Merge pull request #17206 from smoors/20230125173522_new_pr_OpenFold101

enhance OpenFold 1.0.1 for standalone usage

easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb

@@ -33,12 +33,16 @@ dependencies = [
     # OpenFold also requires the AlphaFold modification to OpenMM
     # https://github.com/aqlaboratory/openfold/blob/v1.0.0/scripts/install_third_party_dependencies.sh#L20-L24
     # https://github.com/aqlaboratory/openfold/blob/v1.0.0/lib/openmm.patch
-    ('OpenMM', '7.5.1', '-DeepMind-patch'),
+    ('OpenMM', '7.5.1', '-CUDA-%(cudaver)s-DeepMind-patch'),
 ]
 
 use_pip = True
 
+# flash_attn (FlashAttention) is optional, speeds up MSA attention for sequences with < 1000 residues
 exts_list = [
+    ('flash_attn', '0.2.8', {
+        'checksums': ['b54fee86463cdb9933e8d47e500c52f3eaf283f1c8a9d96099e62acc7dc0be1f'],
+    }),
     ('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'}],
@@ -80,13 +84,36 @@ exts_list = [
     }),
 ]
 
+# _resources_dir = '%(installdir)s/lib/python%(pyshortver)s/site-packages/openfold/resources/'
+# _resources_target_dir = '/databases/bio/%(namelower)s-%(version)s'
+
+postinstallcmds = [
+    'cp -a run_pretrained_openfold.py thread_sequence.py train_openfold.py %(installdir)s/bin',
+    'cp -a scripts %(installdir)s/bin',
+    'chmod -R a+x %(installdir)s/bin',
+    # manually download stereo_chemical_props.txt, openfold parameters and alphafold parameters
+    # see scripts download_alphafold_params.sh, download_openfold_params.sh ,install_third_party_dependencies.sh
+    # download to _resources_target_dir and add symlinks in _resources_dir
+    # or download directly into _resources_dir
+    # 'ln -s %s/stereo_chemical_props.txt %s' % (_resources_target_dir, _resources_dir),
+    # 'ln -s %s/openfold_params %s' % (_resources_target_dir, _resources_dir),
+    # 'ln -s %s/params %s' % (_resources_target_dir, _resources_dir),
+]
+
+fix_python_shebang_for = ['bin/*.py', '/bin/scripts/*.py']
+
+modextrapaths = {
+    'PATH': 'bin/scripts',
+}
+
 sanity_check_paths = {
-    'files': ['bin/pdbfixer'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+    'files': ['bin/pdbfixer', 'bin/run_pretrained_openfold.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'bin/scripts'],
 }
 
 sanity_check_commands = [
     "pdbfixer --help",
+    "run_pretrained_openfold.py --help",
 ]
 
 sanity_pip_check = True

easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb

@@ -0,0 +1,64 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenMM'
+version = '7.5.1'
+versionsuffix = '-CUDA-%(cudaver)s-DeepMind-patch'
+
+homepage = 'https://openmm.org'
+description = "OpenMM is a toolkit for molecular simulation."
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'opt': True}
+
+source_urls = ['https://github.com/openmm/openmm/archive/']
+sources = ['%(version)s.tar.gz']
+patches = [
+    ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'),
+    '%(name)s-7.5.0_fix_path_to_nvcc.patch',
+]
+checksums = [
+    {'7.5.1.tar.gz': 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7'},
+    {'OpenMM-7.5.1_DeepMind.patch': '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6'},
+    {'OpenMM-7.5.0_fix_path_to_nvcc.patch': '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c'},
+]
+
+builddependencies = [
+    ('CMake', '3.20.1'),
+    ('Doxygen', '1.9.1'),
+]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('CUDA', '11.3.1', '', SYSTEM),
+    ('SWIG', '4.0.2'),
+]
+
+# Flags for CUDA-enabled build
+configopts = "-DOPENMM_BUILD_CUDA_LIB=ON"
+
+# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373
+pretestopts = " CTEST_OUTPUT_ON_FAILURE=1"
+local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)"
+runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern
+
+preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && '
+preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && '
+
+# required to install the python API
+installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'],
+    'dirs': []
+}
+
+sanity_check_commands = ["python -m simtk.testInstallation"]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+    'OPENMM_INCLUDE_PATH': 'include',
+    'OPENMM_LIB_PATH': 'lib',
+}
+
+moduleclass = 'bio'