{chem}[foss/2023a] LAMMPS v29Aug2024_update2 w/ kokkos with deepmd plugin by laraPPr · Pull Request #23166 · easybuilders/easybuild-easyconfigs

laraPPr · 2025-06-20T10:54:40Z

(created using eb --new-pr)

{ai}[foss/2023a] DeePMD-kit v3.0.1, Horovod v0.28.1 w/ TensorFlow 2.13.0 #22217

…eepmd-plugin.eb and patches: LAMMPS-29Aug2024_install-deepmd-plugin.patch

github-actions · 2025-06-20T10:55:09Z

Updated software `LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb`

Diff against LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb

easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb

diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb
index 1c4e71cba4..4e0caaae7e 100644
--- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb
+++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb
@@ -1,7 +1,7 @@
 name = 'LAMMPS'
-version = '2Aug2023_update2'
-_cuda_suffix = '-CUDA-%(cudaver)s'
-versionsuffix = '-kokkos' + _cuda_suffix
+version = '29Aug2024_update2'
+versionsuffix = '-kokkos' + "-with-deepmd-plugin"
+local_DeePMDkit_version = '3.0.1'
 
 homepage = 'https://www.lammps.org'
 description = """LAMMPS is a classical molecular dynamics code, and an acronym
@@ -15,65 +15,67 @@ simulation domain. The code is designed to be easy to modify or extend with new
 functionality.
 """
 
-toolchain = {'name': 'foss', 'version': '2024a'}
-toolchainopts = {'openmp': True, 'usempi': True, 'extra_cxxflags': '-D_AMXTILEINTRIN_H_INCLUDED'}
-# '-D_AMXTILEINTRIN_H_INCLUDED' flag is required to avoid the following errors,
-# likely due to an incompatibility between the GCC 13.3.0 and CUDA 12.6.0:
-#   [...]/GCCcore/13.3.0/lib/gcc/x86_64-pc-linux-gnu/13.3.0/include/amxtileintrin.h(42):
-#     error: identifier "__builtin_ia32_ldtilecfg" is undefined
-#   [...]/GCCcore/13.3.0/lib/gcc/x86_64-pc-linux-gnu/13.3.0/include/amxtileintrin.h(49):
-#     error: identifier "__builtin_ia32_sttilecfg" is undefined
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True, 'usempi': True}
 
 # 'https://github.com/lammps/lammps/archive/'
-source_urls = [GITHUB_LOWER_SOURCE]
-sources = ['stable_%(version)s.tar.gz']
+source_urls = [
+    GITHUB_LOWER_SOURCE,
+    'https://github.com/deepmodeling/deepmd-kit/archive/refs/tags/',
+]
+sources = [
+    'stable_%(version)s.tar.gz',
+    {
+        'download_filename': 'v%s.tar.gz' % local_DeePMDkit_version,
+        'filename': 'deepmd-v%s.tar.gz' % local_DeePMDkit_version,
+    },
+]
 patches = [
     'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch',
-    'LAMMPS-2Aug2023_fix-timestep-balance-example.patch',
+    'LAMMPS-29Aug2024_install-deepmd-plugin.patch',
 ]
 checksums = [
-    {'stable_2Aug2023_update2.tar.gz': '3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'},
+    {'stable_29Aug2024_update2.tar.gz': 'f8ca3f021a819ced8658055f7750e235c51b4937ddb621cf1bd7bee08e0b6266'},
+    {'deepmd-v3.0.1.tar.gz': 'e842edbc2714bc948ce708c411e5fed751e67c88d5c493c2978f11c849027dca'},
     {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch':
      '723c944b62b9d28427d25e80a7a67049631702d344df49268a6846aa0cd0fe04'},
-    {'LAMMPS-2Aug2023_fix-timestep-balance-example.patch':
-     '6f68387ced2b4bd0a06e4c3d31b0ffd47042476777d87d8a0ca6b19a4e6a1777'},
+    {'LAMMPS-29Aug2024_install-deepmd-plugin.patch':
+     'e601be73e131ed0740553b6ceff066eca0a7a474aad3d1b9e8dd4409ac6497df'},
 ]
 
 builddependencies = [
-    ('CMake', '3.29.3'),
-    ('pkgconf', '2.2.0'),
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
     ('archspec', '0.2.5'),
 ]
 dependencies = [
-    ('CUDA', '12.6.0', '', SYSTEM),
-    ('UCX-CUDA', '1.16.0', _cuda_suffix),
-    ('NCCL', '2.22.3', _cuda_suffix),
-    ('Python', '3.12.3'),
-    ('libpng', '1.6.43'),
-    ('libjpeg-turbo', '3.0.1'),
+    ('Python', '3.11.3'),
+    ('libpng', '1.6.39'),
+    ('libjpeg-turbo', '2.1.5.1'),
     ('netCDF', '4.9.2'),
-    ('GSL', '2.8'),
-    ('zlib', '1.3.1'),
-    ('gzip', '1.13'),
-    ('cURL', '8.7.1'),
-    ('HDF5', '1.14.5'),
+    ('GSL', '2.7'),
+    ('zlib', '1.2.13'),
+    ('gzip', '1.12'),
+    ('cURL', '8.0.1'),
+    ('HDF5', '1.14.0'),
     ('PCRE', '8.45'),
-    ('libxml2', '2.12.7'),
-    ('FFmpeg', '7.0.2'),
+    ('libxml2', '2.11.4'),
+    ('FFmpeg', '6.0'),
     ('Voro++', '0.4.6'),
-    ('kim-api', '2.4.1'),
+    ('kim-api', '2.3.0'),
     ('Eigen', '3.4.0'),
-    ('PLUMED', '2.9.3'),
-    ('SciPy-bundle', '2024.05'),
+    ('PLUMED', '2.9.0'),
+    ('SciPy-bundle', '2023.07'),
     # VTK package is auto-disabled if this dep is not available
-    ('VTK', '9.3.1'),
+    ('VTK', '9.3.0'),
     # We use a custom build of MDI
     ('MDI', '1.4.26'),
+    ('DeePMD-kit', local_DeePMDkit_version)
 ]
 if ARCH == 'x86_64':
     # TBB and ScaFaCos are an optional dependency when building on Intel arch
     dependencies += [
-        ('tbb', '2021.13.0'),
+        ('tbb', '2021.11.0'),
         ('ScaFaCoS', '1.0.4'),
     ]
 
@@ -92,11 +94,6 @@ if ARCH == 'x86_64':
 # 'INTEL'  - if builing on Intel CPU
 # 'OPENMP' - if OpenMP swithed on in 'toolchainopts'
 
-configopts = ' '.join([
-    '-DCMAKE_CXX_STANDARD=17',
-    '-DCMAKE_CXX_STANDARD_REQUIRED=on',
-])
-
 # include the following extra packages into the build
 general_packages = [
     'AMOEBA',
@@ -192,8 +189,6 @@ general_packages = [
 # - MSCG
 # - QMMM (setup seems complex)
 
-# hardware-specific option
-# note: only the highest capability will be used
-# cuda_compute_capabilities = ['9.0']
+configopts = '-Ddeepmd_source_dir=%%(builddir)s/deepmd-kit-%s' % local_DeePMDkit_version
 
 moduleclass = 'chem'

Diff against LAMMPS-29Aug2024_update2-foss-2024a-kokkos.eb

easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2024a-kokkos.eb

diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2024a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb
index 7b9b8fa3da..4e0caaae7e 100644
--- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2024a-kokkos.eb
+++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb
@@ -1,6 +1,7 @@
 name = 'LAMMPS'
 version = '29Aug2024_update2'
-versionsuffix = '-kokkos'
+versionsuffix = '-kokkos' + "-with-deepmd-plugin"
+local_DeePMDkit_version = '3.0.1'
 
 homepage = 'https://www.lammps.org'
 description = """LAMMPS is a classical molecular dynamics code, and an acronym
@@ -14,53 +15,67 @@ simulation domain. The code is designed to be easy to modify or extend with new
 functionality.
 """
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 # 'https://github.com/lammps/lammps/archive/'
-source_urls = [GITHUB_LOWER_SOURCE]
-sources = ['stable_%(version)s.tar.gz']
+source_urls = [
+    GITHUB_LOWER_SOURCE,
+    'https://github.com/deepmodeling/deepmd-kit/archive/refs/tags/',
+]
+sources = [
+    'stable_%(version)s.tar.gz',
+    {
+        'download_filename': 'v%s.tar.gz' % local_DeePMDkit_version,
+        'filename': 'deepmd-v%s.tar.gz' % local_DeePMDkit_version,
+    },
+]
 patches = [
     'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch',
+    'LAMMPS-29Aug2024_install-deepmd-plugin.patch',
 ]
 checksums = [
     {'stable_29Aug2024_update2.tar.gz': 'f8ca3f021a819ced8658055f7750e235c51b4937ddb621cf1bd7bee08e0b6266'},
+    {'deepmd-v3.0.1.tar.gz': 'e842edbc2714bc948ce708c411e5fed751e67c88d5c493c2978f11c849027dca'},
     {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch':
      '723c944b62b9d28427d25e80a7a67049631702d344df49268a6846aa0cd0fe04'},
+    {'LAMMPS-29Aug2024_install-deepmd-plugin.patch':
+     'e601be73e131ed0740553b6ceff066eca0a7a474aad3d1b9e8dd4409ac6497df'},
 ]
 
 builddependencies = [
-    ('CMake', '3.29.3'),
-    ('pkgconf', '2.2.0'),
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
     ('archspec', '0.2.5'),
 ]
 dependencies = [
-    ('Python', '3.12.3'),
-    ('libpng', '1.6.43'),
-    ('libjpeg-turbo', '3.0.1'),
+    ('Python', '3.11.3'),
+    ('libpng', '1.6.39'),
+    ('libjpeg-turbo', '2.1.5.1'),
     ('netCDF', '4.9.2'),
-    ('GSL', '2.8'),
-    ('zlib', '1.3.1'),
-    ('gzip', '1.13'),
-    ('cURL', '8.7.1'),
-    ('HDF5', '1.14.5'),
+    ('GSL', '2.7'),
+    ('zlib', '1.2.13'),
+    ('gzip', '1.12'),
+    ('cURL', '8.0.1'),
+    ('HDF5', '1.14.0'),
     ('PCRE', '8.45'),
-    ('libxml2', '2.12.7'),
-    ('FFmpeg', '7.0.2'),
+    ('libxml2', '2.11.4'),
+    ('FFmpeg', '6.0'),
     ('Voro++', '0.4.6'),
-    ('kim-api', '2.4.1'),
+    ('kim-api', '2.3.0'),
     ('Eigen', '3.4.0'),
-    ('PLUMED', '2.9.3'),
-    ('SciPy-bundle', '2024.05'),
+    ('PLUMED', '2.9.0'),
+    ('SciPy-bundle', '2023.07'),
     # VTK package is auto-disabled if this dep is not available
-    ('VTK', '9.3.1'),
+    ('VTK', '9.3.0'),
     # We use a custom build of MDI
     ('MDI', '1.4.26'),
+    ('DeePMD-kit', local_DeePMDkit_version)
 ]
 if ARCH == 'x86_64':
     # TBB and ScaFaCos are an optional dependency when building on Intel arch
     dependencies += [
-        ('tbb', '2021.13.0'),
+        ('tbb', '2021.11.0'),
         ('ScaFaCoS', '1.0.4'),
     ]
 
@@ -79,11 +94,6 @@ if ARCH == 'x86_64':
 # 'INTEL'  - if builing on Intel CPU
 # 'OPENMP' - if OpenMP swithed on in 'toolchainopts'
 
-configopts = ' '.join([
-    '-DCMAKE_CXX_STANDARD=17',
-    '-DCMAKE_CXX_STANDARD_REQUIRED=on',
-])
-
 # include the following extra packages into the build
 general_packages = [
     'AMOEBA',
@@ -179,4 +189,6 @@ general_packages = [
 # - MSCG
 # - QMMM (setup seems complex)
 
+configopts = '-Ddeepmd_source_dir=%%(builddir)s/deepmd-kit-%s' % local_DeePMDkit_version
+
 moduleclass = 'chem'

Diff against LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb

easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb

diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb
index 5718be3675..4e0caaae7e 100644
--- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb
+++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb
@@ -1,7 +1,7 @@
 name = 'LAMMPS'
 version = '29Aug2024_update2'
-_cuda_suffix = '-CUDA-%(cudaver)s'
-versionsuffix = '-kokkos' + _cuda_suffix
+versionsuffix = '-kokkos' + "-with-deepmd-plugin"
+local_DeePMDkit_version = '3.0.1'
 
 homepage = 'https://www.lammps.org'
 description = """LAMMPS is a classical molecular dynamics code, and an acronym
@@ -15,62 +15,67 @@ simulation domain. The code is designed to be easy to modify or extend with new
 functionality.
 """
 
-toolchain = {'name': 'foss', 'version': '2024a'}
-toolchainopts = {'openmp': True, 'usempi': True, 'extra_cxxflags': '-D_AMXTILEINTRIN_H_INCLUDED'}
-# '-D_AMXTILEINTRIN_H_INCLUDED' flag is required to avoid the following errors,
-# likely due to an incompatibility between the GCC 13.3.0 and NVCC CUDA 12.6.0:
-#   [...]/GCCcore/13.3.0/lib/gcc/x86_64-pc-linux-gnu/13.3.0/include/amxtileintrin.h(42):
-#     error: identifier "__builtin_ia32_ldtilecfg" is undefined
-#   [...]/GCCcore/13.3.0/lib/gcc/x86_64-pc-linux-gnu/13.3.0/include/amxtileintrin.h(49):
-# error: identifier "__builtin_ia32_sttilecfg" is undefined
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True, 'usempi': True}
 
 # 'https://github.com/lammps/lammps/archive/'
-source_urls = [GITHUB_LOWER_SOURCE]
-sources = ['stable_%(version)s.tar.gz']
+source_urls = [
+    GITHUB_LOWER_SOURCE,
+    'https://github.com/deepmodeling/deepmd-kit/archive/refs/tags/',
+]
+sources = [
+    'stable_%(version)s.tar.gz',
+    {
+        'download_filename': 'v%s.tar.gz' % local_DeePMDkit_version,
+        'filename': 'deepmd-v%s.tar.gz' % local_DeePMDkit_version,
+    },
+]
 patches = [
     'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch',
+    'LAMMPS-29Aug2024_install-deepmd-plugin.patch',
 ]
 checksums = [
     {'stable_29Aug2024_update2.tar.gz': 'f8ca3f021a819ced8658055f7750e235c51b4937ddb621cf1bd7bee08e0b6266'},
+    {'deepmd-v3.0.1.tar.gz': 'e842edbc2714bc948ce708c411e5fed751e67c88d5c493c2978f11c849027dca'},
     {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch':
      '723c944b62b9d28427d25e80a7a67049631702d344df49268a6846aa0cd0fe04'},
+    {'LAMMPS-29Aug2024_install-deepmd-plugin.patch':
+     'e601be73e131ed0740553b6ceff066eca0a7a474aad3d1b9e8dd4409ac6497df'},
 ]
 
 builddependencies = [
-    ('CMake', '3.29.3'),
-    ('pkgconf', '2.2.0'),
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
     ('archspec', '0.2.5'),
 ]
 dependencies = [
-    ('CUDA', '12.6.0', '', SYSTEM),
-    ('UCX-CUDA', '1.16.0', _cuda_suffix),
-    ('NCCL', '2.22.3', _cuda_suffix),
-    ('Python', '3.12.3'),
-    ('libpng', '1.6.43'),
-    ('libjpeg-turbo', '3.0.1'),
+    ('Python', '3.11.3'),
+    ('libpng', '1.6.39'),
+    ('libjpeg-turbo', '2.1.5.1'),
     ('netCDF', '4.9.2'),
-    ('GSL', '2.8'),
-    ('zlib', '1.3.1'),
-    ('gzip', '1.13'),
-    ('cURL', '8.7.1'),
-    ('HDF5', '1.14.5'),
+    ('GSL', '2.7'),
+    ('zlib', '1.2.13'),
+    ('gzip', '1.12'),
+    ('cURL', '8.0.1'),
+    ('HDF5', '1.14.0'),
     ('PCRE', '8.45'),
-    ('libxml2', '2.12.7'),
-    ('FFmpeg', '7.0.2'),
+    ('libxml2', '2.11.4'),
+    ('FFmpeg', '6.0'),
     ('Voro++', '0.4.6'),
-    ('kim-api', '2.4.1'),
+    ('kim-api', '2.3.0'),
     ('Eigen', '3.4.0'),
-    ('PLUMED', '2.9.3'),
-    ('SciPy-bundle', '2024.05'),
+    ('PLUMED', '2.9.0'),
+    ('SciPy-bundle', '2023.07'),
     # VTK package is auto-disabled if this dep is not available
-    ('VTK', '9.3.1'),
+    ('VTK', '9.3.0'),
     # We use a custom build of MDI
     ('MDI', '1.4.26'),
+    ('DeePMD-kit', local_DeePMDkit_version)
 ]
 if ARCH == 'x86_64':
     # TBB and ScaFaCos are an optional dependency when building on Intel arch
     dependencies += [
-        ('tbb', '2021.13.0'),
+        ('tbb', '2021.11.0'),
         ('ScaFaCoS', '1.0.4'),
     ]
 
@@ -89,11 +94,6 @@ if ARCH == 'x86_64':
 # 'INTEL'  - if builing on Intel CPU
 # 'OPENMP' - if OpenMP swithed on in 'toolchainopts'
 
-configopts = ' '.join([
-    '-DCMAKE_CXX_STANDARD=17',
-    '-DCMAKE_CXX_STANDARD_REQUIRED=on',
-])
-
 # include the following extra packages into the build
 general_packages = [
     'AMOEBA',
@@ -189,8 +189,6 @@ general_packages = [
 # - MSCG
 # - QMMM (setup seems complex)
 
-# hardware-specific option
-# note: only the highest capability will be used
-# cuda_compute_capabilities = ['9.0']
+configopts = '-Ddeepmd_source_dir=%%(builddir)s/deepmd-kit-%s' % local_DeePMDkit_version
 
 moduleclass = 'chem'

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>

adding easyconfigs: LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-d…

712cfab

…eepmd-plugin.eb and patches: LAMMPS-29Aug2024_install-deepmd-plugin.patch

laraPPr added the update label Jun 20, 2025

This was referenced Jun 20, 2025

{ai}[foss/2023a] DeePMD-kit v3.0.1, Horovod v0.28.1 w/ TensorFlow 2.13.0 #22217

Open

DeePMD-kit vscentrum/vsc-software-stack#487

Open

{chem}[foss/2023a] LAMMPS v2Aug2023_update2 w/ kokkos CUDA 12.1.1 with deepmd plugin #23167

Open

boegel requested changes Jun 23, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_install-deepmd-plugin.patch

Comment thread easybuild/easyconfigs/l/LAMMPS/LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb Outdated

laraPPr and others added 3 commits June 23, 2025 10:05

use local_DeePMDkit_version

3e1392a

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>

add pacth description

be3772c

rename sourcefile of deepmd

c5c6d9f

Thyre added the 2023a label Aug 18, 2025

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{chem}[foss/2023a] LAMMPS v29Aug2024_update2 w/ kokkos with deepmd plugin#23166

{chem}[foss/2023a] LAMMPS v29Aug2024_update2 w/ kokkos with deepmd plugin#23166
laraPPr wants to merge 4 commits into
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laraPPr:20250620125435_new_pr_LAMMPS29Aug2024_update2

laraPPr commented Jun 20, 2025 •

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laraPPr commented Jun 20, 2025 •

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Updated software `LAMMPS-29Aug2024_update2-foss-2023a-kokkos-with-deepmd-plugin.eb`