pd: support paddle backend and `water/se_e2_a` #4302

HydrogenSulfate · 2024-11-03T07:45:53Z

Split #4157 into several pull requests.

Add core modules of paddle backend(deepmd.pd.*) and related backend module unitests.
Support training/testing/freeze(C++ inference will be supported in subsequent pull request) for example water/se_e2_a.
Add se_e2_a related uinttests

Related PR to be merged:

Support numpy scalar as input type case PaddlePaddle/Paddle#69139

Accuracy test

pytorch

paddle:

deepmd.utils.batch_size                       Adjust batch size from 1024 to 2048
deepmd.utils.batch_size                       Adjust batch size from 2048 to 4096
deepmd.entrypoints.test                       # number of test data : 30 ,
deepmd.entrypoints.test                       Energy MAE         : 7.467160e-02 eV
deepmd.entrypoints.test                       Energy RMSE        : 8.981154e-02 eV
deepmd.entrypoints.test                       Energy MAE/Natoms  : 3.889146e-04 eV
deepmd.entrypoints.test                       Energy RMSE/Natoms : 4.677685e-04 eV
deepmd.entrypoints.test                       Force  MAE         : 4.495974e-02 eV/A
deepmd.entrypoints.test                       Force  RMSE        : 5.883696e-02 eV/A
deepmd.entrypoints.test                       Virial MAE         : 4.683873e+00 eV
deepmd.entrypoints.test                       Virial RMSE        : 6.298489e+00 eV
deepmd.entrypoints.test                       Virial MAE/Natoms  : 2.439517e-02 eV
deepmd.entrypoints.test                       Virial RMSE/Natoms : 3.280463e-02 eV

Summary by CodeRabbit

Release Notes

New Features
- Introduced Paddle backend support, enhancing model training and evaluation capabilities.
- Added new classes and methods for handling Paddle-specific functionalities, including descriptors and fitting networks.
- Expanded testing framework to include Paddle, ensuring consistency with existing backends like TensorFlow and PyTorch.
Bug Fixes
- Improved error handling and compatibility checks for Paddle operations.
Documentation
- Updated documentation to reflect new Paddle features and usage instructions.
Tests
- Added comprehensive tests for Paddle integration, ensuring functionality across various model components.

github-advanced-security

CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.

coderabbitai · 2024-11-03T07:57:05Z

📝 Walkthrough

Walkthrough

The pull request introduces significant enhancements to the DeePMD framework, primarily by integrating PaddlePaddle as a new backend. Key changes include updates to the CI workflow for testing, the addition of new classes and methods for managing PaddlePaddle functionalities, and improvements to existing components to support this integration. The modifications also ensure that the testing framework accommodates Paddle alongside TensorFlow and PyTorch, enhancing the overall testing capabilities of the framework.

Changes

File	Change Summary
`.github/workflows/test_python.yml`	Updated workflow to ignore pushes to branches matching "gh-readonly-queue/**", added concurrency management, and included installation of PaddlePaddle.
`backend/find_paddle.py`	Introduced functions to locate PaddlePaddle library and manage its version requirements.
`deepmd/backend/paddle.py`	Added `PaddleBackend` class to integrate Paddle as a backend with various properties and methods.
`deepmd/main.py`	Updated command-line interface to include a new backend option for PaddlePaddle.
`deepmd/pd/cxx_op.py`	Introduced `load_library` function and `ENABLE_CUSTOMIZED_OP` variable for library management.
`deepmd/pd/entrypoints/main.py`	Added command-line interface for managing DeePMD functionalities, including training and freezing models.
`deepmd/pd/infer/deep_eval.py`	Introduced `DeepEval` class for evaluating models using PaddlePaddle.
`deepmd/pd/model`	Multiple files added for various model components, including atomic models, fitting networks, and utilities for managing model interactions with PaddlePaddle.
`deepmd/pd/utils`	New utility files added for data handling, tensor operations, and environment configurations, supporting PaddlePaddle integration.
`pyproject.toml`	Updated dependencies to include PaddlePaddle for testing and modified build configurations.
`source/tests/consistent`	Enhanced test files to support PaddlePaddle, including conditional imports and new evaluation methods for Paddle models.

Possibly related PRs

feat(dpmodel/jax): add entry point for dpmodel and jax backend #4284: Involves adding an entry point for the dpmodel and jax backend, related to the integration of PaddlePaddle.
ci: install GPU JAX in GPU CI #4293: Updates the CI workflow to install GPU JAX, reflecting enhancements to the testing frameworks relevant to PaddlePaddle integration.

Suggested labels

Python

Suggested reviewers

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HydrogenSulfate · 2024-11-03T10:43:01Z

Hello @njzjz , I have a question about the naming of the functions serialize_from_file and deserialize_to_file. According to the docstring explanations for these two functions and the general meaning of "serialize," why can't these functions be named serialize_to_file and deserialize_from_file instead? I was confused when I first saw these two functions.

njzjz · 2024-11-04T23:20:48Z

Hello @njzjz , I have a question about the naming of the functions serialize_from_file and deserialize_to_file. According to the docstring explanations for these two functions and the general meaning of "serialize," why can't these functions be named serialize_to_file and deserialize_from_file instead? I was confused when I first saw these two functions.

Do you mean serialize_hook and deserialize_hook?

deepmd-kit/deepmd/backend/backend.py

Lines 179 to 201 in 38815b3

    
               @property 
        
               @abstractmethod 
        
               def serialize_hook(self) -> Callable[[str], dict]: 
        
                   """The serialize hook to convert the model file to a dictionary. 
        
                   Returns 
        
                   ------- 
        
                   Callable[[str], dict] 
        
                       The serialize hook of the backend. 
        
                   """ 
        
                   pass 
        
               @property 
        
               @abstractmethod 
        
               def deserialize_hook(self) -> Callable[[str, dict], None]: 
        
                   """The deserialize hook to convert the dictionary to a model file. 
        
                   Returns 
        
                   ------- 
        
                   Callable[[str, dict], None] 
        
                       The deserialize hook of the backend. 
        
                   """ 
        
                   pass

codecov · 2024-11-06T03:44:04Z

Codecov Report

Attention: Patch coverage is 55.19308% with 2019 lines in your changes missing coverage. Please review.

Project coverage is 81.12%. Comparing base (dabedd2) to head (39842ff).

Files with missing lines	Patch %	Lines
deepmd/pd/train/training.py	6.51%	531 Missing ⚠️
deepmd/pd/entrypoints/main.py	17.69%	214 Missing ⚠️
deepmd/pd/utils/stat.py	22.47%	169 Missing ⚠️
deepmd/pd/model/network/network.py	37.83%	138 Missing ⚠️
deepmd/pd/utils/preprocess.py	21.76%	133 Missing ⚠️
deepmd/pd/model/network/init.py	23.85%	83 Missing ⚠️
deepmd/pd/utils/finetune.py	10.60%	59 Missing ⚠️
deepmd/pd/model/task/ener.py	41.66%	56 Missing ⚠️
deepmd/pd/utils/env_mat_stat.py	25.67%	55 Missing ⚠️
deepmd/pd/train/wrapper.py	49.03%	53 Missing ⚠️
... and 29 more

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #4302      +/-   ##
==========================================
- Coverage   84.40%   81.12%   -3.29%     
==========================================
  Files         570      624      +54     
  Lines       53071    57577    +4506     
  Branches     3054     3054              
==========================================
+ Hits        44794    46708    +1914     
- Misses       7318     9909    +2591     
- Partials      959      960       +1

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

HydrogenSulfate added 8 commits November 2, 2024 11:14

add core modules of paddle backend and water/se_e2_a example

48f77f3

add paddle code in consistent test

2082a59

clean env and training

2ae45b8

add more test files

7f03a04

Merge branch 'devel' into add_paddle_backend_core_and_water_se_e2_a

4d1c44c

fix pt->pd

72c9b4e

update test_python.yml

3b1c348

restore .pre-commit-config.yaml

a46dcb5

github-actions bot added the Python label Nov 3, 2024

github-advanced-security bot found potential problems Nov 3, 2024

View reviewed changes

remove redundant file

90f9ff9

wanghan-iapcm requested review from njzjz and iProzd November 3, 2024 09:18

njzjz added this to the v3.1.0 milestone Nov 3, 2024

HydrogenSulfate and others added 3 commits November 3, 2024 18:16

Skip bfloat16 for some cases

0a6baa6

enable prim by default in unitest

4b77e55

[pre-commit.ci] auto fixes from pre-commit.com hooks

6e139a2

for more information, see https://pre-commit.ci

HydrogenSulfate changed the title ~~Add paddle backend core and water se e2 a~~ pd: support paddle backend and water/se_e2_a Nov 4, 2024

HydrogenSulfate mentioned this pull request Nov 4, 2024

Support numpy scalar as input type case PaddlePaddle/Paddle#69139

Merged

HydrogenSulfate added 5 commits November 5, 2024 10:48

fix env code

9437957

Merge branch 'devel' into add_paddle_backend_core_and_water_se_e2_a

f1d762f

Merge branch 'devel' into add_paddle_backend_core_and_water_se_e2_a

8534597

update test_ener.py

c22b45d

add missing pd_class

39842ff

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HydrogenSulfate commented Nov 3, 2024 •

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pd: support paddle backend and water/se_e2_a #4302

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HydrogenSulfate commented Nov 3, 2024 • edited Loading

Accuracy test

pytorch

paddle:

Summary by CodeRabbit

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pd: support paddle backend and `water/se_e2_a` #4302

pd: support paddle backend and `water/se_e2_a` #4302

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