{ai,bio}[foss/2024a] AlphaFold3 v3.0.0.20250220, jax-triton v0.2.0, jaxtyping v0.2.38, dm-tree v0.1.8 w/ CUDA 12.6.0 DRAFT!

[ThomasHoffmann77]

(created using eb --new-pr)

• {devel}[foss/2024a] Triton v3.1.0 w/ CUDA 12.6.0 #22064
• {lib}[foss/2024a] dm-haiku v0.0.13 w/ CUDA 12.6.0 #22028
• {ai}[gfbf/2024a] jax v0.4.34, ml_dtypes v0.5.0 w/ CUDA 12.6.0 WIP #21924
• {lib}[GCC/13.3.0] pybind11_abseil v202402.0 #22153
• {bio}[GCC/13.3.0] dssp v4.4.10, libcifpp v7.0.8, libmcfp v1.3.4, mrc v1.3.13 #22155
• {chem}[foss/2024a] RDKit v2024.09.5 #22166
• {bio}[gompi/2024a] HMMER v3.4 #22172

TODO:

• "alphafold3 3.0.0 requires rdkit, which is not installed." although RDKit is dependency -> add minimal rdkit-2024.03.5.dist-info
• disable fetchcontent
• dssp
• pybind11_abseil
• RDKit: check whether 2024_09_4 (latest) would also work
• Check, whether $TRITON_HOME is used at all. Otherwise remove from module(xxx)footer.
• teststep: run_alphafold_tests.py

[github-actions]

Updated software dm-tree-0.1.9-gfbf-2024a.eb

Diff against dm-tree-0.1.8-GCCcore-12.3.0.eb

easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.9-gfbf-2024a.eb
index bf55444d00..3be4da4929 100644
--- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.9-gfbf-2024a.eb
@@ -1,23 +1,32 @@
 easyblock = 'PythonPackage'
 
 name = 'dm-tree'
-version = '0.1.8'
+version = '0.1.9'
 
 homepage = 'https://github.com/deepmind/tree'
 description = """dm-tree provides tree, a library for working with nested data structures. In a way,
 tree generalizes the builtin map function which only supports flat sequences, and
 allows to apply a function to each "leaf" preserving the overall structure."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430']
+sources = ['dm_tree-%(version)s.tar.gz']
+patches = ['dm-tree-0.1.9_pybind11.patch']
+checksums = [
+    {'dm_tree-0.1.9.tar.gz': 'a4c7db3d3935a5a2d5e4b383fc26c6b0cd6f78c6d4605d3e7b518800ecd5342b'},
+    {'dm-tree-0.1.9_pybind11.patch': '39ae1e40e6a027a6c6e085b20d33fe8de0e8103963c2ae0da665597ed9c6b41b'},
+]
 
 builddependencies = [
-    ('binutils', '2.40'),
-    ('CMake', '3.26.3'),
+    ('pybind11', '2.12.0'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('absl-py', '2.1.0'),
+    ('Abseil', '20240722.0'),
+    ('SciPy-bundle', '2024.05'),
+    ('wrapt', '1.16.0'),
 ]
-dependencies = [('Python', '3.11.3')]
 
 download_dep_fail = True
 

Diff against dm-tree-0.1.8-GCCcore-11.3.0.eb

easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.9-gfbf-2024a.eb
old mode 100755
new mode 100644
index 94b5023db0..3be4da4929
--- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.9-gfbf-2024a.eb
@@ -1,23 +1,32 @@
 easyblock = 'PythonPackage'
 
 name = 'dm-tree'
-version = '0.1.8'
+version = '0.1.9'
 
 homepage = 'https://github.com/deepmind/tree'
 description = """dm-tree provides tree, a library for working with nested data structures. In a way,
 tree generalizes the builtin map function which only supports flat sequences, and
 allows to apply a function to each "leaf" preserving the overall structure."""
 
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430']
+sources = ['dm_tree-%(version)s.tar.gz']
+patches = ['dm-tree-0.1.9_pybind11.patch']
+checksums = [
+    {'dm_tree-0.1.9.tar.gz': 'a4c7db3d3935a5a2d5e4b383fc26c6b0cd6f78c6d4605d3e7b518800ecd5342b'},
+    {'dm-tree-0.1.9_pybind11.patch': '39ae1e40e6a027a6c6e085b20d33fe8de0e8103963c2ae0da665597ed9c6b41b'},
+]
 
 builddependencies = [
-    ('binutils', '2.38'),
-    ('CMake', '3.23.1'),
+    ('pybind11', '2.12.0'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('absl-py', '2.1.0'),
+    ('Abseil', '20240722.0'),
+    ('SciPy-bundle', '2024.05'),
+    ('wrapt', '1.16.0'),
 ]
-dependencies = [('Python', '3.10.4')]
 
 download_dep_fail = True
 

Diff against dm-tree-0.1.6-GCCcore-10.3.0.eb

easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb

diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.9-gfbf-2024a.eb
index de8beea149..3be4da4929 100644
--- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.9-gfbf-2024a.eb
@@ -1,23 +1,32 @@
 easyblock = 'PythonPackage'
 
 name = 'dm-tree'
-version = '0.1.6'
+version = '0.1.9'
 
 homepage = 'https://github.com/deepmind/tree'
 description = """dm-tree provides tree, a library for working with nested data structures. In a way,
 tree generalizes the builtin map function which only supports flat sequences, and
 allows to apply a function to each "leaf" preserving the overall structure."""
 
-toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a']
+sources = ['dm_tree-%(version)s.tar.gz']
+patches = ['dm-tree-0.1.9_pybind11.patch']
+checksums = [
+    {'dm_tree-0.1.9.tar.gz': 'a4c7db3d3935a5a2d5e4b383fc26c6b0cd6f78c6d4605d3e7b518800ecd5342b'},
+    {'dm-tree-0.1.9_pybind11.patch': '39ae1e40e6a027a6c6e085b20d33fe8de0e8103963c2ae0da665597ed9c6b41b'},
+]
 
 builddependencies = [
-    ('binutils', '2.36.1'),
-    ('Bazel', '3.7.2'),
+    ('pybind11', '2.12.0'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('absl-py', '2.1.0'),
+    ('Abseil', '20240722.0'),
+    ('SciPy-bundle', '2024.05'),
+    ('wrapt', '1.16.0'),
 ]
-dependencies = [('Python', '3.9.5')]
 
 download_dep_fail = True
 

[ThomasHoffmann77]

dm-tree pybind11 patch taken from debian: https://udd.debian.org/patches.cgi?src=dm-tree&version=0.1.8-3

[VRehnberg]

Are you still working on this @ThomasHoffmann77?

[ThomasHoffmann77]

Are you still working on this @ThomasHoffmann77?

yes, I am still working on it. First draft is functional. Jax requires some more work to allow offline builds. For RDKit I get one failing test for all our archs except for znver2.
Any of you suggestions would be appreciated @VRehnberg

[VRehnberg]

I'm currently waiting to access the model weights so that I can try this out. But, in the meantime, some initial notes:

• this built fine (I built with --ignore-test-failures to get past failures in RDKit, but it doesn't seem to have been needed for AlphaFold3 at least (haven't checked the rest))
• a version bump of at least AlphaFold to get the latest bugfixes would be good

[ThomasHoffmann77]

I'm currently waiting to access the model weights so that I can try this out. But, in the meantime, some initial notes:

• this built fine (I built with --ignore-test-failures to get past failures in RDKit, but it doesn't seem to have been needed for AlphaFold3 at least (haven't checked the rest))
• a version bump of at least AlphaFold to get the latest bugfixes would be good

Thanks for testing. I'll have a look on it in the afternoon

[ThomasHoffmann77]

I'm currently waiting to access the model weights so that I can try this out. But, in the meantime, some initial notes:

• this built fine (I built with --ignore-test-failures to get past failures in RDKit, but it doesn't seem to have been needed for AlphaFold3 at least (haven't checked the rest))
• a version bump of at least AlphaFold to get the latest bugfixes would be good

Thanks for testing. I'll have a look on it in the afternoon

@VRehnberg I bumped to commit 792e61e and updated some of the dependencies (probably not required).
RDkit is used in common/folding_input.py, constants/periodic_table.py, data/tools/rdkit_utils.py, model/atom_layout/atom_layout.py, model/features.py, and structure/chemical_components.py

[VRehnberg]

@VRehnberg I bumped to commit 792e61e and updated some of the dependencies (probably not required). RDkit is used in common/folding_input.py, constants/periodic_table.py, data/tools/rdkit_utils.py, model/atom_layout/atom_layout.py, model/features.py, and structure/chemical_components.py

@ThomasHoffmann77 I meant latest release v3.0.1. Any reason you're using commits?

[ThomasHoffmann77]

@VRehnberg I bumped to commit 792e61e and updated some of the dependencies (probably not required). RDkit is used in common/folding_input.py, constants/periodic_table.py, data/tools/rdkit_utils.py, model/atom_layout/atom_layout.py, model/features.py, and structure/chemical_components.py

@ThomasHoffmann77 I meant latest release v3.0.1. Any reason you're using commits?

I just was not aware that there has been a release tag. I'll change it to 3.0.1. Thanks