|
246 |
+
"""
|
247 |
+
Recursively finds the batch size in a nested list/tuple/dictionary of lists of tensors.
|
248 |
+
|
249 |
+
Args:
|
250 |
+
data (nested list/tuple/dictionary of `torch.Tensor`): The data from which to find the batch size.
|
251 |
+
|
252 |
+
Returns:
|
253 |
+
`int`: The batch size.
|
254 |
+
"""
|
255 |
+
if isinstance(data, (tuple, list, Mapping)) and (len(data) == 0):
|
256 |
+
raise ValueError(f"Cannot find the batch size from empty {type(data)}.")
|
257 |
+
|
258 |
+
if isinstance(data, (tuple, list)):
|
259 |
+
return find_batch_size(data[0])
|
260 |
+
elif isinstance(data, Mapping):
|
261 |
+
for k in data.keys():
|
262 |
+
return find_batch_size(data[k])
|
263 |
+
elif not isinstance(data, torch.Tensor):
|
264 |
+
raise TypeError(f"Can only find the batch size of tensors but got {type(data)}.")
|
265 |
+
return data.shape[0]
|
266 |
+
|
267 |
+
|
268 |
+
def ignorant_find_batch_size(data):
|
269 |
+
"""
|
270 |
+
Same as [`utils.operations.find_batch_size`] except will ignore if `ValueError` and `TypeErrors` are raised
|
271 |
+
|
272 |
+
Args:
|
273 |
+
data (nested list/tuple/dictionary of `torch.Tensor`): The data from which to find the batch size.
|
274 |
+
|
275 |
+
Returns:
|
276 |
+
`int`: The batch size.
|
277 |
+
"""
|
278 |
+
try:
|
279 |
+
return find_batch_size(data)
|
280 |
+
except (ValueError, TypeError):
|
281 |
+
pass
|
282 |
+
return None
|
283 |
+
|
284 |
+
|
285 |
+
def listify(data):
|
286 |
+
"""
|
287 |
+
Recursively finds tensors in a nested list/tuple/dictionary and converts them to a list of numbers.
|
288 |
+
|
289 |
+
Args:
|
290 |
+
data (nested list/tuple/dictionary of `torch.Tensor`): The data from which to convert to regular numbers.
|
291 |
+
|
292 |
+
Returns:
|
293 |
+
The same data structure as `data` with lists of numbers instead of `torch.Tensor`.
|
294 |
+
"""
|
295 |
+
|
296 |
+
def _convert_to_list(tensor):
|
297 |
+
tensor = tensor.detach().cpu()
|
298 |
+
if tensor.dtype == torch.bfloat16:
|
299 |
+
# As of Numpy 1.21.4, NumPy does not support bfloat16 (see
|
300 |
+
# https://github.com/numpy/numpy/blob/a47ecdea856986cd60eabbd53265c2ca5916ad5d/doc/source/user/basics.types.rst ).
|
301 |
+
# Until Numpy adds bfloat16, we must convert float32.
|
302 |
+
tensor = tensor.to(torch.float32)
|
303 |
+
return tensor.tolist()
|
304 |
+
|
305 |
+
return recursively_apply(_convert_to_list, data)
|
306 |
+
|
307 |
+
|
308 |
+
def _tpu_gather(tensor):
|
309 |
+
def _tpu_gather_one(tensor):
|
310 |
+
if tensor.ndim == 0:
|
311 |
+
tensor = tensor.clone()[None]
|
312 |
+
|
313 |
+
# Can only gather contiguous tensors
|
314 |
+
if not tensor.is_contiguous():
|
315 |
+
tensor = tensor.contiguous()
|
316 |
+
return xm.all_gather(tensor)
|
317 |
+
|
318 |
+
res = recursively_apply(_tpu_gather_one, tensor, error_on_other_type=True)
|
319 |
+
xm.mark_step()
|
320 |
+
return res
|
321 |
+
|
322 |
+
|
323 |
+
def _gpu_gather(tensor):
|
324 |
+
state = PartialState()
|
325 |
+
if is_torch_version(">=", "1.13"):
|
326 |
+
gather_op = torch.distributed.all_gather_into_tensor
|
327 |
+
else:
|
328 |
+
gather_op = torch.distributed._all_gather_base
|
329 |
+
|
330 |
+
def _gpu_gather_one(tensor):
|
331 |
+
if tensor.ndim == 0:
|
332 |
+
tensor = tensor.clone()[None]
|
333 |
+
|
334 |
+
# Can only gather contiguous tensors
|
335 |
+
if not tensor.is_contiguous():
|
336 |
+
tensor = tensor.contiguous()
|
337 |
+
|
338 |
+
if state.backend is not None and state.backend != "gloo":
|
339 |
+
# We use `empty` as `all_gather_into_tensor` slightly
|
340 |
+
# differs from `all_gather` for better efficiency,
|
341 |
+
# and we rely on the number of items in the tensor
|
342 |
+
# rather than its direct shape
|
343 |
+
output_tensors = torch.empty(
|
344 |
+
state.num_processes * tensor.numel(),
|
345 |
+
dtype=tensor.dtype,
|
346 |
+
device=state.device,
|
347 |
+
)
|
348 |
+
gather_op(output_tensors, tensor)
|
349 |
+
return output_tensors.view(-1, *tensor.size()[1:])
|
350 |
+
else:
|
351 |
+
# a backend of `None` is always CPU
|
352 |
+
# also gloo does not support `all_gather_into_tensor`,
|
353 |
+
# which will result in a larger memory overhead for the op
|
354 |
+
output_tensors = [torch.empty_like(tensor) for _ in range(state.num_processes)]
|
355 |
+
torch.distributed.all_gather(output_tensors, tensor)
|
356 |
+
return torch.cat(output_tensors, dim=0)
|
357 |
+
|
358 |
+
return recursively_apply(_gpu_gather_one, tensor, error_on_other_type=True)
|
359 |
+
|
360 |
+
|
361 |
+
class DistributedOperationException(Exception):
|
362 |
+
"""
|
363 |
+
An exception class for distributed operations. Raised if the operation cannot be performed due to the shape of the
|
364 |
+
tensors.
|
365 |
+
"""
|
366 |
+
|
367 |
+
pass
|
368 |
+
|
369 |
+
|
370 |
+
def verify_operation(function):
|
371 |
+
"""
|
372 |
+
Verifies that `tensor` is the same shape across all processes. Only ran if `PartialState().debug` is `True`.
|
373 |
+
"""
|
374 |
+
|
375 |
+
@wraps(function)
|
376 |
+
def wrapper(*args, **kwargs):
|
377 |
+
if PartialState().distributed_type == DistributedType.NO or not PartialState().debug:
|
378 |
+
return function(*args, **kwargs)
|
379 |
+
operation = f"{function.__module__}.{function.__name__}"
|
380 |
+
if "tensor" in kwargs:
|
381 |
+
tensor = kwargs["tensor"]
|
382 |
+
else:
|
383 |
+
tensor = args[0]
|
384 |
+
if PartialState().device.type != find_device(tensor).type:
|
385 |
+
raise DistributedOperationException(
|
386 |
+
f"One or more of the tensors passed to {operation} were not on the {tensor.device.type} while the `Accelerator` is configured for {PartialState().device.type}. "
|
387 |
+
f"Please move it to the {PartialState().device.type} before calling {operation}."
|
388 |
+
)
|
389 |
+
shapes = get_shape(tensor)
|
390 |
+
output = gather_object([shapes])
|
391 |
+
if output[0] is not None:
|
392 |
+
are_same = output.count(output[0]) == len(output)
|
393 |
+
if not are_same:
|
394 |
+
process_shape_str = "\n - ".join([f"Process {i}: {shape}" for i, shape in enumerate(output)])
|
395 |
+
raise DistributedOperationException(
|
396 |
+
f"Cannot apply desired operation due to shape mismatches. "
|
397 |
+
"All shapes across devices must be valid."
|
398 |
+
f"\n\nOperation: `{operation}`\nInput shapes:\n - {process_shape_str}"
|
399 |
+
)
|
400 |
+
return function(*args, **kwargs)
|
401 |
+
|
402 |
+
return wrapper
|
403 |
+
|
404 |
+
|
405 |
+
def chained_operation(function):
|
406 |
+
"""
|
407 |
+
Checks that `verify_operation` failed and if so reports a more helpful error chaining the existing
|
408 |
+
`DistributedOperationException`.
|
409 |
+
"""
|
410 |
+
|
411 |
+
@wraps(function)
|
412 |
+
def wrapper(*args, **kwargs):
|
413 |
+
try:
|
414 |
+
return function(*args, **kwargs)
|
415 |
+
except DistributedOperationException as e:
|
416 |
+
operation = f"{function.__module__}.{function.__name__}"
|
417 |
+
raise DistributedOperationException(
|
418 |
+
f"Error found while calling `{operation}`. Please see the earlier error for more details."
|
419 |
+
) from e
|
420 |
+
|
421 |
+
return wrapper
|
422 |
+
|
423 |
+
|
424 |
+
@verify_operation
|
425 |
+
def gather(tensor):
|
426 |
+
"""
|
427 |
+
Recursively gather tensor in a nested list/tuple/dictionary of tensors from all devices.
|
428 |
+
|
429 |
+
Args:
|
430 |
+
tensor (nested list/tuple/dictionary of `torch.Tensor`):
|
431 |
+
The data to gather.
|
432 |
+
|
433 |
+
Returns:
|
434 |
+
The same data structure as `tensor` with all tensors sent to the proper device.
|
435 |
+
"""
|
436 |
+
if PartialState().distributed_type == DistributedType.XLA:
|
437 |
+
return _tpu_gather(tensor)
|
438 |
+
elif PartialState().distributed_type in TORCH_DISTRIBUTED_OPERATION_TYPES:
|
439 |
+
return _gpu_gather(tensor)
|
440 |
+
else:
|
441 |
+
return tensor
|
442 |
+
|
443 |
+
|
444 |
+
def _gpu_gather_object(object: Any):
|
445 |
+
output_objects = [None for _ in range(PartialState().num_processes)]
|
446 |
+
torch.distributed.all_gather_object(output_objects, object)
|
447 |
+
# all_gather_object returns a list of lists, so we need to flatten it
|
448 |
+
return [x for y in output_objects for x in y]
|
449 |
+
|
450 |
+
|
451 |
+
def gather_object(object: Any):
|
452 |
+
"""
|
453 |
+
Recursively gather object in a nested list/tuple/dictionary of objects from all devices.
|
454 |
+
|
455 |
+
Args:
|
456 |
+
object (nested list/tuple/dictionary of picklable object):
|
457 |
+
The data to gather.
|
458 |
+
|
459 |
+
Returns:
|
460 |
+
The same data structure as `object` with all the objects sent to every device.
|
461 |
+
"""
|
462 |
+
if PartialState().distributed_type == DistributedType.XLA:
|
463 |
+
raise NotImplementedError("gather objects in TPU is not supported")
|
464 |
+
elif PartialState().distributed_type in TORCH_DISTRIBUTED_OPERATION_TYPES:
|
465 |
+
return _gpu_gather_object(object)
|
466 |
+
else:
|
467 |
+
return object
|
468 |
+
|
469 |
+
|
470 |
+
def _gpu_broadcast(data, src=0):
|
471 |
+
def _gpu_broadcast_one(tensor, src=0):
|
472 |
+
torch.distributed.broadcast(tensor, src=src)
|
473 |
+
return tensor
|
474 |
+
|
475 |
+
return recursively_apply(_gpu_broadcast_one, data, error_on_other_type=True, src=src)
|
476 |
+
|
477 |
+
|
478 |
+
def _tpu_broadcast(tensor, src=0, name="broadcast tensor"):
|
479 |
+
if isinstance(tensor, (list, tuple)):
|
480 |
+
return honor_type(tensor, (_tpu_broadcast(t, name=f"{name}_{i}") for i, t in enumerate(tensor)))
|
481 |
+
elif isinstance(tensor, Mapping):
|
482 |
+
return type(tensor)({k: _tpu_broadcast(v, name=f"{name}_{k}") for k, v in tensor.items()})
|
483 |
+
return xm.mesh_reduce(name, tensor, lambda x: x[src])
|
484 |
+
|
485 |
+
|
486 |
+
TENSOR_TYPE_TO_INT = {
|
487 |
+
torch.float: 1,
|
488 |
+
torch.double: 2,
|
489 |
+
torch.half: 3,
|
490 |
+
torch.bfloat16: 4,
|
491 |
+
torch.uint8: 5,
|
492 |
+
torch.int8: 6,
|
493 |
+
torch.int16: 7,
|
494 |
+
torch.int32: 8,
|
495 |
+
torch.int64: 9,
|
496 |
+
torch.bool: 10,
|
497 |
+
}
|
498 |
+
|
499 |
+
TENSOR_INT_TO_DTYPE = {v: k for k, v in TENSOR_TYPE_TO_INT.items()}
|
500 |
+
|
501 |
+
|
502 |
+
def gather_tensor_shape(tensor):
|
503 |
+
"""
|
504 |
+
Grabs the shape of `tensor` only available on one process and returns a tensor of its shape
|
505 |
+
"""
|
506 |
+
# Allocate 80 bytes to store the shape
|
507 |
+
max_tensor_dimension = 2**20
|
508 |
+
state = PartialState()
|
509 |
+
base_tensor = torch.empty(max_tensor_dimension, dtype=torch.int, device=state.device)
|
510 |
+
|
511 |
+
# Since PyTorch can't just send a tensor to another GPU without
|
512 |
+
# knowing its size, we store the size of the tensor with data
|
513 |
+
# in an allocation
|
514 |
+
if tensor is not None:
|
515 |
+
shape = tensor.shape
|
516 |
+
tensor_dtype = TENSOR_TYPE_TO_INT[tensor.dtype]
|
517 |
+
base_tensor[: len(shape) + 1] = torch.tensor(list(shape) + [tensor_dtype], dtype=int)
|
518 |
+
# Perform a reduction to copy the size data onto all GPUs
|
519 |
+
base_tensor = reduce(base_tensor, reduction="sum")
|
520 |
+
base_tensor = base_tensor[base_tensor.nonzero()]
|
521 |
+
# The last non-zero data contains the coded dtype the source tensor is
|
522 |
+
dtype = int(base_tensor[-1:][0])
|
523 |
+
base_tensor = base_tensor[:-1]
|
524 |
+
return base_tensor, dtype
|
525 |
+
|
526 |
+
|
527 |
+
def copy_tensor_to_devices(tensor=None) -> torch.Tensor:
|
528 |
+
"""
|
529 |
+
Copys a tensor that only exists on a single device and broadcasts it to other devices. Differs from `broadcast` as
|
530 |
+
each worker doesn't need to know its shape when used (and tensor can be `None`)
|
531 |
+
|
532 |
+
Args:
|
533 |
+
tensor (`torch.tensor`):
|
534 |
+
The tensor that should be sent to all devices. Must only have it be defined on a single device, the rest
|
535 |
+
should be `None`.
|
536 |
+
"""
|
537 |
+
state = PartialState()
|
538 |
+
shape, dtype = gather_tensor_shape(tensor)
|
539 |
+
if tensor is None:
|
540 |
+
tensor = torch.zeros(shape, dtype=TENSOR_INT_TO_DTYPE[dtype]).to(state.device)
|
541 |
+
return reduce(tensor, reduction="sum")
|
542 |
+
|
543 |
+
|
544 |
+
@verify_operation
|
545 |
+
def broadcast(tensor, from_process: int = 0):
|
546 |
+
"""
|
547 |
+
Recursively broadcast tensor in a nested list/tuple/dictionary of tensors to all devices.
|
548 |
+
|
549 |
+
Args:
|
550 |
+
tensor (nested list/tuple/dictionary of `torch.Tensor`):
|
551 |
+
The data to gather.
|
552 |
+
from_process (`int`, *optional*, defaults to 0):
|
553 |
+
The process from which to send the data
|
554 |
+
|
555 |
+
Returns:
|
556 |
+
The same data structure as `tensor` with all tensors broadcasted to the proper device.
|
557 |
+
"""
|
558 |
+
if PartialState().distributed_type == DistributedType.XLA:
|
559 |
+
return _tpu_broadcast(tensor, src=from_process, name="accelerate.utils.broadcast")
|
560 |
+
elif PartialState().distributed_type in TORCH_DISTRIBUTED_OPERATION_TYPES:
|
561 |
+
return _gpu_broadcast(tensor, src=from_process)
|
562 |
+
else:
|
563 |
+
return tensor
|
564 |
+
|
565 |
+
|
566 |
+
def broadcast_object_list(object_list, from_process: int = 0):
|
567 |
+
"""
|
568 |
+
Broadcast a list of picklable objects form one process to the others.
|
569 |
+
|
570 |
+
Args:
|
571 |
+
object_list (list of picklable objects):
|
572 |
+
The list of objects to broadcast. This list will be modified inplace.
|
573 |
+
from_process (`int`, *optional*, defaults to 0):
|
574 |
+
The process from which to send the data.
|
575 |
+
|
576 |
+
Returns:
|
577 |
+
The same list containing the objects from process 0.
|
578 |
+
"""
|
579 |
+
if PartialState().distributed_type == DistributedType.XLA:
|
580 |
+
for i, obj in enumerate(object_list):
|
581 |
+
object_list[i] = xm.mesh_reduce("accelerate.utils.broadcast_object_list", obj, lambda x: x[from_process])
|
582 |
+
elif PartialState().distributed_type in TORCH_DISTRIBUTED_OPERATION_TYPES:
|
583 |
+
torch.distributed.broadcast_object_list(object_list, src=from_process)
|
584 |
+
return object_list
|
585 |
+
|
586 |
+
|
587 |
+
def slice_tensors(data, tensor_slice, process_index=None, num_processes=None):
|
588 |
+
"""
|
589 |
+
Recursively takes a slice in a nested list/tuple/dictionary of tensors.
|
590 |
+
|
591 |
+
Args:
|
592 |
+
data (nested list/tuple/dictionary of `torch.Tensor`):
|
593 |
+
The data to slice.
|
594 |
+
tensor_slice (`slice`):
|
595 |
+
The slice to take.
|
596 |
+
|
597 |
+
Returns:
|
598 |
+
The same data structure as `data` with all the tensors slices.
|
599 |
+
"""
|
600 |
+
|
601 |
+
def _slice_tensor(tensor, tensor_slice):
|
602 |
+
return tensor[tensor_slice]
|
603 |
+
|
604 |
+
return recursively_apply(_slice_tensor, data, tensor_slice)
|
605 |
+
|
606 |
+
|
607 |
+
def concatenate(data, dim=0):
|
608 |
+
"""
|
609 |
+
Recursively concatenate the tensors in a nested list/tuple/dictionary of lists of tensors with the same shape.
|
610 |
+
|
611 |
+
Args:
|
612 |
+
data (nested list/tuple/dictionary of lists of tensors `torch.Tensor`):
|
613 |
+
The data to concatenate.
|
614 |
+
dim (`int`, *optional*, defaults to 0):
|
615 |
+
The dimension on which to concatenate.
|
616 |
+
|
617 |
+
Returns:
|
618 |
+
The same data structure as `data` with all the tensors concatenated.
|
619 |
+
"""
|
620 |
+
if isinstance(data[0], (tuple, list)):
|
621 |
+
return honor_type(data[0], (concatenate([d[i] for d in data], dim=dim) for i in range(len(data[0]))))
|
622 |
+
elif isinstance(data[0], Mapping):
|
623 |
+
return type(data[0])({k: concatenate([d[k] for d in data], dim=dim) for k in data[0].keys()})
|
624 |
+
elif not isinstance(data[0], torch.Tensor):
|
625 |
+
raise TypeError(f"Can only concatenate tensors but got {type(data[0])}")
|
626 |
+
return torch.cat(data, dim=dim)
|
627 |
+
|
628 |
+
|
629 |
+
class CannotPadNestedTensorWarning(UserWarning):
|
630 |
+
pass
|
631 |
+
|
632 |
+
|
633 |
+
@chained_operation
|
634 |
+
def pad_across_processes(tensor, dim=0, pad_index=0, pad_first=False):
|
635 |
+
"""
|
636 |
+
Recursively pad the tensors in a nested list/tuple/dictionary of tensors from all devices to the same size so they
|
637 |
+
can safely be gathered.
|
638 |
+
|
639 |
+
Args:
|
640 |
+
tensor (nested list/tuple/dictionary of `torch.Tensor`):
|
641 |
+
The data to gather.
|
642 |
+
dim (`int`, *optional*, defaults to 0):
|
643 |
+
The dimension on which to pad.
|
644 |
+
pad_index (`int`, *optional*, defaults to 0):
|
645 |
+
The value with which to pad.
|
646 |
+
pad_first (`bool`, *optional*, defaults to `False`):
|
647 |
+
Whether to pad at the beginning or the end.
|
648 |
+
"""
|
649 |
+
|
650 |
+
def _pad_across_processes(tensor, dim=0, pad_index=0, pad_first=False):
|
651 |
+
if getattr(tensor, "is_nested", False):
|
652 |
+
warnings.warn(
|
653 |
+
"Cannot pad nested tensors without more information. Leaving unprocessed.",
|
654 |
+
CannotPadNestedTensorWarning,
|
655 |
+
)
|
656 |
+
return tensor
|
657 |
+
if dim >= len(tensor.shape):
|
658 |
+
return tensor
|
659 |
+
|
660 |
+
# Gather all sizes
|
661 |
+
size = torch.tensor(tensor.shape, device=tensor.device)[None]
|
662 |
+
sizes = gather(size).cpu()
|
663 |
+
# Then pad to the maximum size
|
664 |
+
max_size = max(s[dim] for s in sizes)
|
665 |
+
if max_size == tensor.shape[dim]:
|
666 |
+
return tensor
|
667 |
+
|
668 |
+
old_size = tensor.shape
|
669 |
+
new_size = list(old_size)
|
670 |
+
new_size[dim] = max_size
|
671 |
+
new_tensor = tensor.new_zeros(tuple(new_size)) + pad_index
|
672 |
+
if pad_first:
|
673 |
+
indices = tuple(
|
674 |
+
slice(max_size - old_size[dim], max_size) if i == dim else slice(None) for i in range(len(new_size))
|
675 |
+
)
|
676 |
+
else:
|
677 |
+
indices = tuple(slice(0, old_size[dim]) if i == dim else slice(None) for i in range(len(new_size)))
|
678 |
+
new_tensor[indices] = tensor
|
679 |
+
return new_tensor
|
680 |
+
|
681 |
+
return recursively_apply(
|
682 |
+
_pad_across_processes, tensor, error_on_other_type=True, dim=dim, pad_index=pad_index, pad_first=pad_first
|
683 |
+
)
|
684 |
+
|
685 |
+
|
686 |
+
def pad_input_tensors(tensor, batch_size, num_processes, dim=0):
|
687 |
+
"""
|
688 |
+
Takes a `tensor` of arbitrary size and pads it so that it can work given `num_processes` needed dimensions.
|
689 |
+
|
690 |
+
New tensors are just the last input repeated.
|
691 |
+
|
692 |
+
E.g.:
|
693 |
+
Tensor: ([3,4,4]) Num processes: 4 Expected result shape: ([4,4,4])
|
694 |
+
|
695 |
+
"""
|
696 |
+
|
697 |
+
def _pad_input_tensors(tensor, batch_size, num_processes, dim=0):
|
698 |
+
remainder = batch_size // num_processes
|
699 |
+
last_inputs = batch_size - (remainder * num_processes)
|
700 |
+
if batch_size // num_processes == 0:
|
701 |
+
to_pad = num_processes - batch_size
|
702 |
+
else:
|
703 |
+
to_pad = num_processes - (batch_size // num_processes)
|
704 |
+
# In the rare case that `to_pad` is negative,
|
705 |
+
# we need to pad the last inputs - the found `to_pad`
|
706 |
+
if last_inputs > to_pad & to_pad < 1:
|
707 |
+
to_pad = last_inputs - to_pad
|
708 |
+
old_size = tensor.shape
|
709 |
+
new_size = list(old_size)
|
710 |
+
new_size[0] = batch_size + to_pad
|
711 |
+
new_tensor = tensor.new_zeros(tuple(new_size))
|
712 |
+
indices = tuple(slice(0, old_size[dim]) if i == dim else slice(None) for i in range(len(new_size)))
|
713 |
+
new_tensor[indices] = tensor
|
714 |
+
return new_tensor
|
715 |
+
|
716 |
+
return recursively_apply(
|
717 |
+
_pad_input_tensors,
|
718 |
+
tensor,
|
719 |
+
error_on_other_type=True,
|
720 |
+
batch_size=batch_size,
|
721 |
+
num_processes=num_processes,
|
722 |
+
dim=dim,
|
723 |
+
)
|
724 |
+
|
725 |
+
|
726 |
+
@verify_operation
|
727 |
+
def reduce(tensor, reduction="mean", scale=1.0):
|
728 |
+
"""
|
729 |
+
Recursively reduce the tensors in a nested list/tuple/dictionary of lists of tensors across all processes by the
|
730 |
+
mean of a given operation.
|
731 |
+
|
732 |
+
Args:
|
733 |
+
tensor (nested list/tuple/dictionary of `torch.Tensor`):
|
734 |
+
The data to reduce.
|
735 |
+
reduction (`str`, *optional*, defaults to `"mean"`):
|
736 |
+
A reduction method. Can be of "mean", "sum", or "none"
|
737 |
+
scale (`float`, *optional*):
|
738 |
+
A default scaling value to be applied after the reduce, only valied on XLA.
|
739 |
+
|
740 |
+
Returns:
|
741 |
+
The same data structure as `data` with all the tensors reduced.
|
742 |
+
"""
|
743 |
+
|
744 |
+
def _reduce_across_processes(tensor, reduction="mean", scale=1.0):
|
745 |
+
state = PartialState()
|
746 |
+
cloned_tensor = tensor.clone()
|
747 |
+
if state.distributed_type == DistributedType.NO:
|
748 |
+
return cloned_tensor
|
749 |
+
if state.distributed_type == DistributedType.XLA:
|
750 |
+
# Some processes may have different HLO graphs than other
|
751 |
+
# processes, for example in the breakpoint API
|
752 |
+
# accelerator.set_trigger(). Use mark_step to make HLOs
|
753 |
+
# the same on all processes.
|
754 |
+
xm.mark_step()
|
755 |
+
xm.all_reduce(xm.REDUCE_SUM, [cloned_tensor], scale)
|
756 |
+
xm.mark_step()
|
757 |
+
elif state.distributed_type.value in TORCH_DISTRIBUTED_OPERATION_TYPES:
|
758 |
+
torch.distributed.all_reduce(cloned_tensor, ReduceOp.SUM)
|
759 |
+
if reduction == "mean":
|
760 |
+
cloned_tensor /= state.num_processes
|
761 |
+
return cloned_tensor
|
762 |
+
|
763 |
+
return recursively_apply(
|
764 |
+
_reduce_across_processes, tensor, error_on_other_type=True, reduction=reduction, scale=scale
|
765 |
+
)
|
766 |
+
|
767 |
+
|
768 |
+
def convert_to_fp32(tensor):
|
769 |
+
"""
|
770 |
+
Recursively converts the elements nested list/tuple/dictionary of tensors in FP16/BF16 precision to FP32.
|
771 |
+
|
772 |
+
Args:
|
773 |
+
tensor (nested list/tuple/dictionary of `torch.Tensor`):
|
774 |
+
The data to convert from FP16/BF16 to FP32.
|
775 |
+
|
776 |
+
Returns:
|
777 |
+
The same data structure as `tensor` with all tensors that were in FP16/BF16 precision converted to FP32.
|
778 |
+
"""
|
779 |
+
|
780 |
+
def _convert_to_fp32(tensor):
|
781 |
+
return tensor.float()
|
782 |
+
|
783 |
+
def _is_fp16_bf16_tensor(tensor):
|
784 |
+
return (is_torch_tensor(tensor) or hasattr(tensor, "dtype")) and tensor.dtype in (
|
785 |
+
torch.float16,
|
786 |
+
torch.bfloat16,
|
787 |
+
)
|
788 |
+
|
789 |
+
return recursively_apply(_convert_to_fp32, tensor, test_type=_is_fp16_bf16_tensor)
|
790 |
+
|
791 |
+
|
792 |
+
class ConvertOutputsToFp32:
|
793 |
+
"""
|
794 |
+
Decorator to apply to a function outputing tensors (like a model forward pass) that ensures the outputs in FP16
|
795 |
+
precision will be convert back to FP32.
|
796 |
+
|
797 |
+
Args:
|
798 |
+
model_forward (`Callable`):
|
799 |
+
The function which outputs we want to treat.
|
800 |
+
|
801 |
+
Returns:
|
802 |
+
The same function as `model_forward` but with converted outputs.
|
803 |
+
"""
|
804 |
+
|
805 |
+
def __init__(self, model_forward):
|
806 |
+
self.model_forward = model_forward
|
807 |
+
update_wrapper(self, model_forward)
|
808 |
+
|
809 |
+
def __call__(self, *args, **kwargs):
|
810 |
+
return convert_to_fp32(self.model_forward(*args, **kwargs))
|
811 |
+
|
812 |
+
def __getstate__(self):
|
813 |
+
raise pickle.PicklingError(
|
814 |
+
"Cannot pickle a prepared model with automatic mixed precision, please unwrap the model with `Accelerator.unwrap_model(model)` before pickling it."
|
815 |
+
)
|
816 |
+
|
817 |
+
|
818 |
+
def convert_outputs_to_fp32(model_forward):
|
819 |
+
model_forward = ConvertOutputsToFp32(model_forward)
|
820 |
+
|
821 |
+
def forward(*args, **kwargs):
|
822 |
+
return model_forward(*args, **kwargs)
|
823 |
+
|
824 |
+
# To act like a decorator so that it can be popped when doing `extract_model_from_parallel`
|
825 |
+
forward.__wrapped__ = model_forward
|
826 |
+
|
827 |
+
return forward
|
828 |
+
|
829 |
+
|
830 |
+
def find_device(data):
|
831 |
+
"""
|
832 |
+
Finds the device on which a nested dict/list/tuple of tensors lies (assuming they are all on the same device).
|
833 |
+
|
834 |
+
Args:
|
835 |
+
(nested list/tuple/dictionary of `torch.Tensor`): The data we want to know the device of.
|
836 |
+
"""
|
837 |
+
if isinstance(data, Mapping):
|
838 |
+
for obj in data.values():
|
839 |
+
device = find_device(obj)
|
840 |
+
if device is not None:
|
841 |
+
return device
|
842 |
+
elif isinstance(data, (tuple, list)):
|
843 |
+
for obj in data:
|
844 |
+
device = find_device(obj)
|
845 |
+
if device is not None:
|
846 |
+
return device
|
847 |
+
elif isinstance(data, torch.Tensor):
|
848 |
+
return data.device
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/random.py
ADDED
@@ -0,0 +1,124 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
import random
|
16 |
+
from typing import List, Optional, Union
|
17 |
+
|
18 |
+
import numpy as np
|
19 |
+
import torch
|
20 |
+
|
21 |
+
from ..state import AcceleratorState
|
22 |
+
from .constants import CUDA_DISTRIBUTED_TYPES
|
23 |
+
from .dataclasses import DistributedType, RNGType
|
24 |
+
from .imports import is_mlu_available, is_npu_available, is_torch_xla_available, is_xpu_available
|
25 |
+
|
26 |
+
|
27 |
+
if is_torch_xla_available():
|
28 |
+
import torch_xla.core.xla_model as xm
|
29 |
+
|
30 |
+
|
31 |
+
def set_seed(seed: int, device_specific: bool = False, deterministic: bool = False):
|
32 |
+
"""
|
33 |
+
Helper function for reproducible behavior to set the seed in `random`, `numpy`, `torch`.
|
34 |
+
|
35 |
+
Args:
|
36 |
+
seed (`int`):
|
37 |
+
The seed to set.
|
38 |
+
device_specific (`bool`, *optional*, defaults to `False`):
|
39 |
+
Whether to differ the seed on each device slightly with `self.process_index`.
|
40 |
+
deterministic (`bool`, *optional*, defaults to `False`):
|
41 |
+
Whether to use deterministic algorithms where available. Can slow down training.
|
42 |
+
"""
|
43 |
+
if device_specific:
|
44 |
+
seed += AcceleratorState().process_index
|
45 |
+
random.seed(seed)
|
46 |
+
np.random.seed(seed)
|
47 |
+
torch.manual_seed(seed)
|
48 |
+
if is_xpu_available():
|
49 |
+
torch.xpu.manual_seed_all(seed)
|
50 |
+
elif is_npu_available():
|
51 |
+
torch.npu.manual_seed_all(seed)
|
52 |
+
elif is_mlu_available():
|
53 |
+
torch.mlu.manual_seed_all(seed)
|
54 |
+
else:
|
55 |
+
torch.cuda.manual_seed_all(seed)
|
56 |
+
# ^^ safe to call this function even if cuda is not available
|
57 |
+
if is_torch_xla_available():
|
58 |
+
xm.set_rng_state(seed)
|
59 |
+
|
60 |
+
if deterministic:
|
61 |
+
torch.use_deterministic_algorithms(True)
|
62 |
+
|
63 |
+
|
64 |
+
def synchronize_rng_state(rng_type: Optional[RNGType] = None, generator: Optional[torch.Generator] = None):
|
65 |
+
# Get the proper rng state
|
66 |
+
if rng_type == RNGType.TORCH:
|
67 |
+
rng_state = torch.get_rng_state()
|
68 |
+
elif rng_type == RNGType.CUDA:
|
69 |
+
rng_state = torch.cuda.get_rng_state()
|
70 |
+
elif rng_type == RNGType.XLA:
|
71 |
+
assert is_torch_xla_available(), "Can't synchronize XLA seeds as torch_xla is unavailable."
|
72 |
+
rng_state = torch.tensor(xm.get_rng_state())
|
73 |
+
elif rng_type == RNGType.NPU:
|
74 |
+
assert is_npu_available(), "Can't synchronize NPU seeds on an environment without NPUs."
|
75 |
+
rng_state = torch.npu.get_rng_state()
|
76 |
+
elif rng_type == RNGType.MLU:
|
77 |
+
assert is_mlu_available(), "Can't synchronize MLU seeds on an environment without MLUs."
|
78 |
+
rng_state = torch.mlu.get_rng_state()
|
79 |
+
elif rng_type == RNGType.XPU:
|
80 |
+
assert is_xpu_available(), "Can't synchronize XPU seeds on an environment without XPUs."
|
81 |
+
rng_state = torch.xpu.get_rng_state()
|
82 |
+
elif rng_type == RNGType.GENERATOR:
|
83 |
+
assert generator is not None, "Need a generator to synchronize its seed."
|
84 |
+
rng_state = generator.get_state()
|
85 |
+
|
86 |
+
# Broadcast the rng state from device 0 to other devices
|
87 |
+
state = AcceleratorState()
|
88 |
+
if state.distributed_type == DistributedType.XLA:
|
89 |
+
rng_state = rng_state.to(xm.xla_device())
|
90 |
+
xm.collective_broadcast([rng_state])
|
91 |
+
xm.mark_step()
|
92 |
+
rng_state = rng_state.cpu()
|
93 |
+
elif (
|
94 |
+
state.distributed_type in CUDA_DISTRIBUTED_TYPES
|
95 |
+
or state.distributed_type == DistributedType.MULTI_MLU
|
96 |
+
or state.distributed_type == DistributedType.MULTI_NPU
|
97 |
+
or state.distributed_type == DistributedType.MULTI_XPU
|
98 |
+
):
|
99 |
+
rng_state = rng_state.to(state.device)
|
100 |
+
torch.distributed.broadcast(rng_state, 0)
|
101 |
+
rng_state = rng_state.cpu()
|
102 |
+
elif state.distributed_type == DistributedType.MULTI_CPU:
|
103 |
+
torch.distributed.broadcast(rng_state, 0)
|
104 |
+
|
105 |
+
# Set the broadcast rng state
|
106 |
+
if rng_type == RNGType.TORCH:
|
107 |
+
torch.set_rng_state(rng_state)
|
108 |
+
elif rng_type == RNGType.CUDA:
|
109 |
+
torch.cuda.set_rng_state(rng_state)
|
110 |
+
elif rng_type == RNGType.NPU:
|
111 |
+
torch.npu.set_rng_state(rng_state)
|
112 |
+
elif rng_type == RNGType.MLU:
|
113 |
+
torch.mlu.set_rng_state(rng_state)
|
114 |
+
elif rng_type == RNGType.XPU:
|
115 |
+
torch.xpu.set_rng_state(rng_state)
|
116 |
+
elif rng_type == RNGType.XLA:
|
117 |
+
xm.set_rng_state(rng_state.item())
|
118 |
+
elif rng_type == RNGType.GENERATOR:
|
119 |
+
generator.set_state(rng_state)
|
120 |
+
|
121 |
+
|
122 |
+
def synchronize_rng_states(rng_types: List[Union[str, RNGType]], generator: Optional[torch.Generator] = None):
|
123 |
+
for rng_type in rng_types:
|
124 |
+
synchronize_rng_state(RNGType(rng_type), generator=generator)
|
llmeval-env/lib/python3.10/site-packages/accelerate/utils/rich.py
ADDED
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# Copyright 2022 The HuggingFace Team. All rights reserved.
|
2 |
+
#
|
3 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
4 |
+
# you may not use this file except in compliance with the License.
|
5 |
+
# You may obtain a copy of the License at
|
6 |
+
#
|
7 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
8 |
+
#
|
9 |
+
# Unless required by applicable law or agreed to in writing, software
|
10 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
11 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
12 |
+
# See the License for the specific language governing permissions and
|
13 |
+
# limitations under the License.
|
14 |
+
|
15 |
+
from .imports import is_rich_available
|
16 |
+
|
17 |
+
|
18 |
+
if is_rich_available():
|
19 |
+
from rich.traceback import install
|
20 |
+
|
21 |
+
install(show_locals=False)
|
22 |
+
|
23 |
+
else:
|
24 |
+
raise ModuleNotFoundError("To use the rich extension, install rich with `pip install rich`")
|
llmeval-env/lib/python3.10/site-packages/mbstrdecoder-1.1.3.dist-info/INSTALLER
ADDED
@@ -0,0 +1 @@
|
|
|
|
|
1 |
+
pip
|
llmeval-env/lib/python3.10/site-packages/mbstrdecoder-1.1.3.dist-info/LICENSE
ADDED
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
MIT License
|
2 |
+
|
3 |
+
Copyright (c) 2016 Tsuyoshi Hombashi
|
4 |
+
|
5 |
+
Permission is hereby granted, free of charge, to any person obtaining a copy
|
6 |
+
of this software and associated documentation files (the "Software"), to deal
|
7 |
+
in the Software without restriction, including without limitation the rights
|
8 |
+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
9 |
+
copies of the Software, and to permit persons to whom the Software is
|
10 |
+
furnished to do so, subject to the following conditions:
|
11 |
+
|
12 |
+
The above copyright notice and this permission notice shall be included in all
|
13 |
+
copies or substantial portions of the Software.
|
14 |
+
|
15 |
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
16 |
+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
17 |
+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
18 |
+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
19 |
+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
20 |
+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
21 |
+
SOFTWARE.
|
llmeval-env/lib/python3.10/site-packages/mbstrdecoder-1.1.3.dist-info/METADATA
ADDED
@@ -0,0 +1,117 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
Metadata-Version: 2.1
|
2 |
+
Name: mbstrdecoder
|
3 |
+
Version: 1.1.3
|
4 |
+
Summary: mbstrdecoder is a Python library for multi-byte character string decoder
|
5 |
+
Home-page: https://github.com/thombashi/mbstrdecoder
|
6 |
+
Author: Tsuyoshi Hombashi
|
7 |
+
Author-email: [email protected]
|
8 |
+
License: MIT License
|
9 |
+
Project-URL: Source, https://github.com/thombashi/mbstrdecoder
|
10 |
+
Project-URL: Tracker, https://github.com/thombashi/mbstrdecoder/issues
|
11 |
+
Keywords: multi-byte character,unicode,decoder
|
12 |
+
Classifier: Development Status :: 5 - Production/Stable
|
13 |
+
Classifier: Intended Audience :: Developers
|
14 |
+
Classifier: Intended Audience :: Information Technology
|
15 |
+
Classifier: License :: OSI Approved :: MIT License
|
16 |
+
Classifier: Operating System :: OS Independent
|
17 |
+
Classifier: Programming Language :: Python :: 3
|
18 |
+
Classifier: Programming Language :: Python :: 3.7
|
19 |
+
Classifier: Programming Language :: Python :: 3.8
|
20 |
+
Classifier: Programming Language :: Python :: 3.9
|
21 |
+
Classifier: Programming Language :: Python :: 3.10
|
22 |
+
Classifier: Programming Language :: Python :: 3.11
|
23 |
+
Classifier: Programming Language :: Python :: 3.12
|
24 |
+
Classifier: Programming Language :: Python :: Implementation :: CPython
|
25 |
+
Classifier: Programming Language :: Python :: Implementation :: PyPy
|
26 |
+
Classifier: Topic :: Software Development :: Libraries
|
27 |
+
Classifier: Topic :: Software Development :: Libraries :: Python Modules
|
28 |
+
Classifier: Topic :: Text Processing
|
29 |
+
Requires-Python: >=3.7
|
30 |
+
Description-Content-Type: text/x-rst
|
31 |
+
License-File: LICENSE
|
32 |
+
Requires-Dist: chardet (<6,>=3.0.4)
|
33 |
+
Provides-Extra: test
|
34 |
+
Requires-Dist: Faker (>=1.0.2) ; extra == 'test'
|
35 |
+
Requires-Dist: pytest (>=6.0.1) ; extra == 'test'
|
36 |
+
Requires-Dist: pytest-md-report (>=0.1) ; extra == 'test'
|
37 |
+
|
38 |
+
.. contents:: **mbstrdecoder**
|
39 |
+
:backlinks: top
|
40 |
+
:local:
|
41 |
+
|
42 |
+
|
43 |
+
Summary
|
44 |
+
=======
|
45 |
+
`mbstrdecoder <https://github.com/thombashi/mbstrdecoder>`__ is a Python library for multi-byte character string decoder.
|
46 |
+
|
47 |
+
|
48 |
+
.. image:: https://badge.fury.io/py/mbstrdecoder.svg
|
49 |
+
:target: https://badge.fury.io/py/mbstrdecoder
|
50 |
+
:alt: PyPI package version
|
51 |
+
|
52 |
+
.. image:: https://img.shields.io/pypi/pyversions/mbstrdecoder.svg
|
53 |
+
:target: https://pypi.org/project/mbstrdecoder
|
54 |
+
:alt: Supported Python versions
|
55 |
+
|
56 |
+
.. image:: https://img.shields.io/pypi/implementation/mbstrdecoder.svg
|
57 |
+
:target: https://pypi.org/project/mbstrdecoder
|
58 |
+
:alt: Supported Python implementations
|
59 |
+
|
60 |
+
.. image:: https://github.com/thombashi/mbstrdecoder/actions/workflows/lint_and_test.yml/badge.svg
|
61 |
+
:target: https://github.com/thombashi/mbstrdecoder/actions/workflows/lint_and_test.yml
|
62 |
+
:alt: CI status of Linux/macOS/Windows
|
63 |
+
|
64 |
+
.. image:: https://coveralls.io/repos/github/thombashi/mbstrdecoder/badge.svg?branch=master
|
65 |
+
:target: https://coveralls.io/github/thombashi/mbstrdecoder?branch=master
|
66 |
+
:alt: Test coverage
|
67 |
+
|
68 |
+
.. image:: https://github.com/thombashi/mbstrdecoder/actions/workflows/codeql-analysis.yml/badge.svg
|
69 |
+
:target: https://github.com/thombashi/mbstrdecoder/actions/workflows/codeql-analysis.yml
|
70 |
+
:alt: CodeQL
|
71 |
+
|
72 |
+
|
73 |
+
Installation
|
74 |
+
============
|
75 |
+
|
76 |
+
Install from PyPI
|
77 |
+
------------------------------
|
78 |
+
::
|
79 |
+
|
80 |
+
pip install mbstrdecoder
|
81 |
+
|
82 |
+
Install from PPA (for Ubuntu)
|
83 |
+
------------------------------
|
84 |
+
::
|
85 |
+
|
86 |
+
sudo add-apt-repository ppa:thombashi/ppa
|
87 |
+
sudo apt update
|
88 |
+
sudo apt install python3-mbstrdecoder
|
89 |
+
|
90 |
+
|
91 |
+
Usage
|
92 |
+
=====
|
93 |
+
|
94 |
+
:Sample Code:
|
95 |
+
.. code:: python
|
96 |
+
|
97 |
+
from mbstrdecoder import MultiByteStrDecoder
|
98 |
+
|
99 |
+
encoded_multibyte_text = "マルチバイト文字".encode("utf-8")
|
100 |
+
decoder = MultiByteStrDecoder(encoded_multibyte_text)
|
101 |
+
|
102 |
+
print("encoded bytes: {}".format(encoded_multibyte_text))
|
103 |
+
print("unicode: {}".format(decoder.unicode_str))
|
104 |
+
print("codec: {}".format(decoder.codec))
|
105 |
+
|
106 |
+
:Output:
|
107 |
+
::
|
108 |
+
|
109 |
+
encoded bytes: b'\xe3\x83\x9e\xe3\x83\xab\xe3\x83\x81\xe3\x83\x90\xe3\x82\xa4\xe3\x83\x88\xe6\x96\x87\xe5\xad\x97'
|
110 |
+
unicode: マルチバイト文字
|
111 |
+
codec: utf_8
|
112 |
+
|
113 |
+
|
114 |
+
Dependencies
|
115 |
+
============
|
116 |
+
- Python 3.7+
|
117 |
+
- `Python package dependencies (automatically installed) <https://github.com/thombashi/mbstrdecoder/network/dependencies>`__
|
llmeval-env/lib/python3.10/site-packages/mbstrdecoder-1.1.3.dist-info/top_level.txt
ADDED
@@ -0,0 +1 @@
|
|
|
|
|
1 |
+
mbstrdecoder
|
llmeval-env/lib/python3.10/site-packages/networkx/__init__.py
ADDED
@@ -0,0 +1,49 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
NetworkX
|
3 |
+
========
|
4 |
+
|
5 |
+
NetworkX is a Python package for the creation, manipulation, and study of the
|
6 |
+
structure, dynamics, and functions of complex networks.
|
7 |
+
|
8 |
+
See https://networkx.org for complete documentation.
|
9 |
+
"""
|
10 |
+
|
11 |
+
__version__ = "3.3"
|
12 |
+
|
13 |
+
|
14 |
+
# These are imported in order as listed
|
15 |
+
from networkx.lazy_imports import _lazy_import
|
16 |
+
|
17 |
+
from networkx.exception import *
|
18 |
+
|
19 |
+
from networkx import utils
|
20 |
+
from networkx.utils import _clear_cache, _dispatchable, config
|
21 |
+
|
22 |
+
from networkx import classes
|
23 |
+
from networkx.classes import filters
|
24 |
+
from networkx.classes import *
|
25 |
+
|
26 |
+
from networkx import convert
|
27 |
+
from networkx.convert import *
|
28 |
+
|
29 |
+
from networkx import convert_matrix
|
30 |
+
from networkx.convert_matrix import *
|
31 |
+
|
32 |
+
from networkx import relabel
|
33 |
+
from networkx.relabel import *
|
34 |
+
|
35 |
+
from networkx import generators
|
36 |
+
from networkx.generators import *
|
37 |
+
|
38 |
+
from networkx import readwrite
|
39 |
+
from networkx.readwrite import *
|
40 |
+
|
41 |
+
# Need to test with SciPy, when available
|
42 |
+
from networkx import algorithms
|
43 |
+
from networkx.algorithms import *
|
44 |
+
|
45 |
+
from networkx import linalg
|
46 |
+
from networkx.linalg import *
|
47 |
+
|
48 |
+
from networkx import drawing
|
49 |
+
from networkx.drawing import *
|
llmeval-env/lib/python3.10/site-packages/networkx/conftest.py
ADDED
@@ -0,0 +1,289 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
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|
|
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|
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|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
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|
|
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|
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|
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|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
Testing
|
3 |
+
=======
|
4 |
+
|
5 |
+
General guidelines for writing good tests:
|
6 |
+
|
7 |
+
- doctests always assume ``import networkx as nx`` so don't add that
|
8 |
+
- prefer pytest fixtures over classes with setup methods.
|
9 |
+
- use the ``@pytest.mark.parametrize`` decorator
|
10 |
+
- use ``pytest.importorskip`` for numpy, scipy, pandas, and matplotlib b/c of PyPy.
|
11 |
+
and add the module to the relevant entries below.
|
12 |
+
|
13 |
+
"""
|
14 |
+
import os
|
15 |
+
import sys
|
16 |
+
import warnings
|
17 |
+
from importlib.metadata import entry_points
|
18 |
+
|
19 |
+
import pytest
|
20 |
+
|
21 |
+
import networkx
|
22 |
+
|
23 |
+
|
24 |
+
def pytest_addoption(parser):
|
25 |
+
parser.addoption(
|
26 |
+
"--runslow", action="store_true", default=False, help="run slow tests"
|
27 |
+
)
|
28 |
+
parser.addoption(
|
29 |
+
"--backend",
|
30 |
+
action="store",
|
31 |
+
default=None,
|
32 |
+
help="Run tests with a backend by auto-converting nx graphs to backend graphs",
|
33 |
+
)
|
34 |
+
parser.addoption(
|
35 |
+
"--fallback-to-nx",
|
36 |
+
action="store_true",
|
37 |
+
default=False,
|
38 |
+
help="Run nx function if a backend doesn't implement a dispatchable function"
|
39 |
+
" (use with --backend)",
|
40 |
+
)
|
41 |
+
|
42 |
+
|
43 |
+
def pytest_configure(config):
|
44 |
+
config.addinivalue_line("markers", "slow: mark test as slow to run")
|
45 |
+
backend = config.getoption("--backend")
|
46 |
+
if backend is None:
|
47 |
+
backend = os.environ.get("NETWORKX_TEST_BACKEND")
|
48 |
+
# nx-loopback backend is only available when testing
|
49 |
+
backends = entry_points(name="nx-loopback", group="networkx.backends")
|
50 |
+
if backends:
|
51 |
+
networkx.utils.backends.backends["nx-loopback"] = next(iter(backends))
|
52 |
+
else:
|
53 |
+
warnings.warn(
|
54 |
+
"\n\n WARNING: Mixed NetworkX configuration! \n\n"
|
55 |
+
" This environment has mixed configuration for networkx.\n"
|
56 |
+
" The test object nx-loopback is not configured correctly.\n"
|
57 |
+
" You should not be seeing this message.\n"
|
58 |
+
" Try `pip install -e .`, or change your PYTHONPATH\n"
|
59 |
+
" Make sure python finds the networkx repo you are testing\n\n"
|
60 |
+
)
|
61 |
+
if backend:
|
62 |
+
networkx.config["backend_priority"] = [backend]
|
63 |
+
fallback_to_nx = config.getoption("--fallback-to-nx")
|
64 |
+
if not fallback_to_nx:
|
65 |
+
fallback_to_nx = os.environ.get("NETWORKX_FALLBACK_TO_NX")
|
66 |
+
networkx.utils.backends._dispatchable._fallback_to_nx = bool(fallback_to_nx)
|
67 |
+
|
68 |
+
|
69 |
+
def pytest_collection_modifyitems(config, items):
|
70 |
+
# Setting this to True here allows tests to be set up before dispatching
|
71 |
+
# any function call to a backend.
|
72 |
+
networkx.utils.backends._dispatchable._is_testing = True
|
73 |
+
if backend_priority := networkx.config["backend_priority"]:
|
74 |
+
# Allow pluggable backends to add markers to tests (such as skip or xfail)
|
75 |
+
# when running in auto-conversion test mode
|
76 |
+
backend = networkx.utils.backends.backends[backend_priority[0]].load()
|
77 |
+
if hasattr(backend, "on_start_tests"):
|
78 |
+
getattr(backend, "on_start_tests")(items)
|
79 |
+
|
80 |
+
if config.getoption("--runslow"):
|
81 |
+
# --runslow given in cli: do not skip slow tests
|
82 |
+
return
|
83 |
+
skip_slow = pytest.mark.skip(reason="need --runslow option to run")
|
84 |
+
for item in items:
|
85 |
+
if "slow" in item.keywords:
|
86 |
+
item.add_marker(skip_slow)
|
87 |
+
|
88 |
+
|
89 |
+
# TODO: The warnings below need to be dealt with, but for now we silence them.
|
90 |
+
@pytest.fixture(autouse=True)
|
91 |
+
def set_warnings():
|
92 |
+
warnings.filterwarnings(
|
93 |
+
"ignore",
|
94 |
+
category=FutureWarning,
|
95 |
+
message="\n\nsingle_target_shortest_path_length",
|
96 |
+
)
|
97 |
+
warnings.filterwarnings(
|
98 |
+
"ignore",
|
99 |
+
category=FutureWarning,
|
100 |
+
message="\n\nshortest_path",
|
101 |
+
)
|
102 |
+
warnings.filterwarnings(
|
103 |
+
"ignore", category=DeprecationWarning, message="\nforest_str is deprecated"
|
104 |
+
)
|
105 |
+
warnings.filterwarnings(
|
106 |
+
"ignore", category=DeprecationWarning, message="\n\nrandom_tree"
|
107 |
+
)
|
108 |
+
warnings.filterwarnings(
|
109 |
+
"ignore", category=DeprecationWarning, message="Edmonds has been deprecated"
|
110 |
+
)
|
111 |
+
warnings.filterwarnings(
|
112 |
+
"ignore",
|
113 |
+
category=DeprecationWarning,
|
114 |
+
message="MultiDiGraph_EdgeKey has been deprecated",
|
115 |
+
)
|
116 |
+
warnings.filterwarnings(
|
117 |
+
"ignore", category=DeprecationWarning, message="\n\nThe `normalized`"
|
118 |
+
)
|
119 |
+
warnings.filterwarnings(
|
120 |
+
"ignore",
|
121 |
+
category=DeprecationWarning,
|
122 |
+
message="The function `join` is deprecated",
|
123 |
+
)
|
124 |
+
warnings.filterwarnings(
|
125 |
+
"ignore",
|
126 |
+
category=DeprecationWarning,
|
127 |
+
message="\n\nstrongly_connected_components_recursive",
|
128 |
+
)
|
129 |
+
warnings.filterwarnings(
|
130 |
+
"ignore", category=DeprecationWarning, message="\n\nall_triplets"
|
131 |
+
)
|
132 |
+
warnings.filterwarnings(
|
133 |
+
"ignore", category=DeprecationWarning, message="\n\nrandom_triad"
|
134 |
+
)
|
135 |
+
warnings.filterwarnings(
|
136 |
+
"ignore", category=DeprecationWarning, message="minimal_d_separator"
|
137 |
+
)
|
138 |
+
warnings.filterwarnings(
|
139 |
+
"ignore", category=DeprecationWarning, message="d_separated"
|
140 |
+
)
|
141 |
+
warnings.filterwarnings("ignore", category=DeprecationWarning, message="\n\nk_core")
|
142 |
+
warnings.filterwarnings(
|
143 |
+
"ignore", category=DeprecationWarning, message="\n\nk_shell"
|
144 |
+
)
|
145 |
+
warnings.filterwarnings(
|
146 |
+
"ignore", category=DeprecationWarning, message="\n\nk_crust"
|
147 |
+
)
|
148 |
+
warnings.filterwarnings(
|
149 |
+
"ignore", category=DeprecationWarning, message="\n\nk_corona"
|
150 |
+
)
|
151 |
+
warnings.filterwarnings(
|
152 |
+
"ignore", category=DeprecationWarning, message="\n\ntotal_spanning_tree_weight"
|
153 |
+
)
|
154 |
+
warnings.filterwarnings(
|
155 |
+
"ignore", category=DeprecationWarning, message=r"\n\nThe 'create=matrix'"
|
156 |
+
)
|
157 |
+
|
158 |
+
|
159 |
+
@pytest.fixture(autouse=True)
|
160 |
+
def add_nx(doctest_namespace):
|
161 |
+
doctest_namespace["nx"] = networkx
|
162 |
+
|
163 |
+
|
164 |
+
# What dependencies are installed?
|
165 |
+
|
166 |
+
try:
|
167 |
+
import numpy
|
168 |
+
|
169 |
+
has_numpy = True
|
170 |
+
except ImportError:
|
171 |
+
has_numpy = False
|
172 |
+
|
173 |
+
try:
|
174 |
+
import scipy
|
175 |
+
|
176 |
+
has_scipy = True
|
177 |
+
except ImportError:
|
178 |
+
has_scipy = False
|
179 |
+
|
180 |
+
try:
|
181 |
+
import matplotlib
|
182 |
+
|
183 |
+
has_matplotlib = True
|
184 |
+
except ImportError:
|
185 |
+
has_matplotlib = False
|
186 |
+
|
187 |
+
try:
|
188 |
+
import pandas
|
189 |
+
|
190 |
+
has_pandas = True
|
191 |
+
except ImportError:
|
192 |
+
has_pandas = False
|
193 |
+
|
194 |
+
try:
|
195 |
+
import pygraphviz
|
196 |
+
|
197 |
+
has_pygraphviz = True
|
198 |
+
except ImportError:
|
199 |
+
has_pygraphviz = False
|
200 |
+
|
201 |
+
try:
|
202 |
+
import pydot
|
203 |
+
|
204 |
+
has_pydot = True
|
205 |
+
except ImportError:
|
206 |
+
has_pydot = False
|
207 |
+
|
208 |
+
try:
|
209 |
+
import sympy
|
210 |
+
|
211 |
+
has_sympy = True
|
212 |
+
except ImportError:
|
213 |
+
has_sympy = False
|
214 |
+
|
215 |
+
|
216 |
+
# List of files that pytest should ignore
|
217 |
+
|
218 |
+
collect_ignore = []
|
219 |
+
|
220 |
+
needs_numpy = [
|
221 |
+
"algorithms/approximation/traveling_salesman.py",
|
222 |
+
"algorithms/centrality/current_flow_closeness.py",
|
223 |
+
"algorithms/node_classification.py",
|
224 |
+
"algorithms/non_randomness.py",
|
225 |
+
"algorithms/shortest_paths/dense.py",
|
226 |
+
"algorithms/tree/mst.py",
|
227 |
+
"generators/expanders.py",
|
228 |
+
"linalg/bethehessianmatrix.py",
|
229 |
+
"linalg/laplacianmatrix.py",
|
230 |
+
"utils/misc.py",
|
231 |
+
"algorithms/centrality/laplacian.py",
|
232 |
+
]
|
233 |
+
needs_scipy = [
|
234 |
+
"algorithms/approximation/traveling_salesman.py",
|
235 |
+
"algorithms/assortativity/correlation.py",
|
236 |
+
"algorithms/assortativity/mixing.py",
|
237 |
+
"algorithms/assortativity/pairs.py",
|
238 |
+
"algorithms/bipartite/matrix.py",
|
239 |
+
"algorithms/bipartite/spectral.py",
|
240 |
+
"algorithms/centrality/current_flow_betweenness.py",
|
241 |
+
"algorithms/centrality/current_flow_betweenness_subset.py",
|
242 |
+
"algorithms/centrality/eigenvector.py",
|
243 |
+
"algorithms/centrality/katz.py",
|
244 |
+
"algorithms/centrality/laplacian.py",
|
245 |
+
"algorithms/centrality/second_order.py",
|
246 |
+
"algorithms/centrality/subgraph_alg.py",
|
247 |
+
"algorithms/communicability_alg.py",
|
248 |
+
"algorithms/community/divisive.py",
|
249 |
+
"algorithms/distance_measures.py",
|
250 |
+
"algorithms/link_analysis/hits_alg.py",
|
251 |
+
"algorithms/link_analysis/pagerank_alg.py",
|
252 |
+
"algorithms/node_classification.py",
|
253 |
+
"algorithms/similarity.py",
|
254 |
+
"algorithms/tree/mst.py",
|
255 |
+
"algorithms/walks.py",
|
256 |
+
"convert_matrix.py",
|
257 |
+
"drawing/layout.py",
|
258 |
+
"drawing/nx_pylab.py",
|
259 |
+
"generators/spectral_graph_forge.py",
|
260 |
+
"generators/expanders.py",
|
261 |
+
"linalg/algebraicconnectivity.py",
|
262 |
+
"linalg/attrmatrix.py",
|
263 |
+
"linalg/bethehessianmatrix.py",
|
264 |
+
"linalg/graphmatrix.py",
|
265 |
+
"linalg/laplacianmatrix.py",
|
266 |
+
"linalg/modularitymatrix.py",
|
267 |
+
"linalg/spectrum.py",
|
268 |
+
"utils/rcm.py",
|
269 |
+
]
|
270 |
+
needs_matplotlib = ["drawing/nx_pylab.py"]
|
271 |
+
needs_pandas = ["convert_matrix.py"]
|
272 |
+
needs_pygraphviz = ["drawing/nx_agraph.py"]
|
273 |
+
needs_pydot = ["drawing/nx_pydot.py"]
|
274 |
+
needs_sympy = ["algorithms/polynomials.py"]
|
275 |
+
|
276 |
+
if not has_numpy:
|
277 |
+
collect_ignore += needs_numpy
|
278 |
+
if not has_scipy:
|
279 |
+
collect_ignore += needs_scipy
|
280 |
+
if not has_matplotlib:
|
281 |
+
collect_ignore += needs_matplotlib
|
282 |
+
if not has_pandas:
|
283 |
+
collect_ignore += needs_pandas
|
284 |
+
if not has_pygraphviz:
|
285 |
+
collect_ignore += needs_pygraphviz
|
286 |
+
if not has_pydot:
|
287 |
+
collect_ignore += needs_pydot
|
288 |
+
if not has_sympy:
|
289 |
+
collect_ignore += needs_sympy
|
llmeval-env/lib/python3.10/site-packages/networkx/convert.py
ADDED
@@ -0,0 +1,494 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
1 |
+
"""Functions to convert NetworkX graphs to and from other formats.
|
2 |
+
|
3 |
+
The preferred way of converting data to a NetworkX graph is through the
|
4 |
+
graph constructor. The constructor calls the to_networkx_graph() function
|
5 |
+
which attempts to guess the input type and convert it automatically.
|
6 |
+
|
7 |
+
Examples
|
8 |
+
--------
|
9 |
+
Create a graph with a single edge from a dictionary of dictionaries
|
10 |
+
|
11 |
+
>>> d = {0: {1: 1}} # dict-of-dicts single edge (0,1)
|
12 |
+
>>> G = nx.Graph(d)
|
13 |
+
|
14 |
+
See Also
|
15 |
+
--------
|
16 |
+
nx_agraph, nx_pydot
|
17 |
+
"""
|
18 |
+
import warnings
|
19 |
+
from collections.abc import Collection, Generator, Iterator
|
20 |
+
|
21 |
+
import networkx as nx
|
22 |
+
|
23 |
+
__all__ = [
|
24 |
+
"to_networkx_graph",
|
25 |
+
"from_dict_of_dicts",
|
26 |
+
"to_dict_of_dicts",
|
27 |
+
"from_dict_of_lists",
|
28 |
+
"to_dict_of_lists",
|
29 |
+
"from_edgelist",
|
30 |
+
"to_edgelist",
|
31 |
+
]
|
32 |
+
|
33 |
+
|
34 |
+
def to_networkx_graph(data, create_using=None, multigraph_input=False):
|
35 |
+
"""Make a NetworkX graph from a known data structure.
|
36 |
+
|
37 |
+
The preferred way to call this is automatically
|
38 |
+
from the class constructor
|
39 |
+
|
40 |
+
>>> d = {0: {1: {"weight": 1}}} # dict-of-dicts single edge (0,1)
|
41 |
+
>>> G = nx.Graph(d)
|
42 |
+
|
43 |
+
instead of the equivalent
|
44 |
+
|
45 |
+
>>> G = nx.from_dict_of_dicts(d)
|
46 |
+
|
47 |
+
Parameters
|
48 |
+
----------
|
49 |
+
data : object to be converted
|
50 |
+
|
51 |
+
Current known types are:
|
52 |
+
any NetworkX graph
|
53 |
+
dict-of-dicts
|
54 |
+
dict-of-lists
|
55 |
+
container (e.g. set, list, tuple) of edges
|
56 |
+
iterator (e.g. itertools.chain) that produces edges
|
57 |
+
generator of edges
|
58 |
+
Pandas DataFrame (row per edge)
|
59 |
+
2D numpy array
|
60 |
+
scipy sparse array
|
61 |
+
pygraphviz agraph
|
62 |
+
|
63 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
64 |
+
Graph type to create. If graph instance, then cleared before populated.
|
65 |
+
|
66 |
+
multigraph_input : bool (default False)
|
67 |
+
If True and data is a dict_of_dicts,
|
68 |
+
try to create a multigraph assuming dict_of_dict_of_lists.
|
69 |
+
If data and create_using are both multigraphs then create
|
70 |
+
a multigraph from a multigraph.
|
71 |
+
|
72 |
+
"""
|
73 |
+
# NX graph
|
74 |
+
if hasattr(data, "adj"):
|
75 |
+
try:
|
76 |
+
result = from_dict_of_dicts(
|
77 |
+
data.adj,
|
78 |
+
create_using=create_using,
|
79 |
+
multigraph_input=data.is_multigraph(),
|
80 |
+
)
|
81 |
+
# data.graph should be dict-like
|
82 |
+
result.graph.update(data.graph)
|
83 |
+
# data.nodes should be dict-like
|
84 |
+
# result.add_node_from(data.nodes.items()) possible but
|
85 |
+
# for custom node_attr_dict_factory which may be hashable
|
86 |
+
# will be unexpected behavior
|
87 |
+
for n, dd in data.nodes.items():
|
88 |
+
result._node[n].update(dd)
|
89 |
+
return result
|
90 |
+
except Exception as err:
|
91 |
+
raise nx.NetworkXError("Input is not a correct NetworkX graph.") from err
|
92 |
+
|
93 |
+
# pygraphviz agraph
|
94 |
+
if hasattr(data, "is_strict"):
|
95 |
+
try:
|
96 |
+
return nx.nx_agraph.from_agraph(data, create_using=create_using)
|
97 |
+
except Exception as err:
|
98 |
+
raise nx.NetworkXError("Input is not a correct pygraphviz graph.") from err
|
99 |
+
|
100 |
+
# dict of dicts/lists
|
101 |
+
if isinstance(data, dict):
|
102 |
+
try:
|
103 |
+
return from_dict_of_dicts(
|
104 |
+
data, create_using=create_using, multigraph_input=multigraph_input
|
105 |
+
)
|
106 |
+
except Exception as err1:
|
107 |
+
if multigraph_input is True:
|
108 |
+
raise nx.NetworkXError(
|
109 |
+
f"converting multigraph_input raised:\n{type(err1)}: {err1}"
|
110 |
+
)
|
111 |
+
try:
|
112 |
+
return from_dict_of_lists(data, create_using=create_using)
|
113 |
+
except Exception as err2:
|
114 |
+
raise TypeError("Input is not known type.") from err2
|
115 |
+
|
116 |
+
# Pandas DataFrame
|
117 |
+
try:
|
118 |
+
import pandas as pd
|
119 |
+
|
120 |
+
if isinstance(data, pd.DataFrame):
|
121 |
+
if data.shape[0] == data.shape[1]:
|
122 |
+
try:
|
123 |
+
return nx.from_pandas_adjacency(data, create_using=create_using)
|
124 |
+
except Exception as err:
|
125 |
+
msg = "Input is not a correct Pandas DataFrame adjacency matrix."
|
126 |
+
raise nx.NetworkXError(msg) from err
|
127 |
+
else:
|
128 |
+
try:
|
129 |
+
return nx.from_pandas_edgelist(
|
130 |
+
data, edge_attr=True, create_using=create_using
|
131 |
+
)
|
132 |
+
except Exception as err:
|
133 |
+
msg = "Input is not a correct Pandas DataFrame edge-list."
|
134 |
+
raise nx.NetworkXError(msg) from err
|
135 |
+
except ImportError:
|
136 |
+
warnings.warn("pandas not found, skipping conversion test.", ImportWarning)
|
137 |
+
|
138 |
+
# numpy array
|
139 |
+
try:
|
140 |
+
import numpy as np
|
141 |
+
|
142 |
+
if isinstance(data, np.ndarray):
|
143 |
+
try:
|
144 |
+
return nx.from_numpy_array(data, create_using=create_using)
|
145 |
+
except Exception as err:
|
146 |
+
raise nx.NetworkXError(
|
147 |
+
f"Failed to interpret array as an adjacency matrix."
|
148 |
+
) from err
|
149 |
+
except ImportError:
|
150 |
+
warnings.warn("numpy not found, skipping conversion test.", ImportWarning)
|
151 |
+
|
152 |
+
# scipy sparse array - any format
|
153 |
+
try:
|
154 |
+
import scipy
|
155 |
+
|
156 |
+
if hasattr(data, "format"):
|
157 |
+
try:
|
158 |
+
return nx.from_scipy_sparse_array(data, create_using=create_using)
|
159 |
+
except Exception as err:
|
160 |
+
raise nx.NetworkXError(
|
161 |
+
"Input is not a correct scipy sparse array type."
|
162 |
+
) from err
|
163 |
+
except ImportError:
|
164 |
+
warnings.warn("scipy not found, skipping conversion test.", ImportWarning)
|
165 |
+
|
166 |
+
# Note: most general check - should remain last in order of execution
|
167 |
+
# Includes containers (e.g. list, set, dict, etc.), generators, and
|
168 |
+
# iterators (e.g. itertools.chain) of edges
|
169 |
+
|
170 |
+
if isinstance(data, Collection | Generator | Iterator):
|
171 |
+
try:
|
172 |
+
return from_edgelist(data, create_using=create_using)
|
173 |
+
except Exception as err:
|
174 |
+
raise nx.NetworkXError("Input is not a valid edge list") from err
|
175 |
+
|
176 |
+
raise nx.NetworkXError("Input is not a known data type for conversion.")
|
177 |
+
|
178 |
+
|
179 |
+
@nx._dispatchable
|
180 |
+
def to_dict_of_lists(G, nodelist=None):
|
181 |
+
"""Returns adjacency representation of graph as a dictionary of lists.
|
182 |
+
|
183 |
+
Parameters
|
184 |
+
----------
|
185 |
+
G : graph
|
186 |
+
A NetworkX graph
|
187 |
+
|
188 |
+
nodelist : list
|
189 |
+
Use only nodes specified in nodelist
|
190 |
+
|
191 |
+
Notes
|
192 |
+
-----
|
193 |
+
Completely ignores edge data for MultiGraph and MultiDiGraph.
|
194 |
+
|
195 |
+
"""
|
196 |
+
if nodelist is None:
|
197 |
+
nodelist = G
|
198 |
+
|
199 |
+
d = {}
|
200 |
+
for n in nodelist:
|
201 |
+
d[n] = [nbr for nbr in G.neighbors(n) if nbr in nodelist]
|
202 |
+
return d
|
203 |
+
|
204 |
+
|
205 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
206 |
+
def from_dict_of_lists(d, create_using=None):
|
207 |
+
"""Returns a graph from a dictionary of lists.
|
208 |
+
|
209 |
+
Parameters
|
210 |
+
----------
|
211 |
+
d : dictionary of lists
|
212 |
+
A dictionary of lists adjacency representation.
|
213 |
+
|
214 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
215 |
+
Graph type to create. If graph instance, then cleared before populated.
|
216 |
+
|
217 |
+
Examples
|
218 |
+
--------
|
219 |
+
>>> dol = {0: [1]} # single edge (0,1)
|
220 |
+
>>> G = nx.from_dict_of_lists(dol)
|
221 |
+
|
222 |
+
or
|
223 |
+
|
224 |
+
>>> G = nx.Graph(dol) # use Graph constructor
|
225 |
+
|
226 |
+
"""
|
227 |
+
G = nx.empty_graph(0, create_using)
|
228 |
+
G.add_nodes_from(d)
|
229 |
+
if G.is_multigraph() and not G.is_directed():
|
230 |
+
# a dict_of_lists can't show multiedges. BUT for undirected graphs,
|
231 |
+
# each edge shows up twice in the dict_of_lists.
|
232 |
+
# So we need to treat this case separately.
|
233 |
+
seen = {}
|
234 |
+
for node, nbrlist in d.items():
|
235 |
+
for nbr in nbrlist:
|
236 |
+
if nbr not in seen:
|
237 |
+
G.add_edge(node, nbr)
|
238 |
+
seen[node] = 1 # don't allow reverse edge to show up
|
239 |
+
else:
|
240 |
+
G.add_edges_from(
|
241 |
+
((node, nbr) for node, nbrlist in d.items() for nbr in nbrlist)
|
242 |
+
)
|
243 |
+
return G
|
244 |
+
|
245 |
+
|
246 |
+
def to_dict_of_dicts(G, nodelist=None, edge_data=None):
|
247 |
+
"""Returns adjacency representation of graph as a dictionary of dictionaries.
|
248 |
+
|
249 |
+
Parameters
|
250 |
+
----------
|
251 |
+
G : graph
|
252 |
+
A NetworkX graph
|
253 |
+
|
254 |
+
nodelist : list
|
255 |
+
Use only nodes specified in nodelist
|
256 |
+
|
257 |
+
edge_data : scalar, optional
|
258 |
+
If provided, the value of the dictionary will be set to `edge_data` for
|
259 |
+
all edges. Usual values could be `1` or `True`. If `edge_data` is
|
260 |
+
`None` (the default), the edgedata in `G` is used, resulting in a
|
261 |
+
dict-of-dict-of-dicts. If `G` is a MultiGraph, the result will be a
|
262 |
+
dict-of-dict-of-dict-of-dicts. See Notes for an approach to customize
|
263 |
+
handling edge data. `edge_data` should *not* be a container.
|
264 |
+
|
265 |
+
Returns
|
266 |
+
-------
|
267 |
+
dod : dict
|
268 |
+
A nested dictionary representation of `G`. Note that the level of
|
269 |
+
nesting depends on the type of `G` and the value of `edge_data`
|
270 |
+
(see Examples).
|
271 |
+
|
272 |
+
See Also
|
273 |
+
--------
|
274 |
+
from_dict_of_dicts, to_dict_of_lists
|
275 |
+
|
276 |
+
Notes
|
277 |
+
-----
|
278 |
+
For a more custom approach to handling edge data, try::
|
279 |
+
|
280 |
+
dod = {
|
281 |
+
n: {nbr: custom(n, nbr, dd) for nbr, dd in nbrdict.items()}
|
282 |
+
for n, nbrdict in G.adj.items()
|
283 |
+
}
|
284 |
+
|
285 |
+
where `custom` returns the desired edge data for each edge between `n` and
|
286 |
+
`nbr`, given existing edge data `dd`.
|
287 |
+
|
288 |
+
Examples
|
289 |
+
--------
|
290 |
+
>>> G = nx.path_graph(3)
|
291 |
+
>>> nx.to_dict_of_dicts(G)
|
292 |
+
{0: {1: {}}, 1: {0: {}, 2: {}}, 2: {1: {}}}
|
293 |
+
|
294 |
+
Edge data is preserved by default (``edge_data=None``), resulting
|
295 |
+
in dict-of-dict-of-dicts where the innermost dictionary contains the
|
296 |
+
edge data:
|
297 |
+
|
298 |
+
>>> G = nx.Graph()
|
299 |
+
>>> G.add_edges_from(
|
300 |
+
... [
|
301 |
+
... (0, 1, {"weight": 1.0}),
|
302 |
+
... (1, 2, {"weight": 2.0}),
|
303 |
+
... (2, 0, {"weight": 1.0}),
|
304 |
+
... ]
|
305 |
+
... )
|
306 |
+
>>> d = nx.to_dict_of_dicts(G)
|
307 |
+
>>> d # doctest: +SKIP
|
308 |
+
{0: {1: {'weight': 1.0}, 2: {'weight': 1.0}},
|
309 |
+
1: {0: {'weight': 1.0}, 2: {'weight': 2.0}},
|
310 |
+
2: {1: {'weight': 2.0}, 0: {'weight': 1.0}}}
|
311 |
+
>>> d[1][2]["weight"]
|
312 |
+
2.0
|
313 |
+
|
314 |
+
If `edge_data` is not `None`, edge data in the original graph (if any) is
|
315 |
+
replaced:
|
316 |
+
|
317 |
+
>>> d = nx.to_dict_of_dicts(G, edge_data=1)
|
318 |
+
>>> d
|
319 |
+
{0: {1: 1, 2: 1}, 1: {0: 1, 2: 1}, 2: {1: 1, 0: 1}}
|
320 |
+
>>> d[1][2]
|
321 |
+
1
|
322 |
+
|
323 |
+
This also applies to MultiGraphs: edge data is preserved by default:
|
324 |
+
|
325 |
+
>>> G = nx.MultiGraph()
|
326 |
+
>>> G.add_edge(0, 1, key="a", weight=1.0)
|
327 |
+
'a'
|
328 |
+
>>> G.add_edge(0, 1, key="b", weight=5.0)
|
329 |
+
'b'
|
330 |
+
>>> d = nx.to_dict_of_dicts(G)
|
331 |
+
>>> d # doctest: +SKIP
|
332 |
+
{0: {1: {'a': {'weight': 1.0}, 'b': {'weight': 5.0}}},
|
333 |
+
1: {0: {'a': {'weight': 1.0}, 'b': {'weight': 5.0}}}}
|
334 |
+
>>> d[0][1]["b"]["weight"]
|
335 |
+
5.0
|
336 |
+
|
337 |
+
But multi edge data is lost if `edge_data` is not `None`:
|
338 |
+
|
339 |
+
>>> d = nx.to_dict_of_dicts(G, edge_data=10)
|
340 |
+
>>> d
|
341 |
+
{0: {1: 10}, 1: {0: 10}}
|
342 |
+
"""
|
343 |
+
dod = {}
|
344 |
+
if nodelist is None:
|
345 |
+
if edge_data is None:
|
346 |
+
for u, nbrdict in G.adjacency():
|
347 |
+
dod[u] = nbrdict.copy()
|
348 |
+
else: # edge_data is not None
|
349 |
+
for u, nbrdict in G.adjacency():
|
350 |
+
dod[u] = dod.fromkeys(nbrdict, edge_data)
|
351 |
+
else: # nodelist is not None
|
352 |
+
if edge_data is None:
|
353 |
+
for u in nodelist:
|
354 |
+
dod[u] = {}
|
355 |
+
for v, data in ((v, data) for v, data in G[u].items() if v in nodelist):
|
356 |
+
dod[u][v] = data
|
357 |
+
else: # nodelist and edge_data are not None
|
358 |
+
for u in nodelist:
|
359 |
+
dod[u] = {}
|
360 |
+
for v in (v for v in G[u] if v in nodelist):
|
361 |
+
dod[u][v] = edge_data
|
362 |
+
return dod
|
363 |
+
|
364 |
+
|
365 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
366 |
+
def from_dict_of_dicts(d, create_using=None, multigraph_input=False):
|
367 |
+
"""Returns a graph from a dictionary of dictionaries.
|
368 |
+
|
369 |
+
Parameters
|
370 |
+
----------
|
371 |
+
d : dictionary of dictionaries
|
372 |
+
A dictionary of dictionaries adjacency representation.
|
373 |
+
|
374 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
375 |
+
Graph type to create. If graph instance, then cleared before populated.
|
376 |
+
|
377 |
+
multigraph_input : bool (default False)
|
378 |
+
When True, the dict `d` is assumed
|
379 |
+
to be a dict-of-dict-of-dict-of-dict structure keyed by
|
380 |
+
node to neighbor to edge keys to edge data for multi-edges.
|
381 |
+
Otherwise this routine assumes dict-of-dict-of-dict keyed by
|
382 |
+
node to neighbor to edge data.
|
383 |
+
|
384 |
+
Examples
|
385 |
+
--------
|
386 |
+
>>> dod = {0: {1: {"weight": 1}}} # single edge (0,1)
|
387 |
+
>>> G = nx.from_dict_of_dicts(dod)
|
388 |
+
|
389 |
+
or
|
390 |
+
|
391 |
+
>>> G = nx.Graph(dod) # use Graph constructor
|
392 |
+
|
393 |
+
"""
|
394 |
+
G = nx.empty_graph(0, create_using)
|
395 |
+
G.add_nodes_from(d)
|
396 |
+
# does dict d represent a MultiGraph or MultiDiGraph?
|
397 |
+
if multigraph_input:
|
398 |
+
if G.is_directed():
|
399 |
+
if G.is_multigraph():
|
400 |
+
G.add_edges_from(
|
401 |
+
(u, v, key, data)
|
402 |
+
for u, nbrs in d.items()
|
403 |
+
for v, datadict in nbrs.items()
|
404 |
+
for key, data in datadict.items()
|
405 |
+
)
|
406 |
+
else:
|
407 |
+
G.add_edges_from(
|
408 |
+
(u, v, data)
|
409 |
+
for u, nbrs in d.items()
|
410 |
+
for v, datadict in nbrs.items()
|
411 |
+
for key, data in datadict.items()
|
412 |
+
)
|
413 |
+
else: # Undirected
|
414 |
+
if G.is_multigraph():
|
415 |
+
seen = set() # don't add both directions of undirected graph
|
416 |
+
for u, nbrs in d.items():
|
417 |
+
for v, datadict in nbrs.items():
|
418 |
+
if (u, v) not in seen:
|
419 |
+
G.add_edges_from(
|
420 |
+
(u, v, key, data) for key, data in datadict.items()
|
421 |
+
)
|
422 |
+
seen.add((v, u))
|
423 |
+
else:
|
424 |
+
seen = set() # don't add both directions of undirected graph
|
425 |
+
for u, nbrs in d.items():
|
426 |
+
for v, datadict in nbrs.items():
|
427 |
+
if (u, v) not in seen:
|
428 |
+
G.add_edges_from(
|
429 |
+
(u, v, data) for key, data in datadict.items()
|
430 |
+
)
|
431 |
+
seen.add((v, u))
|
432 |
+
|
433 |
+
else: # not a multigraph to multigraph transfer
|
434 |
+
if G.is_multigraph() and not G.is_directed():
|
435 |
+
# d can have both representations u-v, v-u in dict. Only add one.
|
436 |
+
# We don't need this check for digraphs since we add both directions,
|
437 |
+
# or for Graph() since it is done implicitly (parallel edges not allowed)
|
438 |
+
seen = set()
|
439 |
+
for u, nbrs in d.items():
|
440 |
+
for v, data in nbrs.items():
|
441 |
+
if (u, v) not in seen:
|
442 |
+
G.add_edge(u, v, key=0)
|
443 |
+
G[u][v][0].update(data)
|
444 |
+
seen.add((v, u))
|
445 |
+
else:
|
446 |
+
G.add_edges_from(
|
447 |
+
((u, v, data) for u, nbrs in d.items() for v, data in nbrs.items())
|
448 |
+
)
|
449 |
+
return G
|
450 |
+
|
451 |
+
|
452 |
+
@nx._dispatchable(preserve_edge_attrs=True)
|
453 |
+
def to_edgelist(G, nodelist=None):
|
454 |
+
"""Returns a list of edges in the graph.
|
455 |
+
|
456 |
+
Parameters
|
457 |
+
----------
|
458 |
+
G : graph
|
459 |
+
A NetworkX graph
|
460 |
+
|
461 |
+
nodelist : list
|
462 |
+
Use only nodes specified in nodelist
|
463 |
+
|
464 |
+
"""
|
465 |
+
if nodelist is None:
|
466 |
+
return G.edges(data=True)
|
467 |
+
return G.edges(nodelist, data=True)
|
468 |
+
|
469 |
+
|
470 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
471 |
+
def from_edgelist(edgelist, create_using=None):
|
472 |
+
"""Returns a graph from a list of edges.
|
473 |
+
|
474 |
+
Parameters
|
475 |
+
----------
|
476 |
+
edgelist : list or iterator
|
477 |
+
Edge tuples
|
478 |
+
|
479 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
480 |
+
Graph type to create. If graph instance, then cleared before populated.
|
481 |
+
|
482 |
+
Examples
|
483 |
+
--------
|
484 |
+
>>> edgelist = [(0, 1)] # single edge (0,1)
|
485 |
+
>>> G = nx.from_edgelist(edgelist)
|
486 |
+
|
487 |
+
or
|
488 |
+
|
489 |
+
>>> G = nx.Graph(edgelist) # use Graph constructor
|
490 |
+
|
491 |
+
"""
|
492 |
+
G = nx.empty_graph(0, create_using)
|
493 |
+
G.add_edges_from(edgelist)
|
494 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/convert_matrix.py
ADDED
@@ -0,0 +1,1202 @@
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|
|
1 |
+
"""Functions to convert NetworkX graphs to and from common data containers
|
2 |
+
like numpy arrays, scipy sparse arrays, and pandas DataFrames.
|
3 |
+
|
4 |
+
The preferred way of converting data to a NetworkX graph is through the
|
5 |
+
graph constructor. The constructor calls the `~networkx.convert.to_networkx_graph`
|
6 |
+
function which attempts to guess the input type and convert it automatically.
|
7 |
+
|
8 |
+
Examples
|
9 |
+
--------
|
10 |
+
Create a 10 node random graph from a numpy array
|
11 |
+
|
12 |
+
>>> import numpy as np
|
13 |
+
>>> rng = np.random.default_rng()
|
14 |
+
>>> a = rng.integers(low=0, high=2, size=(10, 10))
|
15 |
+
>>> DG = nx.from_numpy_array(a, create_using=nx.DiGraph)
|
16 |
+
|
17 |
+
or equivalently:
|
18 |
+
|
19 |
+
>>> DG = nx.DiGraph(a)
|
20 |
+
|
21 |
+
which calls `from_numpy_array` internally based on the type of ``a``.
|
22 |
+
|
23 |
+
See Also
|
24 |
+
--------
|
25 |
+
nx_agraph, nx_pydot
|
26 |
+
"""
|
27 |
+
|
28 |
+
import itertools
|
29 |
+
from collections import defaultdict
|
30 |
+
|
31 |
+
import networkx as nx
|
32 |
+
from networkx.utils import not_implemented_for
|
33 |
+
|
34 |
+
__all__ = [
|
35 |
+
"from_pandas_adjacency",
|
36 |
+
"to_pandas_adjacency",
|
37 |
+
"from_pandas_edgelist",
|
38 |
+
"to_pandas_edgelist",
|
39 |
+
"from_scipy_sparse_array",
|
40 |
+
"to_scipy_sparse_array",
|
41 |
+
"from_numpy_array",
|
42 |
+
"to_numpy_array",
|
43 |
+
]
|
44 |
+
|
45 |
+
|
46 |
+
@nx._dispatchable(edge_attrs="weight")
|
47 |
+
def to_pandas_adjacency(
|
48 |
+
G,
|
49 |
+
nodelist=None,
|
50 |
+
dtype=None,
|
51 |
+
order=None,
|
52 |
+
multigraph_weight=sum,
|
53 |
+
weight="weight",
|
54 |
+
nonedge=0.0,
|
55 |
+
):
|
56 |
+
"""Returns the graph adjacency matrix as a Pandas DataFrame.
|
57 |
+
|
58 |
+
Parameters
|
59 |
+
----------
|
60 |
+
G : graph
|
61 |
+
The NetworkX graph used to construct the Pandas DataFrame.
|
62 |
+
|
63 |
+
nodelist : list, optional
|
64 |
+
The rows and columns are ordered according to the nodes in `nodelist`.
|
65 |
+
If `nodelist` is None, then the ordering is produced by G.nodes().
|
66 |
+
|
67 |
+
multigraph_weight : {sum, min, max}, optional
|
68 |
+
An operator that determines how weights in multigraphs are handled.
|
69 |
+
The default is to sum the weights of the multiple edges.
|
70 |
+
|
71 |
+
weight : string or None, optional
|
72 |
+
The edge attribute that holds the numerical value used for
|
73 |
+
the edge weight. If an edge does not have that attribute, then the
|
74 |
+
value 1 is used instead.
|
75 |
+
|
76 |
+
nonedge : float, optional
|
77 |
+
The matrix values corresponding to nonedges are typically set to zero.
|
78 |
+
However, this could be undesirable if there are matrix values
|
79 |
+
corresponding to actual edges that also have the value zero. If so,
|
80 |
+
one might prefer nonedges to have some other value, such as nan.
|
81 |
+
|
82 |
+
Returns
|
83 |
+
-------
|
84 |
+
df : Pandas DataFrame
|
85 |
+
Graph adjacency matrix
|
86 |
+
|
87 |
+
Notes
|
88 |
+
-----
|
89 |
+
For directed graphs, entry i,j corresponds to an edge from i to j.
|
90 |
+
|
91 |
+
The DataFrame entries are assigned to the weight edge attribute. When
|
92 |
+
an edge does not have a weight attribute, the value of the entry is set to
|
93 |
+
the number 1. For multiple (parallel) edges, the values of the entries
|
94 |
+
are determined by the 'multigraph_weight' parameter. The default is to
|
95 |
+
sum the weight attributes for each of the parallel edges.
|
96 |
+
|
97 |
+
When `nodelist` does not contain every node in `G`, the matrix is built
|
98 |
+
from the subgraph of `G` that is induced by the nodes in `nodelist`.
|
99 |
+
|
100 |
+
The convention used for self-loop edges in graphs is to assign the
|
101 |
+
diagonal matrix entry value to the weight attribute of the edge
|
102 |
+
(or the number 1 if the edge has no weight attribute). If the
|
103 |
+
alternate convention of doubling the edge weight is desired the
|
104 |
+
resulting Pandas DataFrame can be modified as follows::
|
105 |
+
|
106 |
+
>>> import pandas as pd
|
107 |
+
>>> G = nx.Graph([(1, 1), (2, 2)])
|
108 |
+
>>> df = nx.to_pandas_adjacency(G)
|
109 |
+
>>> df
|
110 |
+
1 2
|
111 |
+
1 1.0 0.0
|
112 |
+
2 0.0 1.0
|
113 |
+
>>> diag_idx = list(range(len(df)))
|
114 |
+
>>> df.iloc[diag_idx, diag_idx] *= 2
|
115 |
+
>>> df
|
116 |
+
1 2
|
117 |
+
1 2.0 0.0
|
118 |
+
2 0.0 2.0
|
119 |
+
|
120 |
+
Examples
|
121 |
+
--------
|
122 |
+
>>> G = nx.MultiDiGraph()
|
123 |
+
>>> G.add_edge(0, 1, weight=2)
|
124 |
+
0
|
125 |
+
>>> G.add_edge(1, 0)
|
126 |
+
0
|
127 |
+
>>> G.add_edge(2, 2, weight=3)
|
128 |
+
0
|
129 |
+
>>> G.add_edge(2, 2)
|
130 |
+
1
|
131 |
+
>>> nx.to_pandas_adjacency(G, nodelist=[0, 1, 2], dtype=int)
|
132 |
+
0 1 2
|
133 |
+
0 0 2 0
|
134 |
+
1 1 0 0
|
135 |
+
2 0 0 4
|
136 |
+
|
137 |
+
"""
|
138 |
+
import pandas as pd
|
139 |
+
|
140 |
+
M = to_numpy_array(
|
141 |
+
G,
|
142 |
+
nodelist=nodelist,
|
143 |
+
dtype=dtype,
|
144 |
+
order=order,
|
145 |
+
multigraph_weight=multigraph_weight,
|
146 |
+
weight=weight,
|
147 |
+
nonedge=nonedge,
|
148 |
+
)
|
149 |
+
if nodelist is None:
|
150 |
+
nodelist = list(G)
|
151 |
+
return pd.DataFrame(data=M, index=nodelist, columns=nodelist)
|
152 |
+
|
153 |
+
|
154 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
155 |
+
def from_pandas_adjacency(df, create_using=None):
|
156 |
+
r"""Returns a graph from Pandas DataFrame.
|
157 |
+
|
158 |
+
The Pandas DataFrame is interpreted as an adjacency matrix for the graph.
|
159 |
+
|
160 |
+
Parameters
|
161 |
+
----------
|
162 |
+
df : Pandas DataFrame
|
163 |
+
An adjacency matrix representation of a graph
|
164 |
+
|
165 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
166 |
+
Graph type to create. If graph instance, then cleared before populated.
|
167 |
+
|
168 |
+
Notes
|
169 |
+
-----
|
170 |
+
For directed graphs, explicitly mention create_using=nx.DiGraph,
|
171 |
+
and entry i,j of df corresponds to an edge from i to j.
|
172 |
+
|
173 |
+
If `df` has a single data type for each entry it will be converted to an
|
174 |
+
appropriate Python data type.
|
175 |
+
|
176 |
+
If you have node attributes stored in a separate dataframe `df_nodes`,
|
177 |
+
you can load those attributes to the graph `G` using the following code:
|
178 |
+
|
179 |
+
```
|
180 |
+
df_nodes = pd.DataFrame({"node_id": [1, 2, 3], "attribute1": ["A", "B", "C"]})
|
181 |
+
G.add_nodes_from((n, dict(d)) for n, d in df_nodes.iterrows())
|
182 |
+
```
|
183 |
+
|
184 |
+
If `df` has a user-specified compound data type the names
|
185 |
+
of the data fields will be used as attribute keys in the resulting
|
186 |
+
NetworkX graph.
|
187 |
+
|
188 |
+
See Also
|
189 |
+
--------
|
190 |
+
to_pandas_adjacency
|
191 |
+
|
192 |
+
Examples
|
193 |
+
--------
|
194 |
+
Simple integer weights on edges:
|
195 |
+
|
196 |
+
>>> import pandas as pd
|
197 |
+
>>> pd.options.display.max_columns = 20
|
198 |
+
>>> df = pd.DataFrame([[1, 1], [2, 1]])
|
199 |
+
>>> df
|
200 |
+
0 1
|
201 |
+
0 1 1
|
202 |
+
1 2 1
|
203 |
+
>>> G = nx.from_pandas_adjacency(df)
|
204 |
+
>>> G.name = "Graph from pandas adjacency matrix"
|
205 |
+
>>> print(G)
|
206 |
+
Graph named 'Graph from pandas adjacency matrix' with 2 nodes and 3 edges
|
207 |
+
"""
|
208 |
+
|
209 |
+
try:
|
210 |
+
df = df[df.index]
|
211 |
+
except Exception as err:
|
212 |
+
missing = list(set(df.index).difference(set(df.columns)))
|
213 |
+
msg = f"{missing} not in columns"
|
214 |
+
raise nx.NetworkXError("Columns must match Indices.", msg) from err
|
215 |
+
|
216 |
+
A = df.values
|
217 |
+
G = from_numpy_array(A, create_using=create_using)
|
218 |
+
|
219 |
+
nx.relabel.relabel_nodes(G, dict(enumerate(df.columns)), copy=False)
|
220 |
+
return G
|
221 |
+
|
222 |
+
|
223 |
+
@nx._dispatchable(preserve_edge_attrs=True)
|
224 |
+
def to_pandas_edgelist(
|
225 |
+
G,
|
226 |
+
source="source",
|
227 |
+
target="target",
|
228 |
+
nodelist=None,
|
229 |
+
dtype=None,
|
230 |
+
edge_key=None,
|
231 |
+
):
|
232 |
+
"""Returns the graph edge list as a Pandas DataFrame.
|
233 |
+
|
234 |
+
Parameters
|
235 |
+
----------
|
236 |
+
G : graph
|
237 |
+
The NetworkX graph used to construct the Pandas DataFrame.
|
238 |
+
|
239 |
+
source : str or int, optional
|
240 |
+
A valid column name (string or integer) for the source nodes (for the
|
241 |
+
directed case).
|
242 |
+
|
243 |
+
target : str or int, optional
|
244 |
+
A valid column name (string or integer) for the target nodes (for the
|
245 |
+
directed case).
|
246 |
+
|
247 |
+
nodelist : list, optional
|
248 |
+
Use only nodes specified in nodelist
|
249 |
+
|
250 |
+
dtype : dtype, default None
|
251 |
+
Use to create the DataFrame. Data type to force.
|
252 |
+
Only a single dtype is allowed. If None, infer.
|
253 |
+
|
254 |
+
edge_key : str or int or None, optional (default=None)
|
255 |
+
A valid column name (string or integer) for the edge keys (for the
|
256 |
+
multigraph case). If None, edge keys are not stored in the DataFrame.
|
257 |
+
|
258 |
+
Returns
|
259 |
+
-------
|
260 |
+
df : Pandas DataFrame
|
261 |
+
Graph edge list
|
262 |
+
|
263 |
+
Examples
|
264 |
+
--------
|
265 |
+
>>> G = nx.Graph(
|
266 |
+
... [
|
267 |
+
... ("A", "B", {"cost": 1, "weight": 7}),
|
268 |
+
... ("C", "E", {"cost": 9, "weight": 10}),
|
269 |
+
... ]
|
270 |
+
... )
|
271 |
+
>>> df = nx.to_pandas_edgelist(G, nodelist=["A", "C"])
|
272 |
+
>>> df[["source", "target", "cost", "weight"]]
|
273 |
+
source target cost weight
|
274 |
+
0 A B 1 7
|
275 |
+
1 C E 9 10
|
276 |
+
|
277 |
+
>>> G = nx.MultiGraph([("A", "B", {"cost": 1}), ("A", "B", {"cost": 9})])
|
278 |
+
>>> df = nx.to_pandas_edgelist(G, nodelist=["A", "C"], edge_key="ekey")
|
279 |
+
>>> df[["source", "target", "cost", "ekey"]]
|
280 |
+
source target cost ekey
|
281 |
+
0 A B 1 0
|
282 |
+
1 A B 9 1
|
283 |
+
|
284 |
+
"""
|
285 |
+
import pandas as pd
|
286 |
+
|
287 |
+
if nodelist is None:
|
288 |
+
edgelist = G.edges(data=True)
|
289 |
+
else:
|
290 |
+
edgelist = G.edges(nodelist, data=True)
|
291 |
+
source_nodes = [s for s, _, _ in edgelist]
|
292 |
+
target_nodes = [t for _, t, _ in edgelist]
|
293 |
+
|
294 |
+
all_attrs = set().union(*(d.keys() for _, _, d in edgelist))
|
295 |
+
if source in all_attrs:
|
296 |
+
raise nx.NetworkXError(f"Source name {source!r} is an edge attr name")
|
297 |
+
if target in all_attrs:
|
298 |
+
raise nx.NetworkXError(f"Target name {target!r} is an edge attr name")
|
299 |
+
|
300 |
+
nan = float("nan")
|
301 |
+
edge_attr = {k: [d.get(k, nan) for _, _, d in edgelist] for k in all_attrs}
|
302 |
+
|
303 |
+
if G.is_multigraph() and edge_key is not None:
|
304 |
+
if edge_key in all_attrs:
|
305 |
+
raise nx.NetworkXError(f"Edge key name {edge_key!r} is an edge attr name")
|
306 |
+
edge_keys = [k for _, _, k in G.edges(keys=True)]
|
307 |
+
edgelistdict = {source: source_nodes, target: target_nodes, edge_key: edge_keys}
|
308 |
+
else:
|
309 |
+
edgelistdict = {source: source_nodes, target: target_nodes}
|
310 |
+
|
311 |
+
edgelistdict.update(edge_attr)
|
312 |
+
return pd.DataFrame(edgelistdict, dtype=dtype)
|
313 |
+
|
314 |
+
|
315 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
316 |
+
def from_pandas_edgelist(
|
317 |
+
df,
|
318 |
+
source="source",
|
319 |
+
target="target",
|
320 |
+
edge_attr=None,
|
321 |
+
create_using=None,
|
322 |
+
edge_key=None,
|
323 |
+
):
|
324 |
+
"""Returns a graph from Pandas DataFrame containing an edge list.
|
325 |
+
|
326 |
+
The Pandas DataFrame should contain at least two columns of node names and
|
327 |
+
zero or more columns of edge attributes. Each row will be processed as one
|
328 |
+
edge instance.
|
329 |
+
|
330 |
+
Note: This function iterates over DataFrame.values, which is not
|
331 |
+
guaranteed to retain the data type across columns in the row. This is only
|
332 |
+
a problem if your row is entirely numeric and a mix of ints and floats. In
|
333 |
+
that case, all values will be returned as floats. See the
|
334 |
+
DataFrame.iterrows documentation for an example.
|
335 |
+
|
336 |
+
Parameters
|
337 |
+
----------
|
338 |
+
df : Pandas DataFrame
|
339 |
+
An edge list representation of a graph
|
340 |
+
|
341 |
+
source : str or int
|
342 |
+
A valid column name (string or integer) for the source nodes (for the
|
343 |
+
directed case).
|
344 |
+
|
345 |
+
target : str or int
|
346 |
+
A valid column name (string or integer) for the target nodes (for the
|
347 |
+
directed case).
|
348 |
+
|
349 |
+
edge_attr : str or int, iterable, True, or None
|
350 |
+
A valid column name (str or int) or iterable of column names that are
|
351 |
+
used to retrieve items and add them to the graph as edge attributes.
|
352 |
+
If `True`, all of the remaining columns will be added.
|
353 |
+
If `None`, no edge attributes are added to the graph.
|
354 |
+
|
355 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
356 |
+
Graph type to create. If graph instance, then cleared before populated.
|
357 |
+
|
358 |
+
edge_key : str or None, optional (default=None)
|
359 |
+
A valid column name for the edge keys (for a MultiGraph). The values in
|
360 |
+
this column are used for the edge keys when adding edges if create_using
|
361 |
+
is a multigraph.
|
362 |
+
|
363 |
+
If you have node attributes stored in a separate dataframe `df_nodes`,
|
364 |
+
you can load those attributes to the graph `G` using the following code:
|
365 |
+
|
366 |
+
```
|
367 |
+
df_nodes = pd.DataFrame({"node_id": [1, 2, 3], "attribute1": ["A", "B", "C"]})
|
368 |
+
G.add_nodes_from((n, dict(d)) for n, d in df_nodes.iterrows())
|
369 |
+
```
|
370 |
+
|
371 |
+
See Also
|
372 |
+
--------
|
373 |
+
to_pandas_edgelist
|
374 |
+
|
375 |
+
Examples
|
376 |
+
--------
|
377 |
+
Simple integer weights on edges:
|
378 |
+
|
379 |
+
>>> import pandas as pd
|
380 |
+
>>> pd.options.display.max_columns = 20
|
381 |
+
>>> import numpy as np
|
382 |
+
>>> rng = np.random.RandomState(seed=5)
|
383 |
+
>>> ints = rng.randint(1, 11, size=(3, 2))
|
384 |
+
>>> a = ["A", "B", "C"]
|
385 |
+
>>> b = ["D", "A", "E"]
|
386 |
+
>>> df = pd.DataFrame(ints, columns=["weight", "cost"])
|
387 |
+
>>> df[0] = a
|
388 |
+
>>> df["b"] = b
|
389 |
+
>>> df[["weight", "cost", 0, "b"]]
|
390 |
+
weight cost 0 b
|
391 |
+
0 4 7 A D
|
392 |
+
1 7 1 B A
|
393 |
+
2 10 9 C E
|
394 |
+
>>> G = nx.from_pandas_edgelist(df, 0, "b", ["weight", "cost"])
|
395 |
+
>>> G["E"]["C"]["weight"]
|
396 |
+
10
|
397 |
+
>>> G["E"]["C"]["cost"]
|
398 |
+
9
|
399 |
+
>>> edges = pd.DataFrame(
|
400 |
+
... {
|
401 |
+
... "source": [0, 1, 2],
|
402 |
+
... "target": [2, 2, 3],
|
403 |
+
... "weight": [3, 4, 5],
|
404 |
+
... "color": ["red", "blue", "blue"],
|
405 |
+
... }
|
406 |
+
... )
|
407 |
+
>>> G = nx.from_pandas_edgelist(edges, edge_attr=True)
|
408 |
+
>>> G[0][2]["color"]
|
409 |
+
'red'
|
410 |
+
|
411 |
+
Build multigraph with custom keys:
|
412 |
+
|
413 |
+
>>> edges = pd.DataFrame(
|
414 |
+
... {
|
415 |
+
... "source": [0, 1, 2, 0],
|
416 |
+
... "target": [2, 2, 3, 2],
|
417 |
+
... "my_edge_key": ["A", "B", "C", "D"],
|
418 |
+
... "weight": [3, 4, 5, 6],
|
419 |
+
... "color": ["red", "blue", "blue", "blue"],
|
420 |
+
... }
|
421 |
+
... )
|
422 |
+
>>> G = nx.from_pandas_edgelist(
|
423 |
+
... edges,
|
424 |
+
... edge_key="my_edge_key",
|
425 |
+
... edge_attr=["weight", "color"],
|
426 |
+
... create_using=nx.MultiGraph(),
|
427 |
+
... )
|
428 |
+
>>> G[0][2]
|
429 |
+
AtlasView({'A': {'weight': 3, 'color': 'red'}, 'D': {'weight': 6, 'color': 'blue'}})
|
430 |
+
|
431 |
+
|
432 |
+
"""
|
433 |
+
g = nx.empty_graph(0, create_using)
|
434 |
+
|
435 |
+
if edge_attr is None:
|
436 |
+
g.add_edges_from(zip(df[source], df[target]))
|
437 |
+
return g
|
438 |
+
|
439 |
+
reserved_columns = [source, target]
|
440 |
+
|
441 |
+
# Additional columns requested
|
442 |
+
attr_col_headings = []
|
443 |
+
attribute_data = []
|
444 |
+
if edge_attr is True:
|
445 |
+
attr_col_headings = [c for c in df.columns if c not in reserved_columns]
|
446 |
+
elif isinstance(edge_attr, list | tuple):
|
447 |
+
attr_col_headings = edge_attr
|
448 |
+
else:
|
449 |
+
attr_col_headings = [edge_attr]
|
450 |
+
if len(attr_col_headings) == 0:
|
451 |
+
raise nx.NetworkXError(
|
452 |
+
f"Invalid edge_attr argument: No columns found with name: {attr_col_headings}"
|
453 |
+
)
|
454 |
+
|
455 |
+
try:
|
456 |
+
attribute_data = zip(*[df[col] for col in attr_col_headings])
|
457 |
+
except (KeyError, TypeError) as err:
|
458 |
+
msg = f"Invalid edge_attr argument: {edge_attr}"
|
459 |
+
raise nx.NetworkXError(msg) from err
|
460 |
+
|
461 |
+
if g.is_multigraph():
|
462 |
+
# => append the edge keys from the df to the bundled data
|
463 |
+
if edge_key is not None:
|
464 |
+
try:
|
465 |
+
multigraph_edge_keys = df[edge_key]
|
466 |
+
attribute_data = zip(attribute_data, multigraph_edge_keys)
|
467 |
+
except (KeyError, TypeError) as err:
|
468 |
+
msg = f"Invalid edge_key argument: {edge_key}"
|
469 |
+
raise nx.NetworkXError(msg) from err
|
470 |
+
|
471 |
+
for s, t, attrs in zip(df[source], df[target], attribute_data):
|
472 |
+
if edge_key is not None:
|
473 |
+
attrs, multigraph_edge_key = attrs
|
474 |
+
key = g.add_edge(s, t, key=multigraph_edge_key)
|
475 |
+
else:
|
476 |
+
key = g.add_edge(s, t)
|
477 |
+
|
478 |
+
g[s][t][key].update(zip(attr_col_headings, attrs))
|
479 |
+
else:
|
480 |
+
for s, t, attrs in zip(df[source], df[target], attribute_data):
|
481 |
+
g.add_edge(s, t)
|
482 |
+
g[s][t].update(zip(attr_col_headings, attrs))
|
483 |
+
|
484 |
+
return g
|
485 |
+
|
486 |
+
|
487 |
+
@nx._dispatchable(edge_attrs="weight")
|
488 |
+
def to_scipy_sparse_array(G, nodelist=None, dtype=None, weight="weight", format="csr"):
|
489 |
+
"""Returns the graph adjacency matrix as a SciPy sparse array.
|
490 |
+
|
491 |
+
Parameters
|
492 |
+
----------
|
493 |
+
G : graph
|
494 |
+
The NetworkX graph used to construct the sparse matrix.
|
495 |
+
|
496 |
+
nodelist : list, optional
|
497 |
+
The rows and columns are ordered according to the nodes in `nodelist`.
|
498 |
+
If `nodelist` is None, then the ordering is produced by G.nodes().
|
499 |
+
|
500 |
+
dtype : NumPy data-type, optional
|
501 |
+
A valid NumPy dtype used to initialize the array. If None, then the
|
502 |
+
NumPy default is used.
|
503 |
+
|
504 |
+
weight : string or None optional (default='weight')
|
505 |
+
The edge attribute that holds the numerical value used for
|
506 |
+
the edge weight. If None then all edge weights are 1.
|
507 |
+
|
508 |
+
format : str in {'bsr', 'csr', 'csc', 'coo', 'lil', 'dia', 'dok'}
|
509 |
+
The type of the matrix to be returned (default 'csr'). For
|
510 |
+
some algorithms different implementations of sparse matrices
|
511 |
+
can perform better. See [1]_ for details.
|
512 |
+
|
513 |
+
Returns
|
514 |
+
-------
|
515 |
+
A : SciPy sparse array
|
516 |
+
Graph adjacency matrix.
|
517 |
+
|
518 |
+
Notes
|
519 |
+
-----
|
520 |
+
For directed graphs, matrix entry i,j corresponds to an edge from i to j.
|
521 |
+
|
522 |
+
The matrix entries are populated using the edge attribute held in
|
523 |
+
parameter weight. When an edge does not have that attribute, the
|
524 |
+
value of the entry is 1.
|
525 |
+
|
526 |
+
For multiple edges the matrix values are the sums of the edge weights.
|
527 |
+
|
528 |
+
When `nodelist` does not contain every node in `G`, the adjacency matrix
|
529 |
+
is built from the subgraph of `G` that is induced by the nodes in
|
530 |
+
`nodelist`.
|
531 |
+
|
532 |
+
The convention used for self-loop edges in graphs is to assign the
|
533 |
+
diagonal matrix entry value to the weight attribute of the edge
|
534 |
+
(or the number 1 if the edge has no weight attribute). If the
|
535 |
+
alternate convention of doubling the edge weight is desired the
|
536 |
+
resulting SciPy sparse array can be modified as follows:
|
537 |
+
|
538 |
+
>>> G = nx.Graph([(1, 1)])
|
539 |
+
>>> A = nx.to_scipy_sparse_array(G)
|
540 |
+
>>> print(A.todense())
|
541 |
+
[[1]]
|
542 |
+
>>> A.setdiag(A.diagonal() * 2)
|
543 |
+
>>> print(A.toarray())
|
544 |
+
[[2]]
|
545 |
+
|
546 |
+
Examples
|
547 |
+
--------
|
548 |
+
>>> G = nx.MultiDiGraph()
|
549 |
+
>>> G.add_edge(0, 1, weight=2)
|
550 |
+
0
|
551 |
+
>>> G.add_edge(1, 0)
|
552 |
+
0
|
553 |
+
>>> G.add_edge(2, 2, weight=3)
|
554 |
+
0
|
555 |
+
>>> G.add_edge(2, 2)
|
556 |
+
1
|
557 |
+
>>> S = nx.to_scipy_sparse_array(G, nodelist=[0, 1, 2])
|
558 |
+
>>> print(S.toarray())
|
559 |
+
[[0 2 0]
|
560 |
+
[1 0 0]
|
561 |
+
[0 0 4]]
|
562 |
+
|
563 |
+
References
|
564 |
+
----------
|
565 |
+
.. [1] Scipy Dev. References, "Sparse Matrices",
|
566 |
+
https://docs.scipy.org/doc/scipy/reference/sparse.html
|
567 |
+
"""
|
568 |
+
import scipy as sp
|
569 |
+
|
570 |
+
if len(G) == 0:
|
571 |
+
raise nx.NetworkXError("Graph has no nodes or edges")
|
572 |
+
|
573 |
+
if nodelist is None:
|
574 |
+
nodelist = list(G)
|
575 |
+
nlen = len(G)
|
576 |
+
else:
|
577 |
+
nlen = len(nodelist)
|
578 |
+
if nlen == 0:
|
579 |
+
raise nx.NetworkXError("nodelist has no nodes")
|
580 |
+
nodeset = set(G.nbunch_iter(nodelist))
|
581 |
+
if nlen != len(nodeset):
|
582 |
+
for n in nodelist:
|
583 |
+
if n not in G:
|
584 |
+
raise nx.NetworkXError(f"Node {n} in nodelist is not in G")
|
585 |
+
raise nx.NetworkXError("nodelist contains duplicates.")
|
586 |
+
if nlen < len(G):
|
587 |
+
G = G.subgraph(nodelist)
|
588 |
+
|
589 |
+
index = dict(zip(nodelist, range(nlen)))
|
590 |
+
coefficients = zip(
|
591 |
+
*((index[u], index[v], wt) for u, v, wt in G.edges(data=weight, default=1))
|
592 |
+
)
|
593 |
+
try:
|
594 |
+
row, col, data = coefficients
|
595 |
+
except ValueError:
|
596 |
+
# there is no edge in the subgraph
|
597 |
+
row, col, data = [], [], []
|
598 |
+
|
599 |
+
if G.is_directed():
|
600 |
+
A = sp.sparse.coo_array((data, (row, col)), shape=(nlen, nlen), dtype=dtype)
|
601 |
+
else:
|
602 |
+
# symmetrize matrix
|
603 |
+
d = data + data
|
604 |
+
r = row + col
|
605 |
+
c = col + row
|
606 |
+
# selfloop entries get double counted when symmetrizing
|
607 |
+
# so we subtract the data on the diagonal
|
608 |
+
selfloops = list(nx.selfloop_edges(G, data=weight, default=1))
|
609 |
+
if selfloops:
|
610 |
+
diag_index, diag_data = zip(*((index[u], -wt) for u, v, wt in selfloops))
|
611 |
+
d += diag_data
|
612 |
+
r += diag_index
|
613 |
+
c += diag_index
|
614 |
+
A = sp.sparse.coo_array((d, (r, c)), shape=(nlen, nlen), dtype=dtype)
|
615 |
+
try:
|
616 |
+
return A.asformat(format)
|
617 |
+
except ValueError as err:
|
618 |
+
raise nx.NetworkXError(f"Unknown sparse matrix format: {format}") from err
|
619 |
+
|
620 |
+
|
621 |
+
def _csr_gen_triples(A):
|
622 |
+
"""Converts a SciPy sparse array in **Compressed Sparse Row** format to
|
623 |
+
an iterable of weighted edge triples.
|
624 |
+
|
625 |
+
"""
|
626 |
+
nrows = A.shape[0]
|
627 |
+
indptr, dst_indices, data = A.indptr, A.indices, A.data
|
628 |
+
import numpy as np
|
629 |
+
|
630 |
+
src_indices = np.repeat(np.arange(nrows), np.diff(indptr))
|
631 |
+
return zip(src_indices.tolist(), dst_indices.tolist(), A.data.tolist())
|
632 |
+
|
633 |
+
|
634 |
+
def _csc_gen_triples(A):
|
635 |
+
"""Converts a SciPy sparse array in **Compressed Sparse Column** format to
|
636 |
+
an iterable of weighted edge triples.
|
637 |
+
|
638 |
+
"""
|
639 |
+
ncols = A.shape[1]
|
640 |
+
indptr, src_indices, data = A.indptr, A.indices, A.data
|
641 |
+
import numpy as np
|
642 |
+
|
643 |
+
dst_indices = np.repeat(np.arange(ncols), np.diff(indptr))
|
644 |
+
return zip(src_indices.tolist(), dst_indices.tolist(), A.data.tolist())
|
645 |
+
|
646 |
+
|
647 |
+
def _coo_gen_triples(A):
|
648 |
+
"""Converts a SciPy sparse array in **Coordinate** format to an iterable
|
649 |
+
of weighted edge triples.
|
650 |
+
|
651 |
+
"""
|
652 |
+
return zip(A.row.tolist(), A.col.tolist(), A.data.tolist())
|
653 |
+
|
654 |
+
|
655 |
+
def _dok_gen_triples(A):
|
656 |
+
"""Converts a SciPy sparse array in **Dictionary of Keys** format to an
|
657 |
+
iterable of weighted edge triples.
|
658 |
+
|
659 |
+
"""
|
660 |
+
for (r, c), v in A.items():
|
661 |
+
# Use `v.item()` to convert a NumPy scalar to the appropriate Python scalar
|
662 |
+
yield int(r), int(c), v.item()
|
663 |
+
|
664 |
+
|
665 |
+
def _generate_weighted_edges(A):
|
666 |
+
"""Returns an iterable over (u, v, w) triples, where u and v are adjacent
|
667 |
+
vertices and w is the weight of the edge joining u and v.
|
668 |
+
|
669 |
+
`A` is a SciPy sparse array (in any format).
|
670 |
+
|
671 |
+
"""
|
672 |
+
if A.format == "csr":
|
673 |
+
return _csr_gen_triples(A)
|
674 |
+
if A.format == "csc":
|
675 |
+
return _csc_gen_triples(A)
|
676 |
+
if A.format == "dok":
|
677 |
+
return _dok_gen_triples(A)
|
678 |
+
# If A is in any other format (including COO), convert it to COO format.
|
679 |
+
return _coo_gen_triples(A.tocoo())
|
680 |
+
|
681 |
+
|
682 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
683 |
+
def from_scipy_sparse_array(
|
684 |
+
A, parallel_edges=False, create_using=None, edge_attribute="weight"
|
685 |
+
):
|
686 |
+
"""Creates a new graph from an adjacency matrix given as a SciPy sparse
|
687 |
+
array.
|
688 |
+
|
689 |
+
Parameters
|
690 |
+
----------
|
691 |
+
A: scipy.sparse array
|
692 |
+
An adjacency matrix representation of a graph
|
693 |
+
|
694 |
+
parallel_edges : Boolean
|
695 |
+
If this is True, `create_using` is a multigraph, and `A` is an
|
696 |
+
integer matrix, then entry *(i, j)* in the matrix is interpreted as the
|
697 |
+
number of parallel edges joining vertices *i* and *j* in the graph.
|
698 |
+
If it is False, then the entries in the matrix are interpreted as
|
699 |
+
the weight of a single edge joining the vertices.
|
700 |
+
|
701 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
702 |
+
Graph type to create. If graph instance, then cleared before populated.
|
703 |
+
|
704 |
+
edge_attribute: string
|
705 |
+
Name of edge attribute to store matrix numeric value. The data will
|
706 |
+
have the same type as the matrix entry (int, float, (real,imag)).
|
707 |
+
|
708 |
+
Notes
|
709 |
+
-----
|
710 |
+
For directed graphs, explicitly mention create_using=nx.DiGraph,
|
711 |
+
and entry i,j of A corresponds to an edge from i to j.
|
712 |
+
|
713 |
+
If `create_using` is :class:`networkx.MultiGraph` or
|
714 |
+
:class:`networkx.MultiDiGraph`, `parallel_edges` is True, and the
|
715 |
+
entries of `A` are of type :class:`int`, then this function returns a
|
716 |
+
multigraph (constructed from `create_using`) with parallel edges.
|
717 |
+
In this case, `edge_attribute` will be ignored.
|
718 |
+
|
719 |
+
If `create_using` indicates an undirected multigraph, then only the edges
|
720 |
+
indicated by the upper triangle of the matrix `A` will be added to the
|
721 |
+
graph.
|
722 |
+
|
723 |
+
Examples
|
724 |
+
--------
|
725 |
+
>>> import scipy as sp
|
726 |
+
>>> A = sp.sparse.eye(2, 2, 1)
|
727 |
+
>>> G = nx.from_scipy_sparse_array(A)
|
728 |
+
|
729 |
+
If `create_using` indicates a multigraph and the matrix has only integer
|
730 |
+
entries and `parallel_edges` is False, then the entries will be treated
|
731 |
+
as weights for edges joining the nodes (without creating parallel edges):
|
732 |
+
|
733 |
+
>>> A = sp.sparse.csr_array([[1, 1], [1, 2]])
|
734 |
+
>>> G = nx.from_scipy_sparse_array(A, create_using=nx.MultiGraph)
|
735 |
+
>>> G[1][1]
|
736 |
+
AtlasView({0: {'weight': 2}})
|
737 |
+
|
738 |
+
If `create_using` indicates a multigraph and the matrix has only integer
|
739 |
+
entries and `parallel_edges` is True, then the entries will be treated
|
740 |
+
as the number of parallel edges joining those two vertices:
|
741 |
+
|
742 |
+
>>> A = sp.sparse.csr_array([[1, 1], [1, 2]])
|
743 |
+
>>> G = nx.from_scipy_sparse_array(A, parallel_edges=True, create_using=nx.MultiGraph)
|
744 |
+
>>> G[1][1]
|
745 |
+
AtlasView({0: {'weight': 1}, 1: {'weight': 1}})
|
746 |
+
|
747 |
+
"""
|
748 |
+
G = nx.empty_graph(0, create_using)
|
749 |
+
n, m = A.shape
|
750 |
+
if n != m:
|
751 |
+
raise nx.NetworkXError(f"Adjacency matrix not square: nx,ny={A.shape}")
|
752 |
+
# Make sure we get even the isolated nodes of the graph.
|
753 |
+
G.add_nodes_from(range(n))
|
754 |
+
# Create an iterable over (u, v, w) triples and for each triple, add an
|
755 |
+
# edge from u to v with weight w.
|
756 |
+
triples = _generate_weighted_edges(A)
|
757 |
+
# If the entries in the adjacency matrix are integers, the graph is a
|
758 |
+
# multigraph, and parallel_edges is True, then create parallel edges, each
|
759 |
+
# with weight 1, for each entry in the adjacency matrix. Otherwise, create
|
760 |
+
# one edge for each positive entry in the adjacency matrix and set the
|
761 |
+
# weight of that edge to be the entry in the matrix.
|
762 |
+
if A.dtype.kind in ("i", "u") and G.is_multigraph() and parallel_edges:
|
763 |
+
chain = itertools.chain.from_iterable
|
764 |
+
# The following line is equivalent to:
|
765 |
+
#
|
766 |
+
# for (u, v) in edges:
|
767 |
+
# for d in range(A[u, v]):
|
768 |
+
# G.add_edge(u, v, weight=1)
|
769 |
+
#
|
770 |
+
triples = chain(((u, v, 1) for d in range(w)) for (u, v, w) in triples)
|
771 |
+
# If we are creating an undirected multigraph, only add the edges from the
|
772 |
+
# upper triangle of the matrix. Otherwise, add all the edges. This relies
|
773 |
+
# on the fact that the vertices created in the
|
774 |
+
# `_generated_weighted_edges()` function are actually the row/column
|
775 |
+
# indices for the matrix `A`.
|
776 |
+
#
|
777 |
+
# Without this check, we run into a problem where each edge is added twice
|
778 |
+
# when `G.add_weighted_edges_from()` is invoked below.
|
779 |
+
if G.is_multigraph() and not G.is_directed():
|
780 |
+
triples = ((u, v, d) for u, v, d in triples if u <= v)
|
781 |
+
G.add_weighted_edges_from(triples, weight=edge_attribute)
|
782 |
+
return G
|
783 |
+
|
784 |
+
|
785 |
+
@nx._dispatchable(edge_attrs="weight") # edge attrs may also be obtained from `dtype`
|
786 |
+
def to_numpy_array(
|
787 |
+
G,
|
788 |
+
nodelist=None,
|
789 |
+
dtype=None,
|
790 |
+
order=None,
|
791 |
+
multigraph_weight=sum,
|
792 |
+
weight="weight",
|
793 |
+
nonedge=0.0,
|
794 |
+
):
|
795 |
+
"""Returns the graph adjacency matrix as a NumPy array.
|
796 |
+
|
797 |
+
Parameters
|
798 |
+
----------
|
799 |
+
G : graph
|
800 |
+
The NetworkX graph used to construct the NumPy array.
|
801 |
+
|
802 |
+
nodelist : list, optional
|
803 |
+
The rows and columns are ordered according to the nodes in `nodelist`.
|
804 |
+
If `nodelist` is ``None``, then the ordering is produced by ``G.nodes()``.
|
805 |
+
|
806 |
+
dtype : NumPy data type, optional
|
807 |
+
A NumPy data type used to initialize the array. If None, then the NumPy
|
808 |
+
default is used. The dtype can be structured if `weight=None`, in which
|
809 |
+
case the dtype field names are used to look up edge attributes. The
|
810 |
+
result is a structured array where each named field in the dtype
|
811 |
+
corresponds to the adjacency for that edge attribute. See examples for
|
812 |
+
details.
|
813 |
+
|
814 |
+
order : {'C', 'F'}, optional
|
815 |
+
Whether to store multidimensional data in C- or Fortran-contiguous
|
816 |
+
(row- or column-wise) order in memory. If None, then the NumPy default
|
817 |
+
is used.
|
818 |
+
|
819 |
+
multigraph_weight : callable, optional
|
820 |
+
An function that determines how weights in multigraphs are handled.
|
821 |
+
The function should accept a sequence of weights and return a single
|
822 |
+
value. The default is to sum the weights of the multiple edges.
|
823 |
+
|
824 |
+
weight : string or None optional (default = 'weight')
|
825 |
+
The edge attribute that holds the numerical value used for
|
826 |
+
the edge weight. If an edge does not have that attribute, then the
|
827 |
+
value 1 is used instead. `weight` must be ``None`` if a structured
|
828 |
+
dtype is used.
|
829 |
+
|
830 |
+
nonedge : array_like (default = 0.0)
|
831 |
+
The value used to represent non-edges in the adjacency matrix.
|
832 |
+
The array values corresponding to nonedges are typically set to zero.
|
833 |
+
However, this could be undesirable if there are array values
|
834 |
+
corresponding to actual edges that also have the value zero. If so,
|
835 |
+
one might prefer nonedges to have some other value, such as ``nan``.
|
836 |
+
|
837 |
+
Returns
|
838 |
+
-------
|
839 |
+
A : NumPy ndarray
|
840 |
+
Graph adjacency matrix
|
841 |
+
|
842 |
+
Raises
|
843 |
+
------
|
844 |
+
NetworkXError
|
845 |
+
If `dtype` is a structured dtype and `G` is a multigraph
|
846 |
+
ValueError
|
847 |
+
If `dtype` is a structured dtype and `weight` is not `None`
|
848 |
+
|
849 |
+
See Also
|
850 |
+
--------
|
851 |
+
from_numpy_array
|
852 |
+
|
853 |
+
Notes
|
854 |
+
-----
|
855 |
+
For directed graphs, entry ``i, j`` corresponds to an edge from ``i`` to ``j``.
|
856 |
+
|
857 |
+
Entries in the adjacency matrix are given by the `weight` edge attribute.
|
858 |
+
When an edge does not have a weight attribute, the value of the entry is
|
859 |
+
set to the number 1. For multiple (parallel) edges, the values of the
|
860 |
+
entries are determined by the `multigraph_weight` parameter. The default is
|
861 |
+
to sum the weight attributes for each of the parallel edges.
|
862 |
+
|
863 |
+
When `nodelist` does not contain every node in `G`, the adjacency matrix is
|
864 |
+
built from the subgraph of `G` that is induced by the nodes in `nodelist`.
|
865 |
+
|
866 |
+
The convention used for self-loop edges in graphs is to assign the
|
867 |
+
diagonal array entry value to the weight attribute of the edge
|
868 |
+
(or the number 1 if the edge has no weight attribute). If the
|
869 |
+
alternate convention of doubling the edge weight is desired the
|
870 |
+
resulting NumPy array can be modified as follows:
|
871 |
+
|
872 |
+
>>> import numpy as np
|
873 |
+
>>> G = nx.Graph([(1, 1)])
|
874 |
+
>>> A = nx.to_numpy_array(G)
|
875 |
+
>>> A
|
876 |
+
array([[1.]])
|
877 |
+
>>> A[np.diag_indices_from(A)] *= 2
|
878 |
+
>>> A
|
879 |
+
array([[2.]])
|
880 |
+
|
881 |
+
Examples
|
882 |
+
--------
|
883 |
+
>>> G = nx.MultiDiGraph()
|
884 |
+
>>> G.add_edge(0, 1, weight=2)
|
885 |
+
0
|
886 |
+
>>> G.add_edge(1, 0)
|
887 |
+
0
|
888 |
+
>>> G.add_edge(2, 2, weight=3)
|
889 |
+
0
|
890 |
+
>>> G.add_edge(2, 2)
|
891 |
+
1
|
892 |
+
>>> nx.to_numpy_array(G, nodelist=[0, 1, 2])
|
893 |
+
array([[0., 2., 0.],
|
894 |
+
[1., 0., 0.],
|
895 |
+
[0., 0., 4.]])
|
896 |
+
|
897 |
+
When `nodelist` argument is used, nodes of `G` which do not appear in the `nodelist`
|
898 |
+
and their edges are not included in the adjacency matrix. Here is an example:
|
899 |
+
|
900 |
+
>>> G = nx.Graph()
|
901 |
+
>>> G.add_edge(3, 1)
|
902 |
+
>>> G.add_edge(2, 0)
|
903 |
+
>>> G.add_edge(2, 1)
|
904 |
+
>>> G.add_edge(3, 0)
|
905 |
+
>>> nx.to_numpy_array(G, nodelist=[1, 2, 3])
|
906 |
+
array([[0., 1., 1.],
|
907 |
+
[1., 0., 0.],
|
908 |
+
[1., 0., 0.]])
|
909 |
+
|
910 |
+
This function can also be used to create adjacency matrices for multiple
|
911 |
+
edge attributes with structured dtypes:
|
912 |
+
|
913 |
+
>>> G = nx.Graph()
|
914 |
+
>>> G.add_edge(0, 1, weight=10)
|
915 |
+
>>> G.add_edge(1, 2, cost=5)
|
916 |
+
>>> G.add_edge(2, 3, weight=3, cost=-4.0)
|
917 |
+
>>> dtype = np.dtype([("weight", int), ("cost", float)])
|
918 |
+
>>> A = nx.to_numpy_array(G, dtype=dtype, weight=None)
|
919 |
+
>>> A["weight"]
|
920 |
+
array([[ 0, 10, 0, 0],
|
921 |
+
[10, 0, 1, 0],
|
922 |
+
[ 0, 1, 0, 3],
|
923 |
+
[ 0, 0, 3, 0]])
|
924 |
+
>>> A["cost"]
|
925 |
+
array([[ 0., 1., 0., 0.],
|
926 |
+
[ 1., 0., 5., 0.],
|
927 |
+
[ 0., 5., 0., -4.],
|
928 |
+
[ 0., 0., -4., 0.]])
|
929 |
+
|
930 |
+
As stated above, the argument "nonedge" is useful especially when there are
|
931 |
+
actually edges with weight 0 in the graph. Setting a nonedge value different than 0,
|
932 |
+
makes it much clearer to differentiate such 0-weighted edges and actual nonedge values.
|
933 |
+
|
934 |
+
>>> G = nx.Graph()
|
935 |
+
>>> G.add_edge(3, 1, weight=2)
|
936 |
+
>>> G.add_edge(2, 0, weight=0)
|
937 |
+
>>> G.add_edge(2, 1, weight=0)
|
938 |
+
>>> G.add_edge(3, 0, weight=1)
|
939 |
+
>>> nx.to_numpy_array(G, nonedge=-1.0)
|
940 |
+
array([[-1., 2., -1., 1.],
|
941 |
+
[ 2., -1., 0., -1.],
|
942 |
+
[-1., 0., -1., 0.],
|
943 |
+
[ 1., -1., 0., -1.]])
|
944 |
+
"""
|
945 |
+
import numpy as np
|
946 |
+
|
947 |
+
if nodelist is None:
|
948 |
+
nodelist = list(G)
|
949 |
+
nlen = len(nodelist)
|
950 |
+
|
951 |
+
# Input validation
|
952 |
+
nodeset = set(nodelist)
|
953 |
+
if nodeset - set(G):
|
954 |
+
raise nx.NetworkXError(f"Nodes {nodeset - set(G)} in nodelist is not in G")
|
955 |
+
if len(nodeset) < nlen:
|
956 |
+
raise nx.NetworkXError("nodelist contains duplicates.")
|
957 |
+
|
958 |
+
A = np.full((nlen, nlen), fill_value=nonedge, dtype=dtype, order=order)
|
959 |
+
|
960 |
+
# Corner cases: empty nodelist or graph without any edges
|
961 |
+
if nlen == 0 or G.number_of_edges() == 0:
|
962 |
+
return A
|
963 |
+
|
964 |
+
# If dtype is structured and weight is None, use dtype field names as
|
965 |
+
# edge attributes
|
966 |
+
edge_attrs = None # Only single edge attribute by default
|
967 |
+
if A.dtype.names:
|
968 |
+
if weight is None:
|
969 |
+
edge_attrs = dtype.names
|
970 |
+
else:
|
971 |
+
raise ValueError(
|
972 |
+
"Specifying `weight` not supported for structured dtypes\n."
|
973 |
+
"To create adjacency matrices from structured dtypes, use `weight=None`."
|
974 |
+
)
|
975 |
+
|
976 |
+
# Map nodes to row/col in matrix
|
977 |
+
idx = dict(zip(nodelist, range(nlen)))
|
978 |
+
if len(nodelist) < len(G):
|
979 |
+
G = G.subgraph(nodelist).copy()
|
980 |
+
|
981 |
+
# Collect all edge weights and reduce with `multigraph_weights`
|
982 |
+
if G.is_multigraph():
|
983 |
+
if edge_attrs:
|
984 |
+
raise nx.NetworkXError(
|
985 |
+
"Structured arrays are not supported for MultiGraphs"
|
986 |
+
)
|
987 |
+
d = defaultdict(list)
|
988 |
+
for u, v, wt in G.edges(data=weight, default=1.0):
|
989 |
+
d[(idx[u], idx[v])].append(wt)
|
990 |
+
i, j = np.array(list(d.keys())).T # indices
|
991 |
+
wts = [multigraph_weight(ws) for ws in d.values()] # reduced weights
|
992 |
+
else:
|
993 |
+
i, j, wts = [], [], []
|
994 |
+
|
995 |
+
# Special branch: multi-attr adjacency from structured dtypes
|
996 |
+
if edge_attrs:
|
997 |
+
# Extract edges with all data
|
998 |
+
for u, v, data in G.edges(data=True):
|
999 |
+
i.append(idx[u])
|
1000 |
+
j.append(idx[v])
|
1001 |
+
wts.append(data)
|
1002 |
+
# Map each attribute to the appropriate named field in the
|
1003 |
+
# structured dtype
|
1004 |
+
for attr in edge_attrs:
|
1005 |
+
attr_data = [wt.get(attr, 1.0) for wt in wts]
|
1006 |
+
A[attr][i, j] = attr_data
|
1007 |
+
if not G.is_directed():
|
1008 |
+
A[attr][j, i] = attr_data
|
1009 |
+
return A
|
1010 |
+
|
1011 |
+
for u, v, wt in G.edges(data=weight, default=1.0):
|
1012 |
+
i.append(idx[u])
|
1013 |
+
j.append(idx[v])
|
1014 |
+
wts.append(wt)
|
1015 |
+
|
1016 |
+
# Set array values with advanced indexing
|
1017 |
+
A[i, j] = wts
|
1018 |
+
if not G.is_directed():
|
1019 |
+
A[j, i] = wts
|
1020 |
+
|
1021 |
+
return A
|
1022 |
+
|
1023 |
+
|
1024 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
1025 |
+
def from_numpy_array(A, parallel_edges=False, create_using=None, edge_attr="weight"):
|
1026 |
+
"""Returns a graph from a 2D NumPy array.
|
1027 |
+
|
1028 |
+
The 2D NumPy array is interpreted as an adjacency matrix for the graph.
|
1029 |
+
|
1030 |
+
Parameters
|
1031 |
+
----------
|
1032 |
+
A : a 2D numpy.ndarray
|
1033 |
+
An adjacency matrix representation of a graph
|
1034 |
+
|
1035 |
+
parallel_edges : Boolean
|
1036 |
+
If this is True, `create_using` is a multigraph, and `A` is an
|
1037 |
+
integer array, then entry *(i, j)* in the array is interpreted as the
|
1038 |
+
number of parallel edges joining vertices *i* and *j* in the graph.
|
1039 |
+
If it is False, then the entries in the array are interpreted as
|
1040 |
+
the weight of a single edge joining the vertices.
|
1041 |
+
|
1042 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
1043 |
+
Graph type to create. If graph instance, then cleared before populated.
|
1044 |
+
|
1045 |
+
edge_attr : String, optional (default="weight")
|
1046 |
+
The attribute to which the array values are assigned on each edge. If
|
1047 |
+
it is None, edge attributes will not be assigned.
|
1048 |
+
|
1049 |
+
Notes
|
1050 |
+
-----
|
1051 |
+
For directed graphs, explicitly mention create_using=nx.DiGraph,
|
1052 |
+
and entry i,j of A corresponds to an edge from i to j.
|
1053 |
+
|
1054 |
+
If `create_using` is :class:`networkx.MultiGraph` or
|
1055 |
+
:class:`networkx.MultiDiGraph`, `parallel_edges` is True, and the
|
1056 |
+
entries of `A` are of type :class:`int`, then this function returns a
|
1057 |
+
multigraph (of the same type as `create_using`) with parallel edges.
|
1058 |
+
|
1059 |
+
If `create_using` indicates an undirected multigraph, then only the edges
|
1060 |
+
indicated by the upper triangle of the array `A` will be added to the
|
1061 |
+
graph.
|
1062 |
+
|
1063 |
+
If `edge_attr` is Falsy (False or None), edge attributes will not be
|
1064 |
+
assigned, and the array data will be treated like a binary mask of
|
1065 |
+
edge presence or absence. Otherwise, the attributes will be assigned
|
1066 |
+
as follows:
|
1067 |
+
|
1068 |
+
If the NumPy array has a single data type for each array entry it
|
1069 |
+
will be converted to an appropriate Python data type.
|
1070 |
+
|
1071 |
+
If the NumPy array has a user-specified compound data type the names
|
1072 |
+
of the data fields will be used as attribute keys in the resulting
|
1073 |
+
NetworkX graph.
|
1074 |
+
|
1075 |
+
See Also
|
1076 |
+
--------
|
1077 |
+
to_numpy_array
|
1078 |
+
|
1079 |
+
Examples
|
1080 |
+
--------
|
1081 |
+
Simple integer weights on edges:
|
1082 |
+
|
1083 |
+
>>> import numpy as np
|
1084 |
+
>>> A = np.array([[1, 1], [2, 1]])
|
1085 |
+
>>> G = nx.from_numpy_array(A)
|
1086 |
+
>>> G.edges(data=True)
|
1087 |
+
EdgeDataView([(0, 0, {'weight': 1}), (0, 1, {'weight': 2}), (1, 1, {'weight': 1})])
|
1088 |
+
|
1089 |
+
If `create_using` indicates a multigraph and the array has only integer
|
1090 |
+
entries and `parallel_edges` is False, then the entries will be treated
|
1091 |
+
as weights for edges joining the nodes (without creating parallel edges):
|
1092 |
+
|
1093 |
+
>>> A = np.array([[1, 1], [1, 2]])
|
1094 |
+
>>> G = nx.from_numpy_array(A, create_using=nx.MultiGraph)
|
1095 |
+
>>> G[1][1]
|
1096 |
+
AtlasView({0: {'weight': 2}})
|
1097 |
+
|
1098 |
+
If `create_using` indicates a multigraph and the array has only integer
|
1099 |
+
entries and `parallel_edges` is True, then the entries will be treated
|
1100 |
+
as the number of parallel edges joining those two vertices:
|
1101 |
+
|
1102 |
+
>>> A = np.array([[1, 1], [1, 2]])
|
1103 |
+
>>> temp = nx.MultiGraph()
|
1104 |
+
>>> G = nx.from_numpy_array(A, parallel_edges=True, create_using=temp)
|
1105 |
+
>>> G[1][1]
|
1106 |
+
AtlasView({0: {'weight': 1}, 1: {'weight': 1}})
|
1107 |
+
|
1108 |
+
User defined compound data type on edges:
|
1109 |
+
|
1110 |
+
>>> dt = [("weight", float), ("cost", int)]
|
1111 |
+
>>> A = np.array([[(1.0, 2)]], dtype=dt)
|
1112 |
+
>>> G = nx.from_numpy_array(A)
|
1113 |
+
>>> G.edges()
|
1114 |
+
EdgeView([(0, 0)])
|
1115 |
+
>>> G[0][0]["cost"]
|
1116 |
+
2
|
1117 |
+
>>> G[0][0]["weight"]
|
1118 |
+
1.0
|
1119 |
+
|
1120 |
+
"""
|
1121 |
+
kind_to_python_type = {
|
1122 |
+
"f": float,
|
1123 |
+
"i": int,
|
1124 |
+
"u": int,
|
1125 |
+
"b": bool,
|
1126 |
+
"c": complex,
|
1127 |
+
"S": str,
|
1128 |
+
"U": str,
|
1129 |
+
"V": "void",
|
1130 |
+
}
|
1131 |
+
G = nx.empty_graph(0, create_using)
|
1132 |
+
if A.ndim != 2:
|
1133 |
+
raise nx.NetworkXError(f"Input array must be 2D, not {A.ndim}")
|
1134 |
+
n, m = A.shape
|
1135 |
+
if n != m:
|
1136 |
+
raise nx.NetworkXError(f"Adjacency matrix not square: nx,ny={A.shape}")
|
1137 |
+
dt = A.dtype
|
1138 |
+
try:
|
1139 |
+
python_type = kind_to_python_type[dt.kind]
|
1140 |
+
except Exception as err:
|
1141 |
+
raise TypeError(f"Unknown numpy data type: {dt}") from err
|
1142 |
+
|
1143 |
+
# Make sure we get even the isolated nodes of the graph.
|
1144 |
+
G.add_nodes_from(range(n))
|
1145 |
+
# Get a list of all the entries in the array with nonzero entries. These
|
1146 |
+
# coordinates become edges in the graph. (convert to int from np.int64)
|
1147 |
+
edges = ((int(e[0]), int(e[1])) for e in zip(*A.nonzero()))
|
1148 |
+
# handle numpy constructed data type
|
1149 |
+
if python_type == "void":
|
1150 |
+
# Sort the fields by their offset, then by dtype, then by name.
|
1151 |
+
fields = sorted(
|
1152 |
+
(offset, dtype, name) for name, (dtype, offset) in A.dtype.fields.items()
|
1153 |
+
)
|
1154 |
+
triples = (
|
1155 |
+
(
|
1156 |
+
u,
|
1157 |
+
v,
|
1158 |
+
{}
|
1159 |
+
if edge_attr in [False, None]
|
1160 |
+
else {
|
1161 |
+
name: kind_to_python_type[dtype.kind](val)
|
1162 |
+
for (_, dtype, name), val in zip(fields, A[u, v])
|
1163 |
+
},
|
1164 |
+
)
|
1165 |
+
for u, v in edges
|
1166 |
+
)
|
1167 |
+
# If the entries in the adjacency matrix are integers, the graph is a
|
1168 |
+
# multigraph, and parallel_edges is True, then create parallel edges, each
|
1169 |
+
# with weight 1, for each entry in the adjacency matrix. Otherwise, create
|
1170 |
+
# one edge for each positive entry in the adjacency matrix and set the
|
1171 |
+
# weight of that edge to be the entry in the matrix.
|
1172 |
+
elif python_type is int and G.is_multigraph() and parallel_edges:
|
1173 |
+
chain = itertools.chain.from_iterable
|
1174 |
+
# The following line is equivalent to:
|
1175 |
+
#
|
1176 |
+
# for (u, v) in edges:
|
1177 |
+
# for d in range(A[u, v]):
|
1178 |
+
# G.add_edge(u, v, weight=1)
|
1179 |
+
#
|
1180 |
+
if edge_attr in [False, None]:
|
1181 |
+
triples = chain(((u, v, {}) for d in range(A[u, v])) for (u, v) in edges)
|
1182 |
+
else:
|
1183 |
+
triples = chain(
|
1184 |
+
((u, v, {edge_attr: 1}) for d in range(A[u, v])) for (u, v) in edges
|
1185 |
+
)
|
1186 |
+
else: # basic data type
|
1187 |
+
if edge_attr in [False, None]:
|
1188 |
+
triples = ((u, v, {}) for u, v in edges)
|
1189 |
+
else:
|
1190 |
+
triples = ((u, v, {edge_attr: python_type(A[u, v])}) for u, v in edges)
|
1191 |
+
# If we are creating an undirected multigraph, only add the edges from the
|
1192 |
+
# upper triangle of the matrix. Otherwise, add all the edges. This relies
|
1193 |
+
# on the fact that the vertices created in the
|
1194 |
+
# `_generated_weighted_edges()` function are actually the row/column
|
1195 |
+
# indices for the matrix `A`.
|
1196 |
+
#
|
1197 |
+
# Without this check, we run into a problem where each edge is added twice
|
1198 |
+
# when `G.add_edges_from()` is invoked below.
|
1199 |
+
if G.is_multigraph() and not G.is_directed():
|
1200 |
+
triples = ((u, v, d) for u, v, d in triples if u <= v)
|
1201 |
+
G.add_edges_from(triples)
|
1202 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/exception.py
ADDED
@@ -0,0 +1,125 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
**********
|
3 |
+
Exceptions
|
4 |
+
**********
|
5 |
+
|
6 |
+
Base exceptions and errors for NetworkX.
|
7 |
+
"""
|
8 |
+
|
9 |
+
__all__ = [
|
10 |
+
"HasACycle",
|
11 |
+
"NodeNotFound",
|
12 |
+
"PowerIterationFailedConvergence",
|
13 |
+
"ExceededMaxIterations",
|
14 |
+
"AmbiguousSolution",
|
15 |
+
"NetworkXAlgorithmError",
|
16 |
+
"NetworkXException",
|
17 |
+
"NetworkXError",
|
18 |
+
"NetworkXNoCycle",
|
19 |
+
"NetworkXNoPath",
|
20 |
+
"NetworkXNotImplemented",
|
21 |
+
"NetworkXPointlessConcept",
|
22 |
+
"NetworkXUnbounded",
|
23 |
+
"NetworkXUnfeasible",
|
24 |
+
]
|
25 |
+
|
26 |
+
|
27 |
+
class NetworkXException(Exception):
|
28 |
+
"""Base class for exceptions in NetworkX."""
|
29 |
+
|
30 |
+
|
31 |
+
class NetworkXError(NetworkXException):
|
32 |
+
"""Exception for a serious error in NetworkX"""
|
33 |
+
|
34 |
+
|
35 |
+
class NetworkXPointlessConcept(NetworkXException):
|
36 |
+
"""Raised when a null graph is provided as input to an algorithm
|
37 |
+
that cannot use it.
|
38 |
+
|
39 |
+
The null graph is sometimes considered a pointless concept [1]_,
|
40 |
+
thus the name of the exception.
|
41 |
+
|
42 |
+
References
|
43 |
+
----------
|
44 |
+
.. [1] Harary, F. and Read, R. "Is the Null Graph a Pointless
|
45 |
+
Concept?" In Graphs and Combinatorics Conference, George
|
46 |
+
Washington University. New York: Springer-Verlag, 1973.
|
47 |
+
|
48 |
+
"""
|
49 |
+
|
50 |
+
|
51 |
+
class NetworkXAlgorithmError(NetworkXException):
|
52 |
+
"""Exception for unexpected termination of algorithms."""
|
53 |
+
|
54 |
+
|
55 |
+
class NetworkXUnfeasible(NetworkXAlgorithmError):
|
56 |
+
"""Exception raised by algorithms trying to solve a problem
|
57 |
+
instance that has no feasible solution."""
|
58 |
+
|
59 |
+
|
60 |
+
class NetworkXNoPath(NetworkXUnfeasible):
|
61 |
+
"""Exception for algorithms that should return a path when running
|
62 |
+
on graphs where such a path does not exist."""
|
63 |
+
|
64 |
+
|
65 |
+
class NetworkXNoCycle(NetworkXUnfeasible):
|
66 |
+
"""Exception for algorithms that should return a cycle when running
|
67 |
+
on graphs where such a cycle does not exist."""
|
68 |
+
|
69 |
+
|
70 |
+
class HasACycle(NetworkXException):
|
71 |
+
"""Raised if a graph has a cycle when an algorithm expects that it
|
72 |
+
will have no cycles.
|
73 |
+
|
74 |
+
"""
|
75 |
+
|
76 |
+
|
77 |
+
class NetworkXUnbounded(NetworkXAlgorithmError):
|
78 |
+
"""Exception raised by algorithms trying to solve a maximization
|
79 |
+
or a minimization problem instance that is unbounded."""
|
80 |
+
|
81 |
+
|
82 |
+
class NetworkXNotImplemented(NetworkXException):
|
83 |
+
"""Exception raised by algorithms not implemented for a type of graph."""
|
84 |
+
|
85 |
+
|
86 |
+
class NodeNotFound(NetworkXException):
|
87 |
+
"""Exception raised if requested node is not present in the graph"""
|
88 |
+
|
89 |
+
|
90 |
+
class AmbiguousSolution(NetworkXException):
|
91 |
+
"""Raised if more than one valid solution exists for an intermediary step
|
92 |
+
of an algorithm.
|
93 |
+
|
94 |
+
In the face of ambiguity, refuse the temptation to guess.
|
95 |
+
This may occur, for example, when trying to determine the
|
96 |
+
bipartite node sets in a disconnected bipartite graph when
|
97 |
+
computing bipartite matchings.
|
98 |
+
|
99 |
+
"""
|
100 |
+
|
101 |
+
|
102 |
+
class ExceededMaxIterations(NetworkXException):
|
103 |
+
"""Raised if a loop iterates too many times without breaking.
|
104 |
+
|
105 |
+
This may occur, for example, in an algorithm that computes
|
106 |
+
progressively better approximations to a value but exceeds an
|
107 |
+
iteration bound specified by the user.
|
108 |
+
|
109 |
+
"""
|
110 |
+
|
111 |
+
|
112 |
+
class PowerIterationFailedConvergence(ExceededMaxIterations):
|
113 |
+
"""Raised when the power iteration method fails to converge within a
|
114 |
+
specified iteration limit.
|
115 |
+
|
116 |
+
`num_iterations` is the number of iterations that have been
|
117 |
+
completed when this exception was raised.
|
118 |
+
|
119 |
+
"""
|
120 |
+
|
121 |
+
def __init__(self, num_iterations, *args, **kw):
|
122 |
+
msg = f"power iteration failed to converge within {num_iterations} iterations"
|
123 |
+
exception_message = msg
|
124 |
+
superinit = super().__init__
|
125 |
+
superinit(self, exception_message, *args, **kw)
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/__init__.py
ADDED
@@ -0,0 +1,33 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
A package for generating various graphs in networkx.
|
3 |
+
|
4 |
+
"""
|
5 |
+
from networkx.generators.atlas import *
|
6 |
+
from networkx.generators.classic import *
|
7 |
+
from networkx.generators.cographs import *
|
8 |
+
from networkx.generators.community import *
|
9 |
+
from networkx.generators.degree_seq import *
|
10 |
+
from networkx.generators.directed import *
|
11 |
+
from networkx.generators.duplication import *
|
12 |
+
from networkx.generators.ego import *
|
13 |
+
from networkx.generators.expanders import *
|
14 |
+
from networkx.generators.geometric import *
|
15 |
+
from networkx.generators.harary_graph import *
|
16 |
+
from networkx.generators.internet_as_graphs import *
|
17 |
+
from networkx.generators.intersection import *
|
18 |
+
from networkx.generators.interval_graph import *
|
19 |
+
from networkx.generators.joint_degree_seq import *
|
20 |
+
from networkx.generators.lattice import *
|
21 |
+
from networkx.generators.line import *
|
22 |
+
from networkx.generators.mycielski import *
|
23 |
+
from networkx.generators.nonisomorphic_trees import *
|
24 |
+
from networkx.generators.random_clustered import *
|
25 |
+
from networkx.generators.random_graphs import *
|
26 |
+
from networkx.generators.small import *
|
27 |
+
from networkx.generators.social import *
|
28 |
+
from networkx.generators.spectral_graph_forge import *
|
29 |
+
from networkx.generators.stochastic import *
|
30 |
+
from networkx.generators.sudoku import *
|
31 |
+
from networkx.generators.time_series import *
|
32 |
+
from networkx.generators.trees import *
|
33 |
+
from networkx.generators.triads import *
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/atlas.py
ADDED
@@ -0,0 +1,179 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
Generators for the small graph atlas.
|
3 |
+
"""
|
4 |
+
import gzip
|
5 |
+
import importlib.resources
|
6 |
+
import os
|
7 |
+
import os.path
|
8 |
+
from itertools import islice
|
9 |
+
|
10 |
+
import networkx as nx
|
11 |
+
|
12 |
+
__all__ = ["graph_atlas", "graph_atlas_g"]
|
13 |
+
|
14 |
+
#: The total number of graphs in the atlas.
|
15 |
+
#:
|
16 |
+
#: The graphs are labeled starting from 0 and extending to (but not
|
17 |
+
#: including) this number.
|
18 |
+
NUM_GRAPHS = 1253
|
19 |
+
|
20 |
+
#: The path to the data file containing the graph edge lists.
|
21 |
+
#:
|
22 |
+
#: This is the absolute path of the gzipped text file containing the
|
23 |
+
#: edge list for each graph in the atlas. The file contains one entry
|
24 |
+
#: per graph in the atlas, in sequential order, starting from graph
|
25 |
+
#: number 0 and extending through graph number 1252 (see
|
26 |
+
#: :data:`NUM_GRAPHS`). Each entry looks like
|
27 |
+
#:
|
28 |
+
#: .. sourcecode:: text
|
29 |
+
#:
|
30 |
+
#: GRAPH 6
|
31 |
+
#: NODES 3
|
32 |
+
#: 0 1
|
33 |
+
#: 0 2
|
34 |
+
#:
|
35 |
+
#: where the first two lines are the graph's index in the atlas and the
|
36 |
+
#: number of nodes in the graph, and the remaining lines are the edge
|
37 |
+
#: list.
|
38 |
+
#:
|
39 |
+
#: This file was generated from a Python list of graphs via code like
|
40 |
+
#: the following::
|
41 |
+
#:
|
42 |
+
#: import gzip
|
43 |
+
#: from networkx.generators.atlas import graph_atlas_g
|
44 |
+
#: from networkx.readwrite.edgelist import write_edgelist
|
45 |
+
#:
|
46 |
+
#: with gzip.open('atlas.dat.gz', 'wb') as f:
|
47 |
+
#: for i, G in enumerate(graph_atlas_g()):
|
48 |
+
#: f.write(bytes(f'GRAPH {i}\n', encoding='utf-8'))
|
49 |
+
#: f.write(bytes(f'NODES {len(G)}\n', encoding='utf-8'))
|
50 |
+
#: write_edgelist(G, f, data=False)
|
51 |
+
#:
|
52 |
+
|
53 |
+
# Path to the atlas file
|
54 |
+
ATLAS_FILE = importlib.resources.files("networkx.generators") / "atlas.dat.gz"
|
55 |
+
|
56 |
+
|
57 |
+
def _generate_graphs():
|
58 |
+
"""Sequentially read the file containing the edge list data for the
|
59 |
+
graphs in the atlas and generate the graphs one at a time.
|
60 |
+
|
61 |
+
This function reads the file given in :data:`.ATLAS_FILE`.
|
62 |
+
|
63 |
+
"""
|
64 |
+
with gzip.open(ATLAS_FILE, "rb") as f:
|
65 |
+
line = f.readline()
|
66 |
+
while line and line.startswith(b"GRAPH"):
|
67 |
+
# The first two lines of each entry tell us the index of the
|
68 |
+
# graph in the list and the number of nodes in the graph.
|
69 |
+
# They look like this:
|
70 |
+
#
|
71 |
+
# GRAPH 3
|
72 |
+
# NODES 2
|
73 |
+
#
|
74 |
+
graph_index = int(line[6:].rstrip())
|
75 |
+
line = f.readline()
|
76 |
+
num_nodes = int(line[6:].rstrip())
|
77 |
+
# The remaining lines contain the edge list, until the next
|
78 |
+
# GRAPH line (or until the end of the file).
|
79 |
+
edgelist = []
|
80 |
+
line = f.readline()
|
81 |
+
while line and not line.startswith(b"GRAPH"):
|
82 |
+
edgelist.append(line.rstrip())
|
83 |
+
line = f.readline()
|
84 |
+
G = nx.Graph()
|
85 |
+
G.name = f"G{graph_index}"
|
86 |
+
G.add_nodes_from(range(num_nodes))
|
87 |
+
G.add_edges_from(tuple(map(int, e.split())) for e in edgelist)
|
88 |
+
yield G
|
89 |
+
|
90 |
+
|
91 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
92 |
+
def graph_atlas(i):
|
93 |
+
"""Returns graph number `i` from the Graph Atlas.
|
94 |
+
|
95 |
+
For more information, see :func:`.graph_atlas_g`.
|
96 |
+
|
97 |
+
Parameters
|
98 |
+
----------
|
99 |
+
i : int
|
100 |
+
The index of the graph from the atlas to get. The graph at index
|
101 |
+
0 is assumed to be the null graph.
|
102 |
+
|
103 |
+
Returns
|
104 |
+
-------
|
105 |
+
list
|
106 |
+
A list of :class:`~networkx.Graph` objects, the one at index *i*
|
107 |
+
corresponding to the graph *i* in the Graph Atlas.
|
108 |
+
|
109 |
+
See also
|
110 |
+
--------
|
111 |
+
graph_atlas_g
|
112 |
+
|
113 |
+
Notes
|
114 |
+
-----
|
115 |
+
The time required by this function increases linearly with the
|
116 |
+
argument `i`, since it reads a large file sequentially in order to
|
117 |
+
generate the graph [1]_.
|
118 |
+
|
119 |
+
References
|
120 |
+
----------
|
121 |
+
.. [1] Ronald C. Read and Robin J. Wilson, *An Atlas of Graphs*.
|
122 |
+
Oxford University Press, 1998.
|
123 |
+
|
124 |
+
"""
|
125 |
+
if not (0 <= i < NUM_GRAPHS):
|
126 |
+
raise ValueError(f"index must be between 0 and {NUM_GRAPHS}")
|
127 |
+
return next(islice(_generate_graphs(), i, None))
|
128 |
+
|
129 |
+
|
130 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
131 |
+
def graph_atlas_g():
|
132 |
+
"""Returns the list of all graphs with up to seven nodes named in the
|
133 |
+
Graph Atlas.
|
134 |
+
|
135 |
+
The graphs are listed in increasing order by
|
136 |
+
|
137 |
+
1. number of nodes,
|
138 |
+
2. number of edges,
|
139 |
+
3. degree sequence (for example 111223 < 112222),
|
140 |
+
4. number of automorphisms,
|
141 |
+
|
142 |
+
in that order, with three exceptions as described in the *Notes*
|
143 |
+
section below. This causes the list to correspond with the index of
|
144 |
+
the graphs in the Graph Atlas [atlas]_, with the first graph,
|
145 |
+
``G[0]``, being the null graph.
|
146 |
+
|
147 |
+
Returns
|
148 |
+
-------
|
149 |
+
list
|
150 |
+
A list of :class:`~networkx.Graph` objects, the one at index *i*
|
151 |
+
corresponding to the graph *i* in the Graph Atlas.
|
152 |
+
|
153 |
+
See also
|
154 |
+
--------
|
155 |
+
graph_atlas
|
156 |
+
|
157 |
+
Notes
|
158 |
+
-----
|
159 |
+
This function may be expensive in both time and space, since it
|
160 |
+
reads a large file sequentially in order to populate the list.
|
161 |
+
|
162 |
+
Although the NetworkX atlas functions match the order of graphs
|
163 |
+
given in the "Atlas of Graphs" book, there are (at least) three
|
164 |
+
errors in the ordering described in the book. The following three
|
165 |
+
pairs of nodes violate the lexicographically nondecreasing sorted
|
166 |
+
degree sequence rule:
|
167 |
+
|
168 |
+
- graphs 55 and 56 with degree sequences 001111 and 000112,
|
169 |
+
- graphs 1007 and 1008 with degree sequences 3333444 and 3333336,
|
170 |
+
- graphs 1012 and 1213 with degree sequences 1244555 and 1244456.
|
171 |
+
|
172 |
+
References
|
173 |
+
----------
|
174 |
+
.. [atlas] Ronald C. Read and Robin J. Wilson,
|
175 |
+
*An Atlas of Graphs*.
|
176 |
+
Oxford University Press, 1998.
|
177 |
+
|
178 |
+
"""
|
179 |
+
return list(_generate_graphs())
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/classic.py
ADDED
@@ -0,0 +1,1054 @@
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|
1 |
+
"""Generators for some classic graphs.
|
2 |
+
|
3 |
+
The typical graph builder function is called as follows:
|
4 |
+
|
5 |
+
>>> G = nx.complete_graph(100)
|
6 |
+
|
7 |
+
returning the complete graph on n nodes labeled 0, .., 99
|
8 |
+
as a simple graph. Except for `empty_graph`, all the functions
|
9 |
+
in this module return a Graph class (i.e. a simple, undirected graph).
|
10 |
+
|
11 |
+
"""
|
12 |
+
|
13 |
+
import itertools
|
14 |
+
import numbers
|
15 |
+
|
16 |
+
import networkx as nx
|
17 |
+
from networkx.classes import Graph
|
18 |
+
from networkx.exception import NetworkXError
|
19 |
+
from networkx.utils import nodes_or_number, pairwise
|
20 |
+
|
21 |
+
__all__ = [
|
22 |
+
"balanced_tree",
|
23 |
+
"barbell_graph",
|
24 |
+
"binomial_tree",
|
25 |
+
"complete_graph",
|
26 |
+
"complete_multipartite_graph",
|
27 |
+
"circular_ladder_graph",
|
28 |
+
"circulant_graph",
|
29 |
+
"cycle_graph",
|
30 |
+
"dorogovtsev_goltsev_mendes_graph",
|
31 |
+
"empty_graph",
|
32 |
+
"full_rary_tree",
|
33 |
+
"kneser_graph",
|
34 |
+
"ladder_graph",
|
35 |
+
"lollipop_graph",
|
36 |
+
"null_graph",
|
37 |
+
"path_graph",
|
38 |
+
"star_graph",
|
39 |
+
"tadpole_graph",
|
40 |
+
"trivial_graph",
|
41 |
+
"turan_graph",
|
42 |
+
"wheel_graph",
|
43 |
+
]
|
44 |
+
|
45 |
+
|
46 |
+
# -------------------------------------------------------------------
|
47 |
+
# Some Classic Graphs
|
48 |
+
# -------------------------------------------------------------------
|
49 |
+
|
50 |
+
|
51 |
+
def _tree_edges(n, r):
|
52 |
+
if n == 0:
|
53 |
+
return
|
54 |
+
# helper function for trees
|
55 |
+
# yields edges in rooted tree at 0 with n nodes and branching ratio r
|
56 |
+
nodes = iter(range(n))
|
57 |
+
parents = [next(nodes)] # stack of max length r
|
58 |
+
while parents:
|
59 |
+
source = parents.pop(0)
|
60 |
+
for i in range(r):
|
61 |
+
try:
|
62 |
+
target = next(nodes)
|
63 |
+
parents.append(target)
|
64 |
+
yield source, target
|
65 |
+
except StopIteration:
|
66 |
+
break
|
67 |
+
|
68 |
+
|
69 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
70 |
+
def full_rary_tree(r, n, create_using=None):
|
71 |
+
"""Creates a full r-ary tree of `n` nodes.
|
72 |
+
|
73 |
+
Sometimes called a k-ary, n-ary, or m-ary tree.
|
74 |
+
"... all non-leaf nodes have exactly r children and all levels
|
75 |
+
are full except for some rightmost position of the bottom level
|
76 |
+
(if a leaf at the bottom level is missing, then so are all of the
|
77 |
+
leaves to its right." [1]_
|
78 |
+
|
79 |
+
.. plot::
|
80 |
+
|
81 |
+
>>> nx.draw(nx.full_rary_tree(2, 10))
|
82 |
+
|
83 |
+
Parameters
|
84 |
+
----------
|
85 |
+
r : int
|
86 |
+
branching factor of the tree
|
87 |
+
n : int
|
88 |
+
Number of nodes in the tree
|
89 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
90 |
+
Graph type to create. If graph instance, then cleared before populated.
|
91 |
+
|
92 |
+
Returns
|
93 |
+
-------
|
94 |
+
G : networkx Graph
|
95 |
+
An r-ary tree with n nodes
|
96 |
+
|
97 |
+
References
|
98 |
+
----------
|
99 |
+
.. [1] An introduction to data structures and algorithms,
|
100 |
+
James Andrew Storer, Birkhauser Boston 2001, (page 225).
|
101 |
+
"""
|
102 |
+
G = empty_graph(n, create_using)
|
103 |
+
G.add_edges_from(_tree_edges(n, r))
|
104 |
+
return G
|
105 |
+
|
106 |
+
|
107 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
108 |
+
def kneser_graph(n, k):
|
109 |
+
"""Returns the Kneser Graph with parameters `n` and `k`.
|
110 |
+
|
111 |
+
The Kneser Graph has nodes that are k-tuples (subsets) of the integers
|
112 |
+
between 0 and ``n-1``. Nodes are adjacent if their corresponding sets are disjoint.
|
113 |
+
|
114 |
+
Parameters
|
115 |
+
----------
|
116 |
+
n: int
|
117 |
+
Number of integers from which to make node subsets.
|
118 |
+
Subsets are drawn from ``set(range(n))``.
|
119 |
+
k: int
|
120 |
+
Size of the subsets.
|
121 |
+
|
122 |
+
Returns
|
123 |
+
-------
|
124 |
+
G : NetworkX Graph
|
125 |
+
|
126 |
+
Examples
|
127 |
+
--------
|
128 |
+
>>> G = nx.kneser_graph(5, 2)
|
129 |
+
>>> G.number_of_nodes()
|
130 |
+
10
|
131 |
+
>>> G.number_of_edges()
|
132 |
+
15
|
133 |
+
>>> nx.is_isomorphic(G, nx.petersen_graph())
|
134 |
+
True
|
135 |
+
"""
|
136 |
+
if n <= 0:
|
137 |
+
raise NetworkXError("n should be greater than zero")
|
138 |
+
if k <= 0 or k > n:
|
139 |
+
raise NetworkXError("k should be greater than zero and smaller than n")
|
140 |
+
|
141 |
+
G = nx.Graph()
|
142 |
+
# Create all k-subsets of [0, 1, ..., n-1]
|
143 |
+
subsets = list(itertools.combinations(range(n), k))
|
144 |
+
|
145 |
+
if 2 * k > n:
|
146 |
+
G.add_nodes_from(subsets)
|
147 |
+
|
148 |
+
universe = set(range(n))
|
149 |
+
comb = itertools.combinations # only to make it all fit on one line
|
150 |
+
G.add_edges_from((s, t) for s in subsets for t in comb(universe - set(s), k))
|
151 |
+
return G
|
152 |
+
|
153 |
+
|
154 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
155 |
+
def balanced_tree(r, h, create_using=None):
|
156 |
+
"""Returns the perfectly balanced `r`-ary tree of height `h`.
|
157 |
+
|
158 |
+
.. plot::
|
159 |
+
|
160 |
+
>>> nx.draw(nx.balanced_tree(2, 3))
|
161 |
+
|
162 |
+
Parameters
|
163 |
+
----------
|
164 |
+
r : int
|
165 |
+
Branching factor of the tree; each node will have `r`
|
166 |
+
children.
|
167 |
+
|
168 |
+
h : int
|
169 |
+
Height of the tree.
|
170 |
+
|
171 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
172 |
+
Graph type to create. If graph instance, then cleared before populated.
|
173 |
+
|
174 |
+
Returns
|
175 |
+
-------
|
176 |
+
G : NetworkX graph
|
177 |
+
A balanced `r`-ary tree of height `h`.
|
178 |
+
|
179 |
+
Notes
|
180 |
+
-----
|
181 |
+
This is the rooted tree where all leaves are at distance `h` from
|
182 |
+
the root. The root has degree `r` and all other internal nodes
|
183 |
+
have degree `r + 1`.
|
184 |
+
|
185 |
+
Node labels are integers, starting from zero.
|
186 |
+
|
187 |
+
A balanced tree is also known as a *complete r-ary tree*.
|
188 |
+
|
189 |
+
"""
|
190 |
+
# The number of nodes in the balanced tree is `1 + r + ... + r^h`,
|
191 |
+
# which is computed by using the closed-form formula for a geometric
|
192 |
+
# sum with ratio `r`. In the special case that `r` is 1, the number
|
193 |
+
# of nodes is simply `h + 1` (since the tree is actually a path
|
194 |
+
# graph).
|
195 |
+
if r == 1:
|
196 |
+
n = h + 1
|
197 |
+
else:
|
198 |
+
# This must be an integer if both `r` and `h` are integers. If
|
199 |
+
# they are not, we force integer division anyway.
|
200 |
+
n = (1 - r ** (h + 1)) // (1 - r)
|
201 |
+
return full_rary_tree(r, n, create_using=create_using)
|
202 |
+
|
203 |
+
|
204 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
205 |
+
def barbell_graph(m1, m2, create_using=None):
|
206 |
+
"""Returns the Barbell Graph: two complete graphs connected by a path.
|
207 |
+
|
208 |
+
.. plot::
|
209 |
+
|
210 |
+
>>> nx.draw(nx.barbell_graph(4, 2))
|
211 |
+
|
212 |
+
Parameters
|
213 |
+
----------
|
214 |
+
m1 : int
|
215 |
+
Size of the left and right barbells, must be greater than 2.
|
216 |
+
|
217 |
+
m2 : int
|
218 |
+
Length of the path connecting the barbells.
|
219 |
+
|
220 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
221 |
+
Graph type to create. If graph instance, then cleared before populated.
|
222 |
+
Only undirected Graphs are supported.
|
223 |
+
|
224 |
+
Returns
|
225 |
+
-------
|
226 |
+
G : NetworkX graph
|
227 |
+
A barbell graph.
|
228 |
+
|
229 |
+
Notes
|
230 |
+
-----
|
231 |
+
|
232 |
+
|
233 |
+
Two identical complete graphs $K_{m1}$ form the left and right bells,
|
234 |
+
and are connected by a path $P_{m2}$.
|
235 |
+
|
236 |
+
The `2*m1+m2` nodes are numbered
|
237 |
+
`0, ..., m1-1` for the left barbell,
|
238 |
+
`m1, ..., m1+m2-1` for the path,
|
239 |
+
and `m1+m2, ..., 2*m1+m2-1` for the right barbell.
|
240 |
+
|
241 |
+
The 3 subgraphs are joined via the edges `(m1-1, m1)` and
|
242 |
+
`(m1+m2-1, m1+m2)`. If `m2=0`, this is merely two complete
|
243 |
+
graphs joined together.
|
244 |
+
|
245 |
+
This graph is an extremal example in David Aldous
|
246 |
+
and Jim Fill's e-text on Random Walks on Graphs.
|
247 |
+
|
248 |
+
"""
|
249 |
+
if m1 < 2:
|
250 |
+
raise NetworkXError("Invalid graph description, m1 should be >=2")
|
251 |
+
if m2 < 0:
|
252 |
+
raise NetworkXError("Invalid graph description, m2 should be >=0")
|
253 |
+
|
254 |
+
# left barbell
|
255 |
+
G = complete_graph(m1, create_using)
|
256 |
+
if G.is_directed():
|
257 |
+
raise NetworkXError("Directed Graph not supported")
|
258 |
+
|
259 |
+
# connecting path
|
260 |
+
G.add_nodes_from(range(m1, m1 + m2 - 1))
|
261 |
+
if m2 > 1:
|
262 |
+
G.add_edges_from(pairwise(range(m1, m1 + m2)))
|
263 |
+
|
264 |
+
# right barbell
|
265 |
+
G.add_edges_from(
|
266 |
+
(u, v) for u in range(m1 + m2, 2 * m1 + m2) for v in range(u + 1, 2 * m1 + m2)
|
267 |
+
)
|
268 |
+
|
269 |
+
# connect it up
|
270 |
+
G.add_edge(m1 - 1, m1)
|
271 |
+
if m2 > 0:
|
272 |
+
G.add_edge(m1 + m2 - 1, m1 + m2)
|
273 |
+
|
274 |
+
return G
|
275 |
+
|
276 |
+
|
277 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
278 |
+
def binomial_tree(n, create_using=None):
|
279 |
+
"""Returns the Binomial Tree of order n.
|
280 |
+
|
281 |
+
The binomial tree of order 0 consists of a single node. A binomial tree of order k
|
282 |
+
is defined recursively by linking two binomial trees of order k-1: the root of one is
|
283 |
+
the leftmost child of the root of the other.
|
284 |
+
|
285 |
+
.. plot::
|
286 |
+
|
287 |
+
>>> nx.draw(nx.binomial_tree(3))
|
288 |
+
|
289 |
+
Parameters
|
290 |
+
----------
|
291 |
+
n : int
|
292 |
+
Order of the binomial tree.
|
293 |
+
|
294 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
295 |
+
Graph type to create. If graph instance, then cleared before populated.
|
296 |
+
|
297 |
+
Returns
|
298 |
+
-------
|
299 |
+
G : NetworkX graph
|
300 |
+
A binomial tree of $2^n$ nodes and $2^n - 1$ edges.
|
301 |
+
|
302 |
+
"""
|
303 |
+
G = nx.empty_graph(1, create_using)
|
304 |
+
|
305 |
+
N = 1
|
306 |
+
for i in range(n):
|
307 |
+
# Use G.edges() to ensure 2-tuples. G.edges is 3-tuple for MultiGraph
|
308 |
+
edges = [(u + N, v + N) for (u, v) in G.edges()]
|
309 |
+
G.add_edges_from(edges)
|
310 |
+
G.add_edge(0, N)
|
311 |
+
N *= 2
|
312 |
+
return G
|
313 |
+
|
314 |
+
|
315 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
316 |
+
@nodes_or_number(0)
|
317 |
+
def complete_graph(n, create_using=None):
|
318 |
+
"""Return the complete graph `K_n` with n nodes.
|
319 |
+
|
320 |
+
A complete graph on `n` nodes means that all pairs
|
321 |
+
of distinct nodes have an edge connecting them.
|
322 |
+
|
323 |
+
.. plot::
|
324 |
+
|
325 |
+
>>> nx.draw(nx.complete_graph(5))
|
326 |
+
|
327 |
+
Parameters
|
328 |
+
----------
|
329 |
+
n : int or iterable container of nodes
|
330 |
+
If n is an integer, nodes are from range(n).
|
331 |
+
If n is a container of nodes, those nodes appear in the graph.
|
332 |
+
Warning: n is not checked for duplicates and if present the
|
333 |
+
resulting graph may not be as desired. Make sure you have no duplicates.
|
334 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
335 |
+
Graph type to create. If graph instance, then cleared before populated.
|
336 |
+
|
337 |
+
Examples
|
338 |
+
--------
|
339 |
+
>>> G = nx.complete_graph(9)
|
340 |
+
>>> len(G)
|
341 |
+
9
|
342 |
+
>>> G.size()
|
343 |
+
36
|
344 |
+
>>> G = nx.complete_graph(range(11, 14))
|
345 |
+
>>> list(G.nodes())
|
346 |
+
[11, 12, 13]
|
347 |
+
>>> G = nx.complete_graph(4, nx.DiGraph())
|
348 |
+
>>> G.is_directed()
|
349 |
+
True
|
350 |
+
|
351 |
+
"""
|
352 |
+
_, nodes = n
|
353 |
+
G = empty_graph(nodes, create_using)
|
354 |
+
if len(nodes) > 1:
|
355 |
+
if G.is_directed():
|
356 |
+
edges = itertools.permutations(nodes, 2)
|
357 |
+
else:
|
358 |
+
edges = itertools.combinations(nodes, 2)
|
359 |
+
G.add_edges_from(edges)
|
360 |
+
return G
|
361 |
+
|
362 |
+
|
363 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
364 |
+
def circular_ladder_graph(n, create_using=None):
|
365 |
+
"""Returns the circular ladder graph $CL_n$ of length n.
|
366 |
+
|
367 |
+
$CL_n$ consists of two concentric n-cycles in which
|
368 |
+
each of the n pairs of concentric nodes are joined by an edge.
|
369 |
+
|
370 |
+
Node labels are the integers 0 to n-1
|
371 |
+
|
372 |
+
.. plot::
|
373 |
+
|
374 |
+
>>> nx.draw(nx.circular_ladder_graph(5))
|
375 |
+
|
376 |
+
"""
|
377 |
+
G = ladder_graph(n, create_using)
|
378 |
+
G.add_edge(0, n - 1)
|
379 |
+
G.add_edge(n, 2 * n - 1)
|
380 |
+
return G
|
381 |
+
|
382 |
+
|
383 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
384 |
+
def circulant_graph(n, offsets, create_using=None):
|
385 |
+
r"""Returns the circulant graph $Ci_n(x_1, x_2, ..., x_m)$ with $n$ nodes.
|
386 |
+
|
387 |
+
The circulant graph $Ci_n(x_1, ..., x_m)$ consists of $n$ nodes $0, ..., n-1$
|
388 |
+
such that node $i$ is connected to nodes $(i + x) \mod n$ and $(i - x) \mod n$
|
389 |
+
for all $x$ in $x_1, ..., x_m$. Thus $Ci_n(1)$ is a cycle graph.
|
390 |
+
|
391 |
+
.. plot::
|
392 |
+
|
393 |
+
>>> nx.draw(nx.circulant_graph(10, [1]))
|
394 |
+
|
395 |
+
Parameters
|
396 |
+
----------
|
397 |
+
n : integer
|
398 |
+
The number of nodes in the graph.
|
399 |
+
offsets : list of integers
|
400 |
+
A list of node offsets, $x_1$ up to $x_m$, as described above.
|
401 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
402 |
+
Graph type to create. If graph instance, then cleared before populated.
|
403 |
+
|
404 |
+
Returns
|
405 |
+
-------
|
406 |
+
NetworkX Graph of type create_using
|
407 |
+
|
408 |
+
Examples
|
409 |
+
--------
|
410 |
+
Many well-known graph families are subfamilies of the circulant graphs;
|
411 |
+
for example, to create the cycle graph on n points, we connect every
|
412 |
+
node to nodes on either side (with offset plus or minus one). For n = 10,
|
413 |
+
|
414 |
+
>>> G = nx.circulant_graph(10, [1])
|
415 |
+
>>> edges = [
|
416 |
+
... (0, 9),
|
417 |
+
... (0, 1),
|
418 |
+
... (1, 2),
|
419 |
+
... (2, 3),
|
420 |
+
... (3, 4),
|
421 |
+
... (4, 5),
|
422 |
+
... (5, 6),
|
423 |
+
... (6, 7),
|
424 |
+
... (7, 8),
|
425 |
+
... (8, 9),
|
426 |
+
... ]
|
427 |
+
>>> sorted(edges) == sorted(G.edges())
|
428 |
+
True
|
429 |
+
|
430 |
+
Similarly, we can create the complete graph
|
431 |
+
on 5 points with the set of offsets [1, 2]:
|
432 |
+
|
433 |
+
>>> G = nx.circulant_graph(5, [1, 2])
|
434 |
+
>>> edges = [
|
435 |
+
... (0, 1),
|
436 |
+
... (0, 2),
|
437 |
+
... (0, 3),
|
438 |
+
... (0, 4),
|
439 |
+
... (1, 2),
|
440 |
+
... (1, 3),
|
441 |
+
... (1, 4),
|
442 |
+
... (2, 3),
|
443 |
+
... (2, 4),
|
444 |
+
... (3, 4),
|
445 |
+
... ]
|
446 |
+
>>> sorted(edges) == sorted(G.edges())
|
447 |
+
True
|
448 |
+
|
449 |
+
"""
|
450 |
+
G = empty_graph(n, create_using)
|
451 |
+
for i in range(n):
|
452 |
+
for j in offsets:
|
453 |
+
G.add_edge(i, (i - j) % n)
|
454 |
+
G.add_edge(i, (i + j) % n)
|
455 |
+
return G
|
456 |
+
|
457 |
+
|
458 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
459 |
+
@nodes_or_number(0)
|
460 |
+
def cycle_graph(n, create_using=None):
|
461 |
+
"""Returns the cycle graph $C_n$ of cyclically connected nodes.
|
462 |
+
|
463 |
+
$C_n$ is a path with its two end-nodes connected.
|
464 |
+
|
465 |
+
.. plot::
|
466 |
+
|
467 |
+
>>> nx.draw(nx.cycle_graph(5))
|
468 |
+
|
469 |
+
Parameters
|
470 |
+
----------
|
471 |
+
n : int or iterable container of nodes
|
472 |
+
If n is an integer, nodes are from `range(n)`.
|
473 |
+
If n is a container of nodes, those nodes appear in the graph.
|
474 |
+
Warning: n is not checked for duplicates and if present the
|
475 |
+
resulting graph may not be as desired. Make sure you have no duplicates.
|
476 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
477 |
+
Graph type to create. If graph instance, then cleared before populated.
|
478 |
+
|
479 |
+
Notes
|
480 |
+
-----
|
481 |
+
If create_using is directed, the direction is in increasing order.
|
482 |
+
|
483 |
+
"""
|
484 |
+
_, nodes = n
|
485 |
+
G = empty_graph(nodes, create_using)
|
486 |
+
G.add_edges_from(pairwise(nodes, cyclic=True))
|
487 |
+
return G
|
488 |
+
|
489 |
+
|
490 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
491 |
+
def dorogovtsev_goltsev_mendes_graph(n, create_using=None):
|
492 |
+
"""Returns the hierarchically constructed Dorogovtsev-Goltsev-Mendes graph.
|
493 |
+
|
494 |
+
The Dorogovtsev-Goltsev-Mendes [1]_ procedure produces a scale-free graph
|
495 |
+
deterministically with the following properties for a given `n`:
|
496 |
+
- Total number of nodes = ``3 * (3**n + 1) / 2``
|
497 |
+
- Total number of edges = ``3 ** (n + 1)``
|
498 |
+
|
499 |
+
.. plot::
|
500 |
+
|
501 |
+
>>> nx.draw(nx.dorogovtsev_goltsev_mendes_graph(3))
|
502 |
+
|
503 |
+
Parameters
|
504 |
+
----------
|
505 |
+
n : integer
|
506 |
+
The generation number.
|
507 |
+
|
508 |
+
create_using : NetworkX Graph, optional
|
509 |
+
Graph type to be returned. Directed graphs and multi graphs are not
|
510 |
+
supported.
|
511 |
+
|
512 |
+
Returns
|
513 |
+
-------
|
514 |
+
G : NetworkX Graph
|
515 |
+
|
516 |
+
Examples
|
517 |
+
--------
|
518 |
+
>>> G = nx.dorogovtsev_goltsev_mendes_graph(3)
|
519 |
+
>>> G.number_of_nodes()
|
520 |
+
15
|
521 |
+
>>> G.number_of_edges()
|
522 |
+
27
|
523 |
+
>>> nx.is_planar(G)
|
524 |
+
True
|
525 |
+
|
526 |
+
References
|
527 |
+
----------
|
528 |
+
.. [1] S. N. Dorogovtsev, A. V. Goltsev and J. F. F. Mendes,
|
529 |
+
"Pseudofractal scale-free web", Physical Review E 65, 066122, 2002.
|
530 |
+
https://arxiv.org/pdf/cond-mat/0112143.pdf
|
531 |
+
"""
|
532 |
+
G = empty_graph(0, create_using)
|
533 |
+
if G.is_directed():
|
534 |
+
raise NetworkXError("Directed Graph not supported")
|
535 |
+
if G.is_multigraph():
|
536 |
+
raise NetworkXError("Multigraph not supported")
|
537 |
+
|
538 |
+
G.add_edge(0, 1)
|
539 |
+
if n == 0:
|
540 |
+
return G
|
541 |
+
new_node = 2 # next node to be added
|
542 |
+
for i in range(1, n + 1): # iterate over number of generations.
|
543 |
+
last_generation_edges = list(G.edges())
|
544 |
+
number_of_edges_in_last_generation = len(last_generation_edges)
|
545 |
+
for j in range(number_of_edges_in_last_generation):
|
546 |
+
G.add_edge(new_node, last_generation_edges[j][0])
|
547 |
+
G.add_edge(new_node, last_generation_edges[j][1])
|
548 |
+
new_node += 1
|
549 |
+
return G
|
550 |
+
|
551 |
+
|
552 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
553 |
+
@nodes_or_number(0)
|
554 |
+
def empty_graph(n=0, create_using=None, default=Graph):
|
555 |
+
"""Returns the empty graph with n nodes and zero edges.
|
556 |
+
|
557 |
+
.. plot::
|
558 |
+
|
559 |
+
>>> nx.draw(nx.empty_graph(5))
|
560 |
+
|
561 |
+
Parameters
|
562 |
+
----------
|
563 |
+
n : int or iterable container of nodes (default = 0)
|
564 |
+
If n is an integer, nodes are from `range(n)`.
|
565 |
+
If n is a container of nodes, those nodes appear in the graph.
|
566 |
+
create_using : Graph Instance, Constructor or None
|
567 |
+
Indicator of type of graph to return.
|
568 |
+
If a Graph-type instance, then clear and use it.
|
569 |
+
If None, use the `default` constructor.
|
570 |
+
If a constructor, call it to create an empty graph.
|
571 |
+
default : Graph constructor (optional, default = nx.Graph)
|
572 |
+
The constructor to use if create_using is None.
|
573 |
+
If None, then nx.Graph is used.
|
574 |
+
This is used when passing an unknown `create_using` value
|
575 |
+
through your home-grown function to `empty_graph` and
|
576 |
+
you want a default constructor other than nx.Graph.
|
577 |
+
|
578 |
+
Examples
|
579 |
+
--------
|
580 |
+
>>> G = nx.empty_graph(10)
|
581 |
+
>>> G.number_of_nodes()
|
582 |
+
10
|
583 |
+
>>> G.number_of_edges()
|
584 |
+
0
|
585 |
+
>>> G = nx.empty_graph("ABC")
|
586 |
+
>>> G.number_of_nodes()
|
587 |
+
3
|
588 |
+
>>> sorted(G)
|
589 |
+
['A', 'B', 'C']
|
590 |
+
|
591 |
+
Notes
|
592 |
+
-----
|
593 |
+
The variable create_using should be a Graph Constructor or a
|
594 |
+
"graph"-like object. Constructors, e.g. `nx.Graph` or `nx.MultiGraph`
|
595 |
+
will be used to create the returned graph. "graph"-like objects
|
596 |
+
will be cleared (nodes and edges will be removed) and refitted as
|
597 |
+
an empty "graph" with nodes specified in n. This capability
|
598 |
+
is useful for specifying the class-nature of the resulting empty
|
599 |
+
"graph" (i.e. Graph, DiGraph, MyWeirdGraphClass, etc.).
|
600 |
+
|
601 |
+
The variable create_using has three main uses:
|
602 |
+
Firstly, the variable create_using can be used to create an
|
603 |
+
empty digraph, multigraph, etc. For example,
|
604 |
+
|
605 |
+
>>> n = 10
|
606 |
+
>>> G = nx.empty_graph(n, create_using=nx.DiGraph)
|
607 |
+
|
608 |
+
will create an empty digraph on n nodes.
|
609 |
+
|
610 |
+
Secondly, one can pass an existing graph (digraph, multigraph,
|
611 |
+
etc.) via create_using. For example, if G is an existing graph
|
612 |
+
(resp. digraph, multigraph, etc.), then empty_graph(n, create_using=G)
|
613 |
+
will empty G (i.e. delete all nodes and edges using G.clear())
|
614 |
+
and then add n nodes and zero edges, and return the modified graph.
|
615 |
+
|
616 |
+
Thirdly, when constructing your home-grown graph creation function
|
617 |
+
you can use empty_graph to construct the graph by passing a user
|
618 |
+
defined create_using to empty_graph. In this case, if you want the
|
619 |
+
default constructor to be other than nx.Graph, specify `default`.
|
620 |
+
|
621 |
+
>>> def mygraph(n, create_using=None):
|
622 |
+
... G = nx.empty_graph(n, create_using, nx.MultiGraph)
|
623 |
+
... G.add_edges_from([(0, 1), (0, 1)])
|
624 |
+
... return G
|
625 |
+
>>> G = mygraph(3)
|
626 |
+
>>> G.is_multigraph()
|
627 |
+
True
|
628 |
+
>>> G = mygraph(3, nx.Graph)
|
629 |
+
>>> G.is_multigraph()
|
630 |
+
False
|
631 |
+
|
632 |
+
See also create_empty_copy(G).
|
633 |
+
|
634 |
+
"""
|
635 |
+
if create_using is None:
|
636 |
+
G = default()
|
637 |
+
elif isinstance(create_using, type):
|
638 |
+
G = create_using()
|
639 |
+
elif not hasattr(create_using, "adj"):
|
640 |
+
raise TypeError("create_using is not a valid NetworkX graph type or instance")
|
641 |
+
else:
|
642 |
+
# create_using is a NetworkX style Graph
|
643 |
+
create_using.clear()
|
644 |
+
G = create_using
|
645 |
+
|
646 |
+
_, nodes = n
|
647 |
+
G.add_nodes_from(nodes)
|
648 |
+
return G
|
649 |
+
|
650 |
+
|
651 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
652 |
+
def ladder_graph(n, create_using=None):
|
653 |
+
"""Returns the Ladder graph of length n.
|
654 |
+
|
655 |
+
This is two paths of n nodes, with
|
656 |
+
each pair connected by a single edge.
|
657 |
+
|
658 |
+
Node labels are the integers 0 to 2*n - 1.
|
659 |
+
|
660 |
+
.. plot::
|
661 |
+
|
662 |
+
>>> nx.draw(nx.ladder_graph(5))
|
663 |
+
|
664 |
+
"""
|
665 |
+
G = empty_graph(2 * n, create_using)
|
666 |
+
if G.is_directed():
|
667 |
+
raise NetworkXError("Directed Graph not supported")
|
668 |
+
G.add_edges_from(pairwise(range(n)))
|
669 |
+
G.add_edges_from(pairwise(range(n, 2 * n)))
|
670 |
+
G.add_edges_from((v, v + n) for v in range(n))
|
671 |
+
return G
|
672 |
+
|
673 |
+
|
674 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
675 |
+
@nodes_or_number([0, 1])
|
676 |
+
def lollipop_graph(m, n, create_using=None):
|
677 |
+
"""Returns the Lollipop Graph; ``K_m`` connected to ``P_n``.
|
678 |
+
|
679 |
+
This is the Barbell Graph without the right barbell.
|
680 |
+
|
681 |
+
.. plot::
|
682 |
+
|
683 |
+
>>> nx.draw(nx.lollipop_graph(3, 4))
|
684 |
+
|
685 |
+
Parameters
|
686 |
+
----------
|
687 |
+
m, n : int or iterable container of nodes
|
688 |
+
If an integer, nodes are from ``range(m)`` and ``range(m, m+n)``.
|
689 |
+
If a container of nodes, those nodes appear in the graph.
|
690 |
+
Warning: `m` and `n` are not checked for duplicates and if present the
|
691 |
+
resulting graph may not be as desired. Make sure you have no duplicates.
|
692 |
+
|
693 |
+
The nodes for `m` appear in the complete graph $K_m$ and the nodes
|
694 |
+
for `n` appear in the path $P_n$
|
695 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
696 |
+
Graph type to create. If graph instance, then cleared before populated.
|
697 |
+
|
698 |
+
Returns
|
699 |
+
-------
|
700 |
+
Networkx graph
|
701 |
+
A complete graph with `m` nodes connected to a path of length `n`.
|
702 |
+
|
703 |
+
Notes
|
704 |
+
-----
|
705 |
+
The 2 subgraphs are joined via an edge ``(m-1, m)``.
|
706 |
+
If ``n=0``, this is merely a complete graph.
|
707 |
+
|
708 |
+
(This graph is an extremal example in David Aldous and Jim
|
709 |
+
Fill's etext on Random Walks on Graphs.)
|
710 |
+
|
711 |
+
"""
|
712 |
+
m, m_nodes = m
|
713 |
+
M = len(m_nodes)
|
714 |
+
if M < 2:
|
715 |
+
raise NetworkXError("Invalid description: m should indicate at least 2 nodes")
|
716 |
+
|
717 |
+
n, n_nodes = n
|
718 |
+
if isinstance(m, numbers.Integral) and isinstance(n, numbers.Integral):
|
719 |
+
n_nodes = list(range(M, M + n))
|
720 |
+
N = len(n_nodes)
|
721 |
+
|
722 |
+
# the ball
|
723 |
+
G = complete_graph(m_nodes, create_using)
|
724 |
+
if G.is_directed():
|
725 |
+
raise NetworkXError("Directed Graph not supported")
|
726 |
+
|
727 |
+
# the stick
|
728 |
+
G.add_nodes_from(n_nodes)
|
729 |
+
if N > 1:
|
730 |
+
G.add_edges_from(pairwise(n_nodes))
|
731 |
+
|
732 |
+
if len(G) != M + N:
|
733 |
+
raise NetworkXError("Nodes must be distinct in containers m and n")
|
734 |
+
|
735 |
+
# connect ball to stick
|
736 |
+
if M > 0 and N > 0:
|
737 |
+
G.add_edge(m_nodes[-1], n_nodes[0])
|
738 |
+
return G
|
739 |
+
|
740 |
+
|
741 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
742 |
+
def null_graph(create_using=None):
|
743 |
+
"""Returns the Null graph with no nodes or edges.
|
744 |
+
|
745 |
+
See empty_graph for the use of create_using.
|
746 |
+
|
747 |
+
"""
|
748 |
+
G = empty_graph(0, create_using)
|
749 |
+
return G
|
750 |
+
|
751 |
+
|
752 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
753 |
+
@nodes_or_number(0)
|
754 |
+
def path_graph(n, create_using=None):
|
755 |
+
"""Returns the Path graph `P_n` of linearly connected nodes.
|
756 |
+
|
757 |
+
.. plot::
|
758 |
+
|
759 |
+
>>> nx.draw(nx.path_graph(5))
|
760 |
+
|
761 |
+
Parameters
|
762 |
+
----------
|
763 |
+
n : int or iterable
|
764 |
+
If an integer, nodes are 0 to n - 1.
|
765 |
+
If an iterable of nodes, in the order they appear in the path.
|
766 |
+
Warning: n is not checked for duplicates and if present the
|
767 |
+
resulting graph may not be as desired. Make sure you have no duplicates.
|
768 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
769 |
+
Graph type to create. If graph instance, then cleared before populated.
|
770 |
+
|
771 |
+
"""
|
772 |
+
_, nodes = n
|
773 |
+
G = empty_graph(nodes, create_using)
|
774 |
+
G.add_edges_from(pairwise(nodes))
|
775 |
+
return G
|
776 |
+
|
777 |
+
|
778 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
779 |
+
@nodes_or_number(0)
|
780 |
+
def star_graph(n, create_using=None):
|
781 |
+
"""Return the star graph
|
782 |
+
|
783 |
+
The star graph consists of one center node connected to n outer nodes.
|
784 |
+
|
785 |
+
.. plot::
|
786 |
+
|
787 |
+
>>> nx.draw(nx.star_graph(6))
|
788 |
+
|
789 |
+
Parameters
|
790 |
+
----------
|
791 |
+
n : int or iterable
|
792 |
+
If an integer, node labels are 0 to n with center 0.
|
793 |
+
If an iterable of nodes, the center is the first.
|
794 |
+
Warning: n is not checked for duplicates and if present the
|
795 |
+
resulting graph may not be as desired. Make sure you have no duplicates.
|
796 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
797 |
+
Graph type to create. If graph instance, then cleared before populated.
|
798 |
+
|
799 |
+
Notes
|
800 |
+
-----
|
801 |
+
The graph has n+1 nodes for integer n.
|
802 |
+
So star_graph(3) is the same as star_graph(range(4)).
|
803 |
+
"""
|
804 |
+
n, nodes = n
|
805 |
+
if isinstance(n, numbers.Integral):
|
806 |
+
nodes.append(int(n)) # there should be n+1 nodes
|
807 |
+
G = empty_graph(nodes, create_using)
|
808 |
+
if G.is_directed():
|
809 |
+
raise NetworkXError("Directed Graph not supported")
|
810 |
+
|
811 |
+
if len(nodes) > 1:
|
812 |
+
hub, *spokes = nodes
|
813 |
+
G.add_edges_from((hub, node) for node in spokes)
|
814 |
+
return G
|
815 |
+
|
816 |
+
|
817 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
818 |
+
@nodes_or_number([0, 1])
|
819 |
+
def tadpole_graph(m, n, create_using=None):
|
820 |
+
"""Returns the (m,n)-tadpole graph; ``C_m`` connected to ``P_n``.
|
821 |
+
|
822 |
+
This graph on m+n nodes connects a cycle of size `m` to a path of length `n`.
|
823 |
+
It looks like a tadpole. It is also called a kite graph or a dragon graph.
|
824 |
+
|
825 |
+
.. plot::
|
826 |
+
|
827 |
+
>>> nx.draw(nx.tadpole_graph(3, 5))
|
828 |
+
|
829 |
+
Parameters
|
830 |
+
----------
|
831 |
+
m, n : int or iterable container of nodes
|
832 |
+
If an integer, nodes are from ``range(m)`` and ``range(m,m+n)``.
|
833 |
+
If a container of nodes, those nodes appear in the graph.
|
834 |
+
Warning: `m` and `n` are not checked for duplicates and if present the
|
835 |
+
resulting graph may not be as desired.
|
836 |
+
|
837 |
+
The nodes for `m` appear in the cycle graph $C_m$ and the nodes
|
838 |
+
for `n` appear in the path $P_n$.
|
839 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
840 |
+
Graph type to create. If graph instance, then cleared before populated.
|
841 |
+
|
842 |
+
Returns
|
843 |
+
-------
|
844 |
+
Networkx graph
|
845 |
+
A cycle of size `m` connected to a path of length `n`.
|
846 |
+
|
847 |
+
Raises
|
848 |
+
------
|
849 |
+
NetworkXError
|
850 |
+
If ``m < 2``. The tadpole graph is undefined for ``m<2``.
|
851 |
+
|
852 |
+
Notes
|
853 |
+
-----
|
854 |
+
The 2 subgraphs are joined via an edge ``(m-1, m)``.
|
855 |
+
If ``n=0``, this is a cycle graph.
|
856 |
+
`m` and/or `n` can be a container of nodes instead of an integer.
|
857 |
+
|
858 |
+
"""
|
859 |
+
m, m_nodes = m
|
860 |
+
M = len(m_nodes)
|
861 |
+
if M < 2:
|
862 |
+
raise NetworkXError("Invalid description: m should indicate at least 2 nodes")
|
863 |
+
|
864 |
+
n, n_nodes = n
|
865 |
+
if isinstance(m, numbers.Integral) and isinstance(n, numbers.Integral):
|
866 |
+
n_nodes = list(range(M, M + n))
|
867 |
+
|
868 |
+
# the circle
|
869 |
+
G = cycle_graph(m_nodes, create_using)
|
870 |
+
if G.is_directed():
|
871 |
+
raise NetworkXError("Directed Graph not supported")
|
872 |
+
|
873 |
+
# the stick
|
874 |
+
nx.add_path(G, [m_nodes[-1]] + list(n_nodes))
|
875 |
+
|
876 |
+
return G
|
877 |
+
|
878 |
+
|
879 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
880 |
+
def trivial_graph(create_using=None):
|
881 |
+
"""Return the Trivial graph with one node (with label 0) and no edges.
|
882 |
+
|
883 |
+
.. plot::
|
884 |
+
|
885 |
+
>>> nx.draw(nx.trivial_graph(), with_labels=True)
|
886 |
+
|
887 |
+
"""
|
888 |
+
G = empty_graph(1, create_using)
|
889 |
+
return G
|
890 |
+
|
891 |
+
|
892 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
893 |
+
def turan_graph(n, r):
|
894 |
+
r"""Return the Turan Graph
|
895 |
+
|
896 |
+
The Turan Graph is a complete multipartite graph on $n$ nodes
|
897 |
+
with $r$ disjoint subsets. That is, edges connect each node to
|
898 |
+
every node not in its subset.
|
899 |
+
|
900 |
+
Given $n$ and $r$, we create a complete multipartite graph with
|
901 |
+
$r-(n \mod r)$ partitions of size $n/r$, rounded down, and
|
902 |
+
$n \mod r$ partitions of size $n/r+1$, rounded down.
|
903 |
+
|
904 |
+
.. plot::
|
905 |
+
|
906 |
+
>>> nx.draw(nx.turan_graph(6, 2))
|
907 |
+
|
908 |
+
Parameters
|
909 |
+
----------
|
910 |
+
n : int
|
911 |
+
The number of nodes.
|
912 |
+
r : int
|
913 |
+
The number of partitions.
|
914 |
+
Must be less than or equal to n.
|
915 |
+
|
916 |
+
Notes
|
917 |
+
-----
|
918 |
+
Must satisfy $1 <= r <= n$.
|
919 |
+
The graph has $(r-1)(n^2)/(2r)$ edges, rounded down.
|
920 |
+
"""
|
921 |
+
|
922 |
+
if not 1 <= r <= n:
|
923 |
+
raise NetworkXError("Must satisfy 1 <= r <= n")
|
924 |
+
|
925 |
+
partitions = [n // r] * (r - (n % r)) + [n // r + 1] * (n % r)
|
926 |
+
G = complete_multipartite_graph(*partitions)
|
927 |
+
return G
|
928 |
+
|
929 |
+
|
930 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
931 |
+
@nodes_or_number(0)
|
932 |
+
def wheel_graph(n, create_using=None):
|
933 |
+
"""Return the wheel graph
|
934 |
+
|
935 |
+
The wheel graph consists of a hub node connected to a cycle of (n-1) nodes.
|
936 |
+
|
937 |
+
.. plot::
|
938 |
+
|
939 |
+
>>> nx.draw(nx.wheel_graph(5))
|
940 |
+
|
941 |
+
Parameters
|
942 |
+
----------
|
943 |
+
n : int or iterable
|
944 |
+
If an integer, node labels are 0 to n with center 0.
|
945 |
+
If an iterable of nodes, the center is the first.
|
946 |
+
Warning: n is not checked for duplicates and if present the
|
947 |
+
resulting graph may not be as desired. Make sure you have no duplicates.
|
948 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
949 |
+
Graph type to create. If graph instance, then cleared before populated.
|
950 |
+
|
951 |
+
Node labels are the integers 0 to n - 1.
|
952 |
+
"""
|
953 |
+
_, nodes = n
|
954 |
+
G = empty_graph(nodes, create_using)
|
955 |
+
if G.is_directed():
|
956 |
+
raise NetworkXError("Directed Graph not supported")
|
957 |
+
|
958 |
+
if len(nodes) > 1:
|
959 |
+
hub, *rim = nodes
|
960 |
+
G.add_edges_from((hub, node) for node in rim)
|
961 |
+
if len(rim) > 1:
|
962 |
+
G.add_edges_from(pairwise(rim, cyclic=True))
|
963 |
+
return G
|
964 |
+
|
965 |
+
|
966 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
967 |
+
def complete_multipartite_graph(*subset_sizes):
|
968 |
+
"""Returns the complete multipartite graph with the specified subset sizes.
|
969 |
+
|
970 |
+
.. plot::
|
971 |
+
|
972 |
+
>>> nx.draw(nx.complete_multipartite_graph(1, 2, 3))
|
973 |
+
|
974 |
+
Parameters
|
975 |
+
----------
|
976 |
+
subset_sizes : tuple of integers or tuple of node iterables
|
977 |
+
The arguments can either all be integer number of nodes or they
|
978 |
+
can all be iterables of nodes. If integers, they represent the
|
979 |
+
number of nodes in each subset of the multipartite graph.
|
980 |
+
If iterables, each is used to create the nodes for that subset.
|
981 |
+
The length of subset_sizes is the number of subsets.
|
982 |
+
|
983 |
+
Returns
|
984 |
+
-------
|
985 |
+
G : NetworkX Graph
|
986 |
+
Returns the complete multipartite graph with the specified subsets.
|
987 |
+
|
988 |
+
For each node, the node attribute 'subset' is an integer
|
989 |
+
indicating which subset contains the node.
|
990 |
+
|
991 |
+
Examples
|
992 |
+
--------
|
993 |
+
Creating a complete tripartite graph, with subsets of one, two, and three
|
994 |
+
nodes, respectively.
|
995 |
+
|
996 |
+
>>> G = nx.complete_multipartite_graph(1, 2, 3)
|
997 |
+
>>> [G.nodes[u]["subset"] for u in G]
|
998 |
+
[0, 1, 1, 2, 2, 2]
|
999 |
+
>>> list(G.edges(0))
|
1000 |
+
[(0, 1), (0, 2), (0, 3), (0, 4), (0, 5)]
|
1001 |
+
>>> list(G.edges(2))
|
1002 |
+
[(2, 0), (2, 3), (2, 4), (2, 5)]
|
1003 |
+
>>> list(G.edges(4))
|
1004 |
+
[(4, 0), (4, 1), (4, 2)]
|
1005 |
+
|
1006 |
+
>>> G = nx.complete_multipartite_graph("a", "bc", "def")
|
1007 |
+
>>> [G.nodes[u]["subset"] for u in sorted(G)]
|
1008 |
+
[0, 1, 1, 2, 2, 2]
|
1009 |
+
|
1010 |
+
Notes
|
1011 |
+
-----
|
1012 |
+
This function generalizes several other graph builder functions.
|
1013 |
+
|
1014 |
+
- If no subset sizes are given, this returns the null graph.
|
1015 |
+
- If a single subset size `n` is given, this returns the empty graph on
|
1016 |
+
`n` nodes.
|
1017 |
+
- If two subset sizes `m` and `n` are given, this returns the complete
|
1018 |
+
bipartite graph on `m + n` nodes.
|
1019 |
+
- If subset sizes `1` and `n` are given, this returns the star graph on
|
1020 |
+
`n + 1` nodes.
|
1021 |
+
|
1022 |
+
See also
|
1023 |
+
--------
|
1024 |
+
complete_bipartite_graph
|
1025 |
+
"""
|
1026 |
+
# The complete multipartite graph is an undirected simple graph.
|
1027 |
+
G = Graph()
|
1028 |
+
|
1029 |
+
if len(subset_sizes) == 0:
|
1030 |
+
return G
|
1031 |
+
|
1032 |
+
# set up subsets of nodes
|
1033 |
+
try:
|
1034 |
+
extents = pairwise(itertools.accumulate((0,) + subset_sizes))
|
1035 |
+
subsets = [range(start, end) for start, end in extents]
|
1036 |
+
except TypeError:
|
1037 |
+
subsets = subset_sizes
|
1038 |
+
else:
|
1039 |
+
if any(size < 0 for size in subset_sizes):
|
1040 |
+
raise NetworkXError(f"Negative number of nodes not valid: {subset_sizes}")
|
1041 |
+
|
1042 |
+
# add nodes with subset attribute
|
1043 |
+
# while checking that ints are not mixed with iterables
|
1044 |
+
try:
|
1045 |
+
for i, subset in enumerate(subsets):
|
1046 |
+
G.add_nodes_from(subset, subset=i)
|
1047 |
+
except TypeError as err:
|
1048 |
+
raise NetworkXError("Arguments must be all ints or all iterables") from err
|
1049 |
+
|
1050 |
+
# Across subsets, all nodes should be adjacent.
|
1051 |
+
# We can use itertools.combinations() because undirected.
|
1052 |
+
for subset1, subset2 in itertools.combinations(subsets, 2):
|
1053 |
+
G.add_edges_from(itertools.product(subset1, subset2))
|
1054 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/cographs.py
ADDED
@@ -0,0 +1,67 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
r"""Generators for cographs
|
2 |
+
|
3 |
+
A cograph is a graph containing no path on four vertices.
|
4 |
+
Cographs or $P_4$-free graphs can be obtained from a single vertex
|
5 |
+
by disjoint union and complementation operations.
|
6 |
+
|
7 |
+
References
|
8 |
+
----------
|
9 |
+
.. [0] D.G. Corneil, H. Lerchs, L.Stewart Burlingham,
|
10 |
+
"Complement reducible graphs",
|
11 |
+
Discrete Applied Mathematics, Volume 3, Issue 3, 1981, Pages 163-174,
|
12 |
+
ISSN 0166-218X.
|
13 |
+
"""
|
14 |
+
import networkx as nx
|
15 |
+
from networkx.utils import py_random_state
|
16 |
+
|
17 |
+
__all__ = ["random_cograph"]
|
18 |
+
|
19 |
+
|
20 |
+
@py_random_state(1)
|
21 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
22 |
+
def random_cograph(n, seed=None):
|
23 |
+
r"""Returns a random cograph with $2 ^ n$ nodes.
|
24 |
+
|
25 |
+
A cograph is a graph containing no path on four vertices.
|
26 |
+
Cographs or $P_4$-free graphs can be obtained from a single vertex
|
27 |
+
by disjoint union and complementation operations.
|
28 |
+
|
29 |
+
This generator starts off from a single vertex and performs disjoint
|
30 |
+
union and full join operations on itself.
|
31 |
+
The decision on which operation will take place is random.
|
32 |
+
|
33 |
+
Parameters
|
34 |
+
----------
|
35 |
+
n : int
|
36 |
+
The order of the cograph.
|
37 |
+
seed : integer, random_state, or None (default)
|
38 |
+
Indicator of random number generation state.
|
39 |
+
See :ref:`Randomness<randomness>`.
|
40 |
+
|
41 |
+
Returns
|
42 |
+
-------
|
43 |
+
G : A random graph containing no path on four vertices.
|
44 |
+
|
45 |
+
See Also
|
46 |
+
--------
|
47 |
+
full_join
|
48 |
+
union
|
49 |
+
|
50 |
+
References
|
51 |
+
----------
|
52 |
+
.. [1] D.G. Corneil, H. Lerchs, L.Stewart Burlingham,
|
53 |
+
"Complement reducible graphs",
|
54 |
+
Discrete Applied Mathematics, Volume 3, Issue 3, 1981, Pages 163-174,
|
55 |
+
ISSN 0166-218X.
|
56 |
+
"""
|
57 |
+
R = nx.empty_graph(1)
|
58 |
+
|
59 |
+
for i in range(n):
|
60 |
+
RR = nx.relabel_nodes(R.copy(), lambda x: x + len(R))
|
61 |
+
|
62 |
+
if seed.randint(0, 1) == 0:
|
63 |
+
R = nx.full_join(R, RR)
|
64 |
+
else:
|
65 |
+
R = nx.disjoint_union(R, RR)
|
66 |
+
|
67 |
+
return R
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/community.py
ADDED
@@ -0,0 +1,1069 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
1 |
+
"""Generators for classes of graphs used in studying social networks."""
|
2 |
+
import itertools
|
3 |
+
import math
|
4 |
+
|
5 |
+
import networkx as nx
|
6 |
+
from networkx.utils import py_random_state
|
7 |
+
|
8 |
+
__all__ = [
|
9 |
+
"caveman_graph",
|
10 |
+
"connected_caveman_graph",
|
11 |
+
"relaxed_caveman_graph",
|
12 |
+
"random_partition_graph",
|
13 |
+
"planted_partition_graph",
|
14 |
+
"gaussian_random_partition_graph",
|
15 |
+
"ring_of_cliques",
|
16 |
+
"windmill_graph",
|
17 |
+
"stochastic_block_model",
|
18 |
+
"LFR_benchmark_graph",
|
19 |
+
]
|
20 |
+
|
21 |
+
|
22 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
23 |
+
def caveman_graph(l, k):
|
24 |
+
"""Returns a caveman graph of `l` cliques of size `k`.
|
25 |
+
|
26 |
+
Parameters
|
27 |
+
----------
|
28 |
+
l : int
|
29 |
+
Number of cliques
|
30 |
+
k : int
|
31 |
+
Size of cliques
|
32 |
+
|
33 |
+
Returns
|
34 |
+
-------
|
35 |
+
G : NetworkX Graph
|
36 |
+
caveman graph
|
37 |
+
|
38 |
+
Notes
|
39 |
+
-----
|
40 |
+
This returns an undirected graph, it can be converted to a directed
|
41 |
+
graph using :func:`nx.to_directed`, or a multigraph using
|
42 |
+
``nx.MultiGraph(nx.caveman_graph(l, k))``. Only the undirected version is
|
43 |
+
described in [1]_ and it is unclear which of the directed
|
44 |
+
generalizations is most useful.
|
45 |
+
|
46 |
+
Examples
|
47 |
+
--------
|
48 |
+
>>> G = nx.caveman_graph(3, 3)
|
49 |
+
|
50 |
+
See also
|
51 |
+
--------
|
52 |
+
|
53 |
+
connected_caveman_graph
|
54 |
+
|
55 |
+
References
|
56 |
+
----------
|
57 |
+
.. [1] Watts, D. J. 'Networks, Dynamics, and the Small-World Phenomenon.'
|
58 |
+
Amer. J. Soc. 105, 493-527, 1999.
|
59 |
+
"""
|
60 |
+
# l disjoint cliques of size k
|
61 |
+
G = nx.empty_graph(l * k)
|
62 |
+
if k > 1:
|
63 |
+
for start in range(0, l * k, k):
|
64 |
+
edges = itertools.combinations(range(start, start + k), 2)
|
65 |
+
G.add_edges_from(edges)
|
66 |
+
return G
|
67 |
+
|
68 |
+
|
69 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
70 |
+
def connected_caveman_graph(l, k):
|
71 |
+
"""Returns a connected caveman graph of `l` cliques of size `k`.
|
72 |
+
|
73 |
+
The connected caveman graph is formed by creating `n` cliques of size
|
74 |
+
`k`, then a single edge in each clique is rewired to a node in an
|
75 |
+
adjacent clique.
|
76 |
+
|
77 |
+
Parameters
|
78 |
+
----------
|
79 |
+
l : int
|
80 |
+
number of cliques
|
81 |
+
k : int
|
82 |
+
size of cliques (k at least 2 or NetworkXError is raised)
|
83 |
+
|
84 |
+
Returns
|
85 |
+
-------
|
86 |
+
G : NetworkX Graph
|
87 |
+
connected caveman graph
|
88 |
+
|
89 |
+
Raises
|
90 |
+
------
|
91 |
+
NetworkXError
|
92 |
+
If the size of cliques `k` is smaller than 2.
|
93 |
+
|
94 |
+
Notes
|
95 |
+
-----
|
96 |
+
This returns an undirected graph, it can be converted to a directed
|
97 |
+
graph using :func:`nx.to_directed`, or a multigraph using
|
98 |
+
``nx.MultiGraph(nx.caveman_graph(l, k))``. Only the undirected version is
|
99 |
+
described in [1]_ and it is unclear which of the directed
|
100 |
+
generalizations is most useful.
|
101 |
+
|
102 |
+
Examples
|
103 |
+
--------
|
104 |
+
>>> G = nx.connected_caveman_graph(3, 3)
|
105 |
+
|
106 |
+
References
|
107 |
+
----------
|
108 |
+
.. [1] Watts, D. J. 'Networks, Dynamics, and the Small-World Phenomenon.'
|
109 |
+
Amer. J. Soc. 105, 493-527, 1999.
|
110 |
+
"""
|
111 |
+
if k < 2:
|
112 |
+
raise nx.NetworkXError(
|
113 |
+
"The size of cliques in a connected caveman graph must be at least 2."
|
114 |
+
)
|
115 |
+
|
116 |
+
G = nx.caveman_graph(l, k)
|
117 |
+
for start in range(0, l * k, k):
|
118 |
+
G.remove_edge(start, start + 1)
|
119 |
+
G.add_edge(start, (start - 1) % (l * k))
|
120 |
+
return G
|
121 |
+
|
122 |
+
|
123 |
+
@py_random_state(3)
|
124 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
125 |
+
def relaxed_caveman_graph(l, k, p, seed=None):
|
126 |
+
"""Returns a relaxed caveman graph.
|
127 |
+
|
128 |
+
A relaxed caveman graph starts with `l` cliques of size `k`. Edges are
|
129 |
+
then randomly rewired with probability `p` to link different cliques.
|
130 |
+
|
131 |
+
Parameters
|
132 |
+
----------
|
133 |
+
l : int
|
134 |
+
Number of groups
|
135 |
+
k : int
|
136 |
+
Size of cliques
|
137 |
+
p : float
|
138 |
+
Probability of rewiring each edge.
|
139 |
+
seed : integer, random_state, or None (default)
|
140 |
+
Indicator of random number generation state.
|
141 |
+
See :ref:`Randomness<randomness>`.
|
142 |
+
|
143 |
+
Returns
|
144 |
+
-------
|
145 |
+
G : NetworkX Graph
|
146 |
+
Relaxed Caveman Graph
|
147 |
+
|
148 |
+
Raises
|
149 |
+
------
|
150 |
+
NetworkXError
|
151 |
+
If p is not in [0,1]
|
152 |
+
|
153 |
+
Examples
|
154 |
+
--------
|
155 |
+
>>> G = nx.relaxed_caveman_graph(2, 3, 0.1, seed=42)
|
156 |
+
|
157 |
+
References
|
158 |
+
----------
|
159 |
+
.. [1] Santo Fortunato, Community Detection in Graphs,
|
160 |
+
Physics Reports Volume 486, Issues 3-5, February 2010, Pages 75-174.
|
161 |
+
https://arxiv.org/abs/0906.0612
|
162 |
+
"""
|
163 |
+
G = nx.caveman_graph(l, k)
|
164 |
+
nodes = list(G)
|
165 |
+
for u, v in G.edges():
|
166 |
+
if seed.random() < p: # rewire the edge
|
167 |
+
x = seed.choice(nodes)
|
168 |
+
if G.has_edge(u, x):
|
169 |
+
continue
|
170 |
+
G.remove_edge(u, v)
|
171 |
+
G.add_edge(u, x)
|
172 |
+
return G
|
173 |
+
|
174 |
+
|
175 |
+
@py_random_state(3)
|
176 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
177 |
+
def random_partition_graph(sizes, p_in, p_out, seed=None, directed=False):
|
178 |
+
"""Returns the random partition graph with a partition of sizes.
|
179 |
+
|
180 |
+
A partition graph is a graph of communities with sizes defined by
|
181 |
+
s in sizes. Nodes in the same group are connected with probability
|
182 |
+
p_in and nodes of different groups are connected with probability
|
183 |
+
p_out.
|
184 |
+
|
185 |
+
Parameters
|
186 |
+
----------
|
187 |
+
sizes : list of ints
|
188 |
+
Sizes of groups
|
189 |
+
p_in : float
|
190 |
+
probability of edges with in groups
|
191 |
+
p_out : float
|
192 |
+
probability of edges between groups
|
193 |
+
directed : boolean optional, default=False
|
194 |
+
Whether to create a directed graph
|
195 |
+
seed : integer, random_state, or None (default)
|
196 |
+
Indicator of random number generation state.
|
197 |
+
See :ref:`Randomness<randomness>`.
|
198 |
+
|
199 |
+
Returns
|
200 |
+
-------
|
201 |
+
G : NetworkX Graph or DiGraph
|
202 |
+
random partition graph of size sum(gs)
|
203 |
+
|
204 |
+
Raises
|
205 |
+
------
|
206 |
+
NetworkXError
|
207 |
+
If p_in or p_out is not in [0,1]
|
208 |
+
|
209 |
+
Examples
|
210 |
+
--------
|
211 |
+
>>> G = nx.random_partition_graph([10, 10, 10], 0.25, 0.01)
|
212 |
+
>>> len(G)
|
213 |
+
30
|
214 |
+
>>> partition = G.graph["partition"]
|
215 |
+
>>> len(partition)
|
216 |
+
3
|
217 |
+
|
218 |
+
Notes
|
219 |
+
-----
|
220 |
+
This is a generalization of the planted-l-partition described in
|
221 |
+
[1]_. It allows for the creation of groups of any size.
|
222 |
+
|
223 |
+
The partition is store as a graph attribute 'partition'.
|
224 |
+
|
225 |
+
References
|
226 |
+
----------
|
227 |
+
.. [1] Santo Fortunato 'Community Detection in Graphs' Physical Reports
|
228 |
+
Volume 486, Issue 3-5 p. 75-174. https://arxiv.org/abs/0906.0612
|
229 |
+
"""
|
230 |
+
# Use geometric method for O(n+m) complexity algorithm
|
231 |
+
# partition = nx.community_sets(nx.get_node_attributes(G, 'affiliation'))
|
232 |
+
if not 0.0 <= p_in <= 1.0:
|
233 |
+
raise nx.NetworkXError("p_in must be in [0,1]")
|
234 |
+
if not 0.0 <= p_out <= 1.0:
|
235 |
+
raise nx.NetworkXError("p_out must be in [0,1]")
|
236 |
+
|
237 |
+
# create connection matrix
|
238 |
+
num_blocks = len(sizes)
|
239 |
+
p = [[p_out for s in range(num_blocks)] for r in range(num_blocks)]
|
240 |
+
for r in range(num_blocks):
|
241 |
+
p[r][r] = p_in
|
242 |
+
|
243 |
+
return stochastic_block_model(
|
244 |
+
sizes,
|
245 |
+
p,
|
246 |
+
nodelist=None,
|
247 |
+
seed=seed,
|
248 |
+
directed=directed,
|
249 |
+
selfloops=False,
|
250 |
+
sparse=True,
|
251 |
+
)
|
252 |
+
|
253 |
+
|
254 |
+
@py_random_state(4)
|
255 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
256 |
+
def planted_partition_graph(l, k, p_in, p_out, seed=None, directed=False):
|
257 |
+
"""Returns the planted l-partition graph.
|
258 |
+
|
259 |
+
This model partitions a graph with n=l*k vertices in
|
260 |
+
l groups with k vertices each. Vertices of the same
|
261 |
+
group are linked with a probability p_in, and vertices
|
262 |
+
of different groups are linked with probability p_out.
|
263 |
+
|
264 |
+
Parameters
|
265 |
+
----------
|
266 |
+
l : int
|
267 |
+
Number of groups
|
268 |
+
k : int
|
269 |
+
Number of vertices in each group
|
270 |
+
p_in : float
|
271 |
+
probability of connecting vertices within a group
|
272 |
+
p_out : float
|
273 |
+
probability of connected vertices between groups
|
274 |
+
seed : integer, random_state, or None (default)
|
275 |
+
Indicator of random number generation state.
|
276 |
+
See :ref:`Randomness<randomness>`.
|
277 |
+
directed : bool,optional (default=False)
|
278 |
+
If True return a directed graph
|
279 |
+
|
280 |
+
Returns
|
281 |
+
-------
|
282 |
+
G : NetworkX Graph or DiGraph
|
283 |
+
planted l-partition graph
|
284 |
+
|
285 |
+
Raises
|
286 |
+
------
|
287 |
+
NetworkXError
|
288 |
+
If `p_in`, `p_out` are not in `[0, 1]`
|
289 |
+
|
290 |
+
Examples
|
291 |
+
--------
|
292 |
+
>>> G = nx.planted_partition_graph(4, 3, 0.5, 0.1, seed=42)
|
293 |
+
|
294 |
+
See Also
|
295 |
+
--------
|
296 |
+
random_partition_model
|
297 |
+
|
298 |
+
References
|
299 |
+
----------
|
300 |
+
.. [1] A. Condon, R.M. Karp, Algorithms for graph partitioning
|
301 |
+
on the planted partition model,
|
302 |
+
Random Struct. Algor. 18 (2001) 116-140.
|
303 |
+
|
304 |
+
.. [2] Santo Fortunato 'Community Detection in Graphs' Physical Reports
|
305 |
+
Volume 486, Issue 3-5 p. 75-174. https://arxiv.org/abs/0906.0612
|
306 |
+
"""
|
307 |
+
return random_partition_graph([k] * l, p_in, p_out, seed=seed, directed=directed)
|
308 |
+
|
309 |
+
|
310 |
+
@py_random_state(6)
|
311 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
312 |
+
def gaussian_random_partition_graph(n, s, v, p_in, p_out, directed=False, seed=None):
|
313 |
+
"""Generate a Gaussian random partition graph.
|
314 |
+
|
315 |
+
A Gaussian random partition graph is created by creating k partitions
|
316 |
+
each with a size drawn from a normal distribution with mean s and variance
|
317 |
+
s/v. Nodes are connected within clusters with probability p_in and
|
318 |
+
between clusters with probability p_out[1]
|
319 |
+
|
320 |
+
Parameters
|
321 |
+
----------
|
322 |
+
n : int
|
323 |
+
Number of nodes in the graph
|
324 |
+
s : float
|
325 |
+
Mean cluster size
|
326 |
+
v : float
|
327 |
+
Shape parameter. The variance of cluster size distribution is s/v.
|
328 |
+
p_in : float
|
329 |
+
Probability of intra cluster connection.
|
330 |
+
p_out : float
|
331 |
+
Probability of inter cluster connection.
|
332 |
+
directed : boolean, optional default=False
|
333 |
+
Whether to create a directed graph or not
|
334 |
+
seed : integer, random_state, or None (default)
|
335 |
+
Indicator of random number generation state.
|
336 |
+
See :ref:`Randomness<randomness>`.
|
337 |
+
|
338 |
+
Returns
|
339 |
+
-------
|
340 |
+
G : NetworkX Graph or DiGraph
|
341 |
+
gaussian random partition graph
|
342 |
+
|
343 |
+
Raises
|
344 |
+
------
|
345 |
+
NetworkXError
|
346 |
+
If s is > n
|
347 |
+
If p_in or p_out is not in [0,1]
|
348 |
+
|
349 |
+
Notes
|
350 |
+
-----
|
351 |
+
Note the number of partitions is dependent on s,v and n, and that the
|
352 |
+
last partition may be considerably smaller, as it is sized to simply
|
353 |
+
fill out the nodes [1]
|
354 |
+
|
355 |
+
See Also
|
356 |
+
--------
|
357 |
+
random_partition_graph
|
358 |
+
|
359 |
+
Examples
|
360 |
+
--------
|
361 |
+
>>> G = nx.gaussian_random_partition_graph(100, 10, 10, 0.25, 0.1)
|
362 |
+
>>> len(G)
|
363 |
+
100
|
364 |
+
|
365 |
+
References
|
366 |
+
----------
|
367 |
+
.. [1] Ulrik Brandes, Marco Gaertler, Dorothea Wagner,
|
368 |
+
Experiments on Graph Clustering Algorithms,
|
369 |
+
In the proceedings of the 11th Europ. Symp. Algorithms, 2003.
|
370 |
+
"""
|
371 |
+
if s > n:
|
372 |
+
raise nx.NetworkXError("s must be <= n")
|
373 |
+
assigned = 0
|
374 |
+
sizes = []
|
375 |
+
while True:
|
376 |
+
size = int(seed.gauss(s, s / v + 0.5))
|
377 |
+
if size < 1: # how to handle 0 or negative sizes?
|
378 |
+
continue
|
379 |
+
if assigned + size >= n:
|
380 |
+
sizes.append(n - assigned)
|
381 |
+
break
|
382 |
+
assigned += size
|
383 |
+
sizes.append(size)
|
384 |
+
return random_partition_graph(sizes, p_in, p_out, seed=seed, directed=directed)
|
385 |
+
|
386 |
+
|
387 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
388 |
+
def ring_of_cliques(num_cliques, clique_size):
|
389 |
+
"""Defines a "ring of cliques" graph.
|
390 |
+
|
391 |
+
A ring of cliques graph is consisting of cliques, connected through single
|
392 |
+
links. Each clique is a complete graph.
|
393 |
+
|
394 |
+
Parameters
|
395 |
+
----------
|
396 |
+
num_cliques : int
|
397 |
+
Number of cliques
|
398 |
+
clique_size : int
|
399 |
+
Size of cliques
|
400 |
+
|
401 |
+
Returns
|
402 |
+
-------
|
403 |
+
G : NetworkX Graph
|
404 |
+
ring of cliques graph
|
405 |
+
|
406 |
+
Raises
|
407 |
+
------
|
408 |
+
NetworkXError
|
409 |
+
If the number of cliques is lower than 2 or
|
410 |
+
if the size of cliques is smaller than 2.
|
411 |
+
|
412 |
+
Examples
|
413 |
+
--------
|
414 |
+
>>> G = nx.ring_of_cliques(8, 4)
|
415 |
+
|
416 |
+
See Also
|
417 |
+
--------
|
418 |
+
connected_caveman_graph
|
419 |
+
|
420 |
+
Notes
|
421 |
+
-----
|
422 |
+
The `connected_caveman_graph` graph removes a link from each clique to
|
423 |
+
connect it with the next clique. Instead, the `ring_of_cliques` graph
|
424 |
+
simply adds the link without removing any link from the cliques.
|
425 |
+
"""
|
426 |
+
if num_cliques < 2:
|
427 |
+
raise nx.NetworkXError("A ring of cliques must have at least two cliques")
|
428 |
+
if clique_size < 2:
|
429 |
+
raise nx.NetworkXError("The cliques must have at least two nodes")
|
430 |
+
|
431 |
+
G = nx.Graph()
|
432 |
+
for i in range(num_cliques):
|
433 |
+
edges = itertools.combinations(
|
434 |
+
range(i * clique_size, i * clique_size + clique_size), 2
|
435 |
+
)
|
436 |
+
G.add_edges_from(edges)
|
437 |
+
G.add_edge(
|
438 |
+
i * clique_size + 1, (i + 1) * clique_size % (num_cliques * clique_size)
|
439 |
+
)
|
440 |
+
return G
|
441 |
+
|
442 |
+
|
443 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
444 |
+
def windmill_graph(n, k):
|
445 |
+
"""Generate a windmill graph.
|
446 |
+
A windmill graph is a graph of `n` cliques each of size `k` that are all
|
447 |
+
joined at one node.
|
448 |
+
It can be thought of as taking a disjoint union of `n` cliques of size `k`,
|
449 |
+
selecting one point from each, and contracting all of the selected points.
|
450 |
+
Alternatively, one could generate `n` cliques of size `k-1` and one node
|
451 |
+
that is connected to all other nodes in the graph.
|
452 |
+
|
453 |
+
Parameters
|
454 |
+
----------
|
455 |
+
n : int
|
456 |
+
Number of cliques
|
457 |
+
k : int
|
458 |
+
Size of cliques
|
459 |
+
|
460 |
+
Returns
|
461 |
+
-------
|
462 |
+
G : NetworkX Graph
|
463 |
+
windmill graph with n cliques of size k
|
464 |
+
|
465 |
+
Raises
|
466 |
+
------
|
467 |
+
NetworkXError
|
468 |
+
If the number of cliques is less than two
|
469 |
+
If the size of the cliques are less than two
|
470 |
+
|
471 |
+
Examples
|
472 |
+
--------
|
473 |
+
>>> G = nx.windmill_graph(4, 5)
|
474 |
+
|
475 |
+
Notes
|
476 |
+
-----
|
477 |
+
The node labeled `0` will be the node connected to all other nodes.
|
478 |
+
Note that windmill graphs are usually denoted `Wd(k,n)`, so the parameters
|
479 |
+
are in the opposite order as the parameters of this method.
|
480 |
+
"""
|
481 |
+
if n < 2:
|
482 |
+
msg = "A windmill graph must have at least two cliques"
|
483 |
+
raise nx.NetworkXError(msg)
|
484 |
+
if k < 2:
|
485 |
+
raise nx.NetworkXError("The cliques must have at least two nodes")
|
486 |
+
|
487 |
+
G = nx.disjoint_union_all(
|
488 |
+
itertools.chain(
|
489 |
+
[nx.complete_graph(k)], (nx.complete_graph(k - 1) for _ in range(n - 1))
|
490 |
+
)
|
491 |
+
)
|
492 |
+
G.add_edges_from((0, i) for i in range(k, G.number_of_nodes()))
|
493 |
+
return G
|
494 |
+
|
495 |
+
|
496 |
+
@py_random_state(3)
|
497 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
498 |
+
def stochastic_block_model(
|
499 |
+
sizes, p, nodelist=None, seed=None, directed=False, selfloops=False, sparse=True
|
500 |
+
):
|
501 |
+
"""Returns a stochastic block model graph.
|
502 |
+
|
503 |
+
This model partitions the nodes in blocks of arbitrary sizes, and places
|
504 |
+
edges between pairs of nodes independently, with a probability that depends
|
505 |
+
on the blocks.
|
506 |
+
|
507 |
+
Parameters
|
508 |
+
----------
|
509 |
+
sizes : list of ints
|
510 |
+
Sizes of blocks
|
511 |
+
p : list of list of floats
|
512 |
+
Element (r,s) gives the density of edges going from the nodes
|
513 |
+
of group r to nodes of group s.
|
514 |
+
p must match the number of groups (len(sizes) == len(p)),
|
515 |
+
and it must be symmetric if the graph is undirected.
|
516 |
+
nodelist : list, optional
|
517 |
+
The block tags are assigned according to the node identifiers
|
518 |
+
in nodelist. If nodelist is None, then the ordering is the
|
519 |
+
range [0,sum(sizes)-1].
|
520 |
+
seed : integer, random_state, or None (default)
|
521 |
+
Indicator of random number generation state.
|
522 |
+
See :ref:`Randomness<randomness>`.
|
523 |
+
directed : boolean optional, default=False
|
524 |
+
Whether to create a directed graph or not.
|
525 |
+
selfloops : boolean optional, default=False
|
526 |
+
Whether to include self-loops or not.
|
527 |
+
sparse: boolean optional, default=True
|
528 |
+
Use the sparse heuristic to speed up the generator.
|
529 |
+
|
530 |
+
Returns
|
531 |
+
-------
|
532 |
+
g : NetworkX Graph or DiGraph
|
533 |
+
Stochastic block model graph of size sum(sizes)
|
534 |
+
|
535 |
+
Raises
|
536 |
+
------
|
537 |
+
NetworkXError
|
538 |
+
If probabilities are not in [0,1].
|
539 |
+
If the probability matrix is not square (directed case).
|
540 |
+
If the probability matrix is not symmetric (undirected case).
|
541 |
+
If the sizes list does not match nodelist or the probability matrix.
|
542 |
+
If nodelist contains duplicate.
|
543 |
+
|
544 |
+
Examples
|
545 |
+
--------
|
546 |
+
>>> sizes = [75, 75, 300]
|
547 |
+
>>> probs = [[0.25, 0.05, 0.02], [0.05, 0.35, 0.07], [0.02, 0.07, 0.40]]
|
548 |
+
>>> g = nx.stochastic_block_model(sizes, probs, seed=0)
|
549 |
+
>>> len(g)
|
550 |
+
450
|
551 |
+
>>> H = nx.quotient_graph(g, g.graph["partition"], relabel=True)
|
552 |
+
>>> for v in H.nodes(data=True):
|
553 |
+
... print(round(v[1]["density"], 3))
|
554 |
+
0.245
|
555 |
+
0.348
|
556 |
+
0.405
|
557 |
+
>>> for v in H.edges(data=True):
|
558 |
+
... print(round(1.0 * v[2]["weight"] / (sizes[v[0]] * sizes[v[1]]), 3))
|
559 |
+
0.051
|
560 |
+
0.022
|
561 |
+
0.07
|
562 |
+
|
563 |
+
See Also
|
564 |
+
--------
|
565 |
+
random_partition_graph
|
566 |
+
planted_partition_graph
|
567 |
+
gaussian_random_partition_graph
|
568 |
+
gnp_random_graph
|
569 |
+
|
570 |
+
References
|
571 |
+
----------
|
572 |
+
.. [1] Holland, P. W., Laskey, K. B., & Leinhardt, S.,
|
573 |
+
"Stochastic blockmodels: First steps",
|
574 |
+
Social networks, 5(2), 109-137, 1983.
|
575 |
+
"""
|
576 |
+
# Check if dimensions match
|
577 |
+
if len(sizes) != len(p):
|
578 |
+
raise nx.NetworkXException("'sizes' and 'p' do not match.")
|
579 |
+
# Check for probability symmetry (undirected) and shape (directed)
|
580 |
+
for row in p:
|
581 |
+
if len(p) != len(row):
|
582 |
+
raise nx.NetworkXException("'p' must be a square matrix.")
|
583 |
+
if not directed:
|
584 |
+
p_transpose = [list(i) for i in zip(*p)]
|
585 |
+
for i in zip(p, p_transpose):
|
586 |
+
for j in zip(i[0], i[1]):
|
587 |
+
if abs(j[0] - j[1]) > 1e-08:
|
588 |
+
raise nx.NetworkXException("'p' must be symmetric.")
|
589 |
+
# Check for probability range
|
590 |
+
for row in p:
|
591 |
+
for prob in row:
|
592 |
+
if prob < 0 or prob > 1:
|
593 |
+
raise nx.NetworkXException("Entries of 'p' not in [0,1].")
|
594 |
+
# Check for nodelist consistency
|
595 |
+
if nodelist is not None:
|
596 |
+
if len(nodelist) != sum(sizes):
|
597 |
+
raise nx.NetworkXException("'nodelist' and 'sizes' do not match.")
|
598 |
+
if len(nodelist) != len(set(nodelist)):
|
599 |
+
raise nx.NetworkXException("nodelist contains duplicate.")
|
600 |
+
else:
|
601 |
+
nodelist = range(sum(sizes))
|
602 |
+
|
603 |
+
# Setup the graph conditionally to the directed switch.
|
604 |
+
block_range = range(len(sizes))
|
605 |
+
if directed:
|
606 |
+
g = nx.DiGraph()
|
607 |
+
block_iter = itertools.product(block_range, block_range)
|
608 |
+
else:
|
609 |
+
g = nx.Graph()
|
610 |
+
block_iter = itertools.combinations_with_replacement(block_range, 2)
|
611 |
+
# Split nodelist in a partition (list of sets).
|
612 |
+
size_cumsum = [sum(sizes[0:x]) for x in range(len(sizes) + 1)]
|
613 |
+
g.graph["partition"] = [
|
614 |
+
set(nodelist[size_cumsum[x] : size_cumsum[x + 1]])
|
615 |
+
for x in range(len(size_cumsum) - 1)
|
616 |
+
]
|
617 |
+
# Setup nodes and graph name
|
618 |
+
for block_id, nodes in enumerate(g.graph["partition"]):
|
619 |
+
for node in nodes:
|
620 |
+
g.add_node(node, block=block_id)
|
621 |
+
|
622 |
+
g.name = "stochastic_block_model"
|
623 |
+
|
624 |
+
# Test for edge existence
|
625 |
+
parts = g.graph["partition"]
|
626 |
+
for i, j in block_iter:
|
627 |
+
if i == j:
|
628 |
+
if directed:
|
629 |
+
if selfloops:
|
630 |
+
edges = itertools.product(parts[i], parts[i])
|
631 |
+
else:
|
632 |
+
edges = itertools.permutations(parts[i], 2)
|
633 |
+
else:
|
634 |
+
edges = itertools.combinations(parts[i], 2)
|
635 |
+
if selfloops:
|
636 |
+
edges = itertools.chain(edges, zip(parts[i], parts[i]))
|
637 |
+
for e in edges:
|
638 |
+
if seed.random() < p[i][j]:
|
639 |
+
g.add_edge(*e)
|
640 |
+
else:
|
641 |
+
edges = itertools.product(parts[i], parts[j])
|
642 |
+
if sparse:
|
643 |
+
if p[i][j] == 1: # Test edges cases p_ij = 0 or 1
|
644 |
+
for e in edges:
|
645 |
+
g.add_edge(*e)
|
646 |
+
elif p[i][j] > 0:
|
647 |
+
while True:
|
648 |
+
try:
|
649 |
+
logrand = math.log(seed.random())
|
650 |
+
skip = math.floor(logrand / math.log(1 - p[i][j]))
|
651 |
+
# consume "skip" edges
|
652 |
+
next(itertools.islice(edges, skip, skip), None)
|
653 |
+
e = next(edges)
|
654 |
+
g.add_edge(*e) # __safe
|
655 |
+
except StopIteration:
|
656 |
+
break
|
657 |
+
else:
|
658 |
+
for e in edges:
|
659 |
+
if seed.random() < p[i][j]:
|
660 |
+
g.add_edge(*e) # __safe
|
661 |
+
return g
|
662 |
+
|
663 |
+
|
664 |
+
def _zipf_rv_below(gamma, xmin, threshold, seed):
|
665 |
+
"""Returns a random value chosen from the bounded Zipf distribution.
|
666 |
+
|
667 |
+
Repeatedly draws values from the Zipf distribution until the
|
668 |
+
threshold is met, then returns that value.
|
669 |
+
"""
|
670 |
+
result = nx.utils.zipf_rv(gamma, xmin, seed)
|
671 |
+
while result > threshold:
|
672 |
+
result = nx.utils.zipf_rv(gamma, xmin, seed)
|
673 |
+
return result
|
674 |
+
|
675 |
+
|
676 |
+
def _powerlaw_sequence(gamma, low, high, condition, length, max_iters, seed):
|
677 |
+
"""Returns a list of numbers obeying a constrained power law distribution.
|
678 |
+
|
679 |
+
``gamma`` and ``low`` are the parameters for the Zipf distribution.
|
680 |
+
|
681 |
+
``high`` is the maximum allowed value for values draw from the Zipf
|
682 |
+
distribution. For more information, see :func:`_zipf_rv_below`.
|
683 |
+
|
684 |
+
``condition`` and ``length`` are Boolean-valued functions on
|
685 |
+
lists. While generating the list, random values are drawn and
|
686 |
+
appended to the list until ``length`` is satisfied by the created
|
687 |
+
list. Once ``condition`` is satisfied, the sequence generated in
|
688 |
+
this way is returned.
|
689 |
+
|
690 |
+
``max_iters`` indicates the number of times to generate a list
|
691 |
+
satisfying ``length``. If the number of iterations exceeds this
|
692 |
+
value, :exc:`~networkx.exception.ExceededMaxIterations` is raised.
|
693 |
+
|
694 |
+
seed : integer, random_state, or None (default)
|
695 |
+
Indicator of random number generation state.
|
696 |
+
See :ref:`Randomness<randomness>`.
|
697 |
+
"""
|
698 |
+
for i in range(max_iters):
|
699 |
+
seq = []
|
700 |
+
while not length(seq):
|
701 |
+
seq.append(_zipf_rv_below(gamma, low, high, seed))
|
702 |
+
if condition(seq):
|
703 |
+
return seq
|
704 |
+
raise nx.ExceededMaxIterations("Could not create power law sequence")
|
705 |
+
|
706 |
+
|
707 |
+
def _hurwitz_zeta(x, q, tolerance):
|
708 |
+
"""The Hurwitz zeta function, or the Riemann zeta function of two arguments.
|
709 |
+
|
710 |
+
``x`` must be greater than one and ``q`` must be positive.
|
711 |
+
|
712 |
+
This function repeatedly computes subsequent partial sums until
|
713 |
+
convergence, as decided by ``tolerance``.
|
714 |
+
"""
|
715 |
+
z = 0
|
716 |
+
z_prev = -float("inf")
|
717 |
+
k = 0
|
718 |
+
while abs(z - z_prev) > tolerance:
|
719 |
+
z_prev = z
|
720 |
+
z += 1 / ((k + q) ** x)
|
721 |
+
k += 1
|
722 |
+
return z
|
723 |
+
|
724 |
+
|
725 |
+
def _generate_min_degree(gamma, average_degree, max_degree, tolerance, max_iters):
|
726 |
+
"""Returns a minimum degree from the given average degree."""
|
727 |
+
# Defines zeta function whether or not Scipy is available
|
728 |
+
try:
|
729 |
+
from scipy.special import zeta
|
730 |
+
except ImportError:
|
731 |
+
|
732 |
+
def zeta(x, q):
|
733 |
+
return _hurwitz_zeta(x, q, tolerance)
|
734 |
+
|
735 |
+
min_deg_top = max_degree
|
736 |
+
min_deg_bot = 1
|
737 |
+
min_deg_mid = (min_deg_top - min_deg_bot) / 2 + min_deg_bot
|
738 |
+
itrs = 0
|
739 |
+
mid_avg_deg = 0
|
740 |
+
while abs(mid_avg_deg - average_degree) > tolerance:
|
741 |
+
if itrs > max_iters:
|
742 |
+
raise nx.ExceededMaxIterations("Could not match average_degree")
|
743 |
+
mid_avg_deg = 0
|
744 |
+
for x in range(int(min_deg_mid), max_degree + 1):
|
745 |
+
mid_avg_deg += (x ** (-gamma + 1)) / zeta(gamma, min_deg_mid)
|
746 |
+
if mid_avg_deg > average_degree:
|
747 |
+
min_deg_top = min_deg_mid
|
748 |
+
min_deg_mid = (min_deg_top - min_deg_bot) / 2 + min_deg_bot
|
749 |
+
else:
|
750 |
+
min_deg_bot = min_deg_mid
|
751 |
+
min_deg_mid = (min_deg_top - min_deg_bot) / 2 + min_deg_bot
|
752 |
+
itrs += 1
|
753 |
+
# return int(min_deg_mid + 0.5)
|
754 |
+
return round(min_deg_mid)
|
755 |
+
|
756 |
+
|
757 |
+
def _generate_communities(degree_seq, community_sizes, mu, max_iters, seed):
|
758 |
+
"""Returns a list of sets, each of which represents a community.
|
759 |
+
|
760 |
+
``degree_seq`` is the degree sequence that must be met by the
|
761 |
+
graph.
|
762 |
+
|
763 |
+
``community_sizes`` is the community size distribution that must be
|
764 |
+
met by the generated list of sets.
|
765 |
+
|
766 |
+
``mu`` is a float in the interval [0, 1] indicating the fraction of
|
767 |
+
intra-community edges incident to each node.
|
768 |
+
|
769 |
+
``max_iters`` is the number of times to try to add a node to a
|
770 |
+
community. This must be greater than the length of
|
771 |
+
``degree_seq``, otherwise this function will always fail. If
|
772 |
+
the number of iterations exceeds this value,
|
773 |
+
:exc:`~networkx.exception.ExceededMaxIterations` is raised.
|
774 |
+
|
775 |
+
seed : integer, random_state, or None (default)
|
776 |
+
Indicator of random number generation state.
|
777 |
+
See :ref:`Randomness<randomness>`.
|
778 |
+
|
779 |
+
The communities returned by this are sets of integers in the set {0,
|
780 |
+
..., *n* - 1}, where *n* is the length of ``degree_seq``.
|
781 |
+
|
782 |
+
"""
|
783 |
+
# This assumes the nodes in the graph will be natural numbers.
|
784 |
+
result = [set() for _ in community_sizes]
|
785 |
+
n = len(degree_seq)
|
786 |
+
free = list(range(n))
|
787 |
+
for i in range(max_iters):
|
788 |
+
v = free.pop()
|
789 |
+
c = seed.choice(range(len(community_sizes)))
|
790 |
+
# s = int(degree_seq[v] * (1 - mu) + 0.5)
|
791 |
+
s = round(degree_seq[v] * (1 - mu))
|
792 |
+
# If the community is large enough, add the node to the chosen
|
793 |
+
# community. Otherwise, return it to the list of unaffiliated
|
794 |
+
# nodes.
|
795 |
+
if s < community_sizes[c]:
|
796 |
+
result[c].add(v)
|
797 |
+
else:
|
798 |
+
free.append(v)
|
799 |
+
# If the community is too big, remove a node from it.
|
800 |
+
if len(result[c]) > community_sizes[c]:
|
801 |
+
free.append(result[c].pop())
|
802 |
+
if not free:
|
803 |
+
return result
|
804 |
+
msg = "Could not assign communities; try increasing min_community"
|
805 |
+
raise nx.ExceededMaxIterations(msg)
|
806 |
+
|
807 |
+
|
808 |
+
@py_random_state(11)
|
809 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
810 |
+
def LFR_benchmark_graph(
|
811 |
+
n,
|
812 |
+
tau1,
|
813 |
+
tau2,
|
814 |
+
mu,
|
815 |
+
average_degree=None,
|
816 |
+
min_degree=None,
|
817 |
+
max_degree=None,
|
818 |
+
min_community=None,
|
819 |
+
max_community=None,
|
820 |
+
tol=1.0e-7,
|
821 |
+
max_iters=500,
|
822 |
+
seed=None,
|
823 |
+
):
|
824 |
+
r"""Returns the LFR benchmark graph.
|
825 |
+
|
826 |
+
This algorithm proceeds as follows:
|
827 |
+
|
828 |
+
1) Find a degree sequence with a power law distribution, and minimum
|
829 |
+
value ``min_degree``, which has approximate average degree
|
830 |
+
``average_degree``. This is accomplished by either
|
831 |
+
|
832 |
+
a) specifying ``min_degree`` and not ``average_degree``,
|
833 |
+
b) specifying ``average_degree`` and not ``min_degree``, in which
|
834 |
+
case a suitable minimum degree will be found.
|
835 |
+
|
836 |
+
``max_degree`` can also be specified, otherwise it will be set to
|
837 |
+
``n``. Each node *u* will have $\mu \mathrm{deg}(u)$ edges
|
838 |
+
joining it to nodes in communities other than its own and $(1 -
|
839 |
+
\mu) \mathrm{deg}(u)$ edges joining it to nodes in its own
|
840 |
+
community.
|
841 |
+
2) Generate community sizes according to a power law distribution
|
842 |
+
with exponent ``tau2``. If ``min_community`` and
|
843 |
+
``max_community`` are not specified they will be selected to be
|
844 |
+
``min_degree`` and ``max_degree``, respectively. Community sizes
|
845 |
+
are generated until the sum of their sizes equals ``n``.
|
846 |
+
3) Each node will be randomly assigned a community with the
|
847 |
+
condition that the community is large enough for the node's
|
848 |
+
intra-community degree, $(1 - \mu) \mathrm{deg}(u)$ as
|
849 |
+
described in step 2. If a community grows too large, a random node
|
850 |
+
will be selected for reassignment to a new community, until all
|
851 |
+
nodes have been assigned a community.
|
852 |
+
4) Each node *u* then adds $(1 - \mu) \mathrm{deg}(u)$
|
853 |
+
intra-community edges and $\mu \mathrm{deg}(u)$ inter-community
|
854 |
+
edges.
|
855 |
+
|
856 |
+
Parameters
|
857 |
+
----------
|
858 |
+
n : int
|
859 |
+
Number of nodes in the created graph.
|
860 |
+
|
861 |
+
tau1 : float
|
862 |
+
Power law exponent for the degree distribution of the created
|
863 |
+
graph. This value must be strictly greater than one.
|
864 |
+
|
865 |
+
tau2 : float
|
866 |
+
Power law exponent for the community size distribution in the
|
867 |
+
created graph. This value must be strictly greater than one.
|
868 |
+
|
869 |
+
mu : float
|
870 |
+
Fraction of inter-community edges incident to each node. This
|
871 |
+
value must be in the interval [0, 1].
|
872 |
+
|
873 |
+
average_degree : float
|
874 |
+
Desired average degree of nodes in the created graph. This value
|
875 |
+
must be in the interval [0, *n*]. Exactly one of this and
|
876 |
+
``min_degree`` must be specified, otherwise a
|
877 |
+
:exc:`NetworkXError` is raised.
|
878 |
+
|
879 |
+
min_degree : int
|
880 |
+
Minimum degree of nodes in the created graph. This value must be
|
881 |
+
in the interval [0, *n*]. Exactly one of this and
|
882 |
+
``average_degree`` must be specified, otherwise a
|
883 |
+
:exc:`NetworkXError` is raised.
|
884 |
+
|
885 |
+
max_degree : int
|
886 |
+
Maximum degree of nodes in the created graph. If not specified,
|
887 |
+
this is set to ``n``, the total number of nodes in the graph.
|
888 |
+
|
889 |
+
min_community : int
|
890 |
+
Minimum size of communities in the graph. If not specified, this
|
891 |
+
is set to ``min_degree``.
|
892 |
+
|
893 |
+
max_community : int
|
894 |
+
Maximum size of communities in the graph. If not specified, this
|
895 |
+
is set to ``n``, the total number of nodes in the graph.
|
896 |
+
|
897 |
+
tol : float
|
898 |
+
Tolerance when comparing floats, specifically when comparing
|
899 |
+
average degree values.
|
900 |
+
|
901 |
+
max_iters : int
|
902 |
+
Maximum number of iterations to try to create the community sizes,
|
903 |
+
degree distribution, and community affiliations.
|
904 |
+
|
905 |
+
seed : integer, random_state, or None (default)
|
906 |
+
Indicator of random number generation state.
|
907 |
+
See :ref:`Randomness<randomness>`.
|
908 |
+
|
909 |
+
Returns
|
910 |
+
-------
|
911 |
+
G : NetworkX graph
|
912 |
+
The LFR benchmark graph generated according to the specified
|
913 |
+
parameters.
|
914 |
+
|
915 |
+
Each node in the graph has a node attribute ``'community'`` that
|
916 |
+
stores the community (that is, the set of nodes) that includes
|
917 |
+
it.
|
918 |
+
|
919 |
+
Raises
|
920 |
+
------
|
921 |
+
NetworkXError
|
922 |
+
If any of the parameters do not meet their upper and lower bounds:
|
923 |
+
|
924 |
+
- ``tau1`` and ``tau2`` must be strictly greater than 1.
|
925 |
+
- ``mu`` must be in [0, 1].
|
926 |
+
- ``max_degree`` must be in {1, ..., *n*}.
|
927 |
+
- ``min_community`` and ``max_community`` must be in {0, ...,
|
928 |
+
*n*}.
|
929 |
+
|
930 |
+
If not exactly one of ``average_degree`` and ``min_degree`` is
|
931 |
+
specified.
|
932 |
+
|
933 |
+
If ``min_degree`` is not specified and a suitable ``min_degree``
|
934 |
+
cannot be found.
|
935 |
+
|
936 |
+
ExceededMaxIterations
|
937 |
+
If a valid degree sequence cannot be created within
|
938 |
+
``max_iters`` number of iterations.
|
939 |
+
|
940 |
+
If a valid set of community sizes cannot be created within
|
941 |
+
``max_iters`` number of iterations.
|
942 |
+
|
943 |
+
If a valid community assignment cannot be created within ``10 *
|
944 |
+
n * max_iters`` number of iterations.
|
945 |
+
|
946 |
+
Examples
|
947 |
+
--------
|
948 |
+
Basic usage::
|
949 |
+
|
950 |
+
>>> from networkx.generators.community import LFR_benchmark_graph
|
951 |
+
>>> n = 250
|
952 |
+
>>> tau1 = 3
|
953 |
+
>>> tau2 = 1.5
|
954 |
+
>>> mu = 0.1
|
955 |
+
>>> G = LFR_benchmark_graph(
|
956 |
+
... n, tau1, tau2, mu, average_degree=5, min_community=20, seed=10
|
957 |
+
... )
|
958 |
+
|
959 |
+
Continuing the example above, you can get the communities from the
|
960 |
+
node attributes of the graph::
|
961 |
+
|
962 |
+
>>> communities = {frozenset(G.nodes[v]["community"]) for v in G}
|
963 |
+
|
964 |
+
Notes
|
965 |
+
-----
|
966 |
+
This algorithm differs slightly from the original way it was
|
967 |
+
presented in [1].
|
968 |
+
|
969 |
+
1) Rather than connecting the graph via a configuration model then
|
970 |
+
rewiring to match the intra-community and inter-community
|
971 |
+
degrees, we do this wiring explicitly at the end, which should be
|
972 |
+
equivalent.
|
973 |
+
2) The code posted on the author's website [2] calculates the random
|
974 |
+
power law distributed variables and their average using
|
975 |
+
continuous approximations, whereas we use the discrete
|
976 |
+
distributions here as both degree and community size are
|
977 |
+
discrete.
|
978 |
+
|
979 |
+
Though the authors describe the algorithm as quite robust, testing
|
980 |
+
during development indicates that a somewhat narrower parameter set
|
981 |
+
is likely to successfully produce a graph. Some suggestions have
|
982 |
+
been provided in the event of exceptions.
|
983 |
+
|
984 |
+
References
|
985 |
+
----------
|
986 |
+
.. [1] "Benchmark graphs for testing community detection algorithms",
|
987 |
+
Andrea Lancichinetti, Santo Fortunato, and Filippo Radicchi,
|
988 |
+
Phys. Rev. E 78, 046110 2008
|
989 |
+
.. [2] https://www.santofortunato.net/resources
|
990 |
+
|
991 |
+
"""
|
992 |
+
# Perform some basic parameter validation.
|
993 |
+
if not tau1 > 1:
|
994 |
+
raise nx.NetworkXError("tau1 must be greater than one")
|
995 |
+
if not tau2 > 1:
|
996 |
+
raise nx.NetworkXError("tau2 must be greater than one")
|
997 |
+
if not 0 <= mu <= 1:
|
998 |
+
raise nx.NetworkXError("mu must be in the interval [0, 1]")
|
999 |
+
|
1000 |
+
# Validate parameters for generating the degree sequence.
|
1001 |
+
if max_degree is None:
|
1002 |
+
max_degree = n
|
1003 |
+
elif not 0 < max_degree <= n:
|
1004 |
+
raise nx.NetworkXError("max_degree must be in the interval (0, n]")
|
1005 |
+
if not ((min_degree is None) ^ (average_degree is None)):
|
1006 |
+
raise nx.NetworkXError(
|
1007 |
+
"Must assign exactly one of min_degree and average_degree"
|
1008 |
+
)
|
1009 |
+
if min_degree is None:
|
1010 |
+
min_degree = _generate_min_degree(
|
1011 |
+
tau1, average_degree, max_degree, tol, max_iters
|
1012 |
+
)
|
1013 |
+
|
1014 |
+
# Generate a degree sequence with a power law distribution.
|
1015 |
+
low, high = min_degree, max_degree
|
1016 |
+
|
1017 |
+
def condition(seq):
|
1018 |
+
return sum(seq) % 2 == 0
|
1019 |
+
|
1020 |
+
def length(seq):
|
1021 |
+
return len(seq) >= n
|
1022 |
+
|
1023 |
+
deg_seq = _powerlaw_sequence(tau1, low, high, condition, length, max_iters, seed)
|
1024 |
+
|
1025 |
+
# Validate parameters for generating the community size sequence.
|
1026 |
+
if min_community is None:
|
1027 |
+
min_community = min(deg_seq)
|
1028 |
+
if max_community is None:
|
1029 |
+
max_community = max(deg_seq)
|
1030 |
+
|
1031 |
+
# Generate a community size sequence with a power law distribution.
|
1032 |
+
#
|
1033 |
+
# TODO The original code incremented the number of iterations each
|
1034 |
+
# time a new Zipf random value was drawn from the distribution. This
|
1035 |
+
# differed from the way the number of iterations was incremented in
|
1036 |
+
# `_powerlaw_degree_sequence`, so this code was changed to match
|
1037 |
+
# that one. As a result, this code is allowed many more chances to
|
1038 |
+
# generate a valid community size sequence.
|
1039 |
+
low, high = min_community, max_community
|
1040 |
+
|
1041 |
+
def condition(seq):
|
1042 |
+
return sum(seq) == n
|
1043 |
+
|
1044 |
+
def length(seq):
|
1045 |
+
return sum(seq) >= n
|
1046 |
+
|
1047 |
+
comms = _powerlaw_sequence(tau2, low, high, condition, length, max_iters, seed)
|
1048 |
+
|
1049 |
+
# Generate the communities based on the given degree sequence and
|
1050 |
+
# community sizes.
|
1051 |
+
max_iters *= 10 * n
|
1052 |
+
communities = _generate_communities(deg_seq, comms, mu, max_iters, seed)
|
1053 |
+
|
1054 |
+
# Finally, generate the benchmark graph based on the given
|
1055 |
+
# communities, joining nodes according to the intra- and
|
1056 |
+
# inter-community degrees.
|
1057 |
+
G = nx.Graph()
|
1058 |
+
G.add_nodes_from(range(n))
|
1059 |
+
for c in communities:
|
1060 |
+
for u in c:
|
1061 |
+
while G.degree(u) < round(deg_seq[u] * (1 - mu)):
|
1062 |
+
v = seed.choice(list(c))
|
1063 |
+
G.add_edge(u, v)
|
1064 |
+
while G.degree(u) < deg_seq[u]:
|
1065 |
+
v = seed.choice(range(n))
|
1066 |
+
if v not in c:
|
1067 |
+
G.add_edge(u, v)
|
1068 |
+
G.nodes[u]["community"] = c
|
1069 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/degree_seq.py
ADDED
@@ -0,0 +1,868 @@
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|
|
|
|
|
|
|
1 |
+
"""Generate graphs with a given degree sequence or expected degree sequence.
|
2 |
+
"""
|
3 |
+
|
4 |
+
import heapq
|
5 |
+
import math
|
6 |
+
from itertools import chain, combinations, zip_longest
|
7 |
+
from operator import itemgetter
|
8 |
+
|
9 |
+
import networkx as nx
|
10 |
+
from networkx.utils import py_random_state, random_weighted_sample
|
11 |
+
|
12 |
+
__all__ = [
|
13 |
+
"configuration_model",
|
14 |
+
"directed_configuration_model",
|
15 |
+
"expected_degree_graph",
|
16 |
+
"havel_hakimi_graph",
|
17 |
+
"directed_havel_hakimi_graph",
|
18 |
+
"degree_sequence_tree",
|
19 |
+
"random_degree_sequence_graph",
|
20 |
+
]
|
21 |
+
|
22 |
+
chaini = chain.from_iterable
|
23 |
+
|
24 |
+
|
25 |
+
def _to_stublist(degree_sequence):
|
26 |
+
"""Returns a list of degree-repeated node numbers.
|
27 |
+
|
28 |
+
``degree_sequence`` is a list of nonnegative integers representing
|
29 |
+
the degrees of nodes in a graph.
|
30 |
+
|
31 |
+
This function returns a list of node numbers with multiplicities
|
32 |
+
according to the given degree sequence. For example, if the first
|
33 |
+
element of ``degree_sequence`` is ``3``, then the first node number,
|
34 |
+
``0``, will appear at the head of the returned list three times. The
|
35 |
+
node numbers are assumed to be the numbers zero through
|
36 |
+
``len(degree_sequence) - 1``.
|
37 |
+
|
38 |
+
Examples
|
39 |
+
--------
|
40 |
+
|
41 |
+
>>> degree_sequence = [1, 2, 3]
|
42 |
+
>>> _to_stublist(degree_sequence)
|
43 |
+
[0, 1, 1, 2, 2, 2]
|
44 |
+
|
45 |
+
If a zero appears in the sequence, that means the node exists but
|
46 |
+
has degree zero, so that number will be skipped in the returned
|
47 |
+
list::
|
48 |
+
|
49 |
+
>>> degree_sequence = [2, 0, 1]
|
50 |
+
>>> _to_stublist(degree_sequence)
|
51 |
+
[0, 0, 2]
|
52 |
+
|
53 |
+
"""
|
54 |
+
return list(chaini([n] * d for n, d in enumerate(degree_sequence)))
|
55 |
+
|
56 |
+
|
57 |
+
def _configuration_model(
|
58 |
+
deg_sequence, create_using, directed=False, in_deg_sequence=None, seed=None
|
59 |
+
):
|
60 |
+
"""Helper function for generating either undirected or directed
|
61 |
+
configuration model graphs.
|
62 |
+
|
63 |
+
``deg_sequence`` is a list of nonnegative integers representing the
|
64 |
+
degree of the node whose label is the index of the list element.
|
65 |
+
|
66 |
+
``create_using`` see :func:`~networkx.empty_graph`.
|
67 |
+
|
68 |
+
``directed`` and ``in_deg_sequence`` are required if you want the
|
69 |
+
returned graph to be generated using the directed configuration
|
70 |
+
model algorithm. If ``directed`` is ``False``, then ``deg_sequence``
|
71 |
+
is interpreted as the degree sequence of an undirected graph and
|
72 |
+
``in_deg_sequence`` is ignored. Otherwise, if ``directed`` is
|
73 |
+
``True``, then ``deg_sequence`` is interpreted as the out-degree
|
74 |
+
sequence and ``in_deg_sequence`` as the in-degree sequence of a
|
75 |
+
directed graph.
|
76 |
+
|
77 |
+
.. note::
|
78 |
+
|
79 |
+
``deg_sequence`` and ``in_deg_sequence`` need not be the same
|
80 |
+
length.
|
81 |
+
|
82 |
+
``seed`` is a random.Random or numpy.random.RandomState instance
|
83 |
+
|
84 |
+
This function returns a graph, directed if and only if ``directed``
|
85 |
+
is ``True``, generated according to the configuration model
|
86 |
+
algorithm. For more information on the algorithm, see the
|
87 |
+
:func:`configuration_model` or :func:`directed_configuration_model`
|
88 |
+
functions.
|
89 |
+
|
90 |
+
"""
|
91 |
+
n = len(deg_sequence)
|
92 |
+
G = nx.empty_graph(n, create_using)
|
93 |
+
# If empty, return the null graph immediately.
|
94 |
+
if n == 0:
|
95 |
+
return G
|
96 |
+
# Build a list of available degree-repeated nodes. For example,
|
97 |
+
# for degree sequence [3, 2, 1, 1, 1], the "stub list" is
|
98 |
+
# initially [0, 0, 0, 1, 1, 2, 3, 4], that is, node 0 has degree
|
99 |
+
# 3 and thus is repeated 3 times, etc.
|
100 |
+
#
|
101 |
+
# Also, shuffle the stub list in order to get a random sequence of
|
102 |
+
# node pairs.
|
103 |
+
if directed:
|
104 |
+
pairs = zip_longest(deg_sequence, in_deg_sequence, fillvalue=0)
|
105 |
+
# Unzip the list of pairs into a pair of lists.
|
106 |
+
out_deg, in_deg = zip(*pairs)
|
107 |
+
|
108 |
+
out_stublist = _to_stublist(out_deg)
|
109 |
+
in_stublist = _to_stublist(in_deg)
|
110 |
+
|
111 |
+
seed.shuffle(out_stublist)
|
112 |
+
seed.shuffle(in_stublist)
|
113 |
+
else:
|
114 |
+
stublist = _to_stublist(deg_sequence)
|
115 |
+
# Choose a random balanced bipartition of the stublist, which
|
116 |
+
# gives a random pairing of nodes. In this implementation, we
|
117 |
+
# shuffle the list and then split it in half.
|
118 |
+
n = len(stublist)
|
119 |
+
half = n // 2
|
120 |
+
seed.shuffle(stublist)
|
121 |
+
out_stublist, in_stublist = stublist[:half], stublist[half:]
|
122 |
+
G.add_edges_from(zip(out_stublist, in_stublist))
|
123 |
+
return G
|
124 |
+
|
125 |
+
|
126 |
+
@py_random_state(2)
|
127 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
128 |
+
def configuration_model(deg_sequence, create_using=None, seed=None):
|
129 |
+
"""Returns a random graph with the given degree sequence.
|
130 |
+
|
131 |
+
The configuration model generates a random pseudograph (graph with
|
132 |
+
parallel edges and self loops) by randomly assigning edges to
|
133 |
+
match the given degree sequence.
|
134 |
+
|
135 |
+
Parameters
|
136 |
+
----------
|
137 |
+
deg_sequence : list of nonnegative integers
|
138 |
+
Each list entry corresponds to the degree of a node.
|
139 |
+
create_using : NetworkX graph constructor, optional (default MultiGraph)
|
140 |
+
Graph type to create. If graph instance, then cleared before populated.
|
141 |
+
seed : integer, random_state, or None (default)
|
142 |
+
Indicator of random number generation state.
|
143 |
+
See :ref:`Randomness<randomness>`.
|
144 |
+
|
145 |
+
Returns
|
146 |
+
-------
|
147 |
+
G : MultiGraph
|
148 |
+
A graph with the specified degree sequence.
|
149 |
+
Nodes are labeled starting at 0 with an index
|
150 |
+
corresponding to the position in deg_sequence.
|
151 |
+
|
152 |
+
Raises
|
153 |
+
------
|
154 |
+
NetworkXError
|
155 |
+
If the degree sequence does not have an even sum.
|
156 |
+
|
157 |
+
See Also
|
158 |
+
--------
|
159 |
+
is_graphical
|
160 |
+
|
161 |
+
Notes
|
162 |
+
-----
|
163 |
+
As described by Newman [1]_.
|
164 |
+
|
165 |
+
A non-graphical degree sequence (not realizable by some simple
|
166 |
+
graph) is allowed since this function returns graphs with self
|
167 |
+
loops and parallel edges. An exception is raised if the degree
|
168 |
+
sequence does not have an even sum.
|
169 |
+
|
170 |
+
This configuration model construction process can lead to
|
171 |
+
duplicate edges and loops. You can remove the self-loops and
|
172 |
+
parallel edges (see below) which will likely result in a graph
|
173 |
+
that doesn't have the exact degree sequence specified.
|
174 |
+
|
175 |
+
The density of self-loops and parallel edges tends to decrease as
|
176 |
+
the number of nodes increases. However, typically the number of
|
177 |
+
self-loops will approach a Poisson distribution with a nonzero mean,
|
178 |
+
and similarly for the number of parallel edges. Consider a node
|
179 |
+
with *k* stubs. The probability of being joined to another stub of
|
180 |
+
the same node is basically (*k* - *1*) / *N*, where *k* is the
|
181 |
+
degree and *N* is the number of nodes. So the probability of a
|
182 |
+
self-loop scales like *c* / *N* for some constant *c*. As *N* grows,
|
183 |
+
this means we expect *c* self-loops. Similarly for parallel edges.
|
184 |
+
|
185 |
+
References
|
186 |
+
----------
|
187 |
+
.. [1] M.E.J. Newman, "The structure and function of complex networks",
|
188 |
+
SIAM REVIEW 45-2, pp 167-256, 2003.
|
189 |
+
|
190 |
+
Examples
|
191 |
+
--------
|
192 |
+
You can create a degree sequence following a particular distribution
|
193 |
+
by using the one of the distribution functions in
|
194 |
+
:mod:`~networkx.utils.random_sequence` (or one of your own). For
|
195 |
+
example, to create an undirected multigraph on one hundred nodes
|
196 |
+
with degree sequence chosen from the power law distribution:
|
197 |
+
|
198 |
+
>>> sequence = nx.random_powerlaw_tree_sequence(100, tries=5000)
|
199 |
+
>>> G = nx.configuration_model(sequence)
|
200 |
+
>>> len(G)
|
201 |
+
100
|
202 |
+
>>> actual_degrees = [d for v, d in G.degree()]
|
203 |
+
>>> actual_degrees == sequence
|
204 |
+
True
|
205 |
+
|
206 |
+
The returned graph is a multigraph, which may have parallel
|
207 |
+
edges. To remove any parallel edges from the returned graph:
|
208 |
+
|
209 |
+
>>> G = nx.Graph(G)
|
210 |
+
|
211 |
+
Similarly, to remove self-loops:
|
212 |
+
|
213 |
+
>>> G.remove_edges_from(nx.selfloop_edges(G))
|
214 |
+
|
215 |
+
"""
|
216 |
+
if sum(deg_sequence) % 2 != 0:
|
217 |
+
msg = "Invalid degree sequence: sum of degrees must be even, not odd"
|
218 |
+
raise nx.NetworkXError(msg)
|
219 |
+
|
220 |
+
G = nx.empty_graph(0, create_using, default=nx.MultiGraph)
|
221 |
+
if G.is_directed():
|
222 |
+
raise nx.NetworkXNotImplemented("not implemented for directed graphs")
|
223 |
+
|
224 |
+
G = _configuration_model(deg_sequence, G, seed=seed)
|
225 |
+
|
226 |
+
return G
|
227 |
+
|
228 |
+
|
229 |
+
@py_random_state(3)
|
230 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
231 |
+
def directed_configuration_model(
|
232 |
+
in_degree_sequence, out_degree_sequence, create_using=None, seed=None
|
233 |
+
):
|
234 |
+
"""Returns a directed_random graph with the given degree sequences.
|
235 |
+
|
236 |
+
The configuration model generates a random directed pseudograph
|
237 |
+
(graph with parallel edges and self loops) by randomly assigning
|
238 |
+
edges to match the given degree sequences.
|
239 |
+
|
240 |
+
Parameters
|
241 |
+
----------
|
242 |
+
in_degree_sequence : list of nonnegative integers
|
243 |
+
Each list entry corresponds to the in-degree of a node.
|
244 |
+
out_degree_sequence : list of nonnegative integers
|
245 |
+
Each list entry corresponds to the out-degree of a node.
|
246 |
+
create_using : NetworkX graph constructor, optional (default MultiDiGraph)
|
247 |
+
Graph type to create. If graph instance, then cleared before populated.
|
248 |
+
seed : integer, random_state, or None (default)
|
249 |
+
Indicator of random number generation state.
|
250 |
+
See :ref:`Randomness<randomness>`.
|
251 |
+
|
252 |
+
Returns
|
253 |
+
-------
|
254 |
+
G : MultiDiGraph
|
255 |
+
A graph with the specified degree sequences.
|
256 |
+
Nodes are labeled starting at 0 with an index
|
257 |
+
corresponding to the position in deg_sequence.
|
258 |
+
|
259 |
+
Raises
|
260 |
+
------
|
261 |
+
NetworkXError
|
262 |
+
If the degree sequences do not have the same sum.
|
263 |
+
|
264 |
+
See Also
|
265 |
+
--------
|
266 |
+
configuration_model
|
267 |
+
|
268 |
+
Notes
|
269 |
+
-----
|
270 |
+
Algorithm as described by Newman [1]_.
|
271 |
+
|
272 |
+
A non-graphical degree sequence (not realizable by some simple
|
273 |
+
graph) is allowed since this function returns graphs with self
|
274 |
+
loops and parallel edges. An exception is raised if the degree
|
275 |
+
sequences does not have the same sum.
|
276 |
+
|
277 |
+
This configuration model construction process can lead to
|
278 |
+
duplicate edges and loops. You can remove the self-loops and
|
279 |
+
parallel edges (see below) which will likely result in a graph
|
280 |
+
that doesn't have the exact degree sequence specified. This
|
281 |
+
"finite-size effect" decreases as the size of the graph increases.
|
282 |
+
|
283 |
+
References
|
284 |
+
----------
|
285 |
+
.. [1] Newman, M. E. J. and Strogatz, S. H. and Watts, D. J.
|
286 |
+
Random graphs with arbitrary degree distributions and their applications
|
287 |
+
Phys. Rev. E, 64, 026118 (2001)
|
288 |
+
|
289 |
+
Examples
|
290 |
+
--------
|
291 |
+
One can modify the in- and out-degree sequences from an existing
|
292 |
+
directed graph in order to create a new directed graph. For example,
|
293 |
+
here we modify the directed path graph:
|
294 |
+
|
295 |
+
>>> D = nx.DiGraph([(0, 1), (1, 2), (2, 3)])
|
296 |
+
>>> din = list(d for n, d in D.in_degree())
|
297 |
+
>>> dout = list(d for n, d in D.out_degree())
|
298 |
+
>>> din.append(1)
|
299 |
+
>>> dout[0] = 2
|
300 |
+
>>> # We now expect an edge from node 0 to a new node, node 3.
|
301 |
+
... D = nx.directed_configuration_model(din, dout)
|
302 |
+
|
303 |
+
The returned graph is a directed multigraph, which may have parallel
|
304 |
+
edges. To remove any parallel edges from the returned graph:
|
305 |
+
|
306 |
+
>>> D = nx.DiGraph(D)
|
307 |
+
|
308 |
+
Similarly, to remove self-loops:
|
309 |
+
|
310 |
+
>>> D.remove_edges_from(nx.selfloop_edges(D))
|
311 |
+
|
312 |
+
"""
|
313 |
+
if sum(in_degree_sequence) != sum(out_degree_sequence):
|
314 |
+
msg = "Invalid degree sequences: sequences must have equal sums"
|
315 |
+
raise nx.NetworkXError(msg)
|
316 |
+
|
317 |
+
if create_using is None:
|
318 |
+
create_using = nx.MultiDiGraph
|
319 |
+
|
320 |
+
G = _configuration_model(
|
321 |
+
out_degree_sequence,
|
322 |
+
create_using,
|
323 |
+
directed=True,
|
324 |
+
in_deg_sequence=in_degree_sequence,
|
325 |
+
seed=seed,
|
326 |
+
)
|
327 |
+
|
328 |
+
name = "directed configuration_model {} nodes {} edges"
|
329 |
+
return G
|
330 |
+
|
331 |
+
|
332 |
+
@py_random_state(1)
|
333 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
334 |
+
def expected_degree_graph(w, seed=None, selfloops=True):
|
335 |
+
r"""Returns a random graph with given expected degrees.
|
336 |
+
|
337 |
+
Given a sequence of expected degrees $W=(w_0,w_1,\ldots,w_{n-1})$
|
338 |
+
of length $n$ this algorithm assigns an edge between node $u$ and
|
339 |
+
node $v$ with probability
|
340 |
+
|
341 |
+
.. math::
|
342 |
+
|
343 |
+
p_{uv} = \frac{w_u w_v}{\sum_k w_k} .
|
344 |
+
|
345 |
+
Parameters
|
346 |
+
----------
|
347 |
+
w : list
|
348 |
+
The list of expected degrees.
|
349 |
+
selfloops: bool (default=True)
|
350 |
+
Set to False to remove the possibility of self-loop edges.
|
351 |
+
seed : integer, random_state, or None (default)
|
352 |
+
Indicator of random number generation state.
|
353 |
+
See :ref:`Randomness<randomness>`.
|
354 |
+
|
355 |
+
Returns
|
356 |
+
-------
|
357 |
+
Graph
|
358 |
+
|
359 |
+
Examples
|
360 |
+
--------
|
361 |
+
>>> z = [10 for i in range(100)]
|
362 |
+
>>> G = nx.expected_degree_graph(z)
|
363 |
+
|
364 |
+
Notes
|
365 |
+
-----
|
366 |
+
The nodes have integer labels corresponding to index of expected degrees
|
367 |
+
input sequence.
|
368 |
+
|
369 |
+
The complexity of this algorithm is $\mathcal{O}(n+m)$ where $n$ is the
|
370 |
+
number of nodes and $m$ is the expected number of edges.
|
371 |
+
|
372 |
+
The model in [1]_ includes the possibility of self-loop edges.
|
373 |
+
Set selfloops=False to produce a graph without self loops.
|
374 |
+
|
375 |
+
For finite graphs this model doesn't produce exactly the given
|
376 |
+
expected degree sequence. Instead the expected degrees are as
|
377 |
+
follows.
|
378 |
+
|
379 |
+
For the case without self loops (selfloops=False),
|
380 |
+
|
381 |
+
.. math::
|
382 |
+
|
383 |
+
E[deg(u)] = \sum_{v \ne u} p_{uv}
|
384 |
+
= w_u \left( 1 - \frac{w_u}{\sum_k w_k} \right) .
|
385 |
+
|
386 |
+
|
387 |
+
NetworkX uses the standard convention that a self-loop edge counts 2
|
388 |
+
in the degree of a node, so with self loops (selfloops=True),
|
389 |
+
|
390 |
+
.. math::
|
391 |
+
|
392 |
+
E[deg(u)] = \sum_{v \ne u} p_{uv} + 2 p_{uu}
|
393 |
+
= w_u \left( 1 + \frac{w_u}{\sum_k w_k} \right) .
|
394 |
+
|
395 |
+
References
|
396 |
+
----------
|
397 |
+
.. [1] Fan Chung and L. Lu, Connected components in random graphs with
|
398 |
+
given expected degree sequences, Ann. Combinatorics, 6,
|
399 |
+
pp. 125-145, 2002.
|
400 |
+
.. [2] Joel Miller and Aric Hagberg,
|
401 |
+
Efficient generation of networks with given expected degrees,
|
402 |
+
in Algorithms and Models for the Web-Graph (WAW 2011),
|
403 |
+
Alan Frieze, Paul Horn, and Paweł Prałat (Eds), LNCS 6732,
|
404 |
+
pp. 115-126, 2011.
|
405 |
+
"""
|
406 |
+
n = len(w)
|
407 |
+
G = nx.empty_graph(n)
|
408 |
+
|
409 |
+
# If there are no nodes are no edges in the graph, return the empty graph.
|
410 |
+
if n == 0 or max(w) == 0:
|
411 |
+
return G
|
412 |
+
|
413 |
+
rho = 1 / sum(w)
|
414 |
+
# Sort the weights in decreasing order. The original order of the
|
415 |
+
# weights dictates the order of the (integer) node labels, so we
|
416 |
+
# need to remember the permutation applied in the sorting.
|
417 |
+
order = sorted(enumerate(w), key=itemgetter(1), reverse=True)
|
418 |
+
mapping = {c: u for c, (u, v) in enumerate(order)}
|
419 |
+
seq = [v for u, v in order]
|
420 |
+
last = n
|
421 |
+
if not selfloops:
|
422 |
+
last -= 1
|
423 |
+
for u in range(last):
|
424 |
+
v = u
|
425 |
+
if not selfloops:
|
426 |
+
v += 1
|
427 |
+
factor = seq[u] * rho
|
428 |
+
p = min(seq[v] * factor, 1)
|
429 |
+
while v < n and p > 0:
|
430 |
+
if p != 1:
|
431 |
+
r = seed.random()
|
432 |
+
v += math.floor(math.log(r, 1 - p))
|
433 |
+
if v < n:
|
434 |
+
q = min(seq[v] * factor, 1)
|
435 |
+
if seed.random() < q / p:
|
436 |
+
G.add_edge(mapping[u], mapping[v])
|
437 |
+
v += 1
|
438 |
+
p = q
|
439 |
+
return G
|
440 |
+
|
441 |
+
|
442 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
443 |
+
def havel_hakimi_graph(deg_sequence, create_using=None):
|
444 |
+
"""Returns a simple graph with given degree sequence constructed
|
445 |
+
using the Havel-Hakimi algorithm.
|
446 |
+
|
447 |
+
Parameters
|
448 |
+
----------
|
449 |
+
deg_sequence: list of integers
|
450 |
+
Each integer corresponds to the degree of a node (need not be sorted).
|
451 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
452 |
+
Graph type to create. If graph instance, then cleared before populated.
|
453 |
+
Directed graphs are not allowed.
|
454 |
+
|
455 |
+
Raises
|
456 |
+
------
|
457 |
+
NetworkXException
|
458 |
+
For a non-graphical degree sequence (i.e. one
|
459 |
+
not realizable by some simple graph).
|
460 |
+
|
461 |
+
Notes
|
462 |
+
-----
|
463 |
+
The Havel-Hakimi algorithm constructs a simple graph by
|
464 |
+
successively connecting the node of highest degree to other nodes
|
465 |
+
of highest degree, resorting remaining nodes by degree, and
|
466 |
+
repeating the process. The resulting graph has a high
|
467 |
+
degree-associativity. Nodes are labeled 1,.., len(deg_sequence),
|
468 |
+
corresponding to their position in deg_sequence.
|
469 |
+
|
470 |
+
The basic algorithm is from Hakimi [1]_ and was generalized by
|
471 |
+
Kleitman and Wang [2]_.
|
472 |
+
|
473 |
+
References
|
474 |
+
----------
|
475 |
+
.. [1] Hakimi S., On Realizability of a Set of Integers as
|
476 |
+
Degrees of the Vertices of a Linear Graph. I,
|
477 |
+
Journal of SIAM, 10(3), pp. 496-506 (1962)
|
478 |
+
.. [2] Kleitman D.J. and Wang D.L.
|
479 |
+
Algorithms for Constructing Graphs and Digraphs with Given Valences
|
480 |
+
and Factors Discrete Mathematics, 6(1), pp. 79-88 (1973)
|
481 |
+
"""
|
482 |
+
if not nx.is_graphical(deg_sequence):
|
483 |
+
raise nx.NetworkXError("Invalid degree sequence")
|
484 |
+
|
485 |
+
p = len(deg_sequence)
|
486 |
+
G = nx.empty_graph(p, create_using)
|
487 |
+
if G.is_directed():
|
488 |
+
raise nx.NetworkXError("Directed graphs are not supported")
|
489 |
+
num_degs = [[] for i in range(p)]
|
490 |
+
dmax, dsum, n = 0, 0, 0
|
491 |
+
for d in deg_sequence:
|
492 |
+
# Process only the non-zero integers
|
493 |
+
if d > 0:
|
494 |
+
num_degs[d].append(n)
|
495 |
+
dmax, dsum, n = max(dmax, d), dsum + d, n + 1
|
496 |
+
# Return graph if no edges
|
497 |
+
if n == 0:
|
498 |
+
return G
|
499 |
+
|
500 |
+
modstubs = [(0, 0)] * (dmax + 1)
|
501 |
+
# Successively reduce degree sequence by removing the maximum degree
|
502 |
+
while n > 0:
|
503 |
+
# Retrieve the maximum degree in the sequence
|
504 |
+
while len(num_degs[dmax]) == 0:
|
505 |
+
dmax -= 1
|
506 |
+
# If there are not enough stubs to connect to, then the sequence is
|
507 |
+
# not graphical
|
508 |
+
if dmax > n - 1:
|
509 |
+
raise nx.NetworkXError("Non-graphical integer sequence")
|
510 |
+
|
511 |
+
# Remove largest stub in list
|
512 |
+
source = num_degs[dmax].pop()
|
513 |
+
n -= 1
|
514 |
+
# Reduce the next dmax largest stubs
|
515 |
+
mslen = 0
|
516 |
+
k = dmax
|
517 |
+
for i in range(dmax):
|
518 |
+
while len(num_degs[k]) == 0:
|
519 |
+
k -= 1
|
520 |
+
target = num_degs[k].pop()
|
521 |
+
G.add_edge(source, target)
|
522 |
+
n -= 1
|
523 |
+
if k > 1:
|
524 |
+
modstubs[mslen] = (k - 1, target)
|
525 |
+
mslen += 1
|
526 |
+
# Add back to the list any nonzero stubs that were removed
|
527 |
+
for i in range(mslen):
|
528 |
+
(stubval, stubtarget) = modstubs[i]
|
529 |
+
num_degs[stubval].append(stubtarget)
|
530 |
+
n += 1
|
531 |
+
|
532 |
+
return G
|
533 |
+
|
534 |
+
|
535 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
536 |
+
def directed_havel_hakimi_graph(in_deg_sequence, out_deg_sequence, create_using=None):
|
537 |
+
"""Returns a directed graph with the given degree sequences.
|
538 |
+
|
539 |
+
Parameters
|
540 |
+
----------
|
541 |
+
in_deg_sequence : list of integers
|
542 |
+
Each list entry corresponds to the in-degree of a node.
|
543 |
+
out_deg_sequence : list of integers
|
544 |
+
Each list entry corresponds to the out-degree of a node.
|
545 |
+
create_using : NetworkX graph constructor, optional (default DiGraph)
|
546 |
+
Graph type to create. If graph instance, then cleared before populated.
|
547 |
+
|
548 |
+
Returns
|
549 |
+
-------
|
550 |
+
G : DiGraph
|
551 |
+
A graph with the specified degree sequences.
|
552 |
+
Nodes are labeled starting at 0 with an index
|
553 |
+
corresponding to the position in deg_sequence
|
554 |
+
|
555 |
+
Raises
|
556 |
+
------
|
557 |
+
NetworkXError
|
558 |
+
If the degree sequences are not digraphical.
|
559 |
+
|
560 |
+
See Also
|
561 |
+
--------
|
562 |
+
configuration_model
|
563 |
+
|
564 |
+
Notes
|
565 |
+
-----
|
566 |
+
Algorithm as described by Kleitman and Wang [1]_.
|
567 |
+
|
568 |
+
References
|
569 |
+
----------
|
570 |
+
.. [1] D.J. Kleitman and D.L. Wang
|
571 |
+
Algorithms for Constructing Graphs and Digraphs with Given Valences
|
572 |
+
and Factors Discrete Mathematics, 6(1), pp. 79-88 (1973)
|
573 |
+
"""
|
574 |
+
in_deg_sequence = nx.utils.make_list_of_ints(in_deg_sequence)
|
575 |
+
out_deg_sequence = nx.utils.make_list_of_ints(out_deg_sequence)
|
576 |
+
|
577 |
+
# Process the sequences and form two heaps to store degree pairs with
|
578 |
+
# either zero or nonzero out degrees
|
579 |
+
sumin, sumout = 0, 0
|
580 |
+
nin, nout = len(in_deg_sequence), len(out_deg_sequence)
|
581 |
+
maxn = max(nin, nout)
|
582 |
+
G = nx.empty_graph(maxn, create_using, default=nx.DiGraph)
|
583 |
+
if maxn == 0:
|
584 |
+
return G
|
585 |
+
maxin = 0
|
586 |
+
stubheap, zeroheap = [], []
|
587 |
+
for n in range(maxn):
|
588 |
+
in_deg, out_deg = 0, 0
|
589 |
+
if n < nout:
|
590 |
+
out_deg = out_deg_sequence[n]
|
591 |
+
if n < nin:
|
592 |
+
in_deg = in_deg_sequence[n]
|
593 |
+
if in_deg < 0 or out_deg < 0:
|
594 |
+
raise nx.NetworkXError(
|
595 |
+
"Invalid degree sequences. Sequence values must be positive."
|
596 |
+
)
|
597 |
+
sumin, sumout, maxin = sumin + in_deg, sumout + out_deg, max(maxin, in_deg)
|
598 |
+
if in_deg > 0:
|
599 |
+
stubheap.append((-1 * out_deg, -1 * in_deg, n))
|
600 |
+
elif out_deg > 0:
|
601 |
+
zeroheap.append((-1 * out_deg, n))
|
602 |
+
if sumin != sumout:
|
603 |
+
raise nx.NetworkXError(
|
604 |
+
"Invalid degree sequences. Sequences must have equal sums."
|
605 |
+
)
|
606 |
+
heapq.heapify(stubheap)
|
607 |
+
heapq.heapify(zeroheap)
|
608 |
+
|
609 |
+
modstubs = [(0, 0, 0)] * (maxin + 1)
|
610 |
+
# Successively reduce degree sequence by removing the maximum
|
611 |
+
while stubheap:
|
612 |
+
# Remove first value in the sequence with a non-zero in degree
|
613 |
+
(freeout, freein, target) = heapq.heappop(stubheap)
|
614 |
+
freein *= -1
|
615 |
+
if freein > len(stubheap) + len(zeroheap):
|
616 |
+
raise nx.NetworkXError("Non-digraphical integer sequence")
|
617 |
+
|
618 |
+
# Attach arcs from the nodes with the most stubs
|
619 |
+
mslen = 0
|
620 |
+
for i in range(freein):
|
621 |
+
if zeroheap and (not stubheap or stubheap[0][0] > zeroheap[0][0]):
|
622 |
+
(stubout, stubsource) = heapq.heappop(zeroheap)
|
623 |
+
stubin = 0
|
624 |
+
else:
|
625 |
+
(stubout, stubin, stubsource) = heapq.heappop(stubheap)
|
626 |
+
if stubout == 0:
|
627 |
+
raise nx.NetworkXError("Non-digraphical integer sequence")
|
628 |
+
G.add_edge(stubsource, target)
|
629 |
+
# Check if source is now totally connected
|
630 |
+
if stubout + 1 < 0 or stubin < 0:
|
631 |
+
modstubs[mslen] = (stubout + 1, stubin, stubsource)
|
632 |
+
mslen += 1
|
633 |
+
|
634 |
+
# Add the nodes back to the heaps that still have available stubs
|
635 |
+
for i in range(mslen):
|
636 |
+
stub = modstubs[i]
|
637 |
+
if stub[1] < 0:
|
638 |
+
heapq.heappush(stubheap, stub)
|
639 |
+
else:
|
640 |
+
heapq.heappush(zeroheap, (stub[0], stub[2]))
|
641 |
+
if freeout < 0:
|
642 |
+
heapq.heappush(zeroheap, (freeout, target))
|
643 |
+
|
644 |
+
return G
|
645 |
+
|
646 |
+
|
647 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
648 |
+
def degree_sequence_tree(deg_sequence, create_using=None):
|
649 |
+
"""Make a tree for the given degree sequence.
|
650 |
+
|
651 |
+
A tree has #nodes-#edges=1 so
|
652 |
+
the degree sequence must have
|
653 |
+
len(deg_sequence)-sum(deg_sequence)/2=1
|
654 |
+
"""
|
655 |
+
# The sum of the degree sequence must be even (for any undirected graph).
|
656 |
+
degree_sum = sum(deg_sequence)
|
657 |
+
if degree_sum % 2 != 0:
|
658 |
+
msg = "Invalid degree sequence: sum of degrees must be even, not odd"
|
659 |
+
raise nx.NetworkXError(msg)
|
660 |
+
if len(deg_sequence) - degree_sum // 2 != 1:
|
661 |
+
msg = (
|
662 |
+
"Invalid degree sequence: tree must have number of nodes equal"
|
663 |
+
" to one less than the number of edges"
|
664 |
+
)
|
665 |
+
raise nx.NetworkXError(msg)
|
666 |
+
G = nx.empty_graph(0, create_using)
|
667 |
+
if G.is_directed():
|
668 |
+
raise nx.NetworkXError("Directed Graph not supported")
|
669 |
+
|
670 |
+
# Sort all degrees greater than 1 in decreasing order.
|
671 |
+
#
|
672 |
+
# TODO Does this need to be sorted in reverse order?
|
673 |
+
deg = sorted((s for s in deg_sequence if s > 1), reverse=True)
|
674 |
+
|
675 |
+
# make path graph as backbone
|
676 |
+
n = len(deg) + 2
|
677 |
+
nx.add_path(G, range(n))
|
678 |
+
last = n
|
679 |
+
|
680 |
+
# add the leaves
|
681 |
+
for source in range(1, n - 1):
|
682 |
+
nedges = deg.pop() - 2
|
683 |
+
for target in range(last, last + nedges):
|
684 |
+
G.add_edge(source, target)
|
685 |
+
last += nedges
|
686 |
+
|
687 |
+
# in case we added one too many
|
688 |
+
if len(G) > len(deg_sequence):
|
689 |
+
G.remove_node(0)
|
690 |
+
return G
|
691 |
+
|
692 |
+
|
693 |
+
@py_random_state(1)
|
694 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
695 |
+
def random_degree_sequence_graph(sequence, seed=None, tries=10):
|
696 |
+
r"""Returns a simple random graph with the given degree sequence.
|
697 |
+
|
698 |
+
If the maximum degree $d_m$ in the sequence is $O(m^{1/4})$ then the
|
699 |
+
algorithm produces almost uniform random graphs in $O(m d_m)$ time
|
700 |
+
where $m$ is the number of edges.
|
701 |
+
|
702 |
+
Parameters
|
703 |
+
----------
|
704 |
+
sequence : list of integers
|
705 |
+
Sequence of degrees
|
706 |
+
seed : integer, random_state, or None (default)
|
707 |
+
Indicator of random number generation state.
|
708 |
+
See :ref:`Randomness<randomness>`.
|
709 |
+
tries : int, optional
|
710 |
+
Maximum number of tries to create a graph
|
711 |
+
|
712 |
+
Returns
|
713 |
+
-------
|
714 |
+
G : Graph
|
715 |
+
A graph with the specified degree sequence.
|
716 |
+
Nodes are labeled starting at 0 with an index
|
717 |
+
corresponding to the position in the sequence.
|
718 |
+
|
719 |
+
Raises
|
720 |
+
------
|
721 |
+
NetworkXUnfeasible
|
722 |
+
If the degree sequence is not graphical.
|
723 |
+
NetworkXError
|
724 |
+
If a graph is not produced in specified number of tries
|
725 |
+
|
726 |
+
See Also
|
727 |
+
--------
|
728 |
+
is_graphical, configuration_model
|
729 |
+
|
730 |
+
Notes
|
731 |
+
-----
|
732 |
+
The generator algorithm [1]_ is not guaranteed to produce a graph.
|
733 |
+
|
734 |
+
References
|
735 |
+
----------
|
736 |
+
.. [1] Moshen Bayati, Jeong Han Kim, and Amin Saberi,
|
737 |
+
A sequential algorithm for generating random graphs.
|
738 |
+
Algorithmica, Volume 58, Number 4, 860-910,
|
739 |
+
DOI: 10.1007/s00453-009-9340-1
|
740 |
+
|
741 |
+
Examples
|
742 |
+
--------
|
743 |
+
>>> sequence = [1, 2, 2, 3]
|
744 |
+
>>> G = nx.random_degree_sequence_graph(sequence, seed=42)
|
745 |
+
>>> sorted(d for n, d in G.degree())
|
746 |
+
[1, 2, 2, 3]
|
747 |
+
"""
|
748 |
+
DSRG = DegreeSequenceRandomGraph(sequence, seed)
|
749 |
+
for try_n in range(tries):
|
750 |
+
try:
|
751 |
+
return DSRG.generate()
|
752 |
+
except nx.NetworkXUnfeasible:
|
753 |
+
pass
|
754 |
+
raise nx.NetworkXError(f"failed to generate graph in {tries} tries")
|
755 |
+
|
756 |
+
|
757 |
+
class DegreeSequenceRandomGraph:
|
758 |
+
# class to generate random graphs with a given degree sequence
|
759 |
+
# use random_degree_sequence_graph()
|
760 |
+
def __init__(self, degree, rng):
|
761 |
+
if not nx.is_graphical(degree):
|
762 |
+
raise nx.NetworkXUnfeasible("degree sequence is not graphical")
|
763 |
+
self.rng = rng
|
764 |
+
self.degree = list(degree)
|
765 |
+
# node labels are integers 0,...,n-1
|
766 |
+
self.m = sum(self.degree) / 2.0 # number of edges
|
767 |
+
try:
|
768 |
+
self.dmax = max(self.degree) # maximum degree
|
769 |
+
except ValueError:
|
770 |
+
self.dmax = 0
|
771 |
+
|
772 |
+
def generate(self):
|
773 |
+
# remaining_degree is mapping from int->remaining degree
|
774 |
+
self.remaining_degree = dict(enumerate(self.degree))
|
775 |
+
# add all nodes to make sure we get isolated nodes
|
776 |
+
self.graph = nx.Graph()
|
777 |
+
self.graph.add_nodes_from(self.remaining_degree)
|
778 |
+
# remove zero degree nodes
|
779 |
+
for n, d in list(self.remaining_degree.items()):
|
780 |
+
if d == 0:
|
781 |
+
del self.remaining_degree[n]
|
782 |
+
if len(self.remaining_degree) > 0:
|
783 |
+
# build graph in three phases according to how many unmatched edges
|
784 |
+
self.phase1()
|
785 |
+
self.phase2()
|
786 |
+
self.phase3()
|
787 |
+
return self.graph
|
788 |
+
|
789 |
+
def update_remaining(self, u, v, aux_graph=None):
|
790 |
+
# decrement remaining nodes, modify auxiliary graph if in phase3
|
791 |
+
if aux_graph is not None:
|
792 |
+
# remove edges from auxiliary graph
|
793 |
+
aux_graph.remove_edge(u, v)
|
794 |
+
if self.remaining_degree[u] == 1:
|
795 |
+
del self.remaining_degree[u]
|
796 |
+
if aux_graph is not None:
|
797 |
+
aux_graph.remove_node(u)
|
798 |
+
else:
|
799 |
+
self.remaining_degree[u] -= 1
|
800 |
+
if self.remaining_degree[v] == 1:
|
801 |
+
del self.remaining_degree[v]
|
802 |
+
if aux_graph is not None:
|
803 |
+
aux_graph.remove_node(v)
|
804 |
+
else:
|
805 |
+
self.remaining_degree[v] -= 1
|
806 |
+
|
807 |
+
def p(self, u, v):
|
808 |
+
# degree probability
|
809 |
+
return 1 - self.degree[u] * self.degree[v] / (4.0 * self.m)
|
810 |
+
|
811 |
+
def q(self, u, v):
|
812 |
+
# remaining degree probability
|
813 |
+
norm = max(self.remaining_degree.values()) ** 2
|
814 |
+
return self.remaining_degree[u] * self.remaining_degree[v] / norm
|
815 |
+
|
816 |
+
def suitable_edge(self):
|
817 |
+
"""Returns True if and only if an arbitrary remaining node can
|
818 |
+
potentially be joined with some other remaining node.
|
819 |
+
|
820 |
+
"""
|
821 |
+
nodes = iter(self.remaining_degree)
|
822 |
+
u = next(nodes)
|
823 |
+
return any(v not in self.graph[u] for v in nodes)
|
824 |
+
|
825 |
+
def phase1(self):
|
826 |
+
# choose node pairs from (degree) weighted distribution
|
827 |
+
rem_deg = self.remaining_degree
|
828 |
+
while sum(rem_deg.values()) >= 2 * self.dmax**2:
|
829 |
+
u, v = sorted(random_weighted_sample(rem_deg, 2, self.rng))
|
830 |
+
if self.graph.has_edge(u, v):
|
831 |
+
continue
|
832 |
+
if self.rng.random() < self.p(u, v): # accept edge
|
833 |
+
self.graph.add_edge(u, v)
|
834 |
+
self.update_remaining(u, v)
|
835 |
+
|
836 |
+
def phase2(self):
|
837 |
+
# choose remaining nodes uniformly at random and use rejection sampling
|
838 |
+
remaining_deg = self.remaining_degree
|
839 |
+
rng = self.rng
|
840 |
+
while len(remaining_deg) >= 2 * self.dmax:
|
841 |
+
while True:
|
842 |
+
u, v = sorted(rng.sample(list(remaining_deg.keys()), 2))
|
843 |
+
if self.graph.has_edge(u, v):
|
844 |
+
continue
|
845 |
+
if rng.random() < self.q(u, v):
|
846 |
+
break
|
847 |
+
if rng.random() < self.p(u, v): # accept edge
|
848 |
+
self.graph.add_edge(u, v)
|
849 |
+
self.update_remaining(u, v)
|
850 |
+
|
851 |
+
def phase3(self):
|
852 |
+
# build potential remaining edges and choose with rejection sampling
|
853 |
+
potential_edges = combinations(self.remaining_degree, 2)
|
854 |
+
# build auxiliary graph of potential edges not already in graph
|
855 |
+
H = nx.Graph(
|
856 |
+
[(u, v) for (u, v) in potential_edges if not self.graph.has_edge(u, v)]
|
857 |
+
)
|
858 |
+
rng = self.rng
|
859 |
+
while self.remaining_degree:
|
860 |
+
if not self.suitable_edge():
|
861 |
+
raise nx.NetworkXUnfeasible("no suitable edges left")
|
862 |
+
while True:
|
863 |
+
u, v = sorted(rng.choice(list(H.edges())))
|
864 |
+
if rng.random() < self.q(u, v):
|
865 |
+
break
|
866 |
+
if rng.random() < self.p(u, v): # accept edge
|
867 |
+
self.graph.add_edge(u, v)
|
868 |
+
self.update_remaining(u, v, aux_graph=H)
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/directed.py
ADDED
@@ -0,0 +1,501 @@
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
Generators for some directed graphs, including growing network (GN) graphs and
|
3 |
+
scale-free graphs.
|
4 |
+
|
5 |
+
"""
|
6 |
+
|
7 |
+
import numbers
|
8 |
+
from collections import Counter
|
9 |
+
|
10 |
+
import networkx as nx
|
11 |
+
from networkx.generators.classic import empty_graph
|
12 |
+
from networkx.utils import discrete_sequence, py_random_state, weighted_choice
|
13 |
+
|
14 |
+
__all__ = [
|
15 |
+
"gn_graph",
|
16 |
+
"gnc_graph",
|
17 |
+
"gnr_graph",
|
18 |
+
"random_k_out_graph",
|
19 |
+
"scale_free_graph",
|
20 |
+
]
|
21 |
+
|
22 |
+
|
23 |
+
@py_random_state(3)
|
24 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
25 |
+
def gn_graph(n, kernel=None, create_using=None, seed=None):
|
26 |
+
"""Returns the growing network (GN) digraph with `n` nodes.
|
27 |
+
|
28 |
+
The GN graph is built by adding nodes one at a time with a link to one
|
29 |
+
previously added node. The target node for the link is chosen with
|
30 |
+
probability based on degree. The default attachment kernel is a linear
|
31 |
+
function of the degree of a node.
|
32 |
+
|
33 |
+
The graph is always a (directed) tree.
|
34 |
+
|
35 |
+
Parameters
|
36 |
+
----------
|
37 |
+
n : int
|
38 |
+
The number of nodes for the generated graph.
|
39 |
+
kernel : function
|
40 |
+
The attachment kernel.
|
41 |
+
create_using : NetworkX graph constructor, optional (default DiGraph)
|
42 |
+
Graph type to create. If graph instance, then cleared before populated.
|
43 |
+
seed : integer, random_state, or None (default)
|
44 |
+
Indicator of random number generation state.
|
45 |
+
See :ref:`Randomness<randomness>`.
|
46 |
+
|
47 |
+
Examples
|
48 |
+
--------
|
49 |
+
To create the undirected GN graph, use the :meth:`~DiGraph.to_directed`
|
50 |
+
method::
|
51 |
+
|
52 |
+
>>> D = nx.gn_graph(10) # the GN graph
|
53 |
+
>>> G = D.to_undirected() # the undirected version
|
54 |
+
|
55 |
+
To specify an attachment kernel, use the `kernel` keyword argument::
|
56 |
+
|
57 |
+
>>> D = nx.gn_graph(10, kernel=lambda x: x**1.5) # A_k = k^1.5
|
58 |
+
|
59 |
+
References
|
60 |
+
----------
|
61 |
+
.. [1] P. L. Krapivsky and S. Redner,
|
62 |
+
Organization of Growing Random Networks,
|
63 |
+
Phys. Rev. E, 63, 066123, 2001.
|
64 |
+
"""
|
65 |
+
G = empty_graph(1, create_using, default=nx.DiGraph)
|
66 |
+
if not G.is_directed():
|
67 |
+
raise nx.NetworkXError("create_using must indicate a Directed Graph")
|
68 |
+
|
69 |
+
if kernel is None:
|
70 |
+
|
71 |
+
def kernel(x):
|
72 |
+
return x
|
73 |
+
|
74 |
+
if n == 1:
|
75 |
+
return G
|
76 |
+
|
77 |
+
G.add_edge(1, 0) # get started
|
78 |
+
ds = [1, 1] # degree sequence
|
79 |
+
|
80 |
+
for source in range(2, n):
|
81 |
+
# compute distribution from kernel and degree
|
82 |
+
dist = [kernel(d) for d in ds]
|
83 |
+
# choose target from discrete distribution
|
84 |
+
target = discrete_sequence(1, distribution=dist, seed=seed)[0]
|
85 |
+
G.add_edge(source, target)
|
86 |
+
ds.append(1) # the source has only one link (degree one)
|
87 |
+
ds[target] += 1 # add one to the target link degree
|
88 |
+
return G
|
89 |
+
|
90 |
+
|
91 |
+
@py_random_state(3)
|
92 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
93 |
+
def gnr_graph(n, p, create_using=None, seed=None):
|
94 |
+
"""Returns the growing network with redirection (GNR) digraph with `n`
|
95 |
+
nodes and redirection probability `p`.
|
96 |
+
|
97 |
+
The GNR graph is built by adding nodes one at a time with a link to one
|
98 |
+
previously added node. The previous target node is chosen uniformly at
|
99 |
+
random. With probability `p` the link is instead "redirected" to the
|
100 |
+
successor node of the target.
|
101 |
+
|
102 |
+
The graph is always a (directed) tree.
|
103 |
+
|
104 |
+
Parameters
|
105 |
+
----------
|
106 |
+
n : int
|
107 |
+
The number of nodes for the generated graph.
|
108 |
+
p : float
|
109 |
+
The redirection probability.
|
110 |
+
create_using : NetworkX graph constructor, optional (default DiGraph)
|
111 |
+
Graph type to create. If graph instance, then cleared before populated.
|
112 |
+
seed : integer, random_state, or None (default)
|
113 |
+
Indicator of random number generation state.
|
114 |
+
See :ref:`Randomness<randomness>`.
|
115 |
+
|
116 |
+
Examples
|
117 |
+
--------
|
118 |
+
To create the undirected GNR graph, use the :meth:`~DiGraph.to_directed`
|
119 |
+
method::
|
120 |
+
|
121 |
+
>>> D = nx.gnr_graph(10, 0.5) # the GNR graph
|
122 |
+
>>> G = D.to_undirected() # the undirected version
|
123 |
+
|
124 |
+
References
|
125 |
+
----------
|
126 |
+
.. [1] P. L. Krapivsky and S. Redner,
|
127 |
+
Organization of Growing Random Networks,
|
128 |
+
Phys. Rev. E, 63, 066123, 2001.
|
129 |
+
"""
|
130 |
+
G = empty_graph(1, create_using, default=nx.DiGraph)
|
131 |
+
if not G.is_directed():
|
132 |
+
raise nx.NetworkXError("create_using must indicate a Directed Graph")
|
133 |
+
|
134 |
+
if n == 1:
|
135 |
+
return G
|
136 |
+
|
137 |
+
for source in range(1, n):
|
138 |
+
target = seed.randrange(0, source)
|
139 |
+
if seed.random() < p and target != 0:
|
140 |
+
target = next(G.successors(target))
|
141 |
+
G.add_edge(source, target)
|
142 |
+
return G
|
143 |
+
|
144 |
+
|
145 |
+
@py_random_state(2)
|
146 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
147 |
+
def gnc_graph(n, create_using=None, seed=None):
|
148 |
+
"""Returns the growing network with copying (GNC) digraph with `n` nodes.
|
149 |
+
|
150 |
+
The GNC graph is built by adding nodes one at a time with a link to one
|
151 |
+
previously added node (chosen uniformly at random) and to all of that
|
152 |
+
node's successors.
|
153 |
+
|
154 |
+
Parameters
|
155 |
+
----------
|
156 |
+
n : int
|
157 |
+
The number of nodes for the generated graph.
|
158 |
+
create_using : NetworkX graph constructor, optional (default DiGraph)
|
159 |
+
Graph type to create. If graph instance, then cleared before populated.
|
160 |
+
seed : integer, random_state, or None (default)
|
161 |
+
Indicator of random number generation state.
|
162 |
+
See :ref:`Randomness<randomness>`.
|
163 |
+
|
164 |
+
References
|
165 |
+
----------
|
166 |
+
.. [1] P. L. Krapivsky and S. Redner,
|
167 |
+
Network Growth by Copying,
|
168 |
+
Phys. Rev. E, 71, 036118, 2005k.},
|
169 |
+
"""
|
170 |
+
G = empty_graph(1, create_using, default=nx.DiGraph)
|
171 |
+
if not G.is_directed():
|
172 |
+
raise nx.NetworkXError("create_using must indicate a Directed Graph")
|
173 |
+
|
174 |
+
if n == 1:
|
175 |
+
return G
|
176 |
+
|
177 |
+
for source in range(1, n):
|
178 |
+
target = seed.randrange(0, source)
|
179 |
+
for succ in G.successors(target):
|
180 |
+
G.add_edge(source, succ)
|
181 |
+
G.add_edge(source, target)
|
182 |
+
return G
|
183 |
+
|
184 |
+
|
185 |
+
@py_random_state(6)
|
186 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
187 |
+
def scale_free_graph(
|
188 |
+
n,
|
189 |
+
alpha=0.41,
|
190 |
+
beta=0.54,
|
191 |
+
gamma=0.05,
|
192 |
+
delta_in=0.2,
|
193 |
+
delta_out=0,
|
194 |
+
seed=None,
|
195 |
+
initial_graph=None,
|
196 |
+
):
|
197 |
+
"""Returns a scale-free directed graph.
|
198 |
+
|
199 |
+
Parameters
|
200 |
+
----------
|
201 |
+
n : integer
|
202 |
+
Number of nodes in graph
|
203 |
+
alpha : float
|
204 |
+
Probability for adding a new node connected to an existing node
|
205 |
+
chosen randomly according to the in-degree distribution.
|
206 |
+
beta : float
|
207 |
+
Probability for adding an edge between two existing nodes.
|
208 |
+
One existing node is chosen randomly according the in-degree
|
209 |
+
distribution and the other chosen randomly according to the out-degree
|
210 |
+
distribution.
|
211 |
+
gamma : float
|
212 |
+
Probability for adding a new node connected to an existing node
|
213 |
+
chosen randomly according to the out-degree distribution.
|
214 |
+
delta_in : float
|
215 |
+
Bias for choosing nodes from in-degree distribution.
|
216 |
+
delta_out : float
|
217 |
+
Bias for choosing nodes from out-degree distribution.
|
218 |
+
seed : integer, random_state, or None (default)
|
219 |
+
Indicator of random number generation state.
|
220 |
+
See :ref:`Randomness<randomness>`.
|
221 |
+
initial_graph : MultiDiGraph instance, optional
|
222 |
+
Build the scale-free graph starting from this initial MultiDiGraph,
|
223 |
+
if provided.
|
224 |
+
|
225 |
+
Returns
|
226 |
+
-------
|
227 |
+
MultiDiGraph
|
228 |
+
|
229 |
+
Examples
|
230 |
+
--------
|
231 |
+
Create a scale-free graph on one hundred nodes::
|
232 |
+
|
233 |
+
>>> G = nx.scale_free_graph(100)
|
234 |
+
|
235 |
+
Notes
|
236 |
+
-----
|
237 |
+
The sum of `alpha`, `beta`, and `gamma` must be 1.
|
238 |
+
|
239 |
+
References
|
240 |
+
----------
|
241 |
+
.. [1] B. Bollobás, C. Borgs, J. Chayes, and O. Riordan,
|
242 |
+
Directed scale-free graphs,
|
243 |
+
Proceedings of the fourteenth annual ACM-SIAM Symposium on
|
244 |
+
Discrete Algorithms, 132--139, 2003.
|
245 |
+
"""
|
246 |
+
|
247 |
+
def _choose_node(candidates, node_list, delta):
|
248 |
+
if delta > 0:
|
249 |
+
bias_sum = len(node_list) * delta
|
250 |
+
p_delta = bias_sum / (bias_sum + len(candidates))
|
251 |
+
if seed.random() < p_delta:
|
252 |
+
return seed.choice(node_list)
|
253 |
+
return seed.choice(candidates)
|
254 |
+
|
255 |
+
if initial_graph is not None and hasattr(initial_graph, "_adj"):
|
256 |
+
if not isinstance(initial_graph, nx.MultiDiGraph):
|
257 |
+
raise nx.NetworkXError("initial_graph must be a MultiDiGraph.")
|
258 |
+
G = initial_graph
|
259 |
+
else:
|
260 |
+
# Start with 3-cycle
|
261 |
+
G = nx.MultiDiGraph([(0, 1), (1, 2), (2, 0)])
|
262 |
+
|
263 |
+
if alpha <= 0:
|
264 |
+
raise ValueError("alpha must be > 0.")
|
265 |
+
if beta <= 0:
|
266 |
+
raise ValueError("beta must be > 0.")
|
267 |
+
if gamma <= 0:
|
268 |
+
raise ValueError("gamma must be > 0.")
|
269 |
+
|
270 |
+
if abs(alpha + beta + gamma - 1.0) >= 1e-9:
|
271 |
+
raise ValueError("alpha+beta+gamma must equal 1.")
|
272 |
+
|
273 |
+
if delta_in < 0:
|
274 |
+
raise ValueError("delta_in must be >= 0.")
|
275 |
+
|
276 |
+
if delta_out < 0:
|
277 |
+
raise ValueError("delta_out must be >= 0.")
|
278 |
+
|
279 |
+
# pre-populate degree states
|
280 |
+
vs = sum((count * [idx] for idx, count in G.out_degree()), [])
|
281 |
+
ws = sum((count * [idx] for idx, count in G.in_degree()), [])
|
282 |
+
|
283 |
+
# pre-populate node state
|
284 |
+
node_list = list(G.nodes())
|
285 |
+
|
286 |
+
# see if there already are number-based nodes
|
287 |
+
numeric_nodes = [n for n in node_list if isinstance(n, numbers.Number)]
|
288 |
+
if len(numeric_nodes) > 0:
|
289 |
+
# set cursor for new nodes appropriately
|
290 |
+
cursor = max(int(n.real) for n in numeric_nodes) + 1
|
291 |
+
else:
|
292 |
+
# or start at zero
|
293 |
+
cursor = 0
|
294 |
+
|
295 |
+
while len(G) < n:
|
296 |
+
r = seed.random()
|
297 |
+
|
298 |
+
# random choice in alpha,beta,gamma ranges
|
299 |
+
if r < alpha:
|
300 |
+
# alpha
|
301 |
+
# add new node v
|
302 |
+
v = cursor
|
303 |
+
cursor += 1
|
304 |
+
# also add to node state
|
305 |
+
node_list.append(v)
|
306 |
+
# choose w according to in-degree and delta_in
|
307 |
+
w = _choose_node(ws, node_list, delta_in)
|
308 |
+
|
309 |
+
elif r < alpha + beta:
|
310 |
+
# beta
|
311 |
+
# choose v according to out-degree and delta_out
|
312 |
+
v = _choose_node(vs, node_list, delta_out)
|
313 |
+
# choose w according to in-degree and delta_in
|
314 |
+
w = _choose_node(ws, node_list, delta_in)
|
315 |
+
|
316 |
+
else:
|
317 |
+
# gamma
|
318 |
+
# choose v according to out-degree and delta_out
|
319 |
+
v = _choose_node(vs, node_list, delta_out)
|
320 |
+
# add new node w
|
321 |
+
w = cursor
|
322 |
+
cursor += 1
|
323 |
+
# also add to node state
|
324 |
+
node_list.append(w)
|
325 |
+
|
326 |
+
# add edge to graph
|
327 |
+
G.add_edge(v, w)
|
328 |
+
|
329 |
+
# update degree states
|
330 |
+
vs.append(v)
|
331 |
+
ws.append(w)
|
332 |
+
|
333 |
+
return G
|
334 |
+
|
335 |
+
|
336 |
+
@py_random_state(4)
|
337 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
338 |
+
def random_uniform_k_out_graph(n, k, self_loops=True, with_replacement=True, seed=None):
|
339 |
+
"""Returns a random `k`-out graph with uniform attachment.
|
340 |
+
|
341 |
+
A random `k`-out graph with uniform attachment is a multidigraph
|
342 |
+
generated by the following algorithm. For each node *u*, choose
|
343 |
+
`k` nodes *v* uniformly at random (with replacement). Add a
|
344 |
+
directed edge joining *u* to *v*.
|
345 |
+
|
346 |
+
Parameters
|
347 |
+
----------
|
348 |
+
n : int
|
349 |
+
The number of nodes in the returned graph.
|
350 |
+
|
351 |
+
k : int
|
352 |
+
The out-degree of each node in the returned graph.
|
353 |
+
|
354 |
+
self_loops : bool
|
355 |
+
If True, self-loops are allowed when generating the graph.
|
356 |
+
|
357 |
+
with_replacement : bool
|
358 |
+
If True, neighbors are chosen with replacement and the
|
359 |
+
returned graph will be a directed multigraph. Otherwise,
|
360 |
+
neighbors are chosen without replacement and the returned graph
|
361 |
+
will be a directed graph.
|
362 |
+
|
363 |
+
seed : integer, random_state, or None (default)
|
364 |
+
Indicator of random number generation state.
|
365 |
+
See :ref:`Randomness<randomness>`.
|
366 |
+
|
367 |
+
Returns
|
368 |
+
-------
|
369 |
+
NetworkX graph
|
370 |
+
A `k`-out-regular directed graph generated according to the
|
371 |
+
above algorithm. It will be a multigraph if and only if
|
372 |
+
`with_replacement` is True.
|
373 |
+
|
374 |
+
Raises
|
375 |
+
------
|
376 |
+
ValueError
|
377 |
+
If `with_replacement` is False and `k` is greater than
|
378 |
+
`n`.
|
379 |
+
|
380 |
+
See also
|
381 |
+
--------
|
382 |
+
random_k_out_graph
|
383 |
+
|
384 |
+
Notes
|
385 |
+
-----
|
386 |
+
The return digraph or multidigraph may not be strongly connected, or
|
387 |
+
even weakly connected.
|
388 |
+
|
389 |
+
If `with_replacement` is True, this function is similar to
|
390 |
+
:func:`random_k_out_graph`, if that function had parameter `alpha`
|
391 |
+
set to positive infinity.
|
392 |
+
|
393 |
+
"""
|
394 |
+
if with_replacement:
|
395 |
+
create_using = nx.MultiDiGraph()
|
396 |
+
|
397 |
+
def sample(v, nodes):
|
398 |
+
if not self_loops:
|
399 |
+
nodes = nodes - {v}
|
400 |
+
return (seed.choice(list(nodes)) for i in range(k))
|
401 |
+
|
402 |
+
else:
|
403 |
+
create_using = nx.DiGraph()
|
404 |
+
|
405 |
+
def sample(v, nodes):
|
406 |
+
if not self_loops:
|
407 |
+
nodes = nodes - {v}
|
408 |
+
return seed.sample(list(nodes), k)
|
409 |
+
|
410 |
+
G = nx.empty_graph(n, create_using)
|
411 |
+
nodes = set(G)
|
412 |
+
for u in G:
|
413 |
+
G.add_edges_from((u, v) for v in sample(u, nodes))
|
414 |
+
return G
|
415 |
+
|
416 |
+
|
417 |
+
@py_random_state(4)
|
418 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
419 |
+
def random_k_out_graph(n, k, alpha, self_loops=True, seed=None):
|
420 |
+
"""Returns a random `k`-out graph with preferential attachment.
|
421 |
+
|
422 |
+
A random `k`-out graph with preferential attachment is a
|
423 |
+
multidigraph generated by the following algorithm.
|
424 |
+
|
425 |
+
1. Begin with an empty digraph, and initially set each node to have
|
426 |
+
weight `alpha`.
|
427 |
+
2. Choose a node `u` with out-degree less than `k` uniformly at
|
428 |
+
random.
|
429 |
+
3. Choose a node `v` from with probability proportional to its
|
430 |
+
weight.
|
431 |
+
4. Add a directed edge from `u` to `v`, and increase the weight
|
432 |
+
of `v` by one.
|
433 |
+
5. If each node has out-degree `k`, halt, otherwise repeat from
|
434 |
+
step 2.
|
435 |
+
|
436 |
+
For more information on this model of random graph, see [1].
|
437 |
+
|
438 |
+
Parameters
|
439 |
+
----------
|
440 |
+
n : int
|
441 |
+
The number of nodes in the returned graph.
|
442 |
+
|
443 |
+
k : int
|
444 |
+
The out-degree of each node in the returned graph.
|
445 |
+
|
446 |
+
alpha : float
|
447 |
+
A positive :class:`float` representing the initial weight of
|
448 |
+
each vertex. A higher number means that in step 3 above, nodes
|
449 |
+
will be chosen more like a true uniformly random sample, and a
|
450 |
+
lower number means that nodes are more likely to be chosen as
|
451 |
+
their in-degree increases. If this parameter is not positive, a
|
452 |
+
:exc:`ValueError` is raised.
|
453 |
+
|
454 |
+
self_loops : bool
|
455 |
+
If True, self-loops are allowed when generating the graph.
|
456 |
+
|
457 |
+
seed : integer, random_state, or None (default)
|
458 |
+
Indicator of random number generation state.
|
459 |
+
See :ref:`Randomness<randomness>`.
|
460 |
+
|
461 |
+
Returns
|
462 |
+
-------
|
463 |
+
:class:`~networkx.classes.MultiDiGraph`
|
464 |
+
A `k`-out-regular multidigraph generated according to the above
|
465 |
+
algorithm.
|
466 |
+
|
467 |
+
Raises
|
468 |
+
------
|
469 |
+
ValueError
|
470 |
+
If `alpha` is not positive.
|
471 |
+
|
472 |
+
Notes
|
473 |
+
-----
|
474 |
+
The returned multidigraph may not be strongly connected, or even
|
475 |
+
weakly connected.
|
476 |
+
|
477 |
+
References
|
478 |
+
----------
|
479 |
+
[1]: Peterson, Nicholas R., and Boris Pittel.
|
480 |
+
"Distance between two random `k`-out digraphs, with and without
|
481 |
+
preferential attachment."
|
482 |
+
arXiv preprint arXiv:1311.5961 (2013).
|
483 |
+
<https://arxiv.org/abs/1311.5961>
|
484 |
+
|
485 |
+
"""
|
486 |
+
if alpha < 0:
|
487 |
+
raise ValueError("alpha must be positive")
|
488 |
+
G = nx.empty_graph(n, create_using=nx.MultiDiGraph)
|
489 |
+
weights = Counter({v: alpha for v in G})
|
490 |
+
for i in range(k * n):
|
491 |
+
u = seed.choice([v for v, d in G.out_degree() if d < k])
|
492 |
+
# If self-loops are not allowed, make the source node `u` have
|
493 |
+
# weight zero.
|
494 |
+
if not self_loops:
|
495 |
+
adjustment = Counter({u: weights[u]})
|
496 |
+
else:
|
497 |
+
adjustment = Counter()
|
498 |
+
v = weighted_choice(weights - adjustment, seed=seed)
|
499 |
+
G.add_edge(u, v)
|
500 |
+
weights[v] += 1
|
501 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/duplication.py
ADDED
@@ -0,0 +1,163 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""Functions for generating graphs based on the "duplication" method.
|
2 |
+
|
3 |
+
These graph generators start with a small initial graph then duplicate
|
4 |
+
nodes and (partially) duplicate their edges. These functions are
|
5 |
+
generally inspired by biological networks.
|
6 |
+
|
7 |
+
"""
|
8 |
+
import networkx as nx
|
9 |
+
from networkx.exception import NetworkXError
|
10 |
+
from networkx.utils import py_random_state
|
11 |
+
|
12 |
+
__all__ = ["partial_duplication_graph", "duplication_divergence_graph"]
|
13 |
+
|
14 |
+
|
15 |
+
@py_random_state(4)
|
16 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
17 |
+
def partial_duplication_graph(N, n, p, q, seed=None):
|
18 |
+
"""Returns a random graph using the partial duplication model.
|
19 |
+
|
20 |
+
Parameters
|
21 |
+
----------
|
22 |
+
N : int
|
23 |
+
The total number of nodes in the final graph.
|
24 |
+
|
25 |
+
n : int
|
26 |
+
The number of nodes in the initial clique.
|
27 |
+
|
28 |
+
p : float
|
29 |
+
The probability of joining each neighbor of a node to the
|
30 |
+
duplicate node. Must be a number in the between zero and one,
|
31 |
+
inclusive.
|
32 |
+
|
33 |
+
q : float
|
34 |
+
The probability of joining the source node to the duplicate
|
35 |
+
node. Must be a number in the between zero and one, inclusive.
|
36 |
+
|
37 |
+
seed : integer, random_state, or None (default)
|
38 |
+
Indicator of random number generation state.
|
39 |
+
See :ref:`Randomness<randomness>`.
|
40 |
+
|
41 |
+
Notes
|
42 |
+
-----
|
43 |
+
A graph of nodes is grown by creating a fully connected graph
|
44 |
+
of size `n`. The following procedure is then repeated until
|
45 |
+
a total of `N` nodes have been reached.
|
46 |
+
|
47 |
+
1. A random node, *u*, is picked and a new node, *v*, is created.
|
48 |
+
2. For each neighbor of *u* an edge from the neighbor to *v* is created
|
49 |
+
with probability `p`.
|
50 |
+
3. An edge from *u* to *v* is created with probability `q`.
|
51 |
+
|
52 |
+
This algorithm appears in [1].
|
53 |
+
|
54 |
+
This implementation allows the possibility of generating
|
55 |
+
disconnected graphs.
|
56 |
+
|
57 |
+
References
|
58 |
+
----------
|
59 |
+
.. [1] Knudsen Michael, and Carsten Wiuf. "A Markov chain approach to
|
60 |
+
randomly grown graphs." Journal of Applied Mathematics 2008.
|
61 |
+
<https://doi.org/10.1155/2008/190836>
|
62 |
+
|
63 |
+
"""
|
64 |
+
if p < 0 or p > 1 or q < 0 or q > 1:
|
65 |
+
msg = "partial duplication graph must have 0 <= p, q <= 1."
|
66 |
+
raise NetworkXError(msg)
|
67 |
+
if n > N:
|
68 |
+
raise NetworkXError("partial duplication graph must have n <= N.")
|
69 |
+
|
70 |
+
G = nx.complete_graph(n)
|
71 |
+
for new_node in range(n, N):
|
72 |
+
# Pick a random vertex, u, already in the graph.
|
73 |
+
src_node = seed.randint(0, new_node - 1)
|
74 |
+
|
75 |
+
# Add a new vertex, v, to the graph.
|
76 |
+
G.add_node(new_node)
|
77 |
+
|
78 |
+
# For each neighbor of u...
|
79 |
+
for nbr_node in list(nx.all_neighbors(G, src_node)):
|
80 |
+
# Add the neighbor to v with probability p.
|
81 |
+
if seed.random() < p:
|
82 |
+
G.add_edge(new_node, nbr_node)
|
83 |
+
|
84 |
+
# Join v and u with probability q.
|
85 |
+
if seed.random() < q:
|
86 |
+
G.add_edge(new_node, src_node)
|
87 |
+
return G
|
88 |
+
|
89 |
+
|
90 |
+
@py_random_state(2)
|
91 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
92 |
+
def duplication_divergence_graph(n, p, seed=None):
|
93 |
+
"""Returns an undirected graph using the duplication-divergence model.
|
94 |
+
|
95 |
+
A graph of `n` nodes is created by duplicating the initial nodes
|
96 |
+
and retaining edges incident to the original nodes with a retention
|
97 |
+
probability `p`.
|
98 |
+
|
99 |
+
Parameters
|
100 |
+
----------
|
101 |
+
n : int
|
102 |
+
The desired number of nodes in the graph.
|
103 |
+
p : float
|
104 |
+
The probability for retaining the edge of the replicated node.
|
105 |
+
seed : integer, random_state, or None (default)
|
106 |
+
Indicator of random number generation state.
|
107 |
+
See :ref:`Randomness<randomness>`.
|
108 |
+
|
109 |
+
Returns
|
110 |
+
-------
|
111 |
+
G : Graph
|
112 |
+
|
113 |
+
Raises
|
114 |
+
------
|
115 |
+
NetworkXError
|
116 |
+
If `p` is not a valid probability.
|
117 |
+
If `n` is less than 2.
|
118 |
+
|
119 |
+
Notes
|
120 |
+
-----
|
121 |
+
This algorithm appears in [1].
|
122 |
+
|
123 |
+
This implementation disallows the possibility of generating
|
124 |
+
disconnected graphs.
|
125 |
+
|
126 |
+
References
|
127 |
+
----------
|
128 |
+
.. [1] I. Ispolatov, P. L. Krapivsky, A. Yuryev,
|
129 |
+
"Duplication-divergence model of protein interaction network",
|
130 |
+
Phys. Rev. E, 71, 061911, 2005.
|
131 |
+
|
132 |
+
"""
|
133 |
+
if p > 1 or p < 0:
|
134 |
+
msg = f"NetworkXError p={p} is not in [0,1]."
|
135 |
+
raise nx.NetworkXError(msg)
|
136 |
+
if n < 2:
|
137 |
+
msg = "n must be greater than or equal to 2"
|
138 |
+
raise nx.NetworkXError(msg)
|
139 |
+
|
140 |
+
G = nx.Graph()
|
141 |
+
|
142 |
+
# Initialize the graph with two connected nodes.
|
143 |
+
G.add_edge(0, 1)
|
144 |
+
i = 2
|
145 |
+
while i < n:
|
146 |
+
# Choose a random node from current graph to duplicate.
|
147 |
+
random_node = seed.choice(list(G))
|
148 |
+
# Make the replica.
|
149 |
+
G.add_node(i)
|
150 |
+
# flag indicates whether at least one edge is connected on the replica.
|
151 |
+
flag = False
|
152 |
+
for nbr in G.neighbors(random_node):
|
153 |
+
if seed.random() < p:
|
154 |
+
# Link retention step.
|
155 |
+
G.add_edge(i, nbr)
|
156 |
+
flag = True
|
157 |
+
if not flag:
|
158 |
+
# Delete replica if no edges retained.
|
159 |
+
G.remove_node(i)
|
160 |
+
else:
|
161 |
+
# Successful duplication.
|
162 |
+
i += 1
|
163 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/ego.py
ADDED
@@ -0,0 +1,65 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
Ego graph.
|
3 |
+
"""
|
4 |
+
__all__ = ["ego_graph"]
|
5 |
+
|
6 |
+
import networkx as nx
|
7 |
+
|
8 |
+
|
9 |
+
@nx._dispatchable(preserve_all_attrs=True, returns_graph=True)
|
10 |
+
def ego_graph(G, n, radius=1, center=True, undirected=False, distance=None):
|
11 |
+
"""Returns induced subgraph of neighbors centered at node n within
|
12 |
+
a given radius.
|
13 |
+
|
14 |
+
Parameters
|
15 |
+
----------
|
16 |
+
G : graph
|
17 |
+
A NetworkX Graph or DiGraph
|
18 |
+
|
19 |
+
n : node
|
20 |
+
A single node
|
21 |
+
|
22 |
+
radius : number, optional
|
23 |
+
Include all neighbors of distance<=radius from n.
|
24 |
+
|
25 |
+
center : bool, optional
|
26 |
+
If False, do not include center node in graph
|
27 |
+
|
28 |
+
undirected : bool, optional
|
29 |
+
If True use both in- and out-neighbors of directed graphs.
|
30 |
+
|
31 |
+
distance : key, optional
|
32 |
+
Use specified edge data key as distance. For example, setting
|
33 |
+
distance='weight' will use the edge weight to measure the
|
34 |
+
distance from the node n.
|
35 |
+
|
36 |
+
Notes
|
37 |
+
-----
|
38 |
+
For directed graphs D this produces the "out" neighborhood
|
39 |
+
or successors. If you want the neighborhood of predecessors
|
40 |
+
first reverse the graph with D.reverse(). If you want both
|
41 |
+
directions use the keyword argument undirected=True.
|
42 |
+
|
43 |
+
Node, edge, and graph attributes are copied to the returned subgraph.
|
44 |
+
"""
|
45 |
+
if undirected:
|
46 |
+
if distance is not None:
|
47 |
+
sp, _ = nx.single_source_dijkstra(
|
48 |
+
G.to_undirected(), n, cutoff=radius, weight=distance
|
49 |
+
)
|
50 |
+
else:
|
51 |
+
sp = dict(
|
52 |
+
nx.single_source_shortest_path_length(
|
53 |
+
G.to_undirected(), n, cutoff=radius
|
54 |
+
)
|
55 |
+
)
|
56 |
+
else:
|
57 |
+
if distance is not None:
|
58 |
+
sp, _ = nx.single_source_dijkstra(G, n, cutoff=radius, weight=distance)
|
59 |
+
else:
|
60 |
+
sp = dict(nx.single_source_shortest_path_length(G, n, cutoff=radius))
|
61 |
+
|
62 |
+
H = G.subgraph(sp).copy()
|
63 |
+
if not center:
|
64 |
+
H.remove_node(n)
|
65 |
+
return H
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/expanders.py
ADDED
@@ -0,0 +1,475 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
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|
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|
|
|
|
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|
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|
|
|
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|
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|
|
|
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|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
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|
|
|
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|
|
|
|
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|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
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|
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|
|
|
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|
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|
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|
|
|
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|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""Provides explicit constructions of expander graphs.
|
2 |
+
|
3 |
+
"""
|
4 |
+
import itertools
|
5 |
+
|
6 |
+
import networkx as nx
|
7 |
+
|
8 |
+
__all__ = [
|
9 |
+
"margulis_gabber_galil_graph",
|
10 |
+
"chordal_cycle_graph",
|
11 |
+
"paley_graph",
|
12 |
+
"maybe_regular_expander",
|
13 |
+
"is_regular_expander",
|
14 |
+
"random_regular_expander_graph",
|
15 |
+
]
|
16 |
+
|
17 |
+
|
18 |
+
# Other discrete torus expanders can be constructed by using the following edge
|
19 |
+
# sets. For more information, see Chapter 4, "Expander Graphs", in
|
20 |
+
# "Pseudorandomness", by Salil Vadhan.
|
21 |
+
#
|
22 |
+
# For a directed expander, add edges from (x, y) to:
|
23 |
+
#
|
24 |
+
# (x, y),
|
25 |
+
# ((x + 1) % n, y),
|
26 |
+
# (x, (y + 1) % n),
|
27 |
+
# (x, (x + y) % n),
|
28 |
+
# (-y % n, x)
|
29 |
+
#
|
30 |
+
# For an undirected expander, add the reverse edges.
|
31 |
+
#
|
32 |
+
# Also appearing in the paper of Gabber and Galil:
|
33 |
+
#
|
34 |
+
# (x, y),
|
35 |
+
# (x, (x + y) % n),
|
36 |
+
# (x, (x + y + 1) % n),
|
37 |
+
# ((x + y) % n, y),
|
38 |
+
# ((x + y + 1) % n, y)
|
39 |
+
#
|
40 |
+
# and:
|
41 |
+
#
|
42 |
+
# (x, y),
|
43 |
+
# ((x + 2*y) % n, y),
|
44 |
+
# ((x + (2*y + 1)) % n, y),
|
45 |
+
# ((x + (2*y + 2)) % n, y),
|
46 |
+
# (x, (y + 2*x) % n),
|
47 |
+
# (x, (y + (2*x + 1)) % n),
|
48 |
+
# (x, (y + (2*x + 2)) % n),
|
49 |
+
#
|
50 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
51 |
+
def margulis_gabber_galil_graph(n, create_using=None):
|
52 |
+
r"""Returns the Margulis-Gabber-Galil undirected MultiGraph on `n^2` nodes.
|
53 |
+
|
54 |
+
The undirected MultiGraph is regular with degree `8`. Nodes are integer
|
55 |
+
pairs. The second-largest eigenvalue of the adjacency matrix of the graph
|
56 |
+
is at most `5 \sqrt{2}`, regardless of `n`.
|
57 |
+
|
58 |
+
Parameters
|
59 |
+
----------
|
60 |
+
n : int
|
61 |
+
Determines the number of nodes in the graph: `n^2`.
|
62 |
+
create_using : NetworkX graph constructor, optional (default MultiGraph)
|
63 |
+
Graph type to create. If graph instance, then cleared before populated.
|
64 |
+
|
65 |
+
Returns
|
66 |
+
-------
|
67 |
+
G : graph
|
68 |
+
The constructed undirected multigraph.
|
69 |
+
|
70 |
+
Raises
|
71 |
+
------
|
72 |
+
NetworkXError
|
73 |
+
If the graph is directed or not a multigraph.
|
74 |
+
|
75 |
+
"""
|
76 |
+
G = nx.empty_graph(0, create_using, default=nx.MultiGraph)
|
77 |
+
if G.is_directed() or not G.is_multigraph():
|
78 |
+
msg = "`create_using` must be an undirected multigraph."
|
79 |
+
raise nx.NetworkXError(msg)
|
80 |
+
|
81 |
+
for x, y in itertools.product(range(n), repeat=2):
|
82 |
+
for u, v in (
|
83 |
+
((x + 2 * y) % n, y),
|
84 |
+
((x + (2 * y + 1)) % n, y),
|
85 |
+
(x, (y + 2 * x) % n),
|
86 |
+
(x, (y + (2 * x + 1)) % n),
|
87 |
+
):
|
88 |
+
G.add_edge((x, y), (u, v))
|
89 |
+
G.graph["name"] = f"margulis_gabber_galil_graph({n})"
|
90 |
+
return G
|
91 |
+
|
92 |
+
|
93 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
94 |
+
def chordal_cycle_graph(p, create_using=None):
|
95 |
+
"""Returns the chordal cycle graph on `p` nodes.
|
96 |
+
|
97 |
+
The returned graph is a cycle graph on `p` nodes with chords joining each
|
98 |
+
vertex `x` to its inverse modulo `p`. This graph is a (mildly explicit)
|
99 |
+
3-regular expander [1]_.
|
100 |
+
|
101 |
+
`p` *must* be a prime number.
|
102 |
+
|
103 |
+
Parameters
|
104 |
+
----------
|
105 |
+
p : a prime number
|
106 |
+
|
107 |
+
The number of vertices in the graph. This also indicates where the
|
108 |
+
chordal edges in the cycle will be created.
|
109 |
+
|
110 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
111 |
+
Graph type to create. If graph instance, then cleared before populated.
|
112 |
+
|
113 |
+
Returns
|
114 |
+
-------
|
115 |
+
G : graph
|
116 |
+
The constructed undirected multigraph.
|
117 |
+
|
118 |
+
Raises
|
119 |
+
------
|
120 |
+
NetworkXError
|
121 |
+
|
122 |
+
If `create_using` indicates directed or not a multigraph.
|
123 |
+
|
124 |
+
References
|
125 |
+
----------
|
126 |
+
|
127 |
+
.. [1] Theorem 4.4.2 in A. Lubotzky. "Discrete groups, expanding graphs and
|
128 |
+
invariant measures", volume 125 of Progress in Mathematics.
|
129 |
+
Birkhäuser Verlag, Basel, 1994.
|
130 |
+
|
131 |
+
"""
|
132 |
+
G = nx.empty_graph(0, create_using, default=nx.MultiGraph)
|
133 |
+
if G.is_directed() or not G.is_multigraph():
|
134 |
+
msg = "`create_using` must be an undirected multigraph."
|
135 |
+
raise nx.NetworkXError(msg)
|
136 |
+
|
137 |
+
for x in range(p):
|
138 |
+
left = (x - 1) % p
|
139 |
+
right = (x + 1) % p
|
140 |
+
# Here we apply Fermat's Little Theorem to compute the multiplicative
|
141 |
+
# inverse of x in Z/pZ. By Fermat's Little Theorem,
|
142 |
+
#
|
143 |
+
# x^p = x (mod p)
|
144 |
+
#
|
145 |
+
# Therefore,
|
146 |
+
#
|
147 |
+
# x * x^(p - 2) = 1 (mod p)
|
148 |
+
#
|
149 |
+
# The number 0 is a special case: we just let its inverse be itself.
|
150 |
+
chord = pow(x, p - 2, p) if x > 0 else 0
|
151 |
+
for y in (left, right, chord):
|
152 |
+
G.add_edge(x, y)
|
153 |
+
G.graph["name"] = f"chordal_cycle_graph({p})"
|
154 |
+
return G
|
155 |
+
|
156 |
+
|
157 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
158 |
+
def paley_graph(p, create_using=None):
|
159 |
+
r"""Returns the Paley $\frac{(p-1)}{2}$ -regular graph on $p$ nodes.
|
160 |
+
|
161 |
+
The returned graph is a graph on $\mathbb{Z}/p\mathbb{Z}$ with edges between $x$ and $y$
|
162 |
+
if and only if $x-y$ is a nonzero square in $\mathbb{Z}/p\mathbb{Z}$.
|
163 |
+
|
164 |
+
If $p \equiv 1 \pmod 4$, $-1$ is a square in $\mathbb{Z}/p\mathbb{Z}$ and therefore $x-y$ is a square if and
|
165 |
+
only if $y-x$ is also a square, i.e the edges in the Paley graph are symmetric.
|
166 |
+
|
167 |
+
If $p \equiv 3 \pmod 4$, $-1$ is not a square in $\mathbb{Z}/p\mathbb{Z}$ and therefore either $x-y$ or $y-x$
|
168 |
+
is a square in $\mathbb{Z}/p\mathbb{Z}$ but not both.
|
169 |
+
|
170 |
+
Note that a more general definition of Paley graphs extends this construction
|
171 |
+
to graphs over $q=p^n$ vertices, by using the finite field $F_q$ instead of $\mathbb{Z}/p\mathbb{Z}$.
|
172 |
+
This construction requires to compute squares in general finite fields and is
|
173 |
+
not what is implemented here (i.e `paley_graph(25)` does not return the true
|
174 |
+
Paley graph associated with $5^2$).
|
175 |
+
|
176 |
+
Parameters
|
177 |
+
----------
|
178 |
+
p : int, an odd prime number.
|
179 |
+
|
180 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
181 |
+
Graph type to create. If graph instance, then cleared before populated.
|
182 |
+
|
183 |
+
Returns
|
184 |
+
-------
|
185 |
+
G : graph
|
186 |
+
The constructed directed graph.
|
187 |
+
|
188 |
+
Raises
|
189 |
+
------
|
190 |
+
NetworkXError
|
191 |
+
If the graph is a multigraph.
|
192 |
+
|
193 |
+
References
|
194 |
+
----------
|
195 |
+
Chapter 13 in B. Bollobas, Random Graphs. Second edition.
|
196 |
+
Cambridge Studies in Advanced Mathematics, 73.
|
197 |
+
Cambridge University Press, Cambridge (2001).
|
198 |
+
"""
|
199 |
+
G = nx.empty_graph(0, create_using, default=nx.DiGraph)
|
200 |
+
if G.is_multigraph():
|
201 |
+
msg = "`create_using` cannot be a multigraph."
|
202 |
+
raise nx.NetworkXError(msg)
|
203 |
+
|
204 |
+
# Compute the squares in Z/pZ.
|
205 |
+
# Make it a set to uniquify (there are exactly (p-1)/2 squares in Z/pZ
|
206 |
+
# when is prime).
|
207 |
+
square_set = {(x**2) % p for x in range(1, p) if (x**2) % p != 0}
|
208 |
+
|
209 |
+
for x in range(p):
|
210 |
+
for x2 in square_set:
|
211 |
+
G.add_edge(x, (x + x2) % p)
|
212 |
+
G.graph["name"] = f"paley({p})"
|
213 |
+
return G
|
214 |
+
|
215 |
+
|
216 |
+
@nx.utils.decorators.np_random_state("seed")
|
217 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
218 |
+
def maybe_regular_expander(n, d, *, create_using=None, max_tries=100, seed=None):
|
219 |
+
r"""Utility for creating a random regular expander.
|
220 |
+
|
221 |
+
Returns a random $d$-regular graph on $n$ nodes which is an expander
|
222 |
+
graph with very good probability.
|
223 |
+
|
224 |
+
Parameters
|
225 |
+
----------
|
226 |
+
n : int
|
227 |
+
The number of nodes.
|
228 |
+
d : int
|
229 |
+
The degree of each node.
|
230 |
+
create_using : Graph Instance or Constructor
|
231 |
+
Indicator of type of graph to return.
|
232 |
+
If a Graph-type instance, then clear and use it.
|
233 |
+
If a constructor, call it to create an empty graph.
|
234 |
+
Use the Graph constructor by default.
|
235 |
+
max_tries : int. (default: 100)
|
236 |
+
The number of allowed loops when generating each independent cycle
|
237 |
+
seed : (default: None)
|
238 |
+
Seed used to set random number generation state. See :ref`Randomness<randomness>`.
|
239 |
+
|
240 |
+
Notes
|
241 |
+
-----
|
242 |
+
The nodes are numbered from $0$ to $n - 1$.
|
243 |
+
|
244 |
+
The graph is generated by taking $d / 2$ random independent cycles.
|
245 |
+
|
246 |
+
Joel Friedman proved that in this model the resulting
|
247 |
+
graph is an expander with probability
|
248 |
+
$1 - O(n^{-\tau})$ where $\tau = \lceil (\sqrt{d - 1}) / 2 \rceil - 1$. [1]_
|
249 |
+
|
250 |
+
Examples
|
251 |
+
--------
|
252 |
+
>>> G = nx.maybe_regular_expander(n=200, d=6, seed=8020)
|
253 |
+
|
254 |
+
Returns
|
255 |
+
-------
|
256 |
+
G : graph
|
257 |
+
The constructed undirected graph.
|
258 |
+
|
259 |
+
Raises
|
260 |
+
------
|
261 |
+
NetworkXError
|
262 |
+
If $d % 2 != 0$ as the degree must be even.
|
263 |
+
If $n - 1$ is less than $ 2d $ as the graph is complete at most.
|
264 |
+
If max_tries is reached
|
265 |
+
|
266 |
+
See Also
|
267 |
+
--------
|
268 |
+
is_regular_expander
|
269 |
+
random_regular_expander_graph
|
270 |
+
|
271 |
+
References
|
272 |
+
----------
|
273 |
+
.. [1] Joel Friedman,
|
274 |
+
A Proof of Alon’s Second Eigenvalue Conjecture and Related Problems, 2004
|
275 |
+
https://arxiv.org/abs/cs/0405020
|
276 |
+
|
277 |
+
"""
|
278 |
+
|
279 |
+
import numpy as np
|
280 |
+
|
281 |
+
if n < 1:
|
282 |
+
raise nx.NetworkXError("n must be a positive integer")
|
283 |
+
|
284 |
+
if not (d >= 2):
|
285 |
+
raise nx.NetworkXError("d must be greater than or equal to 2")
|
286 |
+
|
287 |
+
if not (d % 2 == 0):
|
288 |
+
raise nx.NetworkXError("d must be even")
|
289 |
+
|
290 |
+
if not (n - 1 >= d):
|
291 |
+
raise nx.NetworkXError(
|
292 |
+
f"Need n-1>= d to have room for {d//2} independent cycles with {n} nodes"
|
293 |
+
)
|
294 |
+
|
295 |
+
G = nx.empty_graph(n, create_using)
|
296 |
+
|
297 |
+
if n < 2:
|
298 |
+
return G
|
299 |
+
|
300 |
+
cycles = []
|
301 |
+
edges = set()
|
302 |
+
|
303 |
+
# Create d / 2 cycles
|
304 |
+
for i in range(d // 2):
|
305 |
+
iterations = max_tries
|
306 |
+
# Make sure the cycles are independent to have a regular graph
|
307 |
+
while len(edges) != (i + 1) * n:
|
308 |
+
iterations -= 1
|
309 |
+
# Faster than random.permutation(n) since there are only
|
310 |
+
# (n-1)! distinct cycles against n! permutations of size n
|
311 |
+
cycle = seed.permutation(n - 1).tolist()
|
312 |
+
cycle.append(n - 1)
|
313 |
+
|
314 |
+
new_edges = {
|
315 |
+
(u, v)
|
316 |
+
for u, v in nx.utils.pairwise(cycle, cyclic=True)
|
317 |
+
if (u, v) not in edges and (v, u) not in edges
|
318 |
+
}
|
319 |
+
# If the new cycle has no edges in common with previous cycles
|
320 |
+
# then add it to the list otherwise try again
|
321 |
+
if len(new_edges) == n:
|
322 |
+
cycles.append(cycle)
|
323 |
+
edges.update(new_edges)
|
324 |
+
|
325 |
+
if iterations == 0:
|
326 |
+
raise nx.NetworkXError("Too many iterations in maybe_regular_expander")
|
327 |
+
|
328 |
+
G.add_edges_from(edges)
|
329 |
+
|
330 |
+
return G
|
331 |
+
|
332 |
+
|
333 |
+
@nx.utils.not_implemented_for("directed")
|
334 |
+
@nx.utils.not_implemented_for("multigraph")
|
335 |
+
@nx._dispatchable(preserve_edge_attrs={"G": {"weight": 1}})
|
336 |
+
def is_regular_expander(G, *, epsilon=0):
|
337 |
+
r"""Determines whether the graph G is a regular expander. [1]_
|
338 |
+
|
339 |
+
An expander graph is a sparse graph with strong connectivity properties.
|
340 |
+
|
341 |
+
More precisely, this helper checks whether the graph is a
|
342 |
+
regular $(n, d, \lambda)$-expander with $\lambda$ close to
|
343 |
+
the Alon-Boppana bound and given by
|
344 |
+
$\lambda = 2 \sqrt{d - 1} + \epsilon$. [2]_
|
345 |
+
|
346 |
+
In the case where $\epsilon = 0$ then if the graph successfully passes the test
|
347 |
+
it is a Ramanujan graph. [3]_
|
348 |
+
|
349 |
+
A Ramanujan graph has spectral gap almost as large as possible, which makes them
|
350 |
+
excellent expanders.
|
351 |
+
|
352 |
+
Parameters
|
353 |
+
----------
|
354 |
+
G : NetworkX graph
|
355 |
+
epsilon : int, float, default=0
|
356 |
+
|
357 |
+
Returns
|
358 |
+
-------
|
359 |
+
bool
|
360 |
+
Whether the given graph is a regular $(n, d, \lambda)$-expander
|
361 |
+
where $\lambda = 2 \sqrt{d - 1} + \epsilon$.
|
362 |
+
|
363 |
+
Examples
|
364 |
+
--------
|
365 |
+
>>> G = nx.random_regular_expander_graph(20, 4)
|
366 |
+
>>> nx.is_regular_expander(G)
|
367 |
+
True
|
368 |
+
|
369 |
+
See Also
|
370 |
+
--------
|
371 |
+
maybe_regular_expander
|
372 |
+
random_regular_expander_graph
|
373 |
+
|
374 |
+
References
|
375 |
+
----------
|
376 |
+
.. [1] Expander graph, https://en.wikipedia.org/wiki/Expander_graph
|
377 |
+
.. [2] Alon-Boppana bound, https://en.wikipedia.org/wiki/Alon%E2%80%93Boppana_bound
|
378 |
+
.. [3] Ramanujan graphs, https://en.wikipedia.org/wiki/Ramanujan_graph
|
379 |
+
|
380 |
+
"""
|
381 |
+
|
382 |
+
import numpy as np
|
383 |
+
from scipy.sparse.linalg import eigsh
|
384 |
+
|
385 |
+
if epsilon < 0:
|
386 |
+
raise nx.NetworkXError("epsilon must be non negative")
|
387 |
+
|
388 |
+
if not nx.is_regular(G):
|
389 |
+
return False
|
390 |
+
|
391 |
+
_, d = nx.utils.arbitrary_element(G.degree)
|
392 |
+
|
393 |
+
A = nx.adjacency_matrix(G, dtype=float)
|
394 |
+
lams = eigsh(A, which="LM", k=2, return_eigenvectors=False)
|
395 |
+
|
396 |
+
# lambda2 is the second biggest eigenvalue
|
397 |
+
lambda2 = min(lams)
|
398 |
+
|
399 |
+
# Use bool() to convert numpy scalar to Python Boolean
|
400 |
+
return bool(abs(lambda2) < 2 ** np.sqrt(d - 1) + epsilon)
|
401 |
+
|
402 |
+
|
403 |
+
@nx.utils.decorators.np_random_state("seed")
|
404 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
405 |
+
def random_regular_expander_graph(
|
406 |
+
n, d, *, epsilon=0, create_using=None, max_tries=100, seed=None
|
407 |
+
):
|
408 |
+
r"""Returns a random regular expander graph on $n$ nodes with degree $d$.
|
409 |
+
|
410 |
+
An expander graph is a sparse graph with strong connectivity properties. [1]_
|
411 |
+
|
412 |
+
More precisely the returned graph is a $(n, d, \lambda)$-expander with
|
413 |
+
$\lambda = 2 \sqrt{d - 1} + \epsilon$, close to the Alon-Boppana bound. [2]_
|
414 |
+
|
415 |
+
In the case where $\epsilon = 0$ it returns a Ramanujan graph.
|
416 |
+
A Ramanujan graph has spectral gap almost as large as possible,
|
417 |
+
which makes them excellent expanders. [3]_
|
418 |
+
|
419 |
+
Parameters
|
420 |
+
----------
|
421 |
+
n : int
|
422 |
+
The number of nodes.
|
423 |
+
d : int
|
424 |
+
The degree of each node.
|
425 |
+
epsilon : int, float, default=0
|
426 |
+
max_tries : int, (default: 100)
|
427 |
+
The number of allowed loops, also used in the maybe_regular_expander utility
|
428 |
+
seed : (default: None)
|
429 |
+
Seed used to set random number generation state. See :ref`Randomness<randomness>`.
|
430 |
+
|
431 |
+
Raises
|
432 |
+
------
|
433 |
+
NetworkXError
|
434 |
+
If max_tries is reached
|
435 |
+
|
436 |
+
Examples
|
437 |
+
--------
|
438 |
+
>>> G = nx.random_regular_expander_graph(20, 4)
|
439 |
+
>>> nx.is_regular_expander(G)
|
440 |
+
True
|
441 |
+
|
442 |
+
Notes
|
443 |
+
-----
|
444 |
+
This loops over `maybe_regular_expander` and can be slow when
|
445 |
+
$n$ is too big or $\epsilon$ too small.
|
446 |
+
|
447 |
+
See Also
|
448 |
+
--------
|
449 |
+
maybe_regular_expander
|
450 |
+
is_regular_expander
|
451 |
+
|
452 |
+
References
|
453 |
+
----------
|
454 |
+
.. [1] Expander graph, https://en.wikipedia.org/wiki/Expander_graph
|
455 |
+
.. [2] Alon-Boppana bound, https://en.wikipedia.org/wiki/Alon%E2%80%93Boppana_bound
|
456 |
+
.. [3] Ramanujan graphs, https://en.wikipedia.org/wiki/Ramanujan_graph
|
457 |
+
|
458 |
+
"""
|
459 |
+
G = maybe_regular_expander(
|
460 |
+
n, d, create_using=create_using, max_tries=max_tries, seed=seed
|
461 |
+
)
|
462 |
+
iterations = max_tries
|
463 |
+
|
464 |
+
while not is_regular_expander(G, epsilon=epsilon):
|
465 |
+
iterations -= 1
|
466 |
+
G = maybe_regular_expander(
|
467 |
+
n=n, d=d, create_using=create_using, max_tries=max_tries, seed=seed
|
468 |
+
)
|
469 |
+
|
470 |
+
if iterations == 0:
|
471 |
+
raise nx.NetworkXError(
|
472 |
+
"Too many iterations in random_regular_expander_graph"
|
473 |
+
)
|
474 |
+
|
475 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/geometric.py
ADDED
@@ -0,0 +1,1047 @@
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|
|
1 |
+
"""Generators for geometric graphs.
|
2 |
+
"""
|
3 |
+
|
4 |
+
import math
|
5 |
+
from bisect import bisect_left
|
6 |
+
from itertools import accumulate, combinations, product
|
7 |
+
|
8 |
+
import networkx as nx
|
9 |
+
from networkx.utils import py_random_state
|
10 |
+
|
11 |
+
__all__ = [
|
12 |
+
"geometric_edges",
|
13 |
+
"geographical_threshold_graph",
|
14 |
+
"navigable_small_world_graph",
|
15 |
+
"random_geometric_graph",
|
16 |
+
"soft_random_geometric_graph",
|
17 |
+
"thresholded_random_geometric_graph",
|
18 |
+
"waxman_graph",
|
19 |
+
"geometric_soft_configuration_graph",
|
20 |
+
]
|
21 |
+
|
22 |
+
|
23 |
+
@nx._dispatchable(node_attrs="pos_name")
|
24 |
+
def geometric_edges(G, radius, p=2, *, pos_name="pos"):
|
25 |
+
"""Returns edge list of node pairs within `radius` of each other.
|
26 |
+
|
27 |
+
Parameters
|
28 |
+
----------
|
29 |
+
G : networkx graph
|
30 |
+
The graph from which to generate the edge list. The nodes in `G` should
|
31 |
+
have an attribute ``pos`` corresponding to the node position, which is
|
32 |
+
used to compute the distance to other nodes.
|
33 |
+
radius : scalar
|
34 |
+
The distance threshold. Edges are included in the edge list if the
|
35 |
+
distance between the two nodes is less than `radius`.
|
36 |
+
pos_name : string, default="pos"
|
37 |
+
The name of the node attribute which represents the position of each
|
38 |
+
node in 2D coordinates. Every node in the Graph must have this attribute.
|
39 |
+
p : scalar, default=2
|
40 |
+
The `Minkowski distance metric
|
41 |
+
<https://en.wikipedia.org/wiki/Minkowski_distance>`_ used to compute
|
42 |
+
distances. The default value is 2, i.e. Euclidean distance.
|
43 |
+
|
44 |
+
Returns
|
45 |
+
-------
|
46 |
+
edges : list
|
47 |
+
List of edges whose distances are less than `radius`
|
48 |
+
|
49 |
+
Notes
|
50 |
+
-----
|
51 |
+
Radius uses Minkowski distance metric `p`.
|
52 |
+
If scipy is available, `scipy.spatial.cKDTree` is used to speed computation.
|
53 |
+
|
54 |
+
Examples
|
55 |
+
--------
|
56 |
+
Create a graph with nodes that have a "pos" attribute representing 2D
|
57 |
+
coordinates.
|
58 |
+
|
59 |
+
>>> G = nx.Graph()
|
60 |
+
>>> G.add_nodes_from(
|
61 |
+
... [
|
62 |
+
... (0, {"pos": (0, 0)}),
|
63 |
+
... (1, {"pos": (3, 0)}),
|
64 |
+
... (2, {"pos": (8, 0)}),
|
65 |
+
... ]
|
66 |
+
... )
|
67 |
+
>>> nx.geometric_edges(G, radius=1)
|
68 |
+
[]
|
69 |
+
>>> nx.geometric_edges(G, radius=4)
|
70 |
+
[(0, 1)]
|
71 |
+
>>> nx.geometric_edges(G, radius=6)
|
72 |
+
[(0, 1), (1, 2)]
|
73 |
+
>>> nx.geometric_edges(G, radius=9)
|
74 |
+
[(0, 1), (0, 2), (1, 2)]
|
75 |
+
"""
|
76 |
+
# Input validation - every node must have a "pos" attribute
|
77 |
+
for n, pos in G.nodes(data=pos_name):
|
78 |
+
if pos is None:
|
79 |
+
raise nx.NetworkXError(
|
80 |
+
f"Node {n} (and all nodes) must have a '{pos_name}' attribute."
|
81 |
+
)
|
82 |
+
|
83 |
+
# NOTE: See _geometric_edges for the actual implementation. The reason this
|
84 |
+
# is split into two functions is to avoid the overhead of input validation
|
85 |
+
# every time the function is called internally in one of the other
|
86 |
+
# geometric generators
|
87 |
+
return _geometric_edges(G, radius, p, pos_name)
|
88 |
+
|
89 |
+
|
90 |
+
def _geometric_edges(G, radius, p, pos_name):
|
91 |
+
"""
|
92 |
+
Implements `geometric_edges` without input validation. See `geometric_edges`
|
93 |
+
for complete docstring.
|
94 |
+
"""
|
95 |
+
nodes_pos = G.nodes(data=pos_name)
|
96 |
+
try:
|
97 |
+
import scipy as sp
|
98 |
+
except ImportError:
|
99 |
+
# no scipy KDTree so compute by for-loop
|
100 |
+
radius_p = radius**p
|
101 |
+
edges = [
|
102 |
+
(u, v)
|
103 |
+
for (u, pu), (v, pv) in combinations(nodes_pos, 2)
|
104 |
+
if sum(abs(a - b) ** p for a, b in zip(pu, pv)) <= radius_p
|
105 |
+
]
|
106 |
+
return edges
|
107 |
+
# scipy KDTree is available
|
108 |
+
nodes, coords = list(zip(*nodes_pos))
|
109 |
+
kdtree = sp.spatial.cKDTree(coords) # Cannot provide generator.
|
110 |
+
edge_indexes = kdtree.query_pairs(radius, p)
|
111 |
+
edges = [(nodes[u], nodes[v]) for u, v in sorted(edge_indexes)]
|
112 |
+
return edges
|
113 |
+
|
114 |
+
|
115 |
+
@py_random_state(5)
|
116 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
117 |
+
def random_geometric_graph(
|
118 |
+
n, radius, dim=2, pos=None, p=2, seed=None, *, pos_name="pos"
|
119 |
+
):
|
120 |
+
"""Returns a random geometric graph in the unit cube of dimensions `dim`.
|
121 |
+
|
122 |
+
The random geometric graph model places `n` nodes uniformly at
|
123 |
+
random in the unit cube. Two nodes are joined by an edge if the
|
124 |
+
distance between the nodes is at most `radius`.
|
125 |
+
|
126 |
+
Edges are determined using a KDTree when SciPy is available.
|
127 |
+
This reduces the time complexity from $O(n^2)$ to $O(n)$.
|
128 |
+
|
129 |
+
Parameters
|
130 |
+
----------
|
131 |
+
n : int or iterable
|
132 |
+
Number of nodes or iterable of nodes
|
133 |
+
radius: float
|
134 |
+
Distance threshold value
|
135 |
+
dim : int, optional
|
136 |
+
Dimension of graph
|
137 |
+
pos : dict, optional
|
138 |
+
A dictionary keyed by node with node positions as values.
|
139 |
+
p : float, optional
|
140 |
+
Which Minkowski distance metric to use. `p` has to meet the condition
|
141 |
+
``1 <= p <= infinity``.
|
142 |
+
|
143 |
+
If this argument is not specified, the :math:`L^2` metric
|
144 |
+
(the Euclidean distance metric), p = 2 is used.
|
145 |
+
This should not be confused with the `p` of an Erdős-Rényi random
|
146 |
+
graph, which represents probability.
|
147 |
+
seed : integer, random_state, or None (default)
|
148 |
+
Indicator of random number generation state.
|
149 |
+
See :ref:`Randomness<randomness>`.
|
150 |
+
pos_name : string, default="pos"
|
151 |
+
The name of the node attribute which represents the position
|
152 |
+
in 2D coordinates of the node in the returned graph.
|
153 |
+
|
154 |
+
Returns
|
155 |
+
-------
|
156 |
+
Graph
|
157 |
+
A random geometric graph, undirected and without self-loops.
|
158 |
+
Each node has a node attribute ``'pos'`` that stores the
|
159 |
+
position of that node in Euclidean space as provided by the
|
160 |
+
``pos`` keyword argument or, if ``pos`` was not provided, as
|
161 |
+
generated by this function.
|
162 |
+
|
163 |
+
Examples
|
164 |
+
--------
|
165 |
+
Create a random geometric graph on twenty nodes where nodes are joined by
|
166 |
+
an edge if their distance is at most 0.1::
|
167 |
+
|
168 |
+
>>> G = nx.random_geometric_graph(20, 0.1)
|
169 |
+
|
170 |
+
Notes
|
171 |
+
-----
|
172 |
+
This uses a *k*-d tree to build the graph.
|
173 |
+
|
174 |
+
The `pos` keyword argument can be used to specify node positions so you
|
175 |
+
can create an arbitrary distribution and domain for positions.
|
176 |
+
|
177 |
+
For example, to use a 2D Gaussian distribution of node positions with mean
|
178 |
+
(0, 0) and standard deviation 2::
|
179 |
+
|
180 |
+
>>> import random
|
181 |
+
>>> n = 20
|
182 |
+
>>> pos = {i: (random.gauss(0, 2), random.gauss(0, 2)) for i in range(n)}
|
183 |
+
>>> G = nx.random_geometric_graph(n, 0.2, pos=pos)
|
184 |
+
|
185 |
+
References
|
186 |
+
----------
|
187 |
+
.. [1] Penrose, Mathew, *Random Geometric Graphs*,
|
188 |
+
Oxford Studies in Probability, 5, 2003.
|
189 |
+
|
190 |
+
"""
|
191 |
+
# TODO Is this function just a special case of the geographical
|
192 |
+
# threshold graph?
|
193 |
+
#
|
194 |
+
# half_radius = {v: radius / 2 for v in n}
|
195 |
+
# return geographical_threshold_graph(nodes, theta=1, alpha=1,
|
196 |
+
# weight=half_radius)
|
197 |
+
#
|
198 |
+
G = nx.empty_graph(n)
|
199 |
+
# If no positions are provided, choose uniformly random vectors in
|
200 |
+
# Euclidean space of the specified dimension.
|
201 |
+
if pos is None:
|
202 |
+
pos = {v: [seed.random() for i in range(dim)] for v in G}
|
203 |
+
nx.set_node_attributes(G, pos, pos_name)
|
204 |
+
|
205 |
+
G.add_edges_from(_geometric_edges(G, radius, p, pos_name))
|
206 |
+
return G
|
207 |
+
|
208 |
+
|
209 |
+
@py_random_state(6)
|
210 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
211 |
+
def soft_random_geometric_graph(
|
212 |
+
n, radius, dim=2, pos=None, p=2, p_dist=None, seed=None, *, pos_name="pos"
|
213 |
+
):
|
214 |
+
r"""Returns a soft random geometric graph in the unit cube.
|
215 |
+
|
216 |
+
The soft random geometric graph [1] model places `n` nodes uniformly at
|
217 |
+
random in the unit cube in dimension `dim`. Two nodes of distance, `dist`,
|
218 |
+
computed by the `p`-Minkowski distance metric are joined by an edge with
|
219 |
+
probability `p_dist` if the computed distance metric value of the nodes
|
220 |
+
is at most `radius`, otherwise they are not joined.
|
221 |
+
|
222 |
+
Edges within `radius` of each other are determined using a KDTree when
|
223 |
+
SciPy is available. This reduces the time complexity from :math:`O(n^2)`
|
224 |
+
to :math:`O(n)`.
|
225 |
+
|
226 |
+
Parameters
|
227 |
+
----------
|
228 |
+
n : int or iterable
|
229 |
+
Number of nodes or iterable of nodes
|
230 |
+
radius: float
|
231 |
+
Distance threshold value
|
232 |
+
dim : int, optional
|
233 |
+
Dimension of graph
|
234 |
+
pos : dict, optional
|
235 |
+
A dictionary keyed by node with node positions as values.
|
236 |
+
p : float, optional
|
237 |
+
Which Minkowski distance metric to use.
|
238 |
+
`p` has to meet the condition ``1 <= p <= infinity``.
|
239 |
+
|
240 |
+
If this argument is not specified, the :math:`L^2` metric
|
241 |
+
(the Euclidean distance metric), p = 2 is used.
|
242 |
+
|
243 |
+
This should not be confused with the `p` of an Erdős-Rényi random
|
244 |
+
graph, which represents probability.
|
245 |
+
p_dist : function, optional
|
246 |
+
A probability density function computing the probability of
|
247 |
+
connecting two nodes that are of distance, dist, computed by the
|
248 |
+
Minkowski distance metric. The probability density function, `p_dist`,
|
249 |
+
must be any function that takes the metric value as input
|
250 |
+
and outputs a single probability value between 0-1. The scipy.stats
|
251 |
+
package has many probability distribution functions implemented and
|
252 |
+
tools for custom probability distribution definitions [2], and passing
|
253 |
+
the .pdf method of scipy.stats distributions can be used here. If the
|
254 |
+
probability function, `p_dist`, is not supplied, the default function
|
255 |
+
is an exponential distribution with rate parameter :math:`\lambda=1`.
|
256 |
+
seed : integer, random_state, or None (default)
|
257 |
+
Indicator of random number generation state.
|
258 |
+
See :ref:`Randomness<randomness>`.
|
259 |
+
pos_name : string, default="pos"
|
260 |
+
The name of the node attribute which represents the position
|
261 |
+
in 2D coordinates of the node in the returned graph.
|
262 |
+
|
263 |
+
Returns
|
264 |
+
-------
|
265 |
+
Graph
|
266 |
+
A soft random geometric graph, undirected and without self-loops.
|
267 |
+
Each node has a node attribute ``'pos'`` that stores the
|
268 |
+
position of that node in Euclidean space as provided by the
|
269 |
+
``pos`` keyword argument or, if ``pos`` was not provided, as
|
270 |
+
generated by this function.
|
271 |
+
|
272 |
+
Examples
|
273 |
+
--------
|
274 |
+
Default Graph:
|
275 |
+
|
276 |
+
G = nx.soft_random_geometric_graph(50, 0.2)
|
277 |
+
|
278 |
+
Custom Graph:
|
279 |
+
|
280 |
+
Create a soft random geometric graph on 100 uniformly distributed nodes
|
281 |
+
where nodes are joined by an edge with probability computed from an
|
282 |
+
exponential distribution with rate parameter :math:`\lambda=1` if their
|
283 |
+
Euclidean distance is at most 0.2.
|
284 |
+
|
285 |
+
Notes
|
286 |
+
-----
|
287 |
+
This uses a *k*-d tree to build the graph.
|
288 |
+
|
289 |
+
The `pos` keyword argument can be used to specify node positions so you
|
290 |
+
can create an arbitrary distribution and domain for positions.
|
291 |
+
|
292 |
+
For example, to use a 2D Gaussian distribution of node positions with mean
|
293 |
+
(0, 0) and standard deviation 2
|
294 |
+
|
295 |
+
The scipy.stats package can be used to define the probability distribution
|
296 |
+
with the .pdf method used as `p_dist`.
|
297 |
+
|
298 |
+
::
|
299 |
+
|
300 |
+
>>> import random
|
301 |
+
>>> import math
|
302 |
+
>>> n = 100
|
303 |
+
>>> pos = {i: (random.gauss(0, 2), random.gauss(0, 2)) for i in range(n)}
|
304 |
+
>>> p_dist = lambda dist: math.exp(-dist)
|
305 |
+
>>> G = nx.soft_random_geometric_graph(n, 0.2, pos=pos, p_dist=p_dist)
|
306 |
+
|
307 |
+
References
|
308 |
+
----------
|
309 |
+
.. [1] Penrose, Mathew D. "Connectivity of soft random geometric graphs."
|
310 |
+
The Annals of Applied Probability 26.2 (2016): 986-1028.
|
311 |
+
.. [2] scipy.stats -
|
312 |
+
https://docs.scipy.org/doc/scipy/reference/tutorial/stats.html
|
313 |
+
|
314 |
+
"""
|
315 |
+
G = nx.empty_graph(n)
|
316 |
+
G.name = f"soft_random_geometric_graph({n}, {radius}, {dim})"
|
317 |
+
# If no positions are provided, choose uniformly random vectors in
|
318 |
+
# Euclidean space of the specified dimension.
|
319 |
+
if pos is None:
|
320 |
+
pos = {v: [seed.random() for i in range(dim)] for v in G}
|
321 |
+
nx.set_node_attributes(G, pos, pos_name)
|
322 |
+
|
323 |
+
# if p_dist function not supplied the default function is an exponential
|
324 |
+
# distribution with rate parameter :math:`\lambda=1`.
|
325 |
+
if p_dist is None:
|
326 |
+
|
327 |
+
def p_dist(dist):
|
328 |
+
return math.exp(-dist)
|
329 |
+
|
330 |
+
def should_join(edge):
|
331 |
+
u, v = edge
|
332 |
+
dist = (sum(abs(a - b) ** p for a, b in zip(pos[u], pos[v]))) ** (1 / p)
|
333 |
+
return seed.random() < p_dist(dist)
|
334 |
+
|
335 |
+
G.add_edges_from(filter(should_join, _geometric_edges(G, radius, p, pos_name)))
|
336 |
+
return G
|
337 |
+
|
338 |
+
|
339 |
+
@py_random_state(7)
|
340 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
341 |
+
def geographical_threshold_graph(
|
342 |
+
n,
|
343 |
+
theta,
|
344 |
+
dim=2,
|
345 |
+
pos=None,
|
346 |
+
weight=None,
|
347 |
+
metric=None,
|
348 |
+
p_dist=None,
|
349 |
+
seed=None,
|
350 |
+
*,
|
351 |
+
pos_name="pos",
|
352 |
+
weight_name="weight",
|
353 |
+
):
|
354 |
+
r"""Returns a geographical threshold graph.
|
355 |
+
|
356 |
+
The geographical threshold graph model places $n$ nodes uniformly at
|
357 |
+
random in a rectangular domain. Each node $u$ is assigned a weight
|
358 |
+
$w_u$. Two nodes $u$ and $v$ are joined by an edge if
|
359 |
+
|
360 |
+
.. math::
|
361 |
+
|
362 |
+
(w_u + w_v)p_{dist}(r) \ge \theta
|
363 |
+
|
364 |
+
where `r` is the distance between `u` and `v`, `p_dist` is any function of
|
365 |
+
`r`, and :math:`\theta` as the threshold parameter. `p_dist` is used to
|
366 |
+
give weight to the distance between nodes when deciding whether or not
|
367 |
+
they should be connected. The larger `p_dist` is, the more prone nodes
|
368 |
+
separated by `r` are to be connected, and vice versa.
|
369 |
+
|
370 |
+
Parameters
|
371 |
+
----------
|
372 |
+
n : int or iterable
|
373 |
+
Number of nodes or iterable of nodes
|
374 |
+
theta: float
|
375 |
+
Threshold value
|
376 |
+
dim : int, optional
|
377 |
+
Dimension of graph
|
378 |
+
pos : dict
|
379 |
+
Node positions as a dictionary of tuples keyed by node.
|
380 |
+
weight : dict
|
381 |
+
Node weights as a dictionary of numbers keyed by node.
|
382 |
+
metric : function
|
383 |
+
A metric on vectors of numbers (represented as lists or
|
384 |
+
tuples). This must be a function that accepts two lists (or
|
385 |
+
tuples) as input and yields a number as output. The function
|
386 |
+
must also satisfy the four requirements of a `metric`_.
|
387 |
+
Specifically, if $d$ is the function and $x$, $y$,
|
388 |
+
and $z$ are vectors in the graph, then $d$ must satisfy
|
389 |
+
|
390 |
+
1. $d(x, y) \ge 0$,
|
391 |
+
2. $d(x, y) = 0$ if and only if $x = y$,
|
392 |
+
3. $d(x, y) = d(y, x)$,
|
393 |
+
4. $d(x, z) \le d(x, y) + d(y, z)$.
|
394 |
+
|
395 |
+
If this argument is not specified, the Euclidean distance metric is
|
396 |
+
used.
|
397 |
+
|
398 |
+
.. _metric: https://en.wikipedia.org/wiki/Metric_%28mathematics%29
|
399 |
+
p_dist : function, optional
|
400 |
+
Any function used to give weight to the distance between nodes when
|
401 |
+
deciding whether or not they should be connected. `p_dist` was
|
402 |
+
originally conceived as a probability density function giving the
|
403 |
+
probability of connecting two nodes that are of metric distance `r`
|
404 |
+
apart. The implementation here allows for more arbitrary definitions
|
405 |
+
of `p_dist` that do not need to correspond to valid probability
|
406 |
+
density functions. The :mod:`scipy.stats` package has many
|
407 |
+
probability density functions implemented and tools for custom
|
408 |
+
probability density definitions, and passing the ``.pdf`` method of
|
409 |
+
scipy.stats distributions can be used here. If ``p_dist=None``
|
410 |
+
(the default), the exponential function :math:`r^{-2}` is used.
|
411 |
+
seed : integer, random_state, or None (default)
|
412 |
+
Indicator of random number generation state.
|
413 |
+
See :ref:`Randomness<randomness>`.
|
414 |
+
pos_name : string, default="pos"
|
415 |
+
The name of the node attribute which represents the position
|
416 |
+
in 2D coordinates of the node in the returned graph.
|
417 |
+
weight_name : string, default="weight"
|
418 |
+
The name of the node attribute which represents the weight
|
419 |
+
of the node in the returned graph.
|
420 |
+
|
421 |
+
Returns
|
422 |
+
-------
|
423 |
+
Graph
|
424 |
+
A random geographic threshold graph, undirected and without
|
425 |
+
self-loops.
|
426 |
+
|
427 |
+
Each node has a node attribute ``pos`` that stores the
|
428 |
+
position of that node in Euclidean space as provided by the
|
429 |
+
``pos`` keyword argument or, if ``pos`` was not provided, as
|
430 |
+
generated by this function. Similarly, each node has a node
|
431 |
+
attribute ``weight`` that stores the weight of that node as
|
432 |
+
provided or as generated.
|
433 |
+
|
434 |
+
Examples
|
435 |
+
--------
|
436 |
+
Specify an alternate distance metric using the ``metric`` keyword
|
437 |
+
argument. For example, to use the `taxicab metric`_ instead of the
|
438 |
+
default `Euclidean metric`_::
|
439 |
+
|
440 |
+
>>> dist = lambda x, y: sum(abs(a - b) for a, b in zip(x, y))
|
441 |
+
>>> G = nx.geographical_threshold_graph(10, 0.1, metric=dist)
|
442 |
+
|
443 |
+
.. _taxicab metric: https://en.wikipedia.org/wiki/Taxicab_geometry
|
444 |
+
.. _Euclidean metric: https://en.wikipedia.org/wiki/Euclidean_distance
|
445 |
+
|
446 |
+
Notes
|
447 |
+
-----
|
448 |
+
If weights are not specified they are assigned to nodes by drawing randomly
|
449 |
+
from the exponential distribution with rate parameter $\lambda=1$.
|
450 |
+
To specify weights from a different distribution, use the `weight` keyword
|
451 |
+
argument::
|
452 |
+
|
453 |
+
>>> import random
|
454 |
+
>>> n = 20
|
455 |
+
>>> w = {i: random.expovariate(5.0) for i in range(n)}
|
456 |
+
>>> G = nx.geographical_threshold_graph(20, 50, weight=w)
|
457 |
+
|
458 |
+
If node positions are not specified they are randomly assigned from the
|
459 |
+
uniform distribution.
|
460 |
+
|
461 |
+
References
|
462 |
+
----------
|
463 |
+
.. [1] Masuda, N., Miwa, H., Konno, N.:
|
464 |
+
Geographical threshold graphs with small-world and scale-free
|
465 |
+
properties.
|
466 |
+
Physical Review E 71, 036108 (2005)
|
467 |
+
.. [2] Milan Bradonjić, Aric Hagberg and Allon G. Percus,
|
468 |
+
Giant component and connectivity in geographical threshold graphs,
|
469 |
+
in Algorithms and Models for the Web-Graph (WAW 2007),
|
470 |
+
Antony Bonato and Fan Chung (Eds), pp. 209--216, 2007
|
471 |
+
"""
|
472 |
+
G = nx.empty_graph(n)
|
473 |
+
# If no weights are provided, choose them from an exponential
|
474 |
+
# distribution.
|
475 |
+
if weight is None:
|
476 |
+
weight = {v: seed.expovariate(1) for v in G}
|
477 |
+
# If no positions are provided, choose uniformly random vectors in
|
478 |
+
# Euclidean space of the specified dimension.
|
479 |
+
if pos is None:
|
480 |
+
pos = {v: [seed.random() for i in range(dim)] for v in G}
|
481 |
+
# If no distance metric is provided, use Euclidean distance.
|
482 |
+
if metric is None:
|
483 |
+
metric = math.dist
|
484 |
+
nx.set_node_attributes(G, weight, weight_name)
|
485 |
+
nx.set_node_attributes(G, pos, pos_name)
|
486 |
+
|
487 |
+
# if p_dist is not supplied, use default r^-2
|
488 |
+
if p_dist is None:
|
489 |
+
|
490 |
+
def p_dist(r):
|
491 |
+
return r**-2
|
492 |
+
|
493 |
+
# Returns ``True`` if and only if the nodes whose attributes are
|
494 |
+
# ``du`` and ``dv`` should be joined, according to the threshold
|
495 |
+
# condition.
|
496 |
+
def should_join(pair):
|
497 |
+
u, v = pair
|
498 |
+
u_pos, v_pos = pos[u], pos[v]
|
499 |
+
u_weight, v_weight = weight[u], weight[v]
|
500 |
+
return (u_weight + v_weight) * p_dist(metric(u_pos, v_pos)) >= theta
|
501 |
+
|
502 |
+
G.add_edges_from(filter(should_join, combinations(G, 2)))
|
503 |
+
return G
|
504 |
+
|
505 |
+
|
506 |
+
@py_random_state(6)
|
507 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
508 |
+
def waxman_graph(
|
509 |
+
n,
|
510 |
+
beta=0.4,
|
511 |
+
alpha=0.1,
|
512 |
+
L=None,
|
513 |
+
domain=(0, 0, 1, 1),
|
514 |
+
metric=None,
|
515 |
+
seed=None,
|
516 |
+
*,
|
517 |
+
pos_name="pos",
|
518 |
+
):
|
519 |
+
r"""Returns a Waxman random graph.
|
520 |
+
|
521 |
+
The Waxman random graph model places `n` nodes uniformly at random
|
522 |
+
in a rectangular domain. Each pair of nodes at distance `d` is
|
523 |
+
joined by an edge with probability
|
524 |
+
|
525 |
+
.. math::
|
526 |
+
p = \beta \exp(-d / \alpha L).
|
527 |
+
|
528 |
+
This function implements both Waxman models, using the `L` keyword
|
529 |
+
argument.
|
530 |
+
|
531 |
+
* Waxman-1: if `L` is not specified, it is set to be the maximum distance
|
532 |
+
between any pair of nodes.
|
533 |
+
* Waxman-2: if `L` is specified, the distance between a pair of nodes is
|
534 |
+
chosen uniformly at random from the interval `[0, L]`.
|
535 |
+
|
536 |
+
Parameters
|
537 |
+
----------
|
538 |
+
n : int or iterable
|
539 |
+
Number of nodes or iterable of nodes
|
540 |
+
beta: float
|
541 |
+
Model parameter
|
542 |
+
alpha: float
|
543 |
+
Model parameter
|
544 |
+
L : float, optional
|
545 |
+
Maximum distance between nodes. If not specified, the actual distance
|
546 |
+
is calculated.
|
547 |
+
domain : four-tuple of numbers, optional
|
548 |
+
Domain size, given as a tuple of the form `(x_min, y_min, x_max,
|
549 |
+
y_max)`.
|
550 |
+
metric : function
|
551 |
+
A metric on vectors of numbers (represented as lists or
|
552 |
+
tuples). This must be a function that accepts two lists (or
|
553 |
+
tuples) as input and yields a number as output. The function
|
554 |
+
must also satisfy the four requirements of a `metric`_.
|
555 |
+
Specifically, if $d$ is the function and $x$, $y$,
|
556 |
+
and $z$ are vectors in the graph, then $d$ must satisfy
|
557 |
+
|
558 |
+
1. $d(x, y) \ge 0$,
|
559 |
+
2. $d(x, y) = 0$ if and only if $x = y$,
|
560 |
+
3. $d(x, y) = d(y, x)$,
|
561 |
+
4. $d(x, z) \le d(x, y) + d(y, z)$.
|
562 |
+
|
563 |
+
If this argument is not specified, the Euclidean distance metric is
|
564 |
+
used.
|
565 |
+
|
566 |
+
.. _metric: https://en.wikipedia.org/wiki/Metric_%28mathematics%29
|
567 |
+
|
568 |
+
seed : integer, random_state, or None (default)
|
569 |
+
Indicator of random number generation state.
|
570 |
+
See :ref:`Randomness<randomness>`.
|
571 |
+
pos_name : string, default="pos"
|
572 |
+
The name of the node attribute which represents the position
|
573 |
+
in 2D coordinates of the node in the returned graph.
|
574 |
+
|
575 |
+
Returns
|
576 |
+
-------
|
577 |
+
Graph
|
578 |
+
A random Waxman graph, undirected and without self-loops. Each
|
579 |
+
node has a node attribute ``'pos'`` that stores the position of
|
580 |
+
that node in Euclidean space as generated by this function.
|
581 |
+
|
582 |
+
Examples
|
583 |
+
--------
|
584 |
+
Specify an alternate distance metric using the ``metric`` keyword
|
585 |
+
argument. For example, to use the "`taxicab metric`_" instead of the
|
586 |
+
default `Euclidean metric`_::
|
587 |
+
|
588 |
+
>>> dist = lambda x, y: sum(abs(a - b) for a, b in zip(x, y))
|
589 |
+
>>> G = nx.waxman_graph(10, 0.5, 0.1, metric=dist)
|
590 |
+
|
591 |
+
.. _taxicab metric: https://en.wikipedia.org/wiki/Taxicab_geometry
|
592 |
+
.. _Euclidean metric: https://en.wikipedia.org/wiki/Euclidean_distance
|
593 |
+
|
594 |
+
Notes
|
595 |
+
-----
|
596 |
+
Starting in NetworkX 2.0 the parameters alpha and beta align with their
|
597 |
+
usual roles in the probability distribution. In earlier versions their
|
598 |
+
positions in the expression were reversed. Their position in the calling
|
599 |
+
sequence reversed as well to minimize backward incompatibility.
|
600 |
+
|
601 |
+
References
|
602 |
+
----------
|
603 |
+
.. [1] B. M. Waxman, *Routing of multipoint connections*.
|
604 |
+
IEEE J. Select. Areas Commun. 6(9),(1988) 1617--1622.
|
605 |
+
"""
|
606 |
+
G = nx.empty_graph(n)
|
607 |
+
(xmin, ymin, xmax, ymax) = domain
|
608 |
+
# Each node gets a uniformly random position in the given rectangle.
|
609 |
+
pos = {v: (seed.uniform(xmin, xmax), seed.uniform(ymin, ymax)) for v in G}
|
610 |
+
nx.set_node_attributes(G, pos, pos_name)
|
611 |
+
# If no distance metric is provided, use Euclidean distance.
|
612 |
+
if metric is None:
|
613 |
+
metric = math.dist
|
614 |
+
# If the maximum distance L is not specified (that is, we are in the
|
615 |
+
# Waxman-1 model), then find the maximum distance between any pair
|
616 |
+
# of nodes.
|
617 |
+
#
|
618 |
+
# In the Waxman-1 model, join nodes randomly based on distance. In
|
619 |
+
# the Waxman-2 model, join randomly based on random l.
|
620 |
+
if L is None:
|
621 |
+
L = max(metric(x, y) for x, y in combinations(pos.values(), 2))
|
622 |
+
|
623 |
+
def dist(u, v):
|
624 |
+
return metric(pos[u], pos[v])
|
625 |
+
|
626 |
+
else:
|
627 |
+
|
628 |
+
def dist(u, v):
|
629 |
+
return seed.random() * L
|
630 |
+
|
631 |
+
# `pair` is the pair of nodes to decide whether to join.
|
632 |
+
def should_join(pair):
|
633 |
+
return seed.random() < beta * math.exp(-dist(*pair) / (alpha * L))
|
634 |
+
|
635 |
+
G.add_edges_from(filter(should_join, combinations(G, 2)))
|
636 |
+
return G
|
637 |
+
|
638 |
+
|
639 |
+
@py_random_state(5)
|
640 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
641 |
+
def navigable_small_world_graph(n, p=1, q=1, r=2, dim=2, seed=None):
|
642 |
+
r"""Returns a navigable small-world graph.
|
643 |
+
|
644 |
+
A navigable small-world graph is a directed grid with additional long-range
|
645 |
+
connections that are chosen randomly.
|
646 |
+
|
647 |
+
[...] we begin with a set of nodes [...] that are identified with the set
|
648 |
+
of lattice points in an $n \times n$ square,
|
649 |
+
$\{(i, j): i \in \{1, 2, \ldots, n\}, j \in \{1, 2, \ldots, n\}\}$,
|
650 |
+
and we define the *lattice distance* between two nodes $(i, j)$ and
|
651 |
+
$(k, l)$ to be the number of "lattice steps" separating them:
|
652 |
+
$d((i, j), (k, l)) = |k - i| + |l - j|$.
|
653 |
+
|
654 |
+
For a universal constant $p >= 1$, the node $u$ has a directed edge to
|
655 |
+
every other node within lattice distance $p$---these are its *local
|
656 |
+
contacts*. For universal constants $q >= 0$ and $r >= 0$ we also
|
657 |
+
construct directed edges from $u$ to $q$ other nodes (the *long-range
|
658 |
+
contacts*) using independent random trials; the $i$th directed edge from
|
659 |
+
$u$ has endpoint $v$ with probability proportional to $[d(u,v)]^{-r}$.
|
660 |
+
|
661 |
+
-- [1]_
|
662 |
+
|
663 |
+
Parameters
|
664 |
+
----------
|
665 |
+
n : int
|
666 |
+
The length of one side of the lattice; the number of nodes in
|
667 |
+
the graph is therefore $n^2$.
|
668 |
+
p : int
|
669 |
+
The diameter of short range connections. Each node is joined with every
|
670 |
+
other node within this lattice distance.
|
671 |
+
q : int
|
672 |
+
The number of long-range connections for each node.
|
673 |
+
r : float
|
674 |
+
Exponent for decaying probability of connections. The probability of
|
675 |
+
connecting to a node at lattice distance $d$ is $1/d^r$.
|
676 |
+
dim : int
|
677 |
+
Dimension of grid
|
678 |
+
seed : integer, random_state, or None (default)
|
679 |
+
Indicator of random number generation state.
|
680 |
+
See :ref:`Randomness<randomness>`.
|
681 |
+
|
682 |
+
References
|
683 |
+
----------
|
684 |
+
.. [1] J. Kleinberg. The small-world phenomenon: An algorithmic
|
685 |
+
perspective. Proc. 32nd ACM Symposium on Theory of Computing, 2000.
|
686 |
+
"""
|
687 |
+
if p < 1:
|
688 |
+
raise nx.NetworkXException("p must be >= 1")
|
689 |
+
if q < 0:
|
690 |
+
raise nx.NetworkXException("q must be >= 0")
|
691 |
+
if r < 0:
|
692 |
+
raise nx.NetworkXException("r must be >= 0")
|
693 |
+
|
694 |
+
G = nx.DiGraph()
|
695 |
+
nodes = list(product(range(n), repeat=dim))
|
696 |
+
for p1 in nodes:
|
697 |
+
probs = [0]
|
698 |
+
for p2 in nodes:
|
699 |
+
if p1 == p2:
|
700 |
+
continue
|
701 |
+
d = sum((abs(b - a) for a, b in zip(p1, p2)))
|
702 |
+
if d <= p:
|
703 |
+
G.add_edge(p1, p2)
|
704 |
+
probs.append(d**-r)
|
705 |
+
cdf = list(accumulate(probs))
|
706 |
+
for _ in range(q):
|
707 |
+
target = nodes[bisect_left(cdf, seed.uniform(0, cdf[-1]))]
|
708 |
+
G.add_edge(p1, target)
|
709 |
+
return G
|
710 |
+
|
711 |
+
|
712 |
+
@py_random_state(7)
|
713 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
714 |
+
def thresholded_random_geometric_graph(
|
715 |
+
n,
|
716 |
+
radius,
|
717 |
+
theta,
|
718 |
+
dim=2,
|
719 |
+
pos=None,
|
720 |
+
weight=None,
|
721 |
+
p=2,
|
722 |
+
seed=None,
|
723 |
+
*,
|
724 |
+
pos_name="pos",
|
725 |
+
weight_name="weight",
|
726 |
+
):
|
727 |
+
r"""Returns a thresholded random geometric graph in the unit cube.
|
728 |
+
|
729 |
+
The thresholded random geometric graph [1] model places `n` nodes
|
730 |
+
uniformly at random in the unit cube of dimensions `dim`. Each node
|
731 |
+
`u` is assigned a weight :math:`w_u`. Two nodes `u` and `v` are
|
732 |
+
joined by an edge if they are within the maximum connection distance,
|
733 |
+
`radius` computed by the `p`-Minkowski distance and the summation of
|
734 |
+
weights :math:`w_u` + :math:`w_v` is greater than or equal
|
735 |
+
to the threshold parameter `theta`.
|
736 |
+
|
737 |
+
Edges within `radius` of each other are determined using a KDTree when
|
738 |
+
SciPy is available. This reduces the time complexity from :math:`O(n^2)`
|
739 |
+
to :math:`O(n)`.
|
740 |
+
|
741 |
+
Parameters
|
742 |
+
----------
|
743 |
+
n : int or iterable
|
744 |
+
Number of nodes or iterable of nodes
|
745 |
+
radius: float
|
746 |
+
Distance threshold value
|
747 |
+
theta: float
|
748 |
+
Threshold value
|
749 |
+
dim : int, optional
|
750 |
+
Dimension of graph
|
751 |
+
pos : dict, optional
|
752 |
+
A dictionary keyed by node with node positions as values.
|
753 |
+
weight : dict, optional
|
754 |
+
Node weights as a dictionary of numbers keyed by node.
|
755 |
+
p : float, optional (default 2)
|
756 |
+
Which Minkowski distance metric to use. `p` has to meet the condition
|
757 |
+
``1 <= p <= infinity``.
|
758 |
+
|
759 |
+
If this argument is not specified, the :math:`L^2` metric
|
760 |
+
(the Euclidean distance metric), p = 2 is used.
|
761 |
+
|
762 |
+
This should not be confused with the `p` of an Erdős-Rényi random
|
763 |
+
graph, which represents probability.
|
764 |
+
seed : integer, random_state, or None (default)
|
765 |
+
Indicator of random number generation state.
|
766 |
+
See :ref:`Randomness<randomness>`.
|
767 |
+
pos_name : string, default="pos"
|
768 |
+
The name of the node attribute which represents the position
|
769 |
+
in 2D coordinates of the node in the returned graph.
|
770 |
+
weight_name : string, default="weight"
|
771 |
+
The name of the node attribute which represents the weight
|
772 |
+
of the node in the returned graph.
|
773 |
+
|
774 |
+
Returns
|
775 |
+
-------
|
776 |
+
Graph
|
777 |
+
A thresholded random geographic graph, undirected and without
|
778 |
+
self-loops.
|
779 |
+
|
780 |
+
Each node has a node attribute ``'pos'`` that stores the
|
781 |
+
position of that node in Euclidean space as provided by the
|
782 |
+
``pos`` keyword argument or, if ``pos`` was not provided, as
|
783 |
+
generated by this function. Similarly, each node has a nodethre
|
784 |
+
attribute ``'weight'`` that stores the weight of that node as
|
785 |
+
provided or as generated.
|
786 |
+
|
787 |
+
Examples
|
788 |
+
--------
|
789 |
+
Default Graph:
|
790 |
+
|
791 |
+
G = nx.thresholded_random_geometric_graph(50, 0.2, 0.1)
|
792 |
+
|
793 |
+
Custom Graph:
|
794 |
+
|
795 |
+
Create a thresholded random geometric graph on 50 uniformly distributed
|
796 |
+
nodes where nodes are joined by an edge if their sum weights drawn from
|
797 |
+
a exponential distribution with rate = 5 are >= theta = 0.1 and their
|
798 |
+
Euclidean distance is at most 0.2.
|
799 |
+
|
800 |
+
Notes
|
801 |
+
-----
|
802 |
+
This uses a *k*-d tree to build the graph.
|
803 |
+
|
804 |
+
The `pos` keyword argument can be used to specify node positions so you
|
805 |
+
can create an arbitrary distribution and domain for positions.
|
806 |
+
|
807 |
+
For example, to use a 2D Gaussian distribution of node positions with mean
|
808 |
+
(0, 0) and standard deviation 2
|
809 |
+
|
810 |
+
If weights are not specified they are assigned to nodes by drawing randomly
|
811 |
+
from the exponential distribution with rate parameter :math:`\lambda=1`.
|
812 |
+
To specify weights from a different distribution, use the `weight` keyword
|
813 |
+
argument::
|
814 |
+
|
815 |
+
::
|
816 |
+
|
817 |
+
>>> import random
|
818 |
+
>>> import math
|
819 |
+
>>> n = 50
|
820 |
+
>>> pos = {i: (random.gauss(0, 2), random.gauss(0, 2)) for i in range(n)}
|
821 |
+
>>> w = {i: random.expovariate(5.0) for i in range(n)}
|
822 |
+
>>> G = nx.thresholded_random_geometric_graph(n, 0.2, 0.1, 2, pos, w)
|
823 |
+
|
824 |
+
References
|
825 |
+
----------
|
826 |
+
.. [1] http://cole-maclean.github.io/blog/files/thesis.pdf
|
827 |
+
|
828 |
+
"""
|
829 |
+
G = nx.empty_graph(n)
|
830 |
+
G.name = f"thresholded_random_geometric_graph({n}, {radius}, {theta}, {dim})"
|
831 |
+
# If no weights are provided, choose them from an exponential
|
832 |
+
# distribution.
|
833 |
+
if weight is None:
|
834 |
+
weight = {v: seed.expovariate(1) for v in G}
|
835 |
+
# If no positions are provided, choose uniformly random vectors in
|
836 |
+
# Euclidean space of the specified dimension.
|
837 |
+
if pos is None:
|
838 |
+
pos = {v: [seed.random() for i in range(dim)] for v in G}
|
839 |
+
# If no distance metric is provided, use Euclidean distance.
|
840 |
+
nx.set_node_attributes(G, weight, weight_name)
|
841 |
+
nx.set_node_attributes(G, pos, pos_name)
|
842 |
+
|
843 |
+
edges = (
|
844 |
+
(u, v)
|
845 |
+
for u, v in _geometric_edges(G, radius, p, pos_name)
|
846 |
+
if weight[u] + weight[v] >= theta
|
847 |
+
)
|
848 |
+
G.add_edges_from(edges)
|
849 |
+
return G
|
850 |
+
|
851 |
+
|
852 |
+
@py_random_state(5)
|
853 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
854 |
+
def geometric_soft_configuration_graph(
|
855 |
+
*, beta, n=None, gamma=None, mean_degree=None, kappas=None, seed=None
|
856 |
+
):
|
857 |
+
r"""Returns a random graph from the geometric soft configuration model.
|
858 |
+
|
859 |
+
The $\mathbb{S}^1$ model [1]_ is the geometric soft configuration model
|
860 |
+
which is able to explain many fundamental features of real networks such as
|
861 |
+
small-world property, heteregenous degree distributions, high level of
|
862 |
+
clustering, and self-similarity.
|
863 |
+
|
864 |
+
In the geometric soft configuration model, a node $i$ is assigned two hidden
|
865 |
+
variables: a hidden degree $\kappa_i$, quantifying its popularity, influence,
|
866 |
+
or importance, and an angular position $\theta_i$ in a circle abstracting the
|
867 |
+
similarity space, where angular distances between nodes are a proxy for their
|
868 |
+
similarity. Focusing on the angular position, this model is often called
|
869 |
+
the $\mathbb{S}^1$ model (a one-dimensional sphere). The circle's radius is
|
870 |
+
adjusted to $R = N/2\pi$, where $N$ is the number of nodes, so that the density
|
871 |
+
is set to 1 without loss of generality.
|
872 |
+
|
873 |
+
The connection probability between any pair of nodes increases with
|
874 |
+
the product of their hidden degrees (i.e., their combined popularities),
|
875 |
+
and decreases with the angular distance between the two nodes.
|
876 |
+
Specifically, nodes $i$ and $j$ are connected with the probability
|
877 |
+
|
878 |
+
$p_{ij} = \frac{1}{1 + \frac{d_{ij}^\beta}{\left(\mu \kappa_i \kappa_j\right)^{\max(1, \beta)}}}$
|
879 |
+
|
880 |
+
where $d_{ij} = R\Delta\theta_{ij}$ is the arc length of the circle between
|
881 |
+
nodes $i$ and $j$ separated by an angular distance $\Delta\theta_{ij}$.
|
882 |
+
Parameters $\mu$ and $\beta$ (also called inverse temperature) control the
|
883 |
+
average degree and the clustering coefficient, respectively.
|
884 |
+
|
885 |
+
It can be shown [2]_ that the model undergoes a structural phase transition
|
886 |
+
at $\beta=1$ so that for $\beta<1$ networks are unclustered in the thermodynamic
|
887 |
+
limit (when $N\to \infty$) whereas for $\beta>1$ the ensemble generates
|
888 |
+
networks with finite clustering coefficient.
|
889 |
+
|
890 |
+
The $\mathbb{S}^1$ model can be expressed as a purely geometric model
|
891 |
+
$\mathbb{H}^2$ in the hyperbolic plane [3]_ by mapping the hidden degree of
|
892 |
+
each node into a radial coordinate as
|
893 |
+
|
894 |
+
$r_i = \hat{R} - \frac{2 \max(1, \beta)}{\beta \zeta} \ln \left(\frac{\kappa_i}{\kappa_0}\right)$
|
895 |
+
|
896 |
+
where $\hat{R}$ is the radius of the hyperbolic disk and $\zeta$ is the curvature,
|
897 |
+
|
898 |
+
$\hat{R} = \frac{2}{\zeta} \ln \left(\frac{N}{\pi}\right)
|
899 |
+
- \frac{2\max(1, \beta)}{\beta \zeta} \ln (\mu \kappa_0^2)$
|
900 |
+
|
901 |
+
The connection probability then reads
|
902 |
+
|
903 |
+
$p_{ij} = \frac{1}{1 + \exp\left({\frac{\beta\zeta}{2} (x_{ij} - \hat{R})}\right)}$
|
904 |
+
|
905 |
+
where
|
906 |
+
|
907 |
+
$x_{ij} = r_i + r_j + \frac{2}{\zeta} \ln \frac{\Delta\theta_{ij}}{2}$
|
908 |
+
|
909 |
+
is a good approximation of the hyperbolic distance between two nodes separated
|
910 |
+
by an angular distance $\Delta\theta_{ij}$ with radial coordinates $r_i$ and $r_j$.
|
911 |
+
For $\beta > 1$, the curvature $\zeta = 1$, for $\beta < 1$, $\zeta = \beta^{-1}$.
|
912 |
+
|
913 |
+
|
914 |
+
Parameters
|
915 |
+
----------
|
916 |
+
Either `n`, `gamma`, `mean_degree` are provided or `kappas`. The values of
|
917 |
+
`n`, `gamma`, `mean_degree` (if provided) are used to construct a random
|
918 |
+
kappa-dict keyed by node with values sampled from a power-law distribution.
|
919 |
+
|
920 |
+
beta : positive number
|
921 |
+
Inverse temperature, controlling the clustering coefficient.
|
922 |
+
n : int (default: None)
|
923 |
+
Size of the network (number of nodes).
|
924 |
+
If not provided, `kappas` must be provided and holds the nodes.
|
925 |
+
gamma : float (default: None)
|
926 |
+
Exponent of the power-law distribution for hidden degrees `kappas`.
|
927 |
+
If not provided, `kappas` must be provided directly.
|
928 |
+
mean_degree : float (default: None)
|
929 |
+
The mean degree in the network.
|
930 |
+
If not provided, `kappas` must be provided directly.
|
931 |
+
kappas : dict (default: None)
|
932 |
+
A dict keyed by node to its hidden degree value.
|
933 |
+
If not provided, random values are computed based on a power-law
|
934 |
+
distribution using `n`, `gamma` and `mean_degree`.
|
935 |
+
seed : int, random_state, or None (default)
|
936 |
+
Indicator of random number generation state.
|
937 |
+
See :ref:`Randomness<randomness>`.
|
938 |
+
|
939 |
+
Returns
|
940 |
+
-------
|
941 |
+
Graph
|
942 |
+
A random geometric soft configuration graph (undirected with no self-loops).
|
943 |
+
Each node has three node-attributes:
|
944 |
+
|
945 |
+
- ``kappa`` that represents the hidden degree.
|
946 |
+
|
947 |
+
- ``theta`` the position in the similarity space ($\mathbb{S}^1$) which is
|
948 |
+
also the angular position in the hyperbolic plane.
|
949 |
+
|
950 |
+
- ``radius`` the radial position in the hyperbolic plane
|
951 |
+
(based on the hidden degree).
|
952 |
+
|
953 |
+
|
954 |
+
Examples
|
955 |
+
--------
|
956 |
+
Generate a network with specified parameters:
|
957 |
+
|
958 |
+
>>> G = nx.geometric_soft_configuration_graph(beta=1.5, n=100, gamma=2.7, mean_degree=5)
|
959 |
+
|
960 |
+
Create a geometric soft configuration graph with 100 nodes. The $\beta$ parameter
|
961 |
+
is set to 1.5 and the exponent of the powerlaw distribution of the hidden
|
962 |
+
degrees is 2.7 with mean value of 5.
|
963 |
+
|
964 |
+
Generate a network with predefined hidden degrees:
|
965 |
+
|
966 |
+
>>> kappas = {i: 10 for i in range(100)}
|
967 |
+
>>> G = nx.geometric_soft_configuration_graph(beta=2.5, kappas=kappas)
|
968 |
+
|
969 |
+
Create a geometric soft configuration graph with 100 nodes. The $\beta$ parameter
|
970 |
+
is set to 2.5 and all nodes with hidden degree $\kappa=10$.
|
971 |
+
|
972 |
+
|
973 |
+
References
|
974 |
+
----------
|
975 |
+
.. [1] Serrano, M. Á., Krioukov, D., & Boguñá, M. (2008). Self-similarity
|
976 |
+
of complex networks and hidden metric spaces. Physical review letters, 100(7), 078701.
|
977 |
+
|
978 |
+
.. [2] van der Kolk, J., Serrano, M. Á., & Boguñá, M. (2022). An anomalous
|
979 |
+
topological phase transition in spatial random graphs. Communications Physics, 5(1), 245.
|
980 |
+
|
981 |
+
.. [3] Krioukov, D., Papadopoulos, F., Kitsak, M., Vahdat, A., & Boguná, M. (2010).
|
982 |
+
Hyperbolic geometry of complex networks. Physical Review E, 82(3), 036106.
|
983 |
+
|
984 |
+
"""
|
985 |
+
if beta <= 0:
|
986 |
+
raise nx.NetworkXError("The parameter beta cannot be smaller or equal to 0.")
|
987 |
+
|
988 |
+
if kappas is not None:
|
989 |
+
if not all((n is None, gamma is None, mean_degree is None)):
|
990 |
+
raise nx.NetworkXError(
|
991 |
+
"When kappas is input, n, gamma and mean_degree must not be."
|
992 |
+
)
|
993 |
+
|
994 |
+
n = len(kappas)
|
995 |
+
mean_degree = sum(kappas) / len(kappas)
|
996 |
+
else:
|
997 |
+
if any((n is None, gamma is None, mean_degree is None)):
|
998 |
+
raise nx.NetworkXError(
|
999 |
+
"Please provide either kappas, or all 3 of: n, gamma and mean_degree."
|
1000 |
+
)
|
1001 |
+
|
1002 |
+
# Generate `n` hidden degrees from a powerlaw distribution
|
1003 |
+
# with given exponent `gamma` and mean value `mean_degree`
|
1004 |
+
gam_ratio = (gamma - 2) / (gamma - 1)
|
1005 |
+
kappa_0 = mean_degree * gam_ratio * (1 - 1 / n) / (1 - 1 / n**gam_ratio)
|
1006 |
+
base = 1 - 1 / n
|
1007 |
+
power = 1 / (1 - gamma)
|
1008 |
+
kappas = {i: kappa_0 * (1 - seed.random() * base) ** power for i in range(n)}
|
1009 |
+
|
1010 |
+
G = nx.Graph()
|
1011 |
+
R = n / (2 * math.pi)
|
1012 |
+
|
1013 |
+
# Approximate values for mu in the thermodynamic limit (when n -> infinity)
|
1014 |
+
if beta > 1:
|
1015 |
+
mu = beta * math.sin(math.pi / beta) / (2 * math.pi * mean_degree)
|
1016 |
+
elif beta == 1:
|
1017 |
+
mu = 1 / (2 * mean_degree * math.log(n))
|
1018 |
+
else:
|
1019 |
+
mu = (1 - beta) / (2**beta * mean_degree * n ** (1 - beta))
|
1020 |
+
|
1021 |
+
# Generate random positions on a circle
|
1022 |
+
thetas = {k: seed.uniform(0, 2 * math.pi) for k in kappas}
|
1023 |
+
|
1024 |
+
for u in kappas:
|
1025 |
+
for v in list(G):
|
1026 |
+
angle = math.pi - math.fabs(math.pi - math.fabs(thetas[u] - thetas[v]))
|
1027 |
+
dij = math.pow(R * angle, beta)
|
1028 |
+
mu_kappas = math.pow(mu * kappas[u] * kappas[v], max(1, beta))
|
1029 |
+
p_ij = 1 / (1 + dij / mu_kappas)
|
1030 |
+
|
1031 |
+
# Create an edge with a certain connection probability
|
1032 |
+
if seed.random() < p_ij:
|
1033 |
+
G.add_edge(u, v)
|
1034 |
+
G.add_node(u)
|
1035 |
+
|
1036 |
+
nx.set_node_attributes(G, thetas, "theta")
|
1037 |
+
nx.set_node_attributes(G, kappas, "kappa")
|
1038 |
+
|
1039 |
+
# Map hidden degrees into the radial coordiantes
|
1040 |
+
zeta = 1 if beta > 1 else 1 / beta
|
1041 |
+
kappa_min = min(kappas.values())
|
1042 |
+
R_c = 2 * max(1, beta) / (beta * zeta)
|
1043 |
+
R_hat = (2 / zeta) * math.log(n / math.pi) - R_c * math.log(mu * kappa_min)
|
1044 |
+
radii = {node: R_hat - R_c * math.log(kappa) for node, kappa in kappas.items()}
|
1045 |
+
nx.set_node_attributes(G, radii, "radius")
|
1046 |
+
|
1047 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/harary_graph.py
ADDED
@@ -0,0 +1,199 @@
|
|
|
|
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|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""Generators for Harary graphs
|
2 |
+
|
3 |
+
This module gives two generators for the Harary graph, which was
|
4 |
+
introduced by the famous mathematician Frank Harary in his 1962 work [H]_.
|
5 |
+
The first generator gives the Harary graph that maximizes the node
|
6 |
+
connectivity with given number of nodes and given number of edges.
|
7 |
+
The second generator gives the Harary graph that minimizes
|
8 |
+
the number of edges in the graph with given node connectivity and
|
9 |
+
number of nodes.
|
10 |
+
|
11 |
+
References
|
12 |
+
----------
|
13 |
+
.. [H] Harary, F. "The Maximum Connectivity of a Graph."
|
14 |
+
Proc. Nat. Acad. Sci. USA 48, 1142-1146, 1962.
|
15 |
+
|
16 |
+
"""
|
17 |
+
|
18 |
+
import networkx as nx
|
19 |
+
from networkx.exception import NetworkXError
|
20 |
+
|
21 |
+
__all__ = ["hnm_harary_graph", "hkn_harary_graph"]
|
22 |
+
|
23 |
+
|
24 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
25 |
+
def hnm_harary_graph(n, m, create_using=None):
|
26 |
+
"""Returns the Harary graph with given numbers of nodes and edges.
|
27 |
+
|
28 |
+
The Harary graph $H_{n,m}$ is the graph that maximizes node connectivity
|
29 |
+
with $n$ nodes and $m$ edges.
|
30 |
+
|
31 |
+
This maximum node connectivity is known to be floor($2m/n$). [1]_
|
32 |
+
|
33 |
+
Parameters
|
34 |
+
----------
|
35 |
+
n: integer
|
36 |
+
The number of nodes the generated graph is to contain
|
37 |
+
|
38 |
+
m: integer
|
39 |
+
The number of edges the generated graph is to contain
|
40 |
+
|
41 |
+
create_using : NetworkX graph constructor, optional Graph type
|
42 |
+
to create (default=nx.Graph). If graph instance, then cleared
|
43 |
+
before populated.
|
44 |
+
|
45 |
+
Returns
|
46 |
+
-------
|
47 |
+
NetworkX graph
|
48 |
+
The Harary graph $H_{n,m}$.
|
49 |
+
|
50 |
+
See Also
|
51 |
+
--------
|
52 |
+
hkn_harary_graph
|
53 |
+
|
54 |
+
Notes
|
55 |
+
-----
|
56 |
+
This algorithm runs in $O(m)$ time.
|
57 |
+
It is implemented by following the Reference [2]_.
|
58 |
+
|
59 |
+
References
|
60 |
+
----------
|
61 |
+
.. [1] F. T. Boesch, A. Satyanarayana, and C. L. Suffel,
|
62 |
+
"A Survey of Some Network Reliability Analysis and Synthesis Results,"
|
63 |
+
Networks, pp. 99-107, 2009.
|
64 |
+
|
65 |
+
.. [2] Harary, F. "The Maximum Connectivity of a Graph."
|
66 |
+
Proc. Nat. Acad. Sci. USA 48, 1142-1146, 1962.
|
67 |
+
"""
|
68 |
+
|
69 |
+
if n < 1:
|
70 |
+
raise NetworkXError("The number of nodes must be >= 1!")
|
71 |
+
if m < n - 1:
|
72 |
+
raise NetworkXError("The number of edges must be >= n - 1 !")
|
73 |
+
if m > n * (n - 1) // 2:
|
74 |
+
raise NetworkXError("The number of edges must be <= n(n-1)/2")
|
75 |
+
|
76 |
+
# Construct an empty graph with n nodes first
|
77 |
+
H = nx.empty_graph(n, create_using)
|
78 |
+
# Get the floor of average node degree
|
79 |
+
d = 2 * m // n
|
80 |
+
|
81 |
+
# Test the parity of n and d
|
82 |
+
if (n % 2 == 0) or (d % 2 == 0):
|
83 |
+
# Start with a regular graph of d degrees
|
84 |
+
offset = d // 2
|
85 |
+
for i in range(n):
|
86 |
+
for j in range(1, offset + 1):
|
87 |
+
H.add_edge(i, (i - j) % n)
|
88 |
+
H.add_edge(i, (i + j) % n)
|
89 |
+
if d & 1:
|
90 |
+
# in case d is odd; n must be even in this case
|
91 |
+
half = n // 2
|
92 |
+
for i in range(half):
|
93 |
+
# add edges diagonally
|
94 |
+
H.add_edge(i, i + half)
|
95 |
+
# Get the remainder of 2*m modulo n
|
96 |
+
r = 2 * m % n
|
97 |
+
if r > 0:
|
98 |
+
# add remaining edges at offset+1
|
99 |
+
for i in range(r // 2):
|
100 |
+
H.add_edge(i, i + offset + 1)
|
101 |
+
else:
|
102 |
+
# Start with a regular graph of (d - 1) degrees
|
103 |
+
offset = (d - 1) // 2
|
104 |
+
for i in range(n):
|
105 |
+
for j in range(1, offset + 1):
|
106 |
+
H.add_edge(i, (i - j) % n)
|
107 |
+
H.add_edge(i, (i + j) % n)
|
108 |
+
half = n // 2
|
109 |
+
for i in range(m - n * offset):
|
110 |
+
# add the remaining m - n*offset edges between i and i+half
|
111 |
+
H.add_edge(i, (i + half) % n)
|
112 |
+
|
113 |
+
return H
|
114 |
+
|
115 |
+
|
116 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
117 |
+
def hkn_harary_graph(k, n, create_using=None):
|
118 |
+
"""Returns the Harary graph with given node connectivity and node number.
|
119 |
+
|
120 |
+
The Harary graph $H_{k,n}$ is the graph that minimizes the number of
|
121 |
+
edges needed with given node connectivity $k$ and node number $n$.
|
122 |
+
|
123 |
+
This smallest number of edges is known to be ceil($kn/2$) [1]_.
|
124 |
+
|
125 |
+
Parameters
|
126 |
+
----------
|
127 |
+
k: integer
|
128 |
+
The node connectivity of the generated graph
|
129 |
+
|
130 |
+
n: integer
|
131 |
+
The number of nodes the generated graph is to contain
|
132 |
+
|
133 |
+
create_using : NetworkX graph constructor, optional Graph type
|
134 |
+
to create (default=nx.Graph). If graph instance, then cleared
|
135 |
+
before populated.
|
136 |
+
|
137 |
+
Returns
|
138 |
+
-------
|
139 |
+
NetworkX graph
|
140 |
+
The Harary graph $H_{k,n}$.
|
141 |
+
|
142 |
+
See Also
|
143 |
+
--------
|
144 |
+
hnm_harary_graph
|
145 |
+
|
146 |
+
Notes
|
147 |
+
-----
|
148 |
+
This algorithm runs in $O(kn)$ time.
|
149 |
+
It is implemented by following the Reference [2]_.
|
150 |
+
|
151 |
+
References
|
152 |
+
----------
|
153 |
+
.. [1] Weisstein, Eric W. "Harary Graph." From MathWorld--A Wolfram Web
|
154 |
+
Resource. http://mathworld.wolfram.com/HararyGraph.html.
|
155 |
+
|
156 |
+
.. [2] Harary, F. "The Maximum Connectivity of a Graph."
|
157 |
+
Proc. Nat. Acad. Sci. USA 48, 1142-1146, 1962.
|
158 |
+
"""
|
159 |
+
|
160 |
+
if k < 1:
|
161 |
+
raise NetworkXError("The node connectivity must be >= 1!")
|
162 |
+
if n < k + 1:
|
163 |
+
raise NetworkXError("The number of nodes must be >= k+1 !")
|
164 |
+
|
165 |
+
# in case of connectivity 1, simply return the path graph
|
166 |
+
if k == 1:
|
167 |
+
H = nx.path_graph(n, create_using)
|
168 |
+
return H
|
169 |
+
|
170 |
+
# Construct an empty graph with n nodes first
|
171 |
+
H = nx.empty_graph(n, create_using)
|
172 |
+
|
173 |
+
# Test the parity of k and n
|
174 |
+
if (k % 2 == 0) or (n % 2 == 0):
|
175 |
+
# Construct a regular graph with k degrees
|
176 |
+
offset = k // 2
|
177 |
+
for i in range(n):
|
178 |
+
for j in range(1, offset + 1):
|
179 |
+
H.add_edge(i, (i - j) % n)
|
180 |
+
H.add_edge(i, (i + j) % n)
|
181 |
+
if k & 1:
|
182 |
+
# odd degree; n must be even in this case
|
183 |
+
half = n // 2
|
184 |
+
for i in range(half):
|
185 |
+
# add edges diagonally
|
186 |
+
H.add_edge(i, i + half)
|
187 |
+
else:
|
188 |
+
# Construct a regular graph with (k - 1) degrees
|
189 |
+
offset = (k - 1) // 2
|
190 |
+
for i in range(n):
|
191 |
+
for j in range(1, offset + 1):
|
192 |
+
H.add_edge(i, (i - j) % n)
|
193 |
+
H.add_edge(i, (i + j) % n)
|
194 |
+
half = n // 2
|
195 |
+
for i in range(half + 1):
|
196 |
+
# add half+1 edges between i and i+half
|
197 |
+
H.add_edge(i, (i + half) % n)
|
198 |
+
|
199 |
+
return H
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/internet_as_graphs.py
ADDED
@@ -0,0 +1,441 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
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|
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|
|
|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
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|
|
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|
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|
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|
|
|
|
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|
|
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|
|
|
|
|
|
|
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|
|
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|
|
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|
|
|
|
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|
|
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|
|
|
|
|
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|
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|
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|
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|
1 |
+
"""Generates graphs resembling the Internet Autonomous System network"""
|
2 |
+
|
3 |
+
import networkx as nx
|
4 |
+
from networkx.utils import py_random_state
|
5 |
+
|
6 |
+
__all__ = ["random_internet_as_graph"]
|
7 |
+
|
8 |
+
|
9 |
+
def uniform_int_from_avg(a, m, seed):
|
10 |
+
"""Pick a random integer with uniform probability.
|
11 |
+
|
12 |
+
Returns a random integer uniformly taken from a distribution with
|
13 |
+
minimum value 'a' and average value 'm', X~U(a,b), E[X]=m, X in N where
|
14 |
+
b = 2*m - a.
|
15 |
+
|
16 |
+
Notes
|
17 |
+
-----
|
18 |
+
p = (b-floor(b))/2
|
19 |
+
X = X1 + X2; X1~U(a,floor(b)), X2~B(p)
|
20 |
+
E[X] = E[X1] + E[X2] = (floor(b)+a)/2 + (b-floor(b))/2 = (b+a)/2 = m
|
21 |
+
"""
|
22 |
+
|
23 |
+
from math import floor
|
24 |
+
|
25 |
+
assert m >= a
|
26 |
+
b = 2 * m - a
|
27 |
+
p = (b - floor(b)) / 2
|
28 |
+
X1 = round(seed.random() * (floor(b) - a) + a)
|
29 |
+
if seed.random() < p:
|
30 |
+
X2 = 1
|
31 |
+
else:
|
32 |
+
X2 = 0
|
33 |
+
return X1 + X2
|
34 |
+
|
35 |
+
|
36 |
+
def choose_pref_attach(degs, seed):
|
37 |
+
"""Pick a random value, with a probability given by its weight.
|
38 |
+
|
39 |
+
Returns a random choice among degs keys, each of which has a
|
40 |
+
probability proportional to the corresponding dictionary value.
|
41 |
+
|
42 |
+
Parameters
|
43 |
+
----------
|
44 |
+
degs: dictionary
|
45 |
+
It contains the possible values (keys) and the corresponding
|
46 |
+
probabilities (values)
|
47 |
+
seed: random state
|
48 |
+
|
49 |
+
Returns
|
50 |
+
-------
|
51 |
+
v: object
|
52 |
+
A key of degs or None if degs is empty
|
53 |
+
"""
|
54 |
+
|
55 |
+
if len(degs) == 0:
|
56 |
+
return None
|
57 |
+
s = sum(degs.values())
|
58 |
+
if s == 0:
|
59 |
+
return seed.choice(list(degs.keys()))
|
60 |
+
v = seed.random() * s
|
61 |
+
|
62 |
+
nodes = list(degs.keys())
|
63 |
+
i = 0
|
64 |
+
acc = degs[nodes[i]]
|
65 |
+
while v > acc:
|
66 |
+
i += 1
|
67 |
+
acc += degs[nodes[i]]
|
68 |
+
return nodes[i]
|
69 |
+
|
70 |
+
|
71 |
+
class AS_graph_generator:
|
72 |
+
"""Generates random internet AS graphs."""
|
73 |
+
|
74 |
+
def __init__(self, n, seed):
|
75 |
+
"""Initializes variables. Immediate numbers are taken from [1].
|
76 |
+
|
77 |
+
Parameters
|
78 |
+
----------
|
79 |
+
n: integer
|
80 |
+
Number of graph nodes
|
81 |
+
seed: random state
|
82 |
+
Indicator of random number generation state.
|
83 |
+
See :ref:`Randomness<randomness>`.
|
84 |
+
|
85 |
+
Returns
|
86 |
+
-------
|
87 |
+
GG: AS_graph_generator object
|
88 |
+
|
89 |
+
References
|
90 |
+
----------
|
91 |
+
[1] A. Elmokashfi, A. Kvalbein and C. Dovrolis, "On the Scalability of
|
92 |
+
BGP: The Role of Topology Growth," in IEEE Journal on Selected Areas
|
93 |
+
in Communications, vol. 28, no. 8, pp. 1250-1261, October 2010.
|
94 |
+
"""
|
95 |
+
|
96 |
+
self.seed = seed
|
97 |
+
self.n_t = min(n, round(self.seed.random() * 2 + 4)) # num of T nodes
|
98 |
+
self.n_m = round(0.15 * n) # number of M nodes
|
99 |
+
self.n_cp = round(0.05 * n) # number of CP nodes
|
100 |
+
self.n_c = max(0, n - self.n_t - self.n_m - self.n_cp) # number of C nodes
|
101 |
+
|
102 |
+
self.d_m = 2 + (2.5 * n) / 10000 # average multihoming degree for M nodes
|
103 |
+
self.d_cp = 2 + (1.5 * n) / 10000 # avg multihoming degree for CP nodes
|
104 |
+
self.d_c = 1 + (5 * n) / 100000 # average multihoming degree for C nodes
|
105 |
+
|
106 |
+
self.p_m_m = 1 + (2 * n) / 10000 # avg num of peer edges between M and M
|
107 |
+
self.p_cp_m = 0.2 + (2 * n) / 10000 # avg num of peer edges between CP, M
|
108 |
+
self.p_cp_cp = 0.05 + (2 * n) / 100000 # avg num of peer edges btwn CP, CP
|
109 |
+
|
110 |
+
self.t_m = 0.375 # probability M's provider is T
|
111 |
+
self.t_cp = 0.375 # probability CP's provider is T
|
112 |
+
self.t_c = 0.125 # probability C's provider is T
|
113 |
+
|
114 |
+
def t_graph(self):
|
115 |
+
"""Generates the core mesh network of tier one nodes of a AS graph.
|
116 |
+
|
117 |
+
Returns
|
118 |
+
-------
|
119 |
+
G: Networkx Graph
|
120 |
+
Core network
|
121 |
+
"""
|
122 |
+
|
123 |
+
self.G = nx.Graph()
|
124 |
+
for i in range(self.n_t):
|
125 |
+
self.G.add_node(i, type="T")
|
126 |
+
for r in self.regions:
|
127 |
+
self.regions[r].add(i)
|
128 |
+
for j in self.G.nodes():
|
129 |
+
if i != j:
|
130 |
+
self.add_edge(i, j, "peer")
|
131 |
+
self.customers[i] = set()
|
132 |
+
self.providers[i] = set()
|
133 |
+
return self.G
|
134 |
+
|
135 |
+
def add_edge(self, i, j, kind):
|
136 |
+
if kind == "transit":
|
137 |
+
customer = str(i)
|
138 |
+
else:
|
139 |
+
customer = "none"
|
140 |
+
self.G.add_edge(i, j, type=kind, customer=customer)
|
141 |
+
|
142 |
+
def choose_peer_pref_attach(self, node_list):
|
143 |
+
"""Pick a node with a probability weighted by its peer degree.
|
144 |
+
|
145 |
+
Pick a node from node_list with preferential attachment
|
146 |
+
computed only on their peer degree
|
147 |
+
"""
|
148 |
+
|
149 |
+
d = {}
|
150 |
+
for n in node_list:
|
151 |
+
d[n] = self.G.nodes[n]["peers"]
|
152 |
+
return choose_pref_attach(d, self.seed)
|
153 |
+
|
154 |
+
def choose_node_pref_attach(self, node_list):
|
155 |
+
"""Pick a node with a probability weighted by its degree.
|
156 |
+
|
157 |
+
Pick a node from node_list with preferential attachment
|
158 |
+
computed on their degree
|
159 |
+
"""
|
160 |
+
|
161 |
+
degs = dict(self.G.degree(node_list))
|
162 |
+
return choose_pref_attach(degs, self.seed)
|
163 |
+
|
164 |
+
def add_customer(self, i, j):
|
165 |
+
"""Keep the dictionaries 'customers' and 'providers' consistent."""
|
166 |
+
|
167 |
+
self.customers[j].add(i)
|
168 |
+
self.providers[i].add(j)
|
169 |
+
for z in self.providers[j]:
|
170 |
+
self.customers[z].add(i)
|
171 |
+
self.providers[i].add(z)
|
172 |
+
|
173 |
+
def add_node(self, i, kind, reg2prob, avg_deg, t_edge_prob):
|
174 |
+
"""Add a node and its customer transit edges to the graph.
|
175 |
+
|
176 |
+
Parameters
|
177 |
+
----------
|
178 |
+
i: object
|
179 |
+
Identifier of the new node
|
180 |
+
kind: string
|
181 |
+
Type of the new node. Options are: 'M' for middle node, 'CP' for
|
182 |
+
content provider and 'C' for customer.
|
183 |
+
reg2prob: float
|
184 |
+
Probability the new node can be in two different regions.
|
185 |
+
avg_deg: float
|
186 |
+
Average number of transit nodes of which node i is customer.
|
187 |
+
t_edge_prob: float
|
188 |
+
Probability node i establish a customer transit edge with a tier
|
189 |
+
one (T) node
|
190 |
+
|
191 |
+
Returns
|
192 |
+
-------
|
193 |
+
i: object
|
194 |
+
Identifier of the new node
|
195 |
+
"""
|
196 |
+
|
197 |
+
regs = 1 # regions in which node resides
|
198 |
+
if self.seed.random() < reg2prob: # node is in two regions
|
199 |
+
regs = 2
|
200 |
+
node_options = set()
|
201 |
+
|
202 |
+
self.G.add_node(i, type=kind, peers=0)
|
203 |
+
self.customers[i] = set()
|
204 |
+
self.providers[i] = set()
|
205 |
+
self.nodes[kind].add(i)
|
206 |
+
for r in self.seed.sample(list(self.regions), regs):
|
207 |
+
node_options = node_options.union(self.regions[r])
|
208 |
+
self.regions[r].add(i)
|
209 |
+
|
210 |
+
edge_num = uniform_int_from_avg(1, avg_deg, self.seed)
|
211 |
+
|
212 |
+
t_options = node_options.intersection(self.nodes["T"])
|
213 |
+
m_options = node_options.intersection(self.nodes["M"])
|
214 |
+
if i in m_options:
|
215 |
+
m_options.remove(i)
|
216 |
+
d = 0
|
217 |
+
while d < edge_num and (len(t_options) > 0 or len(m_options) > 0):
|
218 |
+
if len(m_options) == 0 or (
|
219 |
+
len(t_options) > 0 and self.seed.random() < t_edge_prob
|
220 |
+
): # add edge to a T node
|
221 |
+
j = self.choose_node_pref_attach(t_options)
|
222 |
+
t_options.remove(j)
|
223 |
+
else:
|
224 |
+
j = self.choose_node_pref_attach(m_options)
|
225 |
+
m_options.remove(j)
|
226 |
+
self.add_edge(i, j, "transit")
|
227 |
+
self.add_customer(i, j)
|
228 |
+
d += 1
|
229 |
+
|
230 |
+
return i
|
231 |
+
|
232 |
+
def add_m_peering_link(self, m, to_kind):
|
233 |
+
"""Add a peering link between two middle tier (M) nodes.
|
234 |
+
|
235 |
+
Target node j is drawn considering a preferential attachment based on
|
236 |
+
other M node peering degree.
|
237 |
+
|
238 |
+
Parameters
|
239 |
+
----------
|
240 |
+
m: object
|
241 |
+
Node identifier
|
242 |
+
to_kind: string
|
243 |
+
type for target node j (must be always M)
|
244 |
+
|
245 |
+
Returns
|
246 |
+
-------
|
247 |
+
success: boolean
|
248 |
+
"""
|
249 |
+
|
250 |
+
# candidates are of type 'M' and are not customers of m
|
251 |
+
node_options = self.nodes["M"].difference(self.customers[m])
|
252 |
+
# candidates are not providers of m
|
253 |
+
node_options = node_options.difference(self.providers[m])
|
254 |
+
# remove self
|
255 |
+
if m in node_options:
|
256 |
+
node_options.remove(m)
|
257 |
+
|
258 |
+
# remove candidates we are already connected to
|
259 |
+
for j in self.G.neighbors(m):
|
260 |
+
if j in node_options:
|
261 |
+
node_options.remove(j)
|
262 |
+
|
263 |
+
if len(node_options) > 0:
|
264 |
+
j = self.choose_peer_pref_attach(node_options)
|
265 |
+
self.add_edge(m, j, "peer")
|
266 |
+
self.G.nodes[m]["peers"] += 1
|
267 |
+
self.G.nodes[j]["peers"] += 1
|
268 |
+
return True
|
269 |
+
else:
|
270 |
+
return False
|
271 |
+
|
272 |
+
def add_cp_peering_link(self, cp, to_kind):
|
273 |
+
"""Add a peering link to a content provider (CP) node.
|
274 |
+
|
275 |
+
Target node j can be CP or M and it is drawn uniformly among the nodes
|
276 |
+
belonging to the same region as cp.
|
277 |
+
|
278 |
+
Parameters
|
279 |
+
----------
|
280 |
+
cp: object
|
281 |
+
Node identifier
|
282 |
+
to_kind: string
|
283 |
+
type for target node j (must be M or CP)
|
284 |
+
|
285 |
+
Returns
|
286 |
+
-------
|
287 |
+
success: boolean
|
288 |
+
"""
|
289 |
+
|
290 |
+
node_options = set()
|
291 |
+
for r in self.regions: # options include nodes in the same region(s)
|
292 |
+
if cp in self.regions[r]:
|
293 |
+
node_options = node_options.union(self.regions[r])
|
294 |
+
|
295 |
+
# options are restricted to the indicated kind ('M' or 'CP')
|
296 |
+
node_options = self.nodes[to_kind].intersection(node_options)
|
297 |
+
|
298 |
+
# remove self
|
299 |
+
if cp in node_options:
|
300 |
+
node_options.remove(cp)
|
301 |
+
|
302 |
+
# remove nodes that are cp's providers
|
303 |
+
node_options = node_options.difference(self.providers[cp])
|
304 |
+
|
305 |
+
# remove nodes we are already connected to
|
306 |
+
for j in self.G.neighbors(cp):
|
307 |
+
if j in node_options:
|
308 |
+
node_options.remove(j)
|
309 |
+
|
310 |
+
if len(node_options) > 0:
|
311 |
+
j = self.seed.sample(list(node_options), 1)[0]
|
312 |
+
self.add_edge(cp, j, "peer")
|
313 |
+
self.G.nodes[cp]["peers"] += 1
|
314 |
+
self.G.nodes[j]["peers"] += 1
|
315 |
+
return True
|
316 |
+
else:
|
317 |
+
return False
|
318 |
+
|
319 |
+
def graph_regions(self, rn):
|
320 |
+
"""Initializes AS network regions.
|
321 |
+
|
322 |
+
Parameters
|
323 |
+
----------
|
324 |
+
rn: integer
|
325 |
+
Number of regions
|
326 |
+
"""
|
327 |
+
|
328 |
+
self.regions = {}
|
329 |
+
for i in range(rn):
|
330 |
+
self.regions["REG" + str(i)] = set()
|
331 |
+
|
332 |
+
def add_peering_links(self, from_kind, to_kind):
|
333 |
+
"""Utility function to add peering links among node groups."""
|
334 |
+
peer_link_method = None
|
335 |
+
if from_kind == "M":
|
336 |
+
peer_link_method = self.add_m_peering_link
|
337 |
+
m = self.p_m_m
|
338 |
+
if from_kind == "CP":
|
339 |
+
peer_link_method = self.add_cp_peering_link
|
340 |
+
if to_kind == "M":
|
341 |
+
m = self.p_cp_m
|
342 |
+
else:
|
343 |
+
m = self.p_cp_cp
|
344 |
+
|
345 |
+
for i in self.nodes[from_kind]:
|
346 |
+
num = uniform_int_from_avg(0, m, self.seed)
|
347 |
+
for _ in range(num):
|
348 |
+
peer_link_method(i, to_kind)
|
349 |
+
|
350 |
+
def generate(self):
|
351 |
+
"""Generates a random AS network graph as described in [1].
|
352 |
+
|
353 |
+
Returns
|
354 |
+
-------
|
355 |
+
G: Graph object
|
356 |
+
|
357 |
+
Notes
|
358 |
+
-----
|
359 |
+
The process steps are the following: first we create the core network
|
360 |
+
of tier one nodes, then we add the middle tier (M), the content
|
361 |
+
provider (CP) and the customer (C) nodes along with their transit edges
|
362 |
+
(link i,j means i is customer of j). Finally we add peering links
|
363 |
+
between M nodes, between M and CP nodes and between CP node couples.
|
364 |
+
For a detailed description of the algorithm, please refer to [1].
|
365 |
+
|
366 |
+
References
|
367 |
+
----------
|
368 |
+
[1] A. Elmokashfi, A. Kvalbein and C. Dovrolis, "On the Scalability of
|
369 |
+
BGP: The Role of Topology Growth," in IEEE Journal on Selected Areas
|
370 |
+
in Communications, vol. 28, no. 8, pp. 1250-1261, October 2010.
|
371 |
+
"""
|
372 |
+
|
373 |
+
self.graph_regions(5)
|
374 |
+
self.customers = {}
|
375 |
+
self.providers = {}
|
376 |
+
self.nodes = {"T": set(), "M": set(), "CP": set(), "C": set()}
|
377 |
+
|
378 |
+
self.t_graph()
|
379 |
+
self.nodes["T"] = set(self.G.nodes())
|
380 |
+
|
381 |
+
i = len(self.nodes["T"])
|
382 |
+
for _ in range(self.n_m):
|
383 |
+
self.nodes["M"].add(self.add_node(i, "M", 0.2, self.d_m, self.t_m))
|
384 |
+
i += 1
|
385 |
+
for _ in range(self.n_cp):
|
386 |
+
self.nodes["CP"].add(self.add_node(i, "CP", 0.05, self.d_cp, self.t_cp))
|
387 |
+
i += 1
|
388 |
+
for _ in range(self.n_c):
|
389 |
+
self.nodes["C"].add(self.add_node(i, "C", 0, self.d_c, self.t_c))
|
390 |
+
i += 1
|
391 |
+
|
392 |
+
self.add_peering_links("M", "M")
|
393 |
+
self.add_peering_links("CP", "M")
|
394 |
+
self.add_peering_links("CP", "CP")
|
395 |
+
|
396 |
+
return self.G
|
397 |
+
|
398 |
+
|
399 |
+
@py_random_state(1)
|
400 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
401 |
+
def random_internet_as_graph(n, seed=None):
|
402 |
+
"""Generates a random undirected graph resembling the Internet AS network
|
403 |
+
|
404 |
+
Parameters
|
405 |
+
----------
|
406 |
+
n: integer in [1000, 10000]
|
407 |
+
Number of graph nodes
|
408 |
+
seed : integer, random_state, or None (default)
|
409 |
+
Indicator of random number generation state.
|
410 |
+
See :ref:`Randomness<randomness>`.
|
411 |
+
|
412 |
+
Returns
|
413 |
+
-------
|
414 |
+
G: Networkx Graph object
|
415 |
+
A randomly generated undirected graph
|
416 |
+
|
417 |
+
Notes
|
418 |
+
-----
|
419 |
+
This algorithm returns an undirected graph resembling the Internet
|
420 |
+
Autonomous System (AS) network, it uses the approach by Elmokashfi et al.
|
421 |
+
[1]_ and it grants the properties described in the related paper [1]_.
|
422 |
+
|
423 |
+
Each node models an autonomous system, with an attribute 'type' specifying
|
424 |
+
its kind; tier-1 (T), mid-level (M), customer (C) or content-provider (CP).
|
425 |
+
Each edge models an ADV communication link (hence, bidirectional) with
|
426 |
+
attributes:
|
427 |
+
|
428 |
+
- type: transit|peer, the kind of commercial agreement between nodes;
|
429 |
+
- customer: <node id>, the identifier of the node acting as customer
|
430 |
+
('none' if type is peer).
|
431 |
+
|
432 |
+
References
|
433 |
+
----------
|
434 |
+
.. [1] A. Elmokashfi, A. Kvalbein and C. Dovrolis, "On the Scalability of
|
435 |
+
BGP: The Role of Topology Growth," in IEEE Journal on Selected Areas
|
436 |
+
in Communications, vol. 28, no. 8, pp. 1250-1261, October 2010.
|
437 |
+
"""
|
438 |
+
|
439 |
+
GG = AS_graph_generator(n, seed)
|
440 |
+
G = GG.generate()
|
441 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/intersection.py
ADDED
@@ -0,0 +1,124 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
Generators for random intersection graphs.
|
3 |
+
"""
|
4 |
+
import networkx as nx
|
5 |
+
from networkx.utils import py_random_state
|
6 |
+
|
7 |
+
__all__ = [
|
8 |
+
"uniform_random_intersection_graph",
|
9 |
+
"k_random_intersection_graph",
|
10 |
+
"general_random_intersection_graph",
|
11 |
+
]
|
12 |
+
|
13 |
+
|
14 |
+
@py_random_state(3)
|
15 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
16 |
+
def uniform_random_intersection_graph(n, m, p, seed=None):
|
17 |
+
"""Returns a uniform random intersection graph.
|
18 |
+
|
19 |
+
Parameters
|
20 |
+
----------
|
21 |
+
n : int
|
22 |
+
The number of nodes in the first bipartite set (nodes)
|
23 |
+
m : int
|
24 |
+
The number of nodes in the second bipartite set (attributes)
|
25 |
+
p : float
|
26 |
+
Probability of connecting nodes between bipartite sets
|
27 |
+
seed : integer, random_state, or None (default)
|
28 |
+
Indicator of random number generation state.
|
29 |
+
See :ref:`Randomness<randomness>`.
|
30 |
+
|
31 |
+
See Also
|
32 |
+
--------
|
33 |
+
gnp_random_graph
|
34 |
+
|
35 |
+
References
|
36 |
+
----------
|
37 |
+
.. [1] K.B. Singer-Cohen, Random Intersection Graphs, 1995,
|
38 |
+
PhD thesis, Johns Hopkins University
|
39 |
+
.. [2] Fill, J. A., Scheinerman, E. R., and Singer-Cohen, K. B.,
|
40 |
+
Random intersection graphs when m = !(n):
|
41 |
+
An equivalence theorem relating the evolution of the g(n, m, p)
|
42 |
+
and g(n, p) models. Random Struct. Algorithms 16, 2 (2000), 156–176.
|
43 |
+
"""
|
44 |
+
from networkx.algorithms import bipartite
|
45 |
+
|
46 |
+
G = bipartite.random_graph(n, m, p, seed)
|
47 |
+
return nx.projected_graph(G, range(n))
|
48 |
+
|
49 |
+
|
50 |
+
@py_random_state(3)
|
51 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
52 |
+
def k_random_intersection_graph(n, m, k, seed=None):
|
53 |
+
"""Returns a intersection graph with randomly chosen attribute sets for
|
54 |
+
each node that are of equal size (k).
|
55 |
+
|
56 |
+
Parameters
|
57 |
+
----------
|
58 |
+
n : int
|
59 |
+
The number of nodes in the first bipartite set (nodes)
|
60 |
+
m : int
|
61 |
+
The number of nodes in the second bipartite set (attributes)
|
62 |
+
k : float
|
63 |
+
Size of attribute set to assign to each node.
|
64 |
+
seed : integer, random_state, or None (default)
|
65 |
+
Indicator of random number generation state.
|
66 |
+
See :ref:`Randomness<randomness>`.
|
67 |
+
|
68 |
+
See Also
|
69 |
+
--------
|
70 |
+
gnp_random_graph, uniform_random_intersection_graph
|
71 |
+
|
72 |
+
References
|
73 |
+
----------
|
74 |
+
.. [1] Godehardt, E., and Jaworski, J.
|
75 |
+
Two models of random intersection graphs and their applications.
|
76 |
+
Electronic Notes in Discrete Mathematics 10 (2001), 129--132.
|
77 |
+
"""
|
78 |
+
G = nx.empty_graph(n + m)
|
79 |
+
mset = range(n, n + m)
|
80 |
+
for v in range(n):
|
81 |
+
targets = seed.sample(mset, k)
|
82 |
+
G.add_edges_from(zip([v] * len(targets), targets))
|
83 |
+
return nx.projected_graph(G, range(n))
|
84 |
+
|
85 |
+
|
86 |
+
@py_random_state(3)
|
87 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
88 |
+
def general_random_intersection_graph(n, m, p, seed=None):
|
89 |
+
"""Returns a random intersection graph with independent probabilities
|
90 |
+
for connections between node and attribute sets.
|
91 |
+
|
92 |
+
Parameters
|
93 |
+
----------
|
94 |
+
n : int
|
95 |
+
The number of nodes in the first bipartite set (nodes)
|
96 |
+
m : int
|
97 |
+
The number of nodes in the second bipartite set (attributes)
|
98 |
+
p : list of floats of length m
|
99 |
+
Probabilities for connecting nodes to each attribute
|
100 |
+
seed : integer, random_state, or None (default)
|
101 |
+
Indicator of random number generation state.
|
102 |
+
See :ref:`Randomness<randomness>`.
|
103 |
+
|
104 |
+
See Also
|
105 |
+
--------
|
106 |
+
gnp_random_graph, uniform_random_intersection_graph
|
107 |
+
|
108 |
+
References
|
109 |
+
----------
|
110 |
+
.. [1] Nikoletseas, S. E., Raptopoulos, C., and Spirakis, P. G.
|
111 |
+
The existence and efficient construction of large independent sets
|
112 |
+
in general random intersection graphs. In ICALP (2004), J. D´ıaz,
|
113 |
+
J. Karhum¨aki, A. Lepist¨o, and D. Sannella, Eds., vol. 3142
|
114 |
+
of Lecture Notes in Computer Science, Springer, pp. 1029–1040.
|
115 |
+
"""
|
116 |
+
if len(p) != m:
|
117 |
+
raise ValueError("Probability list p must have m elements.")
|
118 |
+
G = nx.empty_graph(n + m)
|
119 |
+
mset = range(n, n + m)
|
120 |
+
for u in range(n):
|
121 |
+
for v, q in zip(mset, p):
|
122 |
+
if seed.random() < q:
|
123 |
+
G.add_edge(u, v)
|
124 |
+
return nx.projected_graph(G, range(n))
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/interval_graph.py
ADDED
@@ -0,0 +1,69 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""
|
2 |
+
Generators for interval graph.
|
3 |
+
"""
|
4 |
+
from collections.abc import Sequence
|
5 |
+
|
6 |
+
import networkx as nx
|
7 |
+
|
8 |
+
__all__ = ["interval_graph"]
|
9 |
+
|
10 |
+
|
11 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
12 |
+
def interval_graph(intervals):
|
13 |
+
"""Generates an interval graph for a list of intervals given.
|
14 |
+
|
15 |
+
In graph theory, an interval graph is an undirected graph formed from a set
|
16 |
+
of closed intervals on the real line, with a vertex for each interval
|
17 |
+
and an edge between vertices whose intervals intersect.
|
18 |
+
It is the intersection graph of the intervals.
|
19 |
+
|
20 |
+
More information can be found at:
|
21 |
+
https://en.wikipedia.org/wiki/Interval_graph
|
22 |
+
|
23 |
+
Parameters
|
24 |
+
----------
|
25 |
+
intervals : a sequence of intervals, say (l, r) where l is the left end,
|
26 |
+
and r is the right end of the closed interval.
|
27 |
+
|
28 |
+
Returns
|
29 |
+
-------
|
30 |
+
G : networkx graph
|
31 |
+
|
32 |
+
Examples
|
33 |
+
--------
|
34 |
+
>>> intervals = [(-2, 3), [1, 4], (2, 3), (4, 6)]
|
35 |
+
>>> G = nx.interval_graph(intervals)
|
36 |
+
>>> sorted(G.edges)
|
37 |
+
[((-2, 3), (1, 4)), ((-2, 3), (2, 3)), ((1, 4), (2, 3)), ((1, 4), (4, 6))]
|
38 |
+
|
39 |
+
Raises
|
40 |
+
------
|
41 |
+
:exc:`TypeError`
|
42 |
+
if `intervals` contains None or an element which is not
|
43 |
+
collections.abc.Sequence or not a length of 2.
|
44 |
+
:exc:`ValueError`
|
45 |
+
if `intervals` contains an interval such that min1 > max1
|
46 |
+
where min1,max1 = interval
|
47 |
+
"""
|
48 |
+
intervals = list(intervals)
|
49 |
+
for interval in intervals:
|
50 |
+
if not (isinstance(interval, Sequence) and len(interval) == 2):
|
51 |
+
raise TypeError(
|
52 |
+
"Each interval must have length 2, and be a "
|
53 |
+
"collections.abc.Sequence such as tuple or list."
|
54 |
+
)
|
55 |
+
if interval[0] > interval[1]:
|
56 |
+
raise ValueError(f"Interval must have lower value first. Got {interval}")
|
57 |
+
|
58 |
+
graph = nx.Graph()
|
59 |
+
|
60 |
+
tupled_intervals = [tuple(interval) for interval in intervals]
|
61 |
+
graph.add_nodes_from(tupled_intervals)
|
62 |
+
|
63 |
+
while tupled_intervals:
|
64 |
+
min1, max1 = interval1 = tupled_intervals.pop()
|
65 |
+
for interval2 in tupled_intervals:
|
66 |
+
min2, max2 = interval2
|
67 |
+
if max1 >= min2 and max2 >= min1:
|
68 |
+
graph.add_edge(interval1, interval2)
|
69 |
+
return graph
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/joint_degree_seq.py
ADDED
@@ -0,0 +1,664 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
1 |
+
"""Generate graphs with a given joint degree and directed joint degree"""
|
2 |
+
|
3 |
+
import networkx as nx
|
4 |
+
from networkx.utils import py_random_state
|
5 |
+
|
6 |
+
__all__ = [
|
7 |
+
"is_valid_joint_degree",
|
8 |
+
"is_valid_directed_joint_degree",
|
9 |
+
"joint_degree_graph",
|
10 |
+
"directed_joint_degree_graph",
|
11 |
+
]
|
12 |
+
|
13 |
+
|
14 |
+
@nx._dispatchable(graphs=None)
|
15 |
+
def is_valid_joint_degree(joint_degrees):
|
16 |
+
"""Checks whether the given joint degree dictionary is realizable.
|
17 |
+
|
18 |
+
A *joint degree dictionary* is a dictionary of dictionaries, in
|
19 |
+
which entry ``joint_degrees[k][l]`` is an integer representing the
|
20 |
+
number of edges joining nodes of degree *k* with nodes of degree
|
21 |
+
*l*. Such a dictionary is realizable as a simple graph if and only
|
22 |
+
if the following conditions are satisfied.
|
23 |
+
|
24 |
+
- each entry must be an integer,
|
25 |
+
- the total number of nodes of degree *k*, computed by
|
26 |
+
``sum(joint_degrees[k].values()) / k``, must be an integer,
|
27 |
+
- the total number of edges joining nodes of degree *k* with
|
28 |
+
nodes of degree *l* cannot exceed the total number of possible edges,
|
29 |
+
- each diagonal entry ``joint_degrees[k][k]`` must be even (this is
|
30 |
+
a convention assumed by the :func:`joint_degree_graph` function).
|
31 |
+
|
32 |
+
|
33 |
+
Parameters
|
34 |
+
----------
|
35 |
+
joint_degrees : dictionary of dictionary of integers
|
36 |
+
A joint degree dictionary in which entry ``joint_degrees[k][l]``
|
37 |
+
is the number of edges joining nodes of degree *k* with nodes of
|
38 |
+
degree *l*.
|
39 |
+
|
40 |
+
Returns
|
41 |
+
-------
|
42 |
+
bool
|
43 |
+
Whether the given joint degree dictionary is realizable as a
|
44 |
+
simple graph.
|
45 |
+
|
46 |
+
References
|
47 |
+
----------
|
48 |
+
.. [1] M. Gjoka, M. Kurant, A. Markopoulou, "2.5K Graphs: from Sampling
|
49 |
+
to Generation", IEEE Infocom, 2013.
|
50 |
+
.. [2] I. Stanton, A. Pinar, "Constructing and sampling graphs with a
|
51 |
+
prescribed joint degree distribution", Journal of Experimental
|
52 |
+
Algorithmics, 2012.
|
53 |
+
"""
|
54 |
+
|
55 |
+
degree_count = {}
|
56 |
+
for k in joint_degrees:
|
57 |
+
if k > 0:
|
58 |
+
k_size = sum(joint_degrees[k].values()) / k
|
59 |
+
if not k_size.is_integer():
|
60 |
+
return False
|
61 |
+
degree_count[k] = k_size
|
62 |
+
|
63 |
+
for k in joint_degrees:
|
64 |
+
for l in joint_degrees[k]:
|
65 |
+
if not float(joint_degrees[k][l]).is_integer():
|
66 |
+
return False
|
67 |
+
|
68 |
+
if (k != l) and (joint_degrees[k][l] > degree_count[k] * degree_count[l]):
|
69 |
+
return False
|
70 |
+
elif k == l:
|
71 |
+
if joint_degrees[k][k] > degree_count[k] * (degree_count[k] - 1):
|
72 |
+
return False
|
73 |
+
if joint_degrees[k][k] % 2 != 0:
|
74 |
+
return False
|
75 |
+
|
76 |
+
# if all above conditions have been satisfied then the input
|
77 |
+
# joint degree is realizable as a simple graph.
|
78 |
+
return True
|
79 |
+
|
80 |
+
|
81 |
+
def _neighbor_switch(G, w, unsat, h_node_residual, avoid_node_id=None):
|
82 |
+
"""Releases one free stub for ``w``, while preserving joint degree in G.
|
83 |
+
|
84 |
+
Parameters
|
85 |
+
----------
|
86 |
+
G : NetworkX graph
|
87 |
+
Graph in which the neighbor switch will take place.
|
88 |
+
w : integer
|
89 |
+
Node id for which we will execute this neighbor switch.
|
90 |
+
unsat : set of integers
|
91 |
+
Set of unsaturated node ids that have the same degree as w.
|
92 |
+
h_node_residual: dictionary of integers
|
93 |
+
Keeps track of the remaining stubs for a given node.
|
94 |
+
avoid_node_id: integer
|
95 |
+
Node id to avoid when selecting w_prime.
|
96 |
+
|
97 |
+
Notes
|
98 |
+
-----
|
99 |
+
First, it selects *w_prime*, an unsaturated node that has the same degree
|
100 |
+
as ``w``. Second, it selects *switch_node*, a neighbor node of ``w`` that
|
101 |
+
is not connected to *w_prime*. Then it executes an edge swap i.e. removes
|
102 |
+
(``w``,*switch_node*) and adds (*w_prime*,*switch_node*). Gjoka et. al. [1]
|
103 |
+
prove that such an edge swap is always possible.
|
104 |
+
|
105 |
+
References
|
106 |
+
----------
|
107 |
+
.. [1] M. Gjoka, B. Tillman, A. Markopoulou, "Construction of Simple
|
108 |
+
Graphs with a Target Joint Degree Matrix and Beyond", IEEE Infocom, '15
|
109 |
+
"""
|
110 |
+
|
111 |
+
if (avoid_node_id is None) or (h_node_residual[avoid_node_id] > 1):
|
112 |
+
# select unsaturated node w_prime that has the same degree as w
|
113 |
+
w_prime = next(iter(unsat))
|
114 |
+
else:
|
115 |
+
# assume that the node pair (v,w) has been selected for connection. if
|
116 |
+
# - neighbor_switch is called for node w,
|
117 |
+
# - nodes v and w have the same degree,
|
118 |
+
# - node v=avoid_node_id has only one stub left,
|
119 |
+
# then prevent v=avoid_node_id from being selected as w_prime.
|
120 |
+
|
121 |
+
iter_var = iter(unsat)
|
122 |
+
while True:
|
123 |
+
w_prime = next(iter_var)
|
124 |
+
if w_prime != avoid_node_id:
|
125 |
+
break
|
126 |
+
|
127 |
+
# select switch_node, a neighbor of w, that is not connected to w_prime
|
128 |
+
w_prime_neighbs = G[w_prime] # slightly faster declaring this variable
|
129 |
+
for v in G[w]:
|
130 |
+
if (v not in w_prime_neighbs) and (v != w_prime):
|
131 |
+
switch_node = v
|
132 |
+
break
|
133 |
+
|
134 |
+
# remove edge (w,switch_node), add edge (w_prime,switch_node) and update
|
135 |
+
# data structures
|
136 |
+
G.remove_edge(w, switch_node)
|
137 |
+
G.add_edge(w_prime, switch_node)
|
138 |
+
h_node_residual[w] += 1
|
139 |
+
h_node_residual[w_prime] -= 1
|
140 |
+
if h_node_residual[w_prime] == 0:
|
141 |
+
unsat.remove(w_prime)
|
142 |
+
|
143 |
+
|
144 |
+
@py_random_state(1)
|
145 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
146 |
+
def joint_degree_graph(joint_degrees, seed=None):
|
147 |
+
"""Generates a random simple graph with the given joint degree dictionary.
|
148 |
+
|
149 |
+
Parameters
|
150 |
+
----------
|
151 |
+
joint_degrees : dictionary of dictionary of integers
|
152 |
+
A joint degree dictionary in which entry ``joint_degrees[k][l]`` is the
|
153 |
+
number of edges joining nodes of degree *k* with nodes of degree *l*.
|
154 |
+
seed : integer, random_state, or None (default)
|
155 |
+
Indicator of random number generation state.
|
156 |
+
See :ref:`Randomness<randomness>`.
|
157 |
+
|
158 |
+
Returns
|
159 |
+
-------
|
160 |
+
G : Graph
|
161 |
+
A graph with the specified joint degree dictionary.
|
162 |
+
|
163 |
+
Raises
|
164 |
+
------
|
165 |
+
NetworkXError
|
166 |
+
If *joint_degrees* dictionary is not realizable.
|
167 |
+
|
168 |
+
Notes
|
169 |
+
-----
|
170 |
+
In each iteration of the "while loop" the algorithm picks two disconnected
|
171 |
+
nodes *v* and *w*, of degree *k* and *l* correspondingly, for which
|
172 |
+
``joint_degrees[k][l]`` has not reached its target yet. It then adds
|
173 |
+
edge (*v*, *w*) and increases the number of edges in graph G by one.
|
174 |
+
|
175 |
+
The intelligence of the algorithm lies in the fact that it is always
|
176 |
+
possible to add an edge between such disconnected nodes *v* and *w*,
|
177 |
+
even if one or both nodes do not have free stubs. That is made possible by
|
178 |
+
executing a "neighbor switch", an edge rewiring move that releases
|
179 |
+
a free stub while keeping the joint degree of G the same.
|
180 |
+
|
181 |
+
The algorithm continues for E (number of edges) iterations of
|
182 |
+
the "while loop", at the which point all entries of the given
|
183 |
+
``joint_degrees[k][l]`` have reached their target values and the
|
184 |
+
construction is complete.
|
185 |
+
|
186 |
+
References
|
187 |
+
----------
|
188 |
+
.. [1] M. Gjoka, B. Tillman, A. Markopoulou, "Construction of Simple
|
189 |
+
Graphs with a Target Joint Degree Matrix and Beyond", IEEE Infocom, '15
|
190 |
+
|
191 |
+
Examples
|
192 |
+
--------
|
193 |
+
>>> joint_degrees = {
|
194 |
+
... 1: {4: 1},
|
195 |
+
... 2: {2: 2, 3: 2, 4: 2},
|
196 |
+
... 3: {2: 2, 4: 1},
|
197 |
+
... 4: {1: 1, 2: 2, 3: 1},
|
198 |
+
... }
|
199 |
+
>>> G = nx.joint_degree_graph(joint_degrees)
|
200 |
+
>>>
|
201 |
+
"""
|
202 |
+
|
203 |
+
if not is_valid_joint_degree(joint_degrees):
|
204 |
+
msg = "Input joint degree dict not realizable as a simple graph"
|
205 |
+
raise nx.NetworkXError(msg)
|
206 |
+
|
207 |
+
# compute degree count from joint_degrees
|
208 |
+
degree_count = {k: sum(l.values()) // k for k, l in joint_degrees.items() if k > 0}
|
209 |
+
|
210 |
+
# start with empty N-node graph
|
211 |
+
N = sum(degree_count.values())
|
212 |
+
G = nx.empty_graph(N)
|
213 |
+
|
214 |
+
# for a given degree group, keep the list of all node ids
|
215 |
+
h_degree_nodelist = {}
|
216 |
+
|
217 |
+
# for a given node, keep track of the remaining stubs
|
218 |
+
h_node_residual = {}
|
219 |
+
|
220 |
+
# populate h_degree_nodelist and h_node_residual
|
221 |
+
nodeid = 0
|
222 |
+
for degree, num_nodes in degree_count.items():
|
223 |
+
h_degree_nodelist[degree] = range(nodeid, nodeid + num_nodes)
|
224 |
+
for v in h_degree_nodelist[degree]:
|
225 |
+
h_node_residual[v] = degree
|
226 |
+
nodeid += int(num_nodes)
|
227 |
+
|
228 |
+
# iterate over every degree pair (k,l) and add the number of edges given
|
229 |
+
# for each pair
|
230 |
+
for k in joint_degrees:
|
231 |
+
for l in joint_degrees[k]:
|
232 |
+
# n_edges_add is the number of edges to add for the
|
233 |
+
# degree pair (k,l)
|
234 |
+
n_edges_add = joint_degrees[k][l]
|
235 |
+
|
236 |
+
if (n_edges_add > 0) and (k >= l):
|
237 |
+
# number of nodes with degree k and l
|
238 |
+
k_size = degree_count[k]
|
239 |
+
l_size = degree_count[l]
|
240 |
+
|
241 |
+
# k_nodes and l_nodes consist of all nodes of degree k and l
|
242 |
+
k_nodes = h_degree_nodelist[k]
|
243 |
+
l_nodes = h_degree_nodelist[l]
|
244 |
+
|
245 |
+
# k_unsat and l_unsat consist of nodes of degree k and l that
|
246 |
+
# are unsaturated (nodes that have at least 1 available stub)
|
247 |
+
k_unsat = {v for v in k_nodes if h_node_residual[v] > 0}
|
248 |
+
|
249 |
+
if k != l:
|
250 |
+
l_unsat = {w for w in l_nodes if h_node_residual[w] > 0}
|
251 |
+
else:
|
252 |
+
l_unsat = k_unsat
|
253 |
+
n_edges_add = joint_degrees[k][l] // 2
|
254 |
+
|
255 |
+
while n_edges_add > 0:
|
256 |
+
# randomly pick nodes v and w that have degrees k and l
|
257 |
+
v = k_nodes[seed.randrange(k_size)]
|
258 |
+
w = l_nodes[seed.randrange(l_size)]
|
259 |
+
|
260 |
+
# if nodes v and w are disconnected then attempt to connect
|
261 |
+
if not G.has_edge(v, w) and (v != w):
|
262 |
+
# if node v has no free stubs then do neighbor switch
|
263 |
+
if h_node_residual[v] == 0:
|
264 |
+
_neighbor_switch(G, v, k_unsat, h_node_residual)
|
265 |
+
|
266 |
+
# if node w has no free stubs then do neighbor switch
|
267 |
+
if h_node_residual[w] == 0:
|
268 |
+
if k != l:
|
269 |
+
_neighbor_switch(G, w, l_unsat, h_node_residual)
|
270 |
+
else:
|
271 |
+
_neighbor_switch(
|
272 |
+
G, w, l_unsat, h_node_residual, avoid_node_id=v
|
273 |
+
)
|
274 |
+
|
275 |
+
# add edge (v, w) and update data structures
|
276 |
+
G.add_edge(v, w)
|
277 |
+
h_node_residual[v] -= 1
|
278 |
+
h_node_residual[w] -= 1
|
279 |
+
n_edges_add -= 1
|
280 |
+
|
281 |
+
if h_node_residual[v] == 0:
|
282 |
+
k_unsat.discard(v)
|
283 |
+
if h_node_residual[w] == 0:
|
284 |
+
l_unsat.discard(w)
|
285 |
+
return G
|
286 |
+
|
287 |
+
|
288 |
+
@nx._dispatchable(graphs=None)
|
289 |
+
def is_valid_directed_joint_degree(in_degrees, out_degrees, nkk):
|
290 |
+
"""Checks whether the given directed joint degree input is realizable
|
291 |
+
|
292 |
+
Parameters
|
293 |
+
----------
|
294 |
+
in_degrees : list of integers
|
295 |
+
in degree sequence contains the in degrees of nodes.
|
296 |
+
out_degrees : list of integers
|
297 |
+
out degree sequence contains the out degrees of nodes.
|
298 |
+
nkk : dictionary of dictionary of integers
|
299 |
+
directed joint degree dictionary. for nodes of out degree k (first
|
300 |
+
level of dict) and nodes of in degree l (second level of dict)
|
301 |
+
describes the number of edges.
|
302 |
+
|
303 |
+
Returns
|
304 |
+
-------
|
305 |
+
boolean
|
306 |
+
returns true if given input is realizable, else returns false.
|
307 |
+
|
308 |
+
Notes
|
309 |
+
-----
|
310 |
+
Here is the list of conditions that the inputs (in/out degree sequences,
|
311 |
+
nkk) need to satisfy for simple directed graph realizability:
|
312 |
+
|
313 |
+
- Condition 0: in_degrees and out_degrees have the same length
|
314 |
+
- Condition 1: nkk[k][l] is integer for all k,l
|
315 |
+
- Condition 2: sum(nkk[k])/k = number of nodes with partition id k, is an
|
316 |
+
integer and matching degree sequence
|
317 |
+
- Condition 3: number of edges and non-chords between k and l cannot exceed
|
318 |
+
maximum possible number of edges
|
319 |
+
|
320 |
+
|
321 |
+
References
|
322 |
+
----------
|
323 |
+
[1] B. Tillman, A. Markopoulou, C. T. Butts & M. Gjoka,
|
324 |
+
"Construction of Directed 2K Graphs". In Proc. of KDD 2017.
|
325 |
+
"""
|
326 |
+
V = {} # number of nodes with in/out degree.
|
327 |
+
forbidden = {}
|
328 |
+
if len(in_degrees) != len(out_degrees):
|
329 |
+
return False
|
330 |
+
|
331 |
+
for idx in range(len(in_degrees)):
|
332 |
+
i = in_degrees[idx]
|
333 |
+
o = out_degrees[idx]
|
334 |
+
V[(i, 0)] = V.get((i, 0), 0) + 1
|
335 |
+
V[(o, 1)] = V.get((o, 1), 0) + 1
|
336 |
+
|
337 |
+
forbidden[(o, i)] = forbidden.get((o, i), 0) + 1
|
338 |
+
|
339 |
+
S = {} # number of edges going from in/out degree nodes.
|
340 |
+
for k in nkk:
|
341 |
+
for l in nkk[k]:
|
342 |
+
val = nkk[k][l]
|
343 |
+
if not float(val).is_integer(): # condition 1
|
344 |
+
return False
|
345 |
+
|
346 |
+
if val > 0:
|
347 |
+
S[(k, 1)] = S.get((k, 1), 0) + val
|
348 |
+
S[(l, 0)] = S.get((l, 0), 0) + val
|
349 |
+
# condition 3
|
350 |
+
if val + forbidden.get((k, l), 0) > V[(k, 1)] * V[(l, 0)]:
|
351 |
+
return False
|
352 |
+
|
353 |
+
return all(S[s] / s[0] == V[s] for s in S)
|
354 |
+
|
355 |
+
|
356 |
+
def _directed_neighbor_switch(
|
357 |
+
G, w, unsat, h_node_residual_out, chords, h_partition_in, partition
|
358 |
+
):
|
359 |
+
"""Releases one free stub for node w, while preserving joint degree in G.
|
360 |
+
|
361 |
+
Parameters
|
362 |
+
----------
|
363 |
+
G : networkx directed graph
|
364 |
+
graph within which the edge swap will take place.
|
365 |
+
w : integer
|
366 |
+
node id for which we need to perform a neighbor switch.
|
367 |
+
unsat: set of integers
|
368 |
+
set of node ids that have the same degree as w and are unsaturated.
|
369 |
+
h_node_residual_out: dict of integers
|
370 |
+
for a given node, keeps track of the remaining stubs to be added.
|
371 |
+
chords: set of tuples
|
372 |
+
keeps track of available positions to add edges.
|
373 |
+
h_partition_in: dict of integers
|
374 |
+
for a given node, keeps track of its partition id (in degree).
|
375 |
+
partition: integer
|
376 |
+
partition id to check if chords have to be updated.
|
377 |
+
|
378 |
+
Notes
|
379 |
+
-----
|
380 |
+
First, it selects node w_prime that (1) has the same degree as w and
|
381 |
+
(2) is unsaturated. Then, it selects node v, a neighbor of w, that is
|
382 |
+
not connected to w_prime and does an edge swap i.e. removes (w,v) and
|
383 |
+
adds (w_prime,v). If neighbor switch is not possible for w using
|
384 |
+
w_prime and v, then return w_prime; in [1] it's proven that
|
385 |
+
such unsaturated nodes can be used.
|
386 |
+
|
387 |
+
References
|
388 |
+
----------
|
389 |
+
[1] B. Tillman, A. Markopoulou, C. T. Butts & M. Gjoka,
|
390 |
+
"Construction of Directed 2K Graphs". In Proc. of KDD 2017.
|
391 |
+
"""
|
392 |
+
w_prime = unsat.pop()
|
393 |
+
unsat.add(w_prime)
|
394 |
+
# select node t, a neighbor of w, that is not connected to w_prime
|
395 |
+
w_neighbs = list(G.successors(w))
|
396 |
+
# slightly faster declaring this variable
|
397 |
+
w_prime_neighbs = list(G.successors(w_prime))
|
398 |
+
|
399 |
+
for v in w_neighbs:
|
400 |
+
if (v not in w_prime_neighbs) and w_prime != v:
|
401 |
+
# removes (w,v), add (w_prime,v) and update data structures
|
402 |
+
G.remove_edge(w, v)
|
403 |
+
G.add_edge(w_prime, v)
|
404 |
+
|
405 |
+
if h_partition_in[v] == partition:
|
406 |
+
chords.add((w, v))
|
407 |
+
chords.discard((w_prime, v))
|
408 |
+
|
409 |
+
h_node_residual_out[w] += 1
|
410 |
+
h_node_residual_out[w_prime] -= 1
|
411 |
+
if h_node_residual_out[w_prime] == 0:
|
412 |
+
unsat.remove(w_prime)
|
413 |
+
return None
|
414 |
+
|
415 |
+
# If neighbor switch didn't work, use unsaturated node
|
416 |
+
return w_prime
|
417 |
+
|
418 |
+
|
419 |
+
def _directed_neighbor_switch_rev(
|
420 |
+
G, w, unsat, h_node_residual_in, chords, h_partition_out, partition
|
421 |
+
):
|
422 |
+
"""The reverse of directed_neighbor_switch.
|
423 |
+
|
424 |
+
Parameters
|
425 |
+
----------
|
426 |
+
G : networkx directed graph
|
427 |
+
graph within which the edge swap will take place.
|
428 |
+
w : integer
|
429 |
+
node id for which we need to perform a neighbor switch.
|
430 |
+
unsat: set of integers
|
431 |
+
set of node ids that have the same degree as w and are unsaturated.
|
432 |
+
h_node_residual_in: dict of integers
|
433 |
+
for a given node, keeps track of the remaining stubs to be added.
|
434 |
+
chords: set of tuples
|
435 |
+
keeps track of available positions to add edges.
|
436 |
+
h_partition_out: dict of integers
|
437 |
+
for a given node, keeps track of its partition id (out degree).
|
438 |
+
partition: integer
|
439 |
+
partition id to check if chords have to be updated.
|
440 |
+
|
441 |
+
Notes
|
442 |
+
-----
|
443 |
+
Same operation as directed_neighbor_switch except it handles this operation
|
444 |
+
for incoming edges instead of outgoing.
|
445 |
+
"""
|
446 |
+
w_prime = unsat.pop()
|
447 |
+
unsat.add(w_prime)
|
448 |
+
# slightly faster declaring these as variables.
|
449 |
+
w_neighbs = list(G.predecessors(w))
|
450 |
+
w_prime_neighbs = list(G.predecessors(w_prime))
|
451 |
+
# select node v, a neighbor of w, that is not connected to w_prime.
|
452 |
+
for v in w_neighbs:
|
453 |
+
if (v not in w_prime_neighbs) and w_prime != v:
|
454 |
+
# removes (v,w), add (v,w_prime) and update data structures.
|
455 |
+
G.remove_edge(v, w)
|
456 |
+
G.add_edge(v, w_prime)
|
457 |
+
if h_partition_out[v] == partition:
|
458 |
+
chords.add((v, w))
|
459 |
+
chords.discard((v, w_prime))
|
460 |
+
|
461 |
+
h_node_residual_in[w] += 1
|
462 |
+
h_node_residual_in[w_prime] -= 1
|
463 |
+
if h_node_residual_in[w_prime] == 0:
|
464 |
+
unsat.remove(w_prime)
|
465 |
+
return None
|
466 |
+
|
467 |
+
# If neighbor switch didn't work, use the unsaturated node.
|
468 |
+
return w_prime
|
469 |
+
|
470 |
+
|
471 |
+
@py_random_state(3)
|
472 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
473 |
+
def directed_joint_degree_graph(in_degrees, out_degrees, nkk, seed=None):
|
474 |
+
"""Generates a random simple directed graph with the joint degree.
|
475 |
+
|
476 |
+
Parameters
|
477 |
+
----------
|
478 |
+
degree_seq : list of tuples (of size 3)
|
479 |
+
degree sequence contains tuples of nodes with node id, in degree and
|
480 |
+
out degree.
|
481 |
+
nkk : dictionary of dictionary of integers
|
482 |
+
directed joint degree dictionary, for nodes of out degree k (first
|
483 |
+
level of dict) and nodes of in degree l (second level of dict)
|
484 |
+
describes the number of edges.
|
485 |
+
seed : hashable object, optional
|
486 |
+
Seed for random number generator.
|
487 |
+
|
488 |
+
Returns
|
489 |
+
-------
|
490 |
+
G : Graph
|
491 |
+
A directed graph with the specified inputs.
|
492 |
+
|
493 |
+
Raises
|
494 |
+
------
|
495 |
+
NetworkXError
|
496 |
+
If degree_seq and nkk are not realizable as a simple directed graph.
|
497 |
+
|
498 |
+
|
499 |
+
Notes
|
500 |
+
-----
|
501 |
+
Similarly to the undirected version:
|
502 |
+
In each iteration of the "while loop" the algorithm picks two disconnected
|
503 |
+
nodes v and w, of degree k and l correspondingly, for which nkk[k][l] has
|
504 |
+
not reached its target yet i.e. (for given k,l): n_edges_add < nkk[k][l].
|
505 |
+
It then adds edge (v,w) and always increases the number of edges in graph G
|
506 |
+
by one.
|
507 |
+
|
508 |
+
The intelligence of the algorithm lies in the fact that it is always
|
509 |
+
possible to add an edge between disconnected nodes v and w, for which
|
510 |
+
nkk[degree(v)][degree(w)] has not reached its target, even if one or both
|
511 |
+
nodes do not have free stubs. If either node v or w does not have a free
|
512 |
+
stub, we perform a "neighbor switch", an edge rewiring move that releases a
|
513 |
+
free stub while keeping nkk the same.
|
514 |
+
|
515 |
+
The difference for the directed version lies in the fact that neighbor
|
516 |
+
switches might not be able to rewire, but in these cases unsaturated nodes
|
517 |
+
can be reassigned to use instead, see [1] for detailed description and
|
518 |
+
proofs.
|
519 |
+
|
520 |
+
The algorithm continues for E (number of edges in the graph) iterations of
|
521 |
+
the "while loop", at which point all entries of the given nkk[k][l] have
|
522 |
+
reached their target values and the construction is complete.
|
523 |
+
|
524 |
+
References
|
525 |
+
----------
|
526 |
+
[1] B. Tillman, A. Markopoulou, C. T. Butts & M. Gjoka,
|
527 |
+
"Construction of Directed 2K Graphs". In Proc. of KDD 2017.
|
528 |
+
|
529 |
+
Examples
|
530 |
+
--------
|
531 |
+
>>> in_degrees = [0, 1, 1, 2]
|
532 |
+
>>> out_degrees = [1, 1, 1, 1]
|
533 |
+
>>> nkk = {1: {1: 2, 2: 2}}
|
534 |
+
>>> G = nx.directed_joint_degree_graph(in_degrees, out_degrees, nkk)
|
535 |
+
>>>
|
536 |
+
"""
|
537 |
+
if not is_valid_directed_joint_degree(in_degrees, out_degrees, nkk):
|
538 |
+
msg = "Input is not realizable as a simple graph"
|
539 |
+
raise nx.NetworkXError(msg)
|
540 |
+
|
541 |
+
# start with an empty directed graph.
|
542 |
+
G = nx.DiGraph()
|
543 |
+
|
544 |
+
# for a given group, keep the list of all node ids.
|
545 |
+
h_degree_nodelist_in = {}
|
546 |
+
h_degree_nodelist_out = {}
|
547 |
+
# for a given group, keep the list of all unsaturated node ids.
|
548 |
+
h_degree_nodelist_in_unsat = {}
|
549 |
+
h_degree_nodelist_out_unsat = {}
|
550 |
+
# for a given node, keep track of the remaining stubs to be added.
|
551 |
+
h_node_residual_out = {}
|
552 |
+
h_node_residual_in = {}
|
553 |
+
# for a given node, keep track of the partition id.
|
554 |
+
h_partition_out = {}
|
555 |
+
h_partition_in = {}
|
556 |
+
# keep track of non-chords between pairs of partition ids.
|
557 |
+
non_chords = {}
|
558 |
+
|
559 |
+
# populate data structures
|
560 |
+
for idx, i in enumerate(in_degrees):
|
561 |
+
idx = int(idx)
|
562 |
+
if i > 0:
|
563 |
+
h_degree_nodelist_in.setdefault(i, [])
|
564 |
+
h_degree_nodelist_in_unsat.setdefault(i, set())
|
565 |
+
h_degree_nodelist_in[i].append(idx)
|
566 |
+
h_degree_nodelist_in_unsat[i].add(idx)
|
567 |
+
h_node_residual_in[idx] = i
|
568 |
+
h_partition_in[idx] = i
|
569 |
+
|
570 |
+
for idx, o in enumerate(out_degrees):
|
571 |
+
o = out_degrees[idx]
|
572 |
+
non_chords[(o, in_degrees[idx])] = non_chords.get((o, in_degrees[idx]), 0) + 1
|
573 |
+
idx = int(idx)
|
574 |
+
if o > 0:
|
575 |
+
h_degree_nodelist_out.setdefault(o, [])
|
576 |
+
h_degree_nodelist_out_unsat.setdefault(o, set())
|
577 |
+
h_degree_nodelist_out[o].append(idx)
|
578 |
+
h_degree_nodelist_out_unsat[o].add(idx)
|
579 |
+
h_node_residual_out[idx] = o
|
580 |
+
h_partition_out[idx] = o
|
581 |
+
|
582 |
+
G.add_node(idx)
|
583 |
+
|
584 |
+
nk_in = {}
|
585 |
+
nk_out = {}
|
586 |
+
for p in h_degree_nodelist_in:
|
587 |
+
nk_in[p] = len(h_degree_nodelist_in[p])
|
588 |
+
for p in h_degree_nodelist_out:
|
589 |
+
nk_out[p] = len(h_degree_nodelist_out[p])
|
590 |
+
|
591 |
+
# iterate over every degree pair (k,l) and add the number of edges given
|
592 |
+
# for each pair.
|
593 |
+
for k in nkk:
|
594 |
+
for l in nkk[k]:
|
595 |
+
n_edges_add = nkk[k][l]
|
596 |
+
|
597 |
+
if n_edges_add > 0:
|
598 |
+
# chords contains a random set of potential edges.
|
599 |
+
chords = set()
|
600 |
+
|
601 |
+
k_len = nk_out[k]
|
602 |
+
l_len = nk_in[l]
|
603 |
+
chords_sample = seed.sample(
|
604 |
+
range(k_len * l_len), n_edges_add + non_chords.get((k, l), 0)
|
605 |
+
)
|
606 |
+
|
607 |
+
num = 0
|
608 |
+
while len(chords) < n_edges_add:
|
609 |
+
i = h_degree_nodelist_out[k][chords_sample[num] % k_len]
|
610 |
+
j = h_degree_nodelist_in[l][chords_sample[num] // k_len]
|
611 |
+
num += 1
|
612 |
+
if i != j:
|
613 |
+
chords.add((i, j))
|
614 |
+
|
615 |
+
# k_unsat and l_unsat consist of nodes of in/out degree k and l
|
616 |
+
# that are unsaturated i.e. those nodes that have at least one
|
617 |
+
# available stub
|
618 |
+
k_unsat = h_degree_nodelist_out_unsat[k]
|
619 |
+
l_unsat = h_degree_nodelist_in_unsat[l]
|
620 |
+
|
621 |
+
while n_edges_add > 0:
|
622 |
+
v, w = chords.pop()
|
623 |
+
chords.add((v, w))
|
624 |
+
|
625 |
+
# if node v has no free stubs then do neighbor switch.
|
626 |
+
if h_node_residual_out[v] == 0:
|
627 |
+
_v = _directed_neighbor_switch(
|
628 |
+
G,
|
629 |
+
v,
|
630 |
+
k_unsat,
|
631 |
+
h_node_residual_out,
|
632 |
+
chords,
|
633 |
+
h_partition_in,
|
634 |
+
l,
|
635 |
+
)
|
636 |
+
if _v is not None:
|
637 |
+
v = _v
|
638 |
+
|
639 |
+
# if node w has no free stubs then do neighbor switch.
|
640 |
+
if h_node_residual_in[w] == 0:
|
641 |
+
_w = _directed_neighbor_switch_rev(
|
642 |
+
G,
|
643 |
+
w,
|
644 |
+
l_unsat,
|
645 |
+
h_node_residual_in,
|
646 |
+
chords,
|
647 |
+
h_partition_out,
|
648 |
+
k,
|
649 |
+
)
|
650 |
+
if _w is not None:
|
651 |
+
w = _w
|
652 |
+
|
653 |
+
# add edge (v,w) and update data structures.
|
654 |
+
G.add_edge(v, w)
|
655 |
+
h_node_residual_out[v] -= 1
|
656 |
+
h_node_residual_in[w] -= 1
|
657 |
+
n_edges_add -= 1
|
658 |
+
chords.discard((v, w))
|
659 |
+
|
660 |
+
if h_node_residual_out[v] == 0:
|
661 |
+
k_unsat.discard(v)
|
662 |
+
if h_node_residual_in[w] == 0:
|
663 |
+
l_unsat.discard(w)
|
664 |
+
return G
|
llmeval-env/lib/python3.10/site-packages/networkx/generators/lattice.py
ADDED
@@ -0,0 +1,367 @@
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|
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|
|
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|
|
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|
|
|
|
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|
|
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|
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|
|
|
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|
|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
"""Functions for generating grid graphs and lattices
|
2 |
+
|
3 |
+
The :func:`grid_2d_graph`, :func:`triangular_lattice_graph`, and
|
4 |
+
:func:`hexagonal_lattice_graph` functions correspond to the three
|
5 |
+
`regular tilings of the plane`_, the square, triangular, and hexagonal
|
6 |
+
tilings, respectively. :func:`grid_graph` and :func:`hypercube_graph`
|
7 |
+
are similar for arbitrary dimensions. Useful relevant discussion can
|
8 |
+
be found about `Triangular Tiling`_, and `Square, Hex and Triangle Grids`_
|
9 |
+
|
10 |
+
.. _regular tilings of the plane: https://en.wikipedia.org/wiki/List_of_regular_polytopes_and_compounds#Euclidean_tilings
|
11 |
+
.. _Square, Hex and Triangle Grids: http://www-cs-students.stanford.edu/~amitp/game-programming/grids/
|
12 |
+
.. _Triangular Tiling: https://en.wikipedia.org/wiki/Triangular_tiling
|
13 |
+
|
14 |
+
"""
|
15 |
+
|
16 |
+
from itertools import repeat
|
17 |
+
from math import sqrt
|
18 |
+
|
19 |
+
import networkx as nx
|
20 |
+
from networkx.classes import set_node_attributes
|
21 |
+
from networkx.exception import NetworkXError
|
22 |
+
from networkx.generators.classic import cycle_graph, empty_graph, path_graph
|
23 |
+
from networkx.relabel import relabel_nodes
|
24 |
+
from networkx.utils import flatten, nodes_or_number, pairwise
|
25 |
+
|
26 |
+
__all__ = [
|
27 |
+
"grid_2d_graph",
|
28 |
+
"grid_graph",
|
29 |
+
"hypercube_graph",
|
30 |
+
"triangular_lattice_graph",
|
31 |
+
"hexagonal_lattice_graph",
|
32 |
+
]
|
33 |
+
|
34 |
+
|
35 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
36 |
+
@nodes_or_number([0, 1])
|
37 |
+
def grid_2d_graph(m, n, periodic=False, create_using=None):
|
38 |
+
"""Returns the two-dimensional grid graph.
|
39 |
+
|
40 |
+
The grid graph has each node connected to its four nearest neighbors.
|
41 |
+
|
42 |
+
Parameters
|
43 |
+
----------
|
44 |
+
m, n : int or iterable container of nodes
|
45 |
+
If an integer, nodes are from `range(n)`.
|
46 |
+
If a container, elements become the coordinate of the nodes.
|
47 |
+
|
48 |
+
periodic : bool or iterable
|
49 |
+
If `periodic` is True, both dimensions are periodic. If False, none
|
50 |
+
are periodic. If `periodic` is iterable, it should yield 2 bool
|
51 |
+
values indicating whether the 1st and 2nd axes, respectively, are
|
52 |
+
periodic.
|
53 |
+
|
54 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
55 |
+
Graph type to create. If graph instance, then cleared before populated.
|
56 |
+
|
57 |
+
Returns
|
58 |
+
-------
|
59 |
+
NetworkX graph
|
60 |
+
The (possibly periodic) grid graph of the specified dimensions.
|
61 |
+
|
62 |
+
"""
|
63 |
+
G = empty_graph(0, create_using)
|
64 |
+
row_name, rows = m
|
65 |
+
col_name, cols = n
|
66 |
+
G.add_nodes_from((i, j) for i in rows for j in cols)
|
67 |
+
G.add_edges_from(((i, j), (pi, j)) for pi, i in pairwise(rows) for j in cols)
|
68 |
+
G.add_edges_from(((i, j), (i, pj)) for i in rows for pj, j in pairwise(cols))
|
69 |
+
|
70 |
+
try:
|
71 |
+
periodic_r, periodic_c = periodic
|
72 |
+
except TypeError:
|
73 |
+
periodic_r = periodic_c = periodic
|
74 |
+
|
75 |
+
if periodic_r and len(rows) > 2:
|
76 |
+
first = rows[0]
|
77 |
+
last = rows[-1]
|
78 |
+
G.add_edges_from(((first, j), (last, j)) for j in cols)
|
79 |
+
if periodic_c and len(cols) > 2:
|
80 |
+
first = cols[0]
|
81 |
+
last = cols[-1]
|
82 |
+
G.add_edges_from(((i, first), (i, last)) for i in rows)
|
83 |
+
# both directions for directed
|
84 |
+
if G.is_directed():
|
85 |
+
G.add_edges_from((v, u) for u, v in G.edges())
|
86 |
+
return G
|
87 |
+
|
88 |
+
|
89 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
90 |
+
def grid_graph(dim, periodic=False):
|
91 |
+
"""Returns the *n*-dimensional grid graph.
|
92 |
+
|
93 |
+
The dimension *n* is the length of the list `dim` and the size in
|
94 |
+
each dimension is the value of the corresponding list element.
|
95 |
+
|
96 |
+
Parameters
|
97 |
+
----------
|
98 |
+
dim : list or tuple of numbers or iterables of nodes
|
99 |
+
'dim' is a tuple or list with, for each dimension, either a number
|
100 |
+
that is the size of that dimension or an iterable of nodes for
|
101 |
+
that dimension. The dimension of the grid_graph is the length
|
102 |
+
of `dim`.
|
103 |
+
|
104 |
+
periodic : bool or iterable
|
105 |
+
If `periodic` is True, all dimensions are periodic. If False all
|
106 |
+
dimensions are not periodic. If `periodic` is iterable, it should
|
107 |
+
yield `dim` bool values each of which indicates whether the
|
108 |
+
corresponding axis is periodic.
|
109 |
+
|
110 |
+
Returns
|
111 |
+
-------
|
112 |
+
NetworkX graph
|
113 |
+
The (possibly periodic) grid graph of the specified dimensions.
|
114 |
+
|
115 |
+
Examples
|
116 |
+
--------
|
117 |
+
To produce a 2 by 3 by 4 grid graph, a graph on 24 nodes:
|
118 |
+
|
119 |
+
>>> from networkx import grid_graph
|
120 |
+
>>> G = grid_graph(dim=(2, 3, 4))
|
121 |
+
>>> len(G)
|
122 |
+
24
|
123 |
+
>>> G = grid_graph(dim=(range(7, 9), range(3, 6)))
|
124 |
+
>>> len(G)
|
125 |
+
6
|
126 |
+
"""
|
127 |
+
from networkx.algorithms.operators.product import cartesian_product
|
128 |
+
|
129 |
+
if not dim:
|
130 |
+
return empty_graph(0)
|
131 |
+
|
132 |
+
try:
|
133 |
+
func = (cycle_graph if p else path_graph for p in periodic)
|
134 |
+
except TypeError:
|
135 |
+
func = repeat(cycle_graph if periodic else path_graph)
|
136 |
+
|
137 |
+
G = next(func)(dim[0])
|
138 |
+
for current_dim in dim[1:]:
|
139 |
+
Gnew = next(func)(current_dim)
|
140 |
+
G = cartesian_product(Gnew, G)
|
141 |
+
# graph G is done but has labels of the form (1, (2, (3, 1))) so relabel
|
142 |
+
H = relabel_nodes(G, flatten)
|
143 |
+
return H
|
144 |
+
|
145 |
+
|
146 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
147 |
+
def hypercube_graph(n):
|
148 |
+
"""Returns the *n*-dimensional hypercube graph.
|
149 |
+
|
150 |
+
The nodes are the integers between 0 and ``2 ** n - 1``, inclusive.
|
151 |
+
|
152 |
+
For more information on the hypercube graph, see the Wikipedia
|
153 |
+
article `Hypercube graph`_.
|
154 |
+
|
155 |
+
.. _Hypercube graph: https://en.wikipedia.org/wiki/Hypercube_graph
|
156 |
+
|
157 |
+
Parameters
|
158 |
+
----------
|
159 |
+
n : int
|
160 |
+
The dimension of the hypercube.
|
161 |
+
The number of nodes in the graph will be ``2 ** n``.
|
162 |
+
|
163 |
+
Returns
|
164 |
+
-------
|
165 |
+
NetworkX graph
|
166 |
+
The hypercube graph of dimension *n*.
|
167 |
+
"""
|
168 |
+
dim = n * [2]
|
169 |
+
G = grid_graph(dim)
|
170 |
+
return G
|
171 |
+
|
172 |
+
|
173 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
174 |
+
def triangular_lattice_graph(
|
175 |
+
m, n, periodic=False, with_positions=True, create_using=None
|
176 |
+
):
|
177 |
+
r"""Returns the $m$ by $n$ triangular lattice graph.
|
178 |
+
|
179 |
+
The `triangular lattice graph`_ is a two-dimensional `grid graph`_ in
|
180 |
+
which each square unit has a diagonal edge (each grid unit has a chord).
|
181 |
+
|
182 |
+
The returned graph has $m$ rows and $n$ columns of triangles. Rows and
|
183 |
+
columns include both triangles pointing up and down. Rows form a strip
|
184 |
+
of constant height. Columns form a series of diamond shapes, staggered
|
185 |
+
with the columns on either side. Another way to state the size is that
|
186 |
+
the nodes form a grid of `m+1` rows and `(n + 1) // 2` columns.
|
187 |
+
The odd row nodes are shifted horizontally relative to the even rows.
|
188 |
+
|
189 |
+
Directed graph types have edges pointed up or right.
|
190 |
+
|
191 |
+
Positions of nodes are computed by default or `with_positions is True`.
|
192 |
+
The position of each node (embedded in a euclidean plane) is stored in
|
193 |
+
the graph using equilateral triangles with sidelength 1.
|
194 |
+
The height between rows of nodes is thus $\sqrt(3)/2$.
|
195 |
+
Nodes lie in the first quadrant with the node $(0, 0)$ at the origin.
|
196 |
+
|
197 |
+
.. _triangular lattice graph: http://mathworld.wolfram.com/TriangularGrid.html
|
198 |
+
.. _grid graph: http://www-cs-students.stanford.edu/~amitp/game-programming/grids/
|
199 |
+
.. _Triangular Tiling: https://en.wikipedia.org/wiki/Triangular_tiling
|
200 |
+
|
201 |
+
Parameters
|
202 |
+
----------
|
203 |
+
m : int
|
204 |
+
The number of rows in the lattice.
|
205 |
+
|
206 |
+
n : int
|
207 |
+
The number of columns in the lattice.
|
208 |
+
|
209 |
+
periodic : bool (default: False)
|
210 |
+
If True, join the boundary vertices of the grid using periodic
|
211 |
+
boundary conditions. The join between boundaries is the final row
|
212 |
+
and column of triangles. This means there is one row and one column
|
213 |
+
fewer nodes for the periodic lattice. Periodic lattices require
|
214 |
+
`m >= 3`, `n >= 5` and are allowed but misaligned if `m` or `n` are odd
|
215 |
+
|
216 |
+
with_positions : bool (default: True)
|
217 |
+
Store the coordinates of each node in the graph node attribute 'pos'.
|
218 |
+
The coordinates provide a lattice with equilateral triangles.
|
219 |
+
Periodic positions shift the nodes vertically in a nonlinear way so
|
220 |
+
the edges don't overlap so much.
|
221 |
+
|
222 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
223 |
+
Graph type to create. If graph instance, then cleared before populated.
|
224 |
+
|
225 |
+
Returns
|
226 |
+
-------
|
227 |
+
NetworkX graph
|
228 |
+
The *m* by *n* triangular lattice graph.
|
229 |
+
"""
|
230 |
+
H = empty_graph(0, create_using)
|
231 |
+
if n == 0 or m == 0:
|
232 |
+
return H
|
233 |
+
if periodic:
|
234 |
+
if n < 5 or m < 3:
|
235 |
+
msg = f"m > 2 and n > 4 required for periodic. m={m}, n={n}"
|
236 |
+
raise NetworkXError(msg)
|
237 |
+
|
238 |
+
N = (n + 1) // 2 # number of nodes in row
|
239 |
+
rows = range(m + 1)
|
240 |
+
cols = range(N + 1)
|
241 |
+
# Make grid
|
242 |
+
H.add_edges_from(((i, j), (i + 1, j)) for j in rows for i in cols[:N])
|
243 |
+
H.add_edges_from(((i, j), (i, j + 1)) for j in rows[:m] for i in cols)
|
244 |
+
# add diagonals
|
245 |
+
H.add_edges_from(((i, j), (i + 1, j + 1)) for j in rows[1:m:2] for i in cols[:N])
|
246 |
+
H.add_edges_from(((i + 1, j), (i, j + 1)) for j in rows[:m:2] for i in cols[:N])
|
247 |
+
# identify boundary nodes if periodic
|
248 |
+
from networkx.algorithms.minors import contracted_nodes
|
249 |
+
|
250 |
+
if periodic is True:
|
251 |
+
for i in cols:
|
252 |
+
H = contracted_nodes(H, (i, 0), (i, m))
|
253 |
+
for j in rows[:m]:
|
254 |
+
H = contracted_nodes(H, (0, j), (N, j))
|
255 |
+
elif n % 2:
|
256 |
+
# remove extra nodes
|
257 |
+
H.remove_nodes_from((N, j) for j in rows[1::2])
|
258 |
+
|
259 |
+
# Add position node attributes
|
260 |
+
if with_positions:
|
261 |
+
ii = (i for i in cols for j in rows)
|
262 |
+
jj = (j for i in cols for j in rows)
|
263 |
+
xx = (0.5 * (j % 2) + i for i in cols for j in rows)
|
264 |
+
h = sqrt(3) / 2
|
265 |
+
if periodic:
|
266 |
+
yy = (h * j + 0.01 * i * i for i in cols for j in rows)
|
267 |
+
else:
|
268 |
+
yy = (h * j for i in cols for j in rows)
|
269 |
+
pos = {(i, j): (x, y) for i, j, x, y in zip(ii, jj, xx, yy) if (i, j) in H}
|
270 |
+
set_node_attributes(H, pos, "pos")
|
271 |
+
return H
|
272 |
+
|
273 |
+
|
274 |
+
@nx._dispatchable(graphs=None, returns_graph=True)
|
275 |
+
def hexagonal_lattice_graph(
|
276 |
+
m, n, periodic=False, with_positions=True, create_using=None
|
277 |
+
):
|
278 |
+
"""Returns an `m` by `n` hexagonal lattice graph.
|
279 |
+
|
280 |
+
The *hexagonal lattice graph* is a graph whose nodes and edges are
|
281 |
+
the `hexagonal tiling`_ of the plane.
|
282 |
+
|
283 |
+
The returned graph will have `m` rows and `n` columns of hexagons.
|
284 |
+
`Odd numbered columns`_ are shifted up relative to even numbered columns.
|
285 |
+
|
286 |
+
Positions of nodes are computed by default or `with_positions is True`.
|
287 |
+
Node positions creating the standard embedding in the plane
|
288 |
+
with sidelength 1 and are stored in the node attribute 'pos'.
|
289 |
+
`pos = nx.get_node_attributes(G, 'pos')` creates a dict ready for drawing.
|
290 |
+
|
291 |
+
.. _hexagonal tiling: https://en.wikipedia.org/wiki/Hexagonal_tiling
|
292 |
+
.. _Odd numbered columns: http://www-cs-students.stanford.edu/~amitp/game-programming/grids/
|
293 |
+
|
294 |
+
Parameters
|
295 |
+
----------
|
296 |
+
m : int
|
297 |
+
The number of rows of hexagons in the lattice.
|
298 |
+
|
299 |
+
n : int
|
300 |
+
The number of columns of hexagons in the lattice.
|
301 |
+
|
302 |
+
periodic : bool
|
303 |
+
Whether to make a periodic grid by joining the boundary vertices.
|
304 |
+
For this to work `n` must be even and both `n > 1` and `m > 1`.
|
305 |
+
The periodic connections create another row and column of hexagons
|
306 |
+
so these graphs have fewer nodes as boundary nodes are identified.
|
307 |
+
|
308 |
+
with_positions : bool (default: True)
|
309 |
+
Store the coordinates of each node in the graph node attribute 'pos'.
|
310 |
+
The coordinates provide a lattice with vertical columns of hexagons
|
311 |
+
offset to interleave and cover the plane.
|
312 |
+
Periodic positions shift the nodes vertically in a nonlinear way so
|
313 |
+
the edges don't overlap so much.
|
314 |
+
|
315 |
+
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
316 |
+
Graph type to create. If graph instance, then cleared before populated.
|
317 |
+
If graph is directed, edges will point up or right.
|
318 |
+
|
319 |
+
Returns
|
320 |
+
-------
|
321 |
+
NetworkX graph
|
322 |
+
The *m* by *n* hexagonal lattice graph.
|
323 |
+
"""
|
324 |
+
G = empty_graph(0, create_using)
|
325 |
+
if m == 0 or n == 0:
|
326 |
+
return G
|
327 |
+
if periodic and (n % 2 == 1 or m < 2 or n < 2):
|
328 |
+
msg = "periodic hexagonal lattice needs m > 1, n > 1 and even n"
|
329 |
+
raise NetworkXError(msg)
|
330 |
+
|
331 |
+
M = 2 * m # twice as many nodes as hexagons vertically
|
332 |
+
rows = range(M + 2)
|
333 |
+
cols = range(n + 1)
|
334 |
+
# make lattice
|
335 |
+
col_edges = (((i, j), (i, j + 1)) for i in cols for j in rows[: M + 1])
|
336 |
+
row_edges = (((i, j), (i + 1, j)) for i in cols[:n] for j in rows if i % 2 == j % 2)
|
337 |
+
G.add_edges_from(col_edges)
|
338 |
+
G.add_edges_from(row_edges)
|
339 |
+
# Remove corner nodes with one edge
|
340 |
+
G.remove_node((0, M + 1))
|
341 |
+
G.remove_node((n, (M + 1) * (n % 2)))
|
342 |
+
|
343 |
+
# identify boundary nodes if periodic
|
344 |
+
from networkx.algorithms.minors import contracted_nodes
|
345 |
+
|
346 |
+
if periodic:
|
347 |
+
for i in cols[:n]:
|
348 |
+
G = contracted_nodes(G, (i, 0), (i, M))
|
349 |
+
for i in cols[1:]:
|
350 |
+
G = contracted_nodes(G, (i, 1), (i, M + 1))
|
351 |
+
for j in rows[1:M]:
|
352 |
+
G = contracted_nodes(G, (0, j), (n, j))
|
353 |
+
G.remove_node((n, M))
|
354 |
+
|
355 |
+
# calc position in embedded space
|
356 |
+
ii = (i for i in cols for j in rows)
|
357 |
+
jj = (j for i in cols for j in rows)
|
358 |
+
xx = (0.5 + i + i // 2 + (j % 2) * ((i % 2) - 0.5) for i in cols for j in rows)
|
359 |
+
h = sqrt(3) / 2
|
360 |
+
if periodic:
|
361 |
+
yy = (h * j + 0.01 * i * i for i in cols for j in rows)
|
362 |
+
else:
|
363 |
+
yy = (h * j for i in cols for j in rows)
|
364 |
+
# exclude nodes not in G
|
365 |
+
pos = {(i, j): (x, y) for i, j, x, y in zip(ii, jj, xx, yy) if (i, j) in G}
|
366 |
+
set_node_attributes(G, pos, "pos")
|
367 |
+
return G
|