{bio}[foss/2023a] ColabFold v1.5.5 w/ CUDA 12.1.1 #21672

ThomasHoffmann77 · 2024-10-16T08:24:58Z

(created using eb --new-pr)

boegel · 2024-11-07T08:47:04Z

@ThomasHoffmann77 Can you clarify why this is marked as draft/WIP?

ThomasHoffmann77 · 2024-11-08T07:38:33Z

@ThomasHoffmann77 Can you clarify why this is marked as draft/WIP?

I was waiting for feedback from our users and for a new version tag 1.5.6

easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb

…UDA-12.1.1.eb Co-authored-by: Kenneth Hoste <[email protected]>

github-actions · 2024-11-18T08:57:53Z

Updated software `ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb`

Diff against ColabFold-1.5.2-foss-2022a.eb

easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb
index c8ebee84c1..5a220445ef 100644
--- a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb
@@ -1,54 +1,178 @@
 easyblock = 'PythonBundle'
+# update 1.5.5: Thomas Hoffmann, EMBL Heidelberg
 
 name = 'ColabFold'
-version = '1.5.2'
+version = '1.5.5'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+_sokrypton_commit = '7c09316f71893e532bc15528cce4c1d3cb705f8f'
+_colab_suffix = '-ColabFold'
 
 homepage = 'https://github.com/sokrypton/ColabFold'
 description = """Making protein folding accessible to all. Predict proteins structures both in
 google colab and on your machine."""
 github_account = 'sokrypton'
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+]
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('AlphaFold', '2.3.4', '-%(name)s'),
-    ('matplotlib', '3.5.2'),
-    ('tqdm', '4.64.0'),
-    ('py3Dmol', '2.0.1.post1'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+    ('py3Dmol', '2.1.0'),
+
+
+    ('PyYAML', '6.0'),
+    ('TensorFlow', '2.13.0'),
+    ('Biopython', '1.83'),
+    ('HH-suite', '3.3.0'),
+    ('HMMER', '3.4'),
+    ('Kalign', '3.4.0'),
+    ('jax', '0.4.25', versionsuffix),
+    ('UCX-CUDA', '1.14.1', versionsuffix),
+    ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM),
+    ('NCCL', '2.18.3', versionsuffix),
+    ('OpenMM', '8.0.0', versionsuffix),
+    ('dm-haiku', '0.0.12', versionsuffix),
+    ('dm-tree', '0.1.8'),
 ]
 
+local_scp_commit = '7102c6'
+
+components = [
+    ('stereo_chemical_props', '', {
+        'easyblock': 'Binary',
+        'source_urls': [
+            'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
+        ],
+        'sources': [{
+            'download_filename': 'stereo_chemical_props.txt',
+            'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
+            'extract_cmd': "cp %s .",
+        }],
+        'checksums': ['24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451'],
+    })
+]
+
+
 use_pip = True
 
 exts_list = [
+    ('PDBFixer', '1.9', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'],
+    }),
+    ('tabulate', '0.9.0', {
+        'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'],
+    }),
+    ('websocket-client', '1.5.1', {
+        'modulename': 'websocket',
+        'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'],
+    }),
+    ('docker', '7.0.0', {
+        'checksums': ['323736fb92cd9418fc5e7133bc953e11a9da04f4483f828b527db553f1e7e5a3'],
+    }),
+    ('immutabledict', '4.1.0', {
+        'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+    # Colabfold uses a modified fork of DeepMind's AlphaFold2 (2.3.2). Therefore we provide it as an extension.
+    ('AlphaFold', '20230725-%s' % _sokrypton_commit, {
+        'patches': [
+            'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch',
+            'AlphaFold-2.0.0_n-cpu.patch',
+            'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
+            'AlphaFold-2.3.2_BioPythonPDBData.patch',
+        ],
+        'preinstallopts': " cp %(builddir)s/stereo_chemical_props-7102c6.txt " +
+                          "alphafold/common/stereo_chemical_props.txt &&",
+        'runtest': "python ./run_alphafold_test.py",
+        'source_urls': [
+            'https://github.com/sokrypton/alphafold/archive/',
+        ],
+        'sources': [{
+            'download_filename': '%s.tar.gz' % _sokrypton_commit,
+            'filename': '%(name)s-colabfold-%(version)s.tar.gz'}],
+        'testinstall': True,
+        'checksums': [
+            {'AlphaFold-colabfold-2.3.6.tar.gz': 'a12868525e568091acc5d8e15e9fc389125199786b750243b567ad1c4f89779b'},
+            {'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch':
+             '58cd0ce4094afe76909649abe68034c4fbdb500967f5c818f49b530356dc012b'},
+            {'AlphaFold-2.0.0_n-cpu.patch': 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04'},
+            {'AlphaFold-2.0.1_setup_rm_tfcpu.patch':
+             '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac'},
+            {'AlphaFold-2.3.2_BioPythonPDBData.patch':
+             'e4483a525ae5c4dc5a5f633bed8cf5337c329e64b603ab7b684a9d18cd26a22f'},
+        ],
+    }),
     ('colabfold', version, {
+        'patches': ['%(name)s-%(version)s_relax_requirements.patch'],
+        'preinstallopts': """sed -i 's/^\\(python =.*\\)<=3.10"$/,<=%(pyshortver)s"/;""" +
+                          """s/flow-cpu/flow/' pyproject.toml &&""",
         'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['b3b82e831e241a6ab40f2b0c6d560ac5328c6a0b505a0186c75e397ca1a16477'],
-        # fix requirement on Python 3.10.x revisions and TensorFlow
-        'preinstallopts': r"sed -i 's/^\(python =.*\)<=3.10\"$/\1<3.11\"/;s/flow-cpu/flow/' pyproject.toml &&",
         'use_pip_extras': 'alphafold',
+        'checksums': [
+            {'colabfold-1.5.5.tar.gz': '7fb0ad263c24ec00d46f2dff1611989234bc1351d71653dd06006f2c88f83dcb'},
+            {'colabfold-1.5.5_relax_requirements.patch':
+             'bcbcd7f403fea2e98ea04568d6ef358c72ad4beab762e701903473abf1883d03'},
+        ],
     }),
 ]
 
+_alphafold_buildir = '%%(builddir)s/AlphaFold/alphafold-%s' % _sokrypton_commit
 postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    "cp %s/run_alphafold.py %%(installdir)s/bin/run_alphafold.py" % _alphafold_buildir,
+    "chmod a+x %(installdir)s/bin/run_alphafold*.py",
+    "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
+    "cp -a %s/scripts %%(installdir)s/" % _alphafold_buildir,
     # Copy notebooks to installation directory
     "mkdir %(installdir)s/notebooks",
     "cp AlphaFold2.ipynb ESMFold.ipynb RoseTTAFold.ipynb %(installdir)s/notebooks/",
 ]
 
 sanity_check_paths = {
-    'files': ['bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas'],
+    'files': [
+        'bin/run_alphafold.py', 'bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas',
+        'lib/python%(pyshortver)s/site-packages/alphafold/common/stereo_chemical_props.txt'
+    ],
     'dirs': ['lib/python%(pyshortver)s/site-packages', 'notebooks'],
 }
 
 sanity_check_commands = [
+    "pdbfixer --help",
+    "run_alphafold.py --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
     "colabfold_batch --help",
 ]
 
 sanity_pip_check = True
 
+modextravars = {
+    'TF_FORCE_UNIFIED_MEMORY': '1',
+    'XLA_PYTHON_CLIENT_MEM_FRACTION': '3',
+    # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs/2.3.2',  # please adapt
+    'OPENMM_RELAX': 'CUDA',  # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189
+    # A newer version of UniRef30 (2023_02) is available at:
+    # "https://wwwuser.gwdg.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz.
+    # "Untar to $ALPHAFOLD_DATA_DIR/uniref30/ and set the default version accordingly by changing
+    # the value of ALPHAFOLD_UNIREF30_VER to v2023_02 accordingly:
+    'ALPHAFOLD_UNIREF30_VER': '2021_03',
+}
+
 modloadmsg = """
 %(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks
 """

Diff against ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb

easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb
index 8d8017276a..5a220445ef 100644
--- a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb
@@ -1,56 +1,178 @@
 easyblock = 'PythonBundle'
+# update 1.5.5: Thomas Hoffmann, EMBL Heidelberg
 
 name = 'ColabFold'
-version = '1.5.2'
+version = '1.5.5'
 versionsuffix = '-CUDA-%(cudaver)s'
 
+_sokrypton_commit = '7c09316f71893e532bc15528cce4c1d3cb705f8f'
+_colab_suffix = '-ColabFold'
+
 homepage = 'https://github.com/sokrypton/ColabFold'
 description = """Making protein folding accessible to all. Predict proteins structures both in
 google colab and on your machine."""
 github_account = 'sokrypton'
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+]
 
 dependencies = [
-    ('CUDA', '11.7.0', '', SYSTEM),
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('AlphaFold', '2.3.4', versionsuffix + '-%(name)s'),
-    ('matplotlib', '3.5.2'),
-    ('tqdm', '4.64.0'),
-    ('py3Dmol', '2.0.1.post1'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+    ('py3Dmol', '2.1.0'),
+
+
+    ('PyYAML', '6.0'),
+    ('TensorFlow', '2.13.0'),
+    ('Biopython', '1.83'),
+    ('HH-suite', '3.3.0'),
+    ('HMMER', '3.4'),
+    ('Kalign', '3.4.0'),
+    ('jax', '0.4.25', versionsuffix),
+    ('UCX-CUDA', '1.14.1', versionsuffix),
+    ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM),
+    ('NCCL', '2.18.3', versionsuffix),
+    ('OpenMM', '8.0.0', versionsuffix),
+    ('dm-haiku', '0.0.12', versionsuffix),
+    ('dm-tree', '0.1.8'),
 ]
 
+local_scp_commit = '7102c6'
+
+components = [
+    ('stereo_chemical_props', '', {
+        'easyblock': 'Binary',
+        'source_urls': [
+            'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
+        ],
+        'sources': [{
+            'download_filename': 'stereo_chemical_props.txt',
+            'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
+            'extract_cmd': "cp %s .",
+        }],
+        'checksums': ['24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451'],
+    })
+]
+
+
 use_pip = True
 
 exts_list = [
+    ('PDBFixer', '1.9', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'],
+    }),
+    ('tabulate', '0.9.0', {
+        'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'],
+    }),
+    ('websocket-client', '1.5.1', {
+        'modulename': 'websocket',
+        'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'],
+    }),
+    ('docker', '7.0.0', {
+        'checksums': ['323736fb92cd9418fc5e7133bc953e11a9da04f4483f828b527db553f1e7e5a3'],
+    }),
+    ('immutabledict', '4.1.0', {
+        'checksums': ['93d100ccd2cd09a1fd3f136b9328c6e59529ba341de8bb499437f6819159fe8a'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+    # Colabfold uses a modified fork of DeepMind's AlphaFold2 (2.3.2). Therefore we provide it as an extension.
+    ('AlphaFold', '20230725-%s' % _sokrypton_commit, {
+        'patches': [
+            'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch',
+            'AlphaFold-2.0.0_n-cpu.patch',
+            'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
+            'AlphaFold-2.3.2_BioPythonPDBData.patch',
+        ],
+        'preinstallopts': " cp %(builddir)s/stereo_chemical_props-7102c6.txt " +
+                          "alphafold/common/stereo_chemical_props.txt &&",
+        'runtest': "python ./run_alphafold_test.py",
+        'source_urls': [
+            'https://github.com/sokrypton/alphafold/archive/',
+        ],
+        'sources': [{
+            'download_filename': '%s.tar.gz' % _sokrypton_commit,
+            'filename': '%(name)s-colabfold-%(version)s.tar.gz'}],
+        'testinstall': True,
+        'checksums': [
+            {'AlphaFold-colabfold-2.3.6.tar.gz': 'a12868525e568091acc5d8e15e9fc389125199786b750243b567ad1c4f89779b'},
+            {'AlphaFold-2.3.2_data-dep-paths-shebang-UniRef30.patch':
+             '58cd0ce4094afe76909649abe68034c4fbdb500967f5c818f49b530356dc012b'},
+            {'AlphaFold-2.0.0_n-cpu.patch': 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04'},
+            {'AlphaFold-2.0.1_setup_rm_tfcpu.patch':
+             '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac'},
+            {'AlphaFold-2.3.2_BioPythonPDBData.patch':
+             'e4483a525ae5c4dc5a5f633bed8cf5337c329e64b603ab7b684a9d18cd26a22f'},
+        ],
+    }),
     ('colabfold', version, {
+        'patches': ['%(name)s-%(version)s_relax_requirements.patch'],
+        'preinstallopts': """sed -i 's/^\\(python =.*\\)<=3.10"$/,<=%(pyshortver)s"/;""" +
+                          """s/flow-cpu/flow/' pyproject.toml &&""",
         'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['b3b82e831e241a6ab40f2b0c6d560ac5328c6a0b505a0186c75e397ca1a16477'],
-        # fix requirement on Python 3.10.x revisions and TensorFlow
-        'preinstallopts': r"sed -i 's/^\(python =.*\)<=3.10\"$/\1<3.11\"/;s/flow-cpu/flow/' pyproject.toml &&",
         'use_pip_extras': 'alphafold',
+        'checksums': [
+            {'colabfold-1.5.5.tar.gz': '7fb0ad263c24ec00d46f2dff1611989234bc1351d71653dd06006f2c88f83dcb'},
+            {'colabfold-1.5.5_relax_requirements.patch':
+             'bcbcd7f403fea2e98ea04568d6ef358c72ad4beab762e701903473abf1883d03'},
+        ],
     }),
 ]
 
+_alphafold_buildir = '%%(builddir)s/AlphaFold/alphafold-%s' % _sokrypton_commit
 postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    "cp %s/run_alphafold.py %%(installdir)s/bin/run_alphafold.py" % _alphafold_buildir,
+    "chmod a+x %(installdir)s/bin/run_alphafold*.py",
+    "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
+    "cp -a %s/scripts %%(installdir)s/" % _alphafold_buildir,
     # Copy notebooks to installation directory
     "mkdir %(installdir)s/notebooks",
     "cp AlphaFold2.ipynb ESMFold.ipynb RoseTTAFold.ipynb %(installdir)s/notebooks/",
 ]
 
 sanity_check_paths = {
-    'files': ['bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas'],
+    'files': [
+        'bin/run_alphafold.py', 'bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas',
+        'lib/python%(pyshortver)s/site-packages/alphafold/common/stereo_chemical_props.txt'
+    ],
     'dirs': ['lib/python%(pyshortver)s/site-packages', 'notebooks'],
 }
 
 sanity_check_commands = [
+    "pdbfixer --help",
+    "run_alphafold.py --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
     "colabfold_batch --help",
 ]
 
 sanity_pip_check = True
 
+modextravars = {
+    'TF_FORCE_UNIFIED_MEMORY': '1',
+    'XLA_PYTHON_CLIENT_MEM_FRACTION': '3',
+    # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs/2.3.2',  # please adapt
+    'OPENMM_RELAX': 'CUDA',  # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189
+    # A newer version of UniRef30 (2023_02) is available at:
+    # "https://wwwuser.gwdg.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz.
+    # "Untar to $ALPHAFOLD_DATA_DIR/uniref30/ and set the default version accordingly by changing
+    # the value of ALPHAFOLD_UNIREF30_VER to v2023_02 accordingly:
+    'ALPHAFOLD_UNIREF30_VER': '2021_03',
+}
+
 modloadmsg = """
 %(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks
 """

…UDA-12.1.1.eb Co-authored-by: Kenneth Hoste <[email protected]>

add comment regarding AF2 fork

verdurin · 2025-01-14T15:10:35Z

@ThomasHoffmann77 do you consider this ready for review now?

ThomasHoffmann77 · 2025-01-14T15:25:34Z

@ThomasHoffmann77 do you consider this ready for review now?

I'd say yes.
Not sure, whether the modextravars part requires some more attention. I'd keep it as it is.

verdurin · 2025-01-14T15:56:05Z

Okay, I've re-read your comment, and I see what you mean now.
You want the person installing the module to see this, rather than the user, so they can customise the installation later, if they wish.

Just wondering if something that flashes by during a module installation is the best method.

Deleted postinstallmsg

verdurin · 2025-01-16T16:17:10Z

easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb

@@ -175,11 +175,4 @@ modloadmsg = """
 %(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks
 """

-postinstallmsgs = [


@ThomasHoffmann77 apologies for this extra hassle, but I thought you were going to keep this text and put it as a comment? Seems like valuable information.

Thought the comments in line 169 were enough. However, I'll add some more infos tomorrow

[bio][foss/2023a] ColabFold v1.5.5 w/ CUDA 12.1.1

74574cb

ThomasHoffmann77 marked this pull request as draft October 16, 2024 08:25

ThomasHoffmann77 changed the title ~~[bio][foss/2023a] ColabFold v1.5.5 w/ CUDA 12.1.1~~ {bio}[foss/2023a] ColabFold v1.5.5 w/ CUDA 12.1.1 Oct 16, 2024

add missing patches (duplicates from AlphaFold2)

e5f1c83

boegel added the update label Nov 7, 2024

boegel added this to the 4.x milestone Nov 7, 2024

ThomasHoffmann77 marked this pull request as ready for review November 7, 2024 10:59

laraPPr mentioned this pull request Nov 7, 2024

Colabfold + database vscentrum/vsc-software-stack#452

Open

3 tasks

boegel requested changes Nov 16, 2024

View reviewed changes

ThomasHoffmann77 and others added 2 commits November 18, 2024 09:55

Update easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-C…

c06f39a

…UDA-12.1.1.eb Co-authored-by: Kenneth Hoste <[email protected]>

Update easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-C…

5b77b87

…UDA-12.1.1.eb Co-authored-by: Kenneth Hoste <[email protected]>

ThomasHoffmann77 and others added 3 commits November 18, 2024 09:58

Update easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-C…

bbefe44

…UDA-12.1.1.eb Co-authored-by: Kenneth Hoste <[email protected]>

Update easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.5-foss-2023a-C…

f0fd6ad

…UDA-12.1.1.eb Co-authored-by: Kenneth Hoste <[email protected]>

Update ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb

bd9ed18

add comment regarding AF2 fork

Update ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb

080927d

Deleted postinstallmsg

ThomasHoffmann77 requested review from verdurin and boegel January 15, 2025 21:15

verdurin reviewed Jan 16, 2025

View reviewed changes

Update ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb

bfd9440

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

{bio}[foss/2023a] ColabFold v1.5.5 w/ CUDA 12.1.1 #21672

{bio}[foss/2023a] ColabFold v1.5.5 w/ CUDA 12.1.1 #21672

ThomasHoffmann77 commented Oct 16, 2024

boegel commented Nov 7, 2024

ThomasHoffmann77 commented Nov 8, 2024

github-actions bot commented Nov 18, 2024 •

edited

Loading

verdurin commented Jan 14, 2025

ThomasHoffmann77 commented Jan 14, 2025

verdurin commented Jan 14, 2025 •

edited

Loading

verdurin Jan 16, 2025

ThomasHoffmann77 Jan 16, 2025

{bio}[foss/2023a] ColabFold v1.5.5 w/ CUDA 12.1.1 #21672

Are you sure you want to change the base?

{bio}[foss/2023a] ColabFold v1.5.5 w/ CUDA 12.1.1 #21672

Conversation

ThomasHoffmann77 commented Oct 16, 2024

boegel commented Nov 7, 2024

ThomasHoffmann77 commented Nov 8, 2024

github-actions bot commented Nov 18, 2024 • edited Loading

Updated software ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb

verdurin commented Jan 14, 2025

ThomasHoffmann77 commented Jan 14, 2025

verdurin commented Jan 14, 2025 • edited Loading

verdurin Jan 16, 2025

Choose a reason for hiding this comment

ThomasHoffmann77 Jan 16, 2025

Choose a reason for hiding this comment

github-actions bot commented Nov 18, 2024 •

edited

Loading

Updated software `ColabFold-1.5.5-foss-2023a-CUDA-12.1.1.eb`

verdurin commented Jan 14, 2025 •

edited

Loading