diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index d6332594c4b..05ffdaeea4e 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -10,12 +10,9 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), # required for installing dm-tree ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), + ('CMake', '3.20.1'), ] dependencies = [ @@ -32,34 +29,14 @@ dependencies = [ ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -163,8 +140,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } @@ -177,11 +153,6 @@ sanity_check_commands = [ sanity_pip_check = True -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - # these allow to make predictions on proteins that would typically be too long to fit into GPU memory; # see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py modextravars = { diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb index bb34b753f32..bb289e74a36 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb @@ -9,12 +9,9 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), # required for installing dm-tree ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), + ('CMake', '3.20.1'), ] dependencies = [ @@ -27,34 +24,14 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('jax', '0.2.24'), # also provides absl-py + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -158,8 +135,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } @@ -172,11 +148,6 @@ sanity_check_commands = [ sanity_pip_check = True -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - modextravars = { # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt } diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 5b4a6edac04..3307a0c7c2b 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -10,12 +10,9 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), # required for installing dm-tree ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), + ('CMake', '3.20.1'), ] dependencies = [ @@ -32,34 +29,14 @@ dependencies = [ ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -166,8 +143,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } @@ -180,11 +156,6 @@ sanity_check_commands = [ sanity_pip_check = True -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - # these allow to make predictions on proteins that would typically be too long to fit into GPU memory; # see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py modextravars = { diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb index a864581a569..749bb12b07b 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb @@ -9,12 +9,9 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), # required for installing dm-tree ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), + ('CMake', '3.20.1'), ] dependencies = [ @@ -27,34 +24,14 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('jax', '0.3.9'), # also provides absl-py + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -161,8 +138,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'files': ['bin/alphafold', 'bin/pdbfixer', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } @@ -175,11 +151,6 @@ sanity_check_commands = [ sanity_pip_check = True -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - modextravars = { # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt }