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{bio}[foss/2024a] Boltz-2 v2.2.1 w/ CUDA 12.6.0 #25228

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{bio}[foss/2024a] Boltz-2 v2.2.1 w/ CUDA 12.6.0 #25228

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ff72a1f
adding easyconfigs: Boltz-2-2.2.1-foss-2024a-CUDA-12.6.0.eb
migueldiascosta Feb 6, 2026
ed013b1
use source from github, add missing dependencies for tests, etc
migueldiascosta Feb 6, 2026
7a6a2ca
add non-CUDA variant
migueldiascosta Feb 6, 2026
4932f74
fix style
migueldiascosta Feb 6, 2026
14dbbf4
Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…
bedroge Mar 31, 2026
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95 changes: 95 additions & 0 deletions easybuild/easyconfigs/b/Boltz-2/Boltz-2-2.2.1-foss-2024a-CUDA-12.6.0.eb
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Original file line number Diff line number Diff line change
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easyblock = 'PythonBundle'

name = 'Boltz-2'
version = '2.2.1'
versionsuffix = '-CUDA-%(cudaver)s'

homepage = 'https://github.com/jwohlwend/boltz'
description = """
Boltz-2 is a new biomolecular foundation model that goes beyond AlphaFold3 and Boltz-1
by jointly modeling complex structures and binding affinities, a critical component towards accurate molecular design.
"""

toolchain = {'name': 'foss', 'version': '2024a'}

builddependencies = [
('hatchling', '1.27.0'),
]
dependencies = [
('CUDA', '12.6.0', '', SYSTEM),
('Python', '3.12.3'),
('Python-bundle-PyPI', '2024.06'),
('SciPy-bundle', '2024.05'),
('Biopython', '1.84'),
('PyYAML', '6.0.2'),
('PyTorch', '2.7.1', '-CUDA-%(cudaver)s'),
('Hydra', '1.3.2'),
('PyTorch-Lightning', '2.5.6', '-CUDA-%(cudaver)s'),
('RDKit', '2025.03.3'),
('dm-tree', '0.1.9'),
('einops', '0.8.1'),
('gemmi', '0.7.1'),
('numba', '0.60.0'),
('scikit-learn', '1.6.1'),
('wandb', '0.20.1'),
]

exts_list = [
('urllib3', '2.0.7', {
'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'],
}),
('ihm', '1.7', {
'checksums': ['f7d3b9a76d9652f7091bbd1c6bea044a1d40b35bcba9b64c8e51a061fc2463de'],
}),
('frozendict', '2.4.5', {
'checksums': ['fd7add309789595c044c0155a0bddfa9d20c77f65de1e33a14aa3033b936ef63'],
}),
('types-requests', '2.32.0.20240914', {
'modulename': False,
'checksums': ['2850e178db3919d9bf809e434eef65ba49d0e7e33ac92d588f4a5e295fffd405'],
}),
('einx', '0.3.0', {
'checksums': ['17ff87c6a0f68ab358c1da489f00e95f1de106fd12ff17d0fb3e210aaa1e5f8c'],
}),
('fairscale', '0.4.13', {
'checksums': ['1b797825c427f5dba92253fd0d8daa574e8bd651a2423497775fab1b30cfb768'],
}),
('mashumaro', '3.14', {
'checksums': ['5ef6f2b963892cbe9a4ceb3441dfbea37f8c3412523f25d42e9b3a7186555f1d'],
}),
('modelcif', '1.2', {
'checksums': ['517d2a7be67c96fd56dcc3b50cf7bb0b130958c325653d9925f9a5dbfe151d78'],
}),
('chembl-structure-pipeline', '1.2.4', {
'checksums': ['e381500ac815ded31cc4841d1fbfe7c089788a07f2fbaa9bb818b52facfa9030'],
}),
('packaging', '25.0', {
'checksums': ['d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f'],
}),
('opt-einsum', '3.4.0', {
'modulename': 'opt_einsum',
'checksums': ['96ca72f1b886d148241348783498194c577fa30a8faac108586b14f1ba4473ac'],
}),
('cuequivariance', '0.8.1', {
'checksums': ['f398dd0b61f80894994ef12a6ac7dd844e3d301a5486b99ff17d0082f1e22b4c'],
}),
('cuequivariance-torch', '0.8.1', {
'checksums': ['03a924b7a4c57bed87ca3d0345218eb805d8d2e848f5f5c57192a2e4a8ebc3db'],
}),
('cuequivariance-ops-torch-cu12', '0.8.1', {
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@bedroge bedroge Apr 8, 2026

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I got a failing sanity check due to a missing dependency for this package:

cuequivariance-ops-torch-cu12 0.8.1 requires cuequivariance-ops-cu12, which is not installed.

'source_tmpl':
'cuequivariance_ops_torch_cu12-0.8.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl',
'checksums': ['839a262c6bb461684e7d929f5bf4b96c2fa58a5308e64c213ec7835fb1c3907e'],
}),
('boltz', version, {
'checksums': ['dfbc5847a9d378a1e24829ff53c3faa182fb945775074712c130a3884710736d'],
'preinstallopts': 'sed -i -e \'s/==.*/\\",/g\' pyproject.toml && ',
'source_urls': ['https://github.com/jwohlwend/boltz/archive/refs/tags/'],
'source_tmpl': 'v%(version)s.tar.gz',
'runtest': 'export HOME=%(builddir)s && cd %(start_dir)s && pytest -svv tests/',
'testinstall': True}),
]

sanity_check_commands = ["boltz 2>&1 | grep 'Usage: boltz'"]

moduleclass = 'bio'
88 changes: 88 additions & 0 deletions easybuild/easyconfigs/b/Boltz-2/Boltz-2-2.2.1-foss-2024a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
easyblock = 'PythonBundle'

name = 'Boltz-2'
version = '2.2.1'

homepage = 'https://github.com/jwohlwend/boltz'
description = """
Boltz-2 is a new biomolecular foundation model that goes beyond AlphaFold3 and Boltz-1
by jointly modeling complex structures and binding affinities, a critical component towards accurate molecular design.
"""

toolchain = {'name': 'foss', 'version': '2024a'}

builddependencies = [
('hatchling', '1.27.0'),
]
dependencies = [
('Python', '3.12.3'),
('Python-bundle-PyPI', '2024.06'),
('SciPy-bundle', '2024.05'),
('Biopython', '1.84'),
('PyYAML', '6.0.2'),
('PyTorch', '2.6.0'),
('Hydra', '1.3.2'),
('PyTorch-Lightning', '2.5.2'),
('RDKit', '2025.03.3'),
('dm-tree', '0.1.9'),
('einops', '0.8.1'),
('gemmi', '0.7.1'),
('numba', '0.60.0'),
('scikit-learn', '1.6.1'),
('wandb', '0.20.1'),
]

exts_list = [
('urllib3', '2.0.7', {
'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'],
}),
('ihm', '1.7', {
'checksums': ['f7d3b9a76d9652f7091bbd1c6bea044a1d40b35bcba9b64c8e51a061fc2463de'],
}),
('frozendict', '2.4.5', {
'checksums': ['fd7add309789595c044c0155a0bddfa9d20c77f65de1e33a14aa3033b936ef63'],
}),
('types-requests', '2.32.0.20240914', {
'modulename': False,
'checksums': ['2850e178db3919d9bf809e434eef65ba49d0e7e33ac92d588f4a5e295fffd405'],
}),
('einx', '0.3.0', {
'checksums': ['17ff87c6a0f68ab358c1da489f00e95f1de106fd12ff17d0fb3e210aaa1e5f8c'],
}),
('fairscale', '0.4.13', {
'checksums': ['1b797825c427f5dba92253fd0d8daa574e8bd651a2423497775fab1b30cfb768'],
}),
('mashumaro', '3.14', {
'checksums': ['5ef6f2b963892cbe9a4ceb3441dfbea37f8c3412523f25d42e9b3a7186555f1d'],
}),
('modelcif', '1.2', {
'checksums': ['517d2a7be67c96fd56dcc3b50cf7bb0b130958c325653d9925f9a5dbfe151d78'],
}),
('chembl-structure-pipeline', '1.2.4', {
'checksums': ['e381500ac815ded31cc4841d1fbfe7c089788a07f2fbaa9bb818b52facfa9030'],
}),
('packaging', '25.0', {
'checksums': ['d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f'],
}),
('opt-einsum', '3.4.0', {
'modulename': 'opt_einsum',
'checksums': ['96ca72f1b886d148241348783498194c577fa30a8faac108586b14f1ba4473ac'],
}),
('cuequivariance', '0.8.1', {
'checksums': ['f398dd0b61f80894994ef12a6ac7dd844e3d301a5486b99ff17d0082f1e22b4c'],
}),
('cuequivariance-torch', '0.8.1', {
'checksums': ['03a924b7a4c57bed87ca3d0345218eb805d8d2e848f5f5c57192a2e4a8ebc3db'],
}),
('boltz', version, {
'checksums': ['dfbc5847a9d378a1e24829ff53c3faa182fb945775074712c130a3884710736d'],
'preinstallopts': 'sed -i -e \'s/==.*/\\",/g\' pyproject.toml && ',
'source_urls': ['https://github.com/jwohlwend/boltz/archive/refs/tags/'],
'source_tmpl': 'v%(version)s.tar.gz',
'runtest': 'export HOME=%(builddir)s && cd %(start_dir)s && pytest -svv tests/',
'testinstall': True}),
]

sanity_check_commands = ["boltz 2>&1 | grep 'Usage: boltz'"]

moduleclass = 'bio'
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