{bio}[foss/2021a] AlphaFold v2.2.2 w/ Python 3.9.5 + CUDA 11.3.1

easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb

@@ -0,0 +1,198 @@
+easyblock = 'PythonBundle'
+
+name = 'AlphaFold'
+version = '2.2.0'
+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', '0.2.28', 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-2.1.2_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-2.1_fix-alphafold-tests.patch',
+        ],
+        'checksums': [
+            '37c92f31895c1f2cd5d8529176bc27a8d7db7659fff64e0c5f3f99ea35aadfb0',  # v2.2.0.tar.gz
+            '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
+            '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
+            '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48',  # AlphaFold-2.1.2_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
+            # AlphaFold-2.1_fix-alphafold-tests.patch
+            '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588',
+        ],
+        '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', '0.11.2', {
+        'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'],
+    }),
+    ('chex', '0.1.1', {
+        'checksums': ['f319f04568d1a75951f59129973a7852eedab93c4a94f382a65c4d718d9857c1'],
+    }),
+    ('tabulate', '0.8.9', {
+        'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'],
+    }),
+    ('jmp', '0.0.2', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['fdb5cec0d10aab4116c2770f24b2adf4f503fcfbb96ce8ef583e1879bdbf1b9b'],
+    }),
+    ('dm-haiku', '0.0.6', {
+        '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': ['bb038d7b6eae50ad8b59aecaad7b26180261f155c9a789d071133cb2596dc616'],
+    }),
+    ('dm-tree', '0.1.6', {
+        'modulename': 'tree',
+        'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'],
+    }),
+    ('websocket-client', '1.3.1', {
+        'modulename': 'websocket',
+        'checksums': ['6278a75065395418283f887de7c3beafb3aa68dada5cacbe4b214e8d26da499b'],
+    }),
+    ('docker', '5.0.3', {
+        'checksums': ['d916a26b62970e7c2f554110ed6af04c7ccff8e9f81ad17d0d40c75637e227fb'],
+    }),
+    ('immutabledict', '2.2.1', {
+        'checksums': ['1ddb0edf1bb6c70d0197eb90ce1fe2b2d58502334f5fdfde72d7c633d723ec3a'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+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'

easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb

@@ -0,0 +1,129 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'PythonBundle'
+
+name = 'jax'
+version = '0.2.28'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://pypi.python.org/pypi/jax'
+description = """Composable transformations of Python+NumPy programs:
+differentiate, vectorize, JIT to GPU/TPU, and more"""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+builddependencies = [
+    ('Bazel', '3.7.2'),
+    ('pytest-xdist', '2.3.0'),
+    # git 2.x required to fetch repository 'io_bazel_rules_docker'
+    ('git', '2.32.0', '-nodocs'),
+]
+
+dependencies = [
+    ('CUDA', '11.3.1', '', True),
+    ('cuDNN', '8.2.1.32', versionsuffix, True),
+    ('NCCL', '2.10.3', versionsuffix),
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('flatbuffers-python', '2.0'),
+    ('typing-extensions', '3.10.0.0'),
+]
+
+# running the tests with lots of cores results in test failures because not enough threads can be started,
+# and running with a single core also results in systematic test failures
+# 4 cores seems to work best
+parallel = 4
+
+# downloading TensorFlow tarball to avoid that Bazel downloads it during the build
+# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE
+local_tf_commit = 'e662039f98d2b6a0d8242887d0881bae04e2d590'
+local_tf_dir = 'tensorflow-%s' % local_tf_commit
+local_tf_builddir = '%(builddir)s/' + local_tf_dir
+
+# replace remote TensorFlow repository with the local one from EB
+local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && "
+local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir
+
+use_pip = True
+
+default_easyblock = 'PythonPackage'
+default_component_specs = {
+    'sources': [SOURCE_TAR_GZ],
+    'source_urls': [PYPI_SOURCE],
+    'start_dir': '%(name)s-%(version)s',
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'download_dep_fail': True,
+}
+
+components = [
+    ('absl-py', '0.13.0', {
+        'options': {'modulename': 'absl'},
+        'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'],
+    }),
+    ('jaxlib', '0.1.76', {
+        'sources': [
+            '%(name)s-v%(version)s.tar.gz',
+            {
+                'download_filename': '%s.tar.gz' % local_tf_commit,
+                'filename': 'tensorflow-%s.tar.gz' % local_tf_commit,
+            }
+        ],
+        'source_urls': [
+            'https://github.com/google/jax/archive/',
+            'https://github.com/tensorflow/tensorflow/archive/'
+        ],
+        'patches': [
+            ('jaxlib_local-tensorflow-repo.sed', '.'),
+            'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch',
+            ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir),
+        ],
+        'checksums': [
+            # jaxlib-v0.1.76.tar.gz
+            '6d5e185906dbc8f0f6589c5bc0569ae049bfe6346c271db73d5077f1fda41c7c',
+            # tensorflow-e662039f98d2b6a0d8242887d0881bae04e2d590.tar.gz
+            '8d6604640c8092abf640ccfb7222f6f941ee7b409d30292f6261ce3c86e23fab',
+            # jaxlib_local-tensorflow-repo.sed
+            'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5',
+            # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch
+            'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631',
+            # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch
+            '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db',
+        ],
+        'start_dir': 'jax-jaxlib-v%(version)s',
+        'prebuildopts': local_jax_prebuildopts,
+    }),
+]
+
+exts_list = [
+    ('opt_einsum', '3.3.0', {
+        'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/google/jax/archive/'],
+        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
+        'patches': [
+            'jax-0.2.19_fix-update-of-cache-access-time.patch',
+            'jax-0.2.24-foss-2021a_unimplemented.patch',
+        ],
+        'checksums': [
+            '7c6ffb14c2069d75c0721ec21b35ee253f0f368b84b9ec9459f0870ed902bfa7',  # jax-v0.2.28.tar.gz
+            # jax-0.2.19_fix-update-of-cache-access-time.patch
+            'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806',
+            # jax-0.2.24-foss-2021a_unimplemented.patch
+            '96fe1b15b55611727b0ae76409b89c44ae21a1c10002507ca8e3c06c2b134f4e',
+        ],
+        # deliberately not testing in parallel, as that results in (additional) failing tests;
+        # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing,
+        # see https://github.com/google/jax/issues/7323 and
+        # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst;
+        # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs;
+        # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores;
+        'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform "
+                   "JAX_ENABLE_X64=true pytest tests",
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'