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 support for PaddlePaddle in the DeePMD framework, enhancing model training and evaluation capabilities.
- Added new backend options and configuration files for multitask models.
- Implemented new classes and methods for handling Paddle-specific functionalities, including descriptor calculations and model evaluations.
- Enhanced the command-line interface to include Paddle as a backend option.
- Expanded the functionality for managing Paddle dependencies and configurations in the testing framework.
Bug Fixes
- Improved error handling and robustness in various components across the framework.
Tests
- Expanded the test suite to include Paddle-specific tests, ensuring consistency and reliability across different backends.
- Introduced unit tests for new functionalities related to Paddle, including model evaluations and descriptor calculations.
- Added tests to validate force gradient calculations and smoothness properties in models.
- Implemented tests for neighbor statistics and region transformations, ensuring accuracy in calculations.
Documentation
- Updated documentation across multiple modules to reflect new features and usage instructions.

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 updates across multiple files to enhance the integration of PaddlePaddle within the DeepMD framework. Key changes include updates to workflow configurations for testing, the addition of new classes and methods for Paddle-specific functionalities, and enhancements to existing tests to accommodate Paddle. The updates also include new JSON configuration files for models, improvements in error handling, and the introduction of new utility functions, all aimed at expanding the framework's capabilities and ensuring compatibility with PaddlePaddle.

Changes

File Path	Change Summary
`.github/workflows/test_python.yml`	Added `branches-ignore` for certain branches and a `merge_group` for job concurrency management. A new installation step for PaddlePaddle added in `testpython` job.
`backend/find_paddle.py`	Introduced functions for locating PaddlePaddle library and managing its version requirements.
`deepmd/backend/paddle.py`	Added `PaddleBackend` class with methods for backend availability and model serialization.
`deepmd/main.py`	Enhanced command-line interface to include a new backend option for Paddle.
`deepmd/pd/entrypoints/__init__.py`	Added SPDX license identifier.
`deepmd/pd/entrypoints/main.py`	Implemented command-line functionalities for managing model training and evaluation.
`deepmd/pd/infer/deep_eval.py`	Introduced `DeepEval` class for evaluating models in Paddle.
`deepmd/pd/infer/inference.py`	Added `Tester` class for testing DeePMD models.
`deepmd/pd/loss/__init__.py`	New module for loss functions initialized with imports.
`deepmd/pd/loss/ener.py`	Introduced `EnergyStdLoss` class for computing energy-related losses.
`deepmd/pd/loss/loss.py`	Added `TaskLoss` class for defining loss function interfaces.
`deepmd/pd/model/__init__.py`	Added SPDX license identifier.
`deepmd/pd/model/atomic_model/__init__.py`	New module documentation added for atomic models.
`deepmd/pd/model/atomic_model/base_atomic_model.py`	Introduced `BaseAtomicModel` class for managing atomic contributions.
`deepmd/pd/model/atomic_model/dp_atomic_model.py`	Added `DPAtomicModel` class for atomic predictions.
`deepmd/pd/model/atomic_model/energy_atomic_model.py`	Introduced `DPEnergyAtomicModel` for energy atomic modeling.
`deepmd/pd/model/descriptor/__init__.py`	New module for descriptor initialization.
`deepmd/pd/model/descriptor/base_descriptor.py`	Added `BaseDescriptor` for descriptor functionalities.
`deepmd/pd/model/descriptor/descriptor.py`	Introduced `DescriptorBlock` class for descriptor implementations.
`deepmd/pd/model/descriptor/env_mat.py`	Added functions for constructing environment matrices.
`deepmd/pd/model/descriptor/se_a.py`	Introduced `DescrptSeA` class for specific descriptor calculations.
`deepmd/pd/model/model/__init__.py`	Updated model framework with detailed docstring and internal functions.
`deepmd/pd/model/model/dp_model.py`	Added `DPModelCommon` class for common model methods.
`deepmd/pd/model/model/ener_model.py`	Introduced `EnergyModel` class for energy-related predictions.
`deepmd/pd/model/model/frozen.py`	Added `FrozenModel` class for loading models from frozen states.
`deepmd/pd/model/model/make_model.py`	Introduced `make_model` function for model creation.
`deepmd/pd/model/model/model.py`	Added `BaseModel` class for foundational model functionalities.
`deepmd/pd/model/model/transform_output.py`	Introduced functions for transforming model outputs.
`deepmd/pd/model/network/__init__.py`	Added SPDX license identifier.
`deepmd/pd/model/network/init.py`	Introduced tensor initialization functions for Paddle.
`deepmd/pd/model/network/mlp.py`	Implemented MLP architecture with various layer classes.
`deepmd/pd/model/network/network.py`	Enhanced type embedding network functionalities.
`deepmd/pd/model/task/__init__.py`	New module initialization for task-related classes.
`deepmd/pd/model/task/base_fitting.py`	Introduced `BaseFitting` class for fitting networks.
`deepmd/pd/model/task/ener.py`	Added `EnergyFittingNet` class for energy fitting networks.
`deepmd/pd/model/task/fitting.py`	Introduced `Fitting` class for multitask fitting networks.
`deepmd/pd/model/task/invar_fitting.py`	Added `InvarFitting` class for invariant fitting networks.
`deepmd/pd/model/task/task.py`	Added SPDX license identifier.
`deepmd/pd/train/__init__.py`	Introduced SPDX license identifier.
`deepmd/pd/train/training.py`	Added `Trainer` class for managing the training process.
`deepmd/pd/train/wrapper.py`	Introduced `ModelWrapper` class for encapsulating models.
`deepmd/pd/utils/__init__.py`	Added SPDX license identifier.
`deepmd/pd/utils/auto_batch_size.py`	Introduced `AutoBatchSize` class for managing batch sizes.
`deepmd/pd/utils/dataloader.py`	Added `DpLoaderSet` class for parallelized data loading.
`deepmd/pd/utils/dataset.py`	Introduced `DeepmdDataSetForLoader` class for managing datasets.
`deepmd/pd/utils/decomp.py`	Added functions for high-order differentiation.
`deepmd/pd/utils/dp_random.py`	Introduced `dp_random.py` for random number generation utilities.
`deepmd/pd/utils/env.py`	Enhanced environment configuration functionalities.
`deepmd/pd/utils/env_mat_stat.py`	Added `EnvMatStat` classes for environmental matrix statistics.
`deepmd/pd/utils/exclude_mask.py`	Introduced `AtomExcludeMask` and `PairExcludeMask` classes for handling exclusion masks.
`deepmd/pd/utils/finetune.py`	Added functions for fine-tuning models.
`deepmd/pd/utils/multi_task.py`	Introduced functions for preprocessing shared parameters in multitask models.
`deepmd/pd/utils/neighbor_stat.py`	Added `NeighborStatOP` and `NeighborStat` classes for neighbor statistics.
`deepmd/pd/utils/nlist.py`	Introduced functions for managing neighbor lists.
`deepmd/pd/utils/preprocess.py`	Added `compute_smooth_weight` function for calculating smooth weights.
`deepmd/pd/utils/region.py`	Introduced functions for coordinate transformations.
`deepmd/pd/utils/serialization.py`	Added serialization and deserialization functions for models.
`deepmd/pd/utils/stat.py`	Introduced functions for computing and managing statistical data.
`deepmd/pd/utils/update_sel.py`	Added `UpdateSel` class for managing selection updates.
`deepmd/pd/utils/utils.py`	Enhanced `ActivationFn` class and utility functions for tensor operations.
`deepmd/utils/batch_size.py`	Updated `AutoBatchSize` class for handling batch operations.
`deepmd/utils/data.py`	Introduced `get_item_paddle` method for Paddle data retrieval.
`pyproject.toml`	Updated dependency management and testing configurations for Paddle.
`source/tests/consistent/common.py`	Added support for Paddle in the testing framework.
`source/tests/consistent/descriptor/common.py`	Introduced Paddle evaluation methods in descriptor tests.
`source/tests/consistent/descriptor/test_se_e2_a.py`	Enhanced descriptor tests to include Paddle functionality.
`source/tests/consistent/fitting/common.py`	Added Paddle conditional checks in fitting tests.
`source/tests/consistent/fitting/test_ener.py`	Enhanced energy fitting tests to support Paddle.
`source/tests/consistent/model/common.py`	Introduced Paddle utilities in model tests.
`source/tests/consistent/model/test_ener.py`	Integrated Paddle into energy model tests.
`source/tests/consistent/test_activation.py`	Added Paddle activation function tests.
`source/tests/consistent/test_type_embedding.py`	Enhanced type embedding tests to support Paddle.
`source/tests/pd/__init__.py`	Added license identifier and initialization for Paddle.
`source/tests/pd/model/test_force_grad.py`	Introduced unit tests for force gradient calculations.
`source/tests/pd/model/test_jit.py`	Added unit tests for JIT compilation functionality.
`source/tests/pd/model/test_null_input.py`	Established tests for null input scenarios.
`source/tests/pd/model/test_smooth.py`	Introduced tests for model smoothness properties.
`source/tests/pd/test_change_bias.py`	Added tests for changing model output bias.
`deepmd/dpmodel/model/make_model.py`	Enhanced model creation functions with additional methods.
`source/tests/consistent/test_neighbor_stat.py`	Added Paddle support in neighbor statistics tests.
`source/tests/pd/model/test_descriptor.py`	Established tests for descriptor functionality.
`source/tests/pd/model/test_embedding_net.py`	Introduced tests for embedding networks.
`source/tests/pd/model/test_model.py`	Added tests for model behavior and consistency across frameworks.
`source/tests/pd/model/water/se_atten.json`	New JSON configuration for model parameters.
`source/tests/pd/model/water/multitask.json`	New JSON configuration for multitask model parameters.

Sequence Diagram(s)

sequenceDiagram
    participant CI as CI Workflow
    participant Test as Test Runner
    participant Paddle as Paddle Backend
    participant Model as DeepMD Model

    CI->>Test: Trigger Tests
    Test->>Paddle: Check Paddle Installation
    alt Paddle Installed
        Test->>Model: Load Model
        Model->>Paddle: Run Model Evaluation
        Paddle-->>Model: Return Results
        Test-->>CI: Report Success
    else Paddle Not Installed
        Test-->>CI: Report Skipped Tests
    end

Possibly related PRs

ci: install GPU JAX in GPU CI #4293: The changes in the main PR regarding the workflow configuration for testing Python and the addition of PaddlePaddle are related to the installation of GPU JAX in the CI, as both involve enhancing the testing framework to accommodate new dependencies.
fix: consistent DPA-1 model #4320: The modifications to the DescrptHybrid class in the retrieved PR enhance the configurability of descriptors, which aligns with the main PR's focus on expanding the testing framework to include PaddlePaddle, indicating a broader effort to improve model handling across different frameworks.
fix(dp/pt): support auto sel for dpa2 #4323: The updates to the DescrptDPA2 class in this PR, which enhance the selection update process, are relevant as they reflect ongoing improvements in model descriptors that may be tested or utilized in the updated testing workflows introduced in the main PR.

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njzjz
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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 79.67517% with 876 lines in your changes missing coverage. Please review.

Project coverage is 83.19%. Comparing base (0ad4289) to head (7e05c35).
Report is 106 commits behind head on devel.

Files with missing lines	Patch %	Lines
deepmd/pd/train/training.py	76.48%	139 Missing ⚠️
deepmd/pd/infer/deep_eval.py	44.00%	98 Missing ⚠️
deepmd/pd/model/network/init.py	23.85%	83 Missing ⚠️
deepmd/pd/entrypoints/main.py	66.82%	71 Missing ⚠️
deepmd/pd/utils/stat.py	75.68%	53 Missing ⚠️
deepmd/pd/model/network/network.py	57.14%	45 Missing ⚠️
deepmd/pd/model/network/mlp.py	73.91%	36 Missing ⚠️
deepmd/pd/model/task/fitting.py	84.28%	33 Missing ⚠️
deepmd/pd/utils/dataloader.py	82.24%	30 Missing ⚠️
deepmd/pd/model/model/frozen.py	53.33%	28 Missing ⚠️
... and 30 more

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #4302      +/-   ##
==========================================
- Coverage   84.50%   83.19%   -1.31%     
==========================================
  Files         596      649      +53     
  Lines       56665    60967    +4302     
  Branches     3459     3461       +2     
==========================================
+ Hits        47884    50721    +2837     
- Misses       7654     9118    +1464     
- Partials     1127     1128       +1

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

…y to coverage newly added code

njzjz · 2024-11-06T22:33:03Z

Attention: Patch coverage is 55.25965% with 2016 lines in your changes missing coverage. Please review.

About 2000+ lines have yet to be tested in the CI. Could you take a look at the coverage report?

HydrogenSulfate · 2024-11-15T04:46:42Z

I have some additional comments. We can merge this PR after v3.0.0 is released and the r3.0 branch is checked out.

Thanks for the comments, redundant files&codes were removed.

Copilot

Copilot reviewed 121 out of 136 changed files in this pull request and generated no suggestions.

Files not reviewed (15)

deepmd/pd/infer/init.py: Evaluated as low risk
deepmd/pd/entrypoints/init.py: Evaluated as low risk
deepmd/dpmodel/model/make_model.py: Evaluated as low risk
deepmd/main.py: Evaluated as low risk
.github/workflows/test_python.yml: Evaluated as low risk
deepmd/pd/model/init.py: Evaluated as low risk
.github/workflows/test_cuda.yml: Evaluated as low risk
deepmd/pd/model/atomic_model/dp_atomic_model.py: Evaluated as low risk
deepmd/pd/model/atomic_model/energy_atomic_model.py: Evaluated as low risk
deepmd/pd/model/descriptor/env_mat.py: Evaluated as low risk
deepmd/pd/model/descriptor/base_descriptor.py: Evaluated as low risk
deepmd/pd/loss/loss.py: Evaluated as low risk
deepmd/pd/model/descriptor/descriptor.py: Evaluated as low risk
deepmd/pd/model/descriptor/init.py: Evaluated as low risk
deepmd/pd/model/atomic_model/init.py: Evaluated as low risk

njzjz · 2024-11-25T07:28:12Z

@coderabbitai resolve

njzjz · 2024-11-25T07:34:37Z

@coderabbitai resolve

njzjz · 2024-11-25T07:51:26Z

@coderabbitai resolve

... It seems to be not working. The comments may be required to be manually resolved

coderabbitai · 2024-11-25T07:51:57Z

@njzjz: Sorry that the resolve command didn't work earlier. I have now resolved the comments for you.

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njzjz · 2024-11-25T08:39:26Z

@HydrogenSulfate A segfault appears in the GPU test. https://github.com/deepmodeling/deepmd-kit/actions/runs/12005580706/job/33462440790

HydrogenSulfate · 2024-11-25T08:44:23Z

@HydrogenSulfate A segfault appears in the GPU test. https://github.com/deepmodeling/deepmd-kit/actions/runs/12005580706/job/33462440790

Thanks for report, I will check it out

HydrogenSulfate · 2024-11-27T05:23:45Z

@HydrogenSulfate A segfault appears in the GPU test. https://github.com/deepmodeling/deepmd-kit/actions/runs/12005580706/job/33462440790

I have make a new environment with cuda11.8 and installed the nightly build paddle(3.0.0.dev20241126), but all paddle tests running successfully as below.

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2022 NVIDIA Corporation
Built on Wed_Sep_21_10:33:58_PDT_2022
Cuda compilation tools, release 11.8, V11.8.89
Build cuda_11.8.r11.8/compiler.31833905_0

It seems a weird issue and is there any way to get the detailed error log from Test CUDA?

njzjz · 2024-11-27T06:17:45Z

It seems a weird issue and is there any way to get the detailed error log from Test CUDA?

It's run in a docker container, so I think it may be reproducible.

Btw, the image is nvidia/cuda:12.6.2-cudnn-devel-ubuntu22.04

njzjz · 2024-11-27T06:46:47Z

A bit strange, but the segfault disappeared.

HydrogenSulfate · 2024-11-27T08:37:09Z

It seems a weird issue and is there any way to get the detailed error log from Test CUDA?

It's run in a docker container, so I think it may be reproducible.

Btw, the image is nvidia/cuda:12.6.2-cudnn-devel-ubuntu22.04

If we can add -v or -vv to pytest's argument(e.g. pytest -vv source/test/) so the test log can be a bit more detailed(but might not clear enough...)

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 iProzd and njzjz 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

use paddle Tensor instead of numpy array in pd/test_auto_batch_size.p…

07cd98e

…y to coverage newly added code

njzjz approved these changes Nov 15, 2024

View reviewed changes

njzjz requested a review from Copilot November 15, 2024 19:38

Copilot AI reviewed Nov 15, 2024

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iProzd approved these changes Nov 23, 2024

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njzjz assigned wanghan-iapcm Nov 24, 2024

HydrogenSulfate mentioned this pull request Nov 25, 2024

pd: support dpa1 #4414

Merged

9 tasks

njzjz enabled auto-merge November 25, 2024 07:28

njzjz unassigned wanghan-iapcm Nov 25, 2024

njzjz added this pull request to the merge queue Nov 25, 2024

github-merge-queue bot removed this pull request from the merge queue due to failed status checks Nov 25, 2024

njzjz added the Test CUDA Trigger test CUDA workflow label Nov 27, 2024

github-actions bot removed the Test CUDA Trigger test CUDA workflow label Nov 27, 2024

njzjz enabled auto-merge November 27, 2024 06:46

njzjz added this pull request to the merge queue Nov 27, 2024

Merged via the queue into deepmodeling:devel with commit 4a45fe5 Nov 27, 2024
63 checks passed

HydrogenSulfate mentioned this pull request Jan 15, 2025

Integrate paddle backend in devel branch #4157

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This was referenced Jul 22, 2025

[WIP] pd: support dpa2/dpa3 inference #4846

Closed

feat(pt): support zbl finetune #4849

Merged

pd: support paddle backend and water/se_e2_a #4302

pd: support paddle backend and water/se_e2_a #4302

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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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