{bio}[foss/2023a] BindCraft v1.1.0, PyRosetta v4.release-387, dm-haiku v0.0.13 #21791

PetrKralCZ · 2024-11-06T13:44:34Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#429

…e-387-gompi-2023a.eb, dm-haiku-0.0.13-foss-2023a.eb

github-actions · 2024-11-06T13:45:06Z

Updated software `dm-haiku-0.0.13-foss-2023a.eb`

Diff against dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb
index f66f10ec55..532f9092e7 100644
--- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.12-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb
@@ -1,9 +1,7 @@
-# update 0.0.12: Thomas Hoffmann (EMBL) 
 easyblock = 'PythonBundle'
 
 name = 'dm-haiku'
-version = '0.0.12'
-versionsuffix = '-CUDA-%(cudaver)s'
+version = '0.0.13'
 
 homepage = 'https://github.com/deepmind/dm-haiku'
 description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural
@@ -14,34 +12,20 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
-    ('jax', '0.4.25', versionsuffix),  # required by jmp, also provides absl-py
-    ('PyYAML', '6.0'),
-    ('CUDA', '12.1.1', '', SYSTEM),
-    ('tensorstore', '0.1.65'),
-    ('protobuf-python', '4.24.0'),
-    ('Optax', '0.2.2', versionsuffix),
+    ('jax', '0.4.25'),  # required by jmp, also provides absl-py
 ]
 
 use_pip = True
 
 exts_list = [
     ('jmp', '0.0.4', {
-        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['6aa7adbddf2bd574b28c7faf6e81a735eb11f53386447896909c6968dc36807d'],
     }),
-    ('flax', '0.8.4', {
-        'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'],
-    }),
-    ('nest_asyncio', '1.6.0', {
-        'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'],
-    }),
-    ('orbax_checkpoint', '0.5.18', {
-        'modulename': 'orbax.checkpoint',
-        'preinstallopts': """sed -i 's/jax >= 0.4.25/&\\*/g' pyproject.toml &&""",
-        'checksums': ['29f5d311b412760bd6a2fecab3bdbf75407bc00dc6d0457d19478258ecc8fa6d'],
-    }),
-    (name, version, {
+    ('dm_haiku', version, {
         'modulename': 'haiku',
-        'checksums': ['ba0b3acf71433156737fe342c486da11727e5e6c9e054245f4f9b8f0b53eb608'],
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['ee9562c68a059f146ad07f555ca591cb8c11ef751afecc38353863562bd23f43'],
     }),
 ]

Diff against dm-haiku-0.0.9-foss-2022a-CUDA-11.7.0.eb

easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb
index b2e1c44658..532f9092e7 100644
--- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb
@@ -1,31 +1,31 @@
 easyblock = 'PythonBundle'
 
 name = 'dm-haiku'
-version = '0.0.9'
-versionsuffix = '-CUDA-%(cudaver)s'
+version = '0.0.13'
 
 homepage = 'https://github.com/deepmind/dm-haiku'
 description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural
 network library for TensorFlow."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('CUDA', '11.7.0', '', SYSTEM),
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('jax', '0.3.25', versionsuffix),  # required by jmp, also provides absl-py
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25'),  # required by jmp, also provides absl-py
 ]
 
 use_pip = True
 
 exts_list = [
     ('jmp', '0.0.4', {
-        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['6aa7adbddf2bd574b28c7faf6e81a735eb11f53386447896909c6968dc36807d'],
     }),
-    (name, version, {
+    ('dm_haiku', version, {
         'modulename': 'haiku',
-        'checksums': ['97752b32cdbe5a3e2d1c60ea884d33eb4b36e7d410000f0d61b571417c925435'],
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['ee9562c68a059f146ad07f555ca591cb8c11ef751afecc38353863562bd23f43'],
     }),
 ]

Diff against dm-haiku-0.0.9-foss-2022a.eb

easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a.eb

diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb
index a27a9594b4..532f9092e7 100644
--- a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a.eb
+++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb
@@ -1,29 +1,31 @@
 easyblock = 'PythonBundle'
 
 name = 'dm-haiku'
-version = '0.0.9'
+version = '0.0.13'
 
 homepage = 'https://github.com/deepmind/dm-haiku'
 description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural
 network library for TensorFlow."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('jax', '0.3.25'),  # required by jmp, also provides absl-py
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25'),  # required by jmp, also provides absl-py
 ]
 
 use_pip = True
 
 exts_list = [
     ('jmp', '0.0.4', {
-        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['6aa7adbddf2bd574b28c7faf6e81a735eb11f53386447896909c6968dc36807d'],
     }),
-    (name, version, {
+    ('dm_haiku', version, {
         'modulename': 'haiku',
-        'checksums': ['97752b32cdbe5a3e2d1c60ea884d33eb4b36e7d410000f0d61b571417c925435'],
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['ee9562c68a059f146ad07f555ca591cb8c11ef751afecc38353863562bd23f43'],
     }),
 ]

Updated software `PyRosetta-4.release-387-gompi-2023a.eb`

Diff against PyRosetta-4.release-384-gompi-2022a.eb

easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb
index 5769add932..c37102d5a8 100644
--- a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb
+++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'PyRosetta'
-version = '4.release-384'
+version = '4.release-387'
 
 homepage = 'https://www.pyrosetta.org/'
 description = """
@@ -10,26 +10,26 @@ suite. It enables users to design their own custom molecular modeling algorithms
 sampling methods and energy functions.
 """
 
-toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 toolchainopts = {'usempi': True}
 
-builddependencies = [('binutils', '2.38')]
+builddependencies = [('binutils', '2.40')]
 
 dependencies = [
-    ('Python', '3.10.4'),
+    ('Python', '3.11.3'),
 ]
 
 use_pip = True
 
 local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2'
-local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python310.linux/'
+local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python311.linux/'
 
 exts_list = [
     (name, version, {
         'source_tmpl': local_source_tmpl,
         'source_urls': [local_source_urls],
         'start_dir': 'setup',
-        'checksums': ['630108f2bac166563fd2a4046a1d82e51e14693bb0e20dd3174e71c02b0760c2'],
+        'checksums': ['42a10efd16cba7739d87a5c4035a2cd8792bc193804963fc26bb2f82f7ac2a1a'],
     }),
 ]

Diff against PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb

easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb

diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb
index 37b027f656..c37102d5a8 100644
--- a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb
+++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb
@@ -1,34 +1,38 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'PyRosetta'
-version = '4.release-292'
-versionsuffix = '-Python-%(pyver)s'
-description = """PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite.
-It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods
-and energy functions."""
+version = '4.release-387'
+
 homepage = 'https://www.pyrosetta.org/'
+description = """
+PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling
+suite. It enables users to design their own custom molecular modeling algorithms using Rosetta
+sampling methods and energy functions.
+"""
 
-toolchain = {'name': 'GCCcore', 'version': '8.3.0'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchainopts = {'usempi': True}
 
-# After aquiring a license here https://els2.comotion.uw.edu/product/pyrosetta,
-# PyRosetta4.Release.python37.linux.release-292.tar.bz2 can be downloaded from
-# https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python37.linux/
-sources = ['%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2']
+builddependencies = [('binutils', '2.40')]
 
-checksums = [
-    'bffe04acb515628200129ded6f0a2ceeeef70f71d59c041f4390764954acac02'
+dependencies = [
+    ('Python', '3.11.3'),
 ]
 
-builddependencies = [('binutils', '2.32')]
+use_pip = True
 
-dependencies = [
-    ('Python', '3.7.4'),
-]
+local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2'
+local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python311.linux/'
 
-start_dir = "setup"
+exts_list = [
+    (name, version, {
+        'source_tmpl': local_source_tmpl,
+        'source_urls': [local_source_urls],
+        'start_dir': 'setup',
+        'checksums': ['42a10efd16cba7739d87a5c4035a2cd8792bc193804963fc26bb2f82f7ac2a1a'],
+    }),
+]
 
-download_dep_fail = True
-use_pip = True
 sanity_pip_check = True
 
 moduleclass = 'bio'

PetrKralCZ · 2024-11-06T14:25:58Z

@boegelbot please test @ generoso

boegelbot · 2024-11-06T14:30:12Z

@PetrKralCZ: Request for testing this PR well received on login1

PR test command 'EB_PR=21791 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21791 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14635

Test results coming soon (I hope)...

- notification for comment with ID 2459896698 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-11-06T14:58:07Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
cns4 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/cf644512385c662efad7a5e1b93388db for a full test report.

PetrKralCZ · 2024-11-06T14:59:48Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-06T15:00:18Z

@PetrKralCZ: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21791 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21791 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5203

Test results coming soon (I hope)...

- notification for comment with ID 2459980906 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-11-06T15:14:13Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/bc285f86ab676fa19964749d88b20b09 for a full test report.

boegel

lgtm

boegel · 2024-11-13T10:16:48Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3143.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/e4160c299e23830c8fd750d6b86db84e for a full test report.

boegel · 2024-11-13T10:20:10Z

Going in, thanks @PetrKralCZ!

adding easyconfigs: BindCraft-1.1.0-foss-2023a.eb, PyRosetta-4.releas…

fd5dcd3

…e-387-gompi-2023a.eb, dm-haiku-0.0.13-foss-2023a.eb

PetrKralCZ added new update labels Nov 6, 2024

PetrKralCZ mentioned this pull request Nov 6, 2024

BindCraft vscentrum/vsc-software-stack#429

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boegel added this to the release after 4.9.4 milestone Nov 13, 2024

boegel approved these changes Nov 13, 2024

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boegel merged commit 116d032 into easybuilders:develop Nov 13, 2024
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{bio}[foss/2023a] BindCraft v1.1.0, PyRosetta v4.release-387, dm-haiku v0.0.13 #21791

{bio}[foss/2023a] BindCraft v1.1.0, PyRosetta v4.release-387, dm-haiku v0.0.13 #21791

PetrKralCZ commented Nov 6, 2024 •

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{bio}[foss/2023a] BindCraft v1.1.0, PyRosetta v4.release-387, dm-haiku v0.0.13 #21791

{bio}[foss/2023a] BindCraft v1.1.0, PyRosetta v4.release-387, dm-haiku v0.0.13 #21791

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PetrKralCZ commented Nov 6, 2024 • edited Loading

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Updated software dm-haiku-0.0.13-foss-2023a.eb

Updated software PyRosetta-4.release-387-gompi-2023a.eb

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PetrKralCZ commented Nov 6, 2024 •

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Updated software `dm-haiku-0.0.13-foss-2023a.eb`

Updated software `PyRosetta-4.release-387-gompi-2023a.eb`