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dingye18 and others added 30 commits January 29, 2023 16:59
* Update the c interface with deepmd

* Remove the setting to GPUNode for DeepPot

* Improved the packaging of the plugin

* Remove simtk in import modules

* Small edit on version control in setup.py

* Add ci config yaml

* Fix bug in github actions

* Build up the environment for CI unit test

* Update github actions run on self-hosted runners

* Update image to ghcr.io

* Add docker login to ghcr.io

* Update ci.yml

* Update ci.yml

* Update ci.yml

* Add credentials in image pul

* Update ci

* Update ci

* Update ci

* Test

* Small fixs for github actions running in container

* Update env variable name

* Update env variable name

* Update env variable name

* Minor fix

* Update env variable name

* test

* test

* Update test for CUDA platform

* remove redundant files

* Remove depend in CUDA toolkit include

* Update container image

* Fix bug in load conda environment

* Fix bug in load conda environment

* Debug

* Debug

* Debug

* Debug

* Small updates in image name
* Update the c interface with deepmd

* Remove the setting to GPUNode for DeepPot

* Improved the packaging of the plugin

* Remove simtk in import modules

* Small edit on version control in setup.py

* Add ci config yaml

* Fix bug in github actions

* Build up the environment for CI unit test

* Update github actions run on self-hosted runners

* Update image to ghcr.io

* Add docker login to ghcr.io

* Update ci.yml

* Update ci.yml

* Update ci.yml

* Add credentials in image pul

* Update ci

* Update ci

* Update ci

* Test

* Small fixs for github actions running in container

* Update env variable name

* Update env variable name

* Update env variable name

* Minor fix

* Update env variable name

* test

* test

* Update test for CUDA platform

* remove redundant files

* Remove depend in CUDA toolkit include

* Update container image

* Fix bug in load conda environment

* Fix bug in load conda environment

* Debug

* Debug

* Debug

* Debug

* Small updates in image name

* Configure CI with ci.yml (#1)

* Update the c interface with deepmd

* Remove the setting to GPUNode for DeepPot

* Improved the packaging of the plugin

* Remove simtk in import modules

* Small edit on version control in setup.py

* Add ci config yaml

* Fix bug in github actions

* Build up the environment for CI unit test

* Update github actions run on self-hosted runners

* Update image to ghcr.io

* Add docker login to ghcr.io

* Update ci.yml

* Update ci.yml

* Update ci.yml

* Add credentials in image pul

* Update ci

* Update ci

* Update ci

* Test

* Small fixs for github actions running in container

* Update env variable name

* Update env variable name

* Update env variable name

* Minor fix

* Update env variable name

* test

* test

* Update test for CUDA platform

* remove redundant files

* Remove depend in CUDA toolkit include

* Update container image

* Fix bug in load conda environment

* Fix bug in load conda environment

* Debug

* Debug

* Debug

* Debug

* Small updates in image name

* Update readme

* Utilized pytest in CI.

* Small fix

* Small fix

* Small fix

* Fix bug

* Fix bug in pytest

* Update

* Fix bug in pytest

* Update the test for python interface

* Refactor the user interface of dp plugin.

* Update __init__.py

* Update test_deepmd_nve.py

* Update test_dp_plugin_nve.py

* Add tests for nvt, npt, alchemical simulations

* Fix bug in alchemical simulation.

* Updaste unit test threshold

* Updaste unit test threshold

* Update the simulation templates in tests.

* Add support for DP/MM with dixed DP region

* Avoid unit test

* Refactor dp (#3)

* Refactor DP plugin

* Avoid unit test

* Small fix in python

* Update the unit test for dp.mm with fixed region

* Small update in ci.yml

* Add support for dp mask

* Add support for DP/MM with adaptive DP region.

* Add support of dp mask for reference platform

* Fix bugs in adaptive dp region simulation

* Update file name for pytest

* Refactor dp (#4)

* Refactor DP plugin

* Avoid unit test

* Small fix in python

* Update the unit test for dp.mm with fixed region

* Small update in ci.yml

* Add support for dp mask

* Add support for DP/MM with adaptive DP region.

* Add support of dp mask for reference platform

* Fix bugs in adaptive dp region simulation

* Update file name for pytest

* Update image in ci workflow

* Fix bug in ci workflow

* Fix in ci workflow

* Fix in ci workflow

* Refactor dp (#5)

* Refactor DP plugin

* Avoid unit test

* Small fix in python

* Update the unit test for dp.mm with fixed region

* Small update in ci.yml

* Add support for dp mask

* Add support for DP/MM with adaptive DP region.

* Add support of dp mask for reference platform

* Fix bugs in adaptive dp region simulation

* Update file name for pytest

* Update image in ci workflow

* Fix bug in ci workflow

* Small fix

* Test the support for dp mask

* Add test for dp adaptive with multi regions

* Add test for dp adaptive with multi regions

* Small fix in unit test

* Update deepmd C++ API with C API.
* Configure CI with ci.yml (#1)

* Update the c interface with deepmd

* Remove the setting to GPUNode for DeepPot

* Improved the packaging of the plugin

* Remove simtk in import modules

* Small edit on version control in setup.py

* Add ci config yaml

* Fix bug in github actions

* Build up the environment for CI unit test

* Update github actions run on self-hosted runners

* Update image to ghcr.io

* Add docker login to ghcr.io

* Update ci.yml

* Update ci.yml

* Update ci.yml

* Add credentials in image pul

* Update ci

* Update ci

* Update ci

* Test

* Small fixs for github actions running in container

* Update env variable name

* Update env variable name

* Update env variable name

* Minor fix

* Update env variable name

* test

* test

* Update test for CUDA platform

* remove redundant files

* Remove depend in CUDA toolkit include

* Update container image

* Fix bug in load conda environment

* Fix bug in load conda environment

* Debug

* Debug

* Debug

* Debug

* Small updates in image name

* Refactor plugin for support C API of DeePMD-kit (#6)

* Update the c interface with deepmd

* Remove the setting to GPUNode for DeepPot

* Improved the packaging of the plugin

* Remove simtk in import modules

* Small edit on version control in setup.py

* Add ci config yaml

* Fix bug in github actions

* Build up the environment for CI unit test

* Update github actions run on self-hosted runners

* Update image to ghcr.io

* Add docker login to ghcr.io

* Update ci.yml

* Update ci.yml

* Update ci.yml

* Add credentials in image pul

* Update ci

* Update ci

* Update ci

* Test

* Small fixs for github actions running in container

* Update env variable name

* Update env variable name

* Update env variable name

* Minor fix

* Update env variable name

* test

* test

* Update test for CUDA platform

* remove redundant files

* Remove depend in CUDA toolkit include

* Update container image

* Fix bug in load conda environment

* Fix bug in load conda environment

* Debug

* Debug

* Debug

* Debug

* Small updates in image name

* Configure CI with ci.yml (#1)

* Update the c interface with deepmd

* Remove the setting to GPUNode for DeepPot

* Improved the packaging of the plugin

* Remove simtk in import modules

* Small edit on version control in setup.py

* Add ci config yaml

* Fix bug in github actions

* Build up the environment for CI unit test

* Update github actions run on self-hosted runners

* Update image to ghcr.io

* Add docker login to ghcr.io

* Update ci.yml

* Update ci.yml

* Update ci.yml

* Add credentials in image pul

* Update ci

* Update ci

* Update ci

* Test

* Small fixs for github actions running in container

* Update env variable name

* Update env variable name

* Update env variable name

* Minor fix

* Update env variable name

* test

* test

* Update test for CUDA platform

* remove redundant files

* Remove depend in CUDA toolkit include

* Update container image

* Fix bug in load conda environment

* Fix bug in load conda environment

* Debug

* Debug

* Debug

* Debug

* Small updates in image name

* Update readme

* Utilized pytest in CI.

* Small fix

* Small fix

* Small fix

* Fix bug

* Fix bug in pytest

* Update

* Fix bug in pytest

* Update the test for python interface

* Refactor the user interface of dp plugin.

* Update __init__.py

* Update test_deepmd_nve.py

* Update test_dp_plugin_nve.py

* Add tests for nvt, npt, alchemical simulations

* Fix bug in alchemical simulation.

* Updaste unit test threshold

* Updaste unit test threshold

* Update the simulation templates in tests.

* Add support for DP/MM with dixed DP region

* Avoid unit test

* Refactor dp (#3)

* Refactor DP plugin

* Avoid unit test

* Small fix in python

* Update the unit test for dp.mm with fixed region

* Small update in ci.yml

* Add support for dp mask

* Add support for DP/MM with adaptive DP region.

* Add support of dp mask for reference platform

* Fix bugs in adaptive dp region simulation

* Update file name for pytest

* Refactor dp (#4)

* Refactor DP plugin

* Avoid unit test

* Small fix in python

* Update the unit test for dp.mm with fixed region

* Small update in ci.yml

* Add support for dp mask

* Add support for DP/MM with adaptive DP region.

* Add support of dp mask for reference platform

* Fix bugs in adaptive dp region simulation

* Update file name for pytest

* Update image in ci workflow

* Fix bug in ci workflow

* Fix in ci workflow

* Fix in ci workflow

* Refactor dp (#5)

* Refactor DP plugin

* Avoid unit test

* Small fix in python

* Update the unit test for dp.mm with fixed region

* Small update in ci.yml

* Add support for dp mask

* Add support for DP/MM with adaptive DP region.

* Add support of dp mask for reference platform

* Fix bugs in adaptive dp region simulation

* Update file name for pytest

* Update image in ci workflow

* Fix bug in ci workflow

* Small fix

* Test the support for dp mask

* Add test for dp adaptive with multi regions

* Add test for dp adaptive with multi regions

* Small fix in unit test

* Update deepmd C++ API with C API.

* Move pb to lfs

* Move pb to lfs

* Update the download link to libdeepmd_c package

* update readme

* Add setGPURank function in Deep Potential model

* Update Readme.
@dingye18 dingye18 self-assigned this May 16, 2025
@dingye18 dingye18 requested a review from Copilot May 16, 2025 02:47
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Pull Request Overview

This pull request adds conda packaging support by incorporating a build script, conda recipe files, and an updated installation guide while also updating test logging comments and parameters. Key changes include:

  • Adjusting test scripts to correctly indicate that total energy is logged instead of temperature.
  • Adding conda packaging metadata, build scripts, and a patch for CUDA.
  • Updating the CMakeLists.txt to conditionally reinstall the DeepMD library for conda environments.

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file
File Description
python/tests/test_deepmd_dp_region.py Updated comments and main test call parameters for energy logging.
platforms/cuda/include/CudaDeepmdKernels.h Removed outdated comments regarding alchemical simulation.
README.md Added a conda-installation section and introduced a spelling issue.
CMakeLists.txt Added options to reinstall DeepMD lib for conda, with enhanced messaging.
.conda/meta.yaml Added conda packaging recipe metadata.
.conda/cuda_platform.patch Updated tests subdirectory inclusion via patch.
.conda/conda_build_config.yaml Added channel sources configuration.
.conda/build.sh Introduced the build script for conda packaging.

dingye18 and others added 2 commits May 16, 2025 10:58
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@dingye18 dingye18 requested a review from Copilot May 16, 2025 02:59
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Pull Request Overview

This PR adds conda packaging support by introducing packaging scripts, configuration files, and installation instructions while making minor comment and parameter updates in test files and the CUDA kernel header.

  • Updated test comments to reflect energy info instead of temperature
  • Revised conda packaging setup with new meta.yaml, build.sh, and supporting files
  • Enhanced CMakeLists.txt messages and included a conda-specific build option

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file
File Description
python/tests/test_deepmd_dp_region.py Updated comments and main test parameters to reflect energy-based results
platforms/cuda/include/CudaDeepmdKernels.h Removed outdated comments regarding alchemical simulation
README.md Added conda installation instructions
CMakeLists.txt Added conda-specific build options and improved Python/SWIG detection messages
.conda/meta.yaml Introduced the recipe for the conda package with appropriate dependencies
.conda/cuda_platform.patch Modified tests subdirectory inclusion in the CUDA platform build configuration
.conda/conda_build_config.yaml Added conda build configuration for linux-64 and ppc64le platforms
.conda/build.sh Added build script that automates library download, build, installation, and cleanup
Comments suppressed due to low confidence (2)

platforms/cuda/include/CudaDeepmdKernels.h:57

  • The removal of outdated comments regarding alchemical simulation is clear; please ensure any related obsolete code or documentation is updated accordingly.
// graph_file 1 and 2 are used for alchemical simulation.

.conda/build.sh:18

  • [nitpick] Verify that removing the entire '${PREFIX}/libdeepmd_c' directory does not impact runtime dependencies, and consider adding a comment to clarify this cleanup step.
rm -r ${PREFIX}/libdeepmd_c

@dingye18 dingye18 removed their assignment May 16, 2025
@dingye18 dingye18 requested a review from HDsky May 16, 2025 03:19
dingye18

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@dingye18 dingye18 merged commit d78280c into JingHuangLab:master May 20, 2025
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2 participants