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{bio}[foss/2021a] AlphaFold v2.1.1 w/ Python 3.9.5 (+ CUDA 11.3.1) #14500

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{bio}[foss/2021a] AlphaFold v2.1.1 w/ Python 3.9.5 (+ CUDA 11.3.1) #14500

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4ed8fc0
adding easyconfigs: AlphaFold-2.1.1-foss-2021a-CUDA-11.3.1.eb, AlphaF…
branfosj Dec 4, 2021
e6570c2
add UCX-CUDA dep and push the CUDA dep earlier in the list
branfosj Dec 7, 2021
1143008
Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…
branfosj Dec 8, 2021
5ccad02
Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…
boegel Dec 9, 2021
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193 changes: 193 additions & 0 deletions easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-foss-2021a-CUDA-11.3.1.eb
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easyblock = 'PythonBundle'

name = 'AlphaFold'
version = '2.1.1'
versionsuffix = '-CUDA-%(cudaver)s'

homepage = 'https://deepmind.com/research/case-studies/alphafold'
description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known"

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'),
]

dependencies = [
('Python', '3.9.5'),
('CUDA', '11.3.1', '', True),
('SciPy-bundle', '2021.05'),
('PyYAML', '5.4.1'),
('TensorFlow', '2.6.0', versionsuffix),
('Biopython', '1.79'),
('HH-suite', '3.3.0'),
('HMMER', '3.3.2'),
('Kalign', '3.3.1'),
('jax', '0.2.24', versionsuffix), # also provides absl-py
('UCX-CUDA', '1.10.0', versionsuffix),
('cuDNN', '8.2.1.32', versionsuffix, True),
('NCCL', '2.10.3', versionsuffix),
]
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': [
'https://github.com/deepmind/alphafold/archive/refs/tags/',
'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
],
'sources': [
{
'download_filename': 'v%(version)s.tar.gz',
'filename': SOURCE_TAR_GZ,
},
{
'download_filename': 'stereo_chemical_props.txt',
'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
'extract_cmd': "cp %s .",
},
],
'patches': [
'AlphaFold-2.0.0_fix-packages.patch',
'AlphaFold-2.1.0_data-dep-paths.patch',
'AlphaFold-2.0.0_n-cpu.patch',
'AlphaFold-2.1.0_fix-scp-path.patch',
'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
'AlphaFold-2.0.1_relax_gpu.patch'
],
'checksums': [
'1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz
'24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt
'826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch
'ecd1b240fdcd30110879dc4a88880405ae3fafb0f93f95f14fe30f6562148e13', # AlphaFold-2.1.0_data-dep-paths.patch
'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch
'5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch
'1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch
'3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch
],
'start_dir': 'alphafold-%(version)s',
'use_pip': True,
}),
]

use_pip = True

exts_list = [
('PDBFixer', '1.7', {
'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'],
}),
('toolz', '0.11.1', {
'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'],
}),
('chex', '0.0.8', {
'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'],
}),
('tabulate', '0.8.9', {
'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'],
}),
('dm-haiku', '0.0.4', {
'modulename': 'haiku',
'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'],
}),
('dm-tree', '0.1.6', {
'modulename': 'tree',
'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'],
}),
('websocket-client', '1.2.1', {
'modulename': 'websocket',
'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'],
}),
('docker', '5.0.0', {
'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'],
}),
('immutabledict', '2.1.0', {
'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'],
}),
('contextlib2', '21.6.0', {
'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
}),
('ml_collections', '0.1.0', {
'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'],
}),
]

postinstallcmds = [
"mkdir -p %(installdir)s/bin",
# run_alphafold.py script is missing a shebang...
"echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
"cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py",
"chmod a+x %(installdir)s/bin/run_alphafold.py",
"cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
"cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/",
"cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
# run tests for run_alphafold.py script;
# shouldn't do this in sanity check to avoid breaking use of --module-only
"PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
"python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py",
]

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'],
'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
}

sanity_check_commands = [
"pdbfixer --help",
"python -m simtk.testInstallation",
"python -c 'import alphafold'",
"alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
]

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 = {
'TF_FORCE_UNIFIED_MEMORY': '1',
'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0',
# 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt
'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189
}

moduleclass = 'bio'
179 changes: 179 additions & 0 deletions easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-foss-2021a.eb
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easyblock = 'PythonBundle'

name = 'AlphaFold'
version = '2.1.1'

homepage = 'https://deepmind.com/research/case-studies/alphafold'
description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known"

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'),
]

dependencies = [
('Python', '3.9.5'),
('SciPy-bundle', '2021.05'),
('PyYAML', '5.4.1'),
('TensorFlow', '2.6.0'),
('Biopython', '1.79'),
('HH-suite', '3.3.0'),
('HMMER', '3.3.2'),
('Kalign', '3.3.1'),
('jax', '0.2.24'), # also provides absl-py
]
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': [
'https://github.com/deepmind/alphafold/archive/refs/tags/',
'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
],
'sources': [
{
'download_filename': 'v%(version)s.tar.gz',
'filename': SOURCE_TAR_GZ,
},
{
'download_filename': 'stereo_chemical_props.txt',
'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
'extract_cmd': "cp %s .",
},
],
'patches': [
'AlphaFold-2.0.0_fix-packages.patch',
'AlphaFold-2.1.0_data-dep-paths.patch',
'AlphaFold-2.0.0_n-cpu.patch',
'AlphaFold-2.1.0_fix-scp-path.patch',
'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
'AlphaFold-2.0.1_relax_gpu.patch'
],
'checksums': [
'1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz
'24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt
'826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch
'ecd1b240fdcd30110879dc4a88880405ae3fafb0f93f95f14fe30f6562148e13', # AlphaFold-2.1.0_data-dep-paths.patch
'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch
'5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch
'1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch
'3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch
],
'start_dir': 'alphafold-%(version)s',
'use_pip': True,
}),
]

use_pip = True

exts_list = [
('PDBFixer', '1.7', {
'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'],
}),
('toolz', '0.11.1', {
'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'],
}),
('chex', '0.0.8', {
'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'],
}),
('tabulate', '0.8.9', {
'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'],
}),
('dm-haiku', '0.0.4', {
'modulename': 'haiku',
'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'],
}),
('dm-tree', '0.1.6', {
'modulename': 'tree',
'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'],
}),
('websocket-client', '1.2.1', {
'modulename': 'websocket',
'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'],
}),
('docker', '5.0.0', {
'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'],
}),
('immutabledict', '2.1.0', {
'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'],
}),
('contextlib2', '21.6.0', {
'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
}),
('ml_collections', '0.1.0', {
'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'],
}),
]

postinstallcmds = [
"mkdir -p %(installdir)s/bin",
# run_alphafold.py script is missing a shebang...
"echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
"cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py",
"chmod a+x %(installdir)s/bin/run_alphafold.py",
"cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
"cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/",
"cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
# run tests for run_alphafold.py script;
# shouldn't do this in sanity check to avoid breaking use of --module-only
"PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
"python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py",
]

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'],
'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
}

sanity_check_commands = [
"pdbfixer --help",
"python -m simtk.testInstallation",
"python -c 'import alphafold'",
"alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
]

sanity_pip_check = True

modextrapaths = {
'OPENMM_INCLUDE_PATH': 'include',
'OPENMM_LIB_PATH': 'lib',
}

moduleclass = 'bio'