{bio}[foss/2024a] AlphaFold3 WIP by jpecar · Pull Request #21864 · easybuilders/easybuild-easyconfigs

jpecar · 2024-11-18T11:18:39Z

(created using eb --new-pr)

github-actions · 2024-11-18T11:20:50Z

Updated software `Boost.Python-NumPy-1.85.0-gfbf-2024a.eb`

Diff against Boost.Python-NumPy-1.79.0-foss-2022a.eb

easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.79.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.79.0-foss-2022a.eb b/easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.85.0-gfbf-2024a.eb
index f9fa7521f3..453b8d4b1a 100644
--- a/easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.79.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.85.0-gfbf-2024a.eb
@@ -1,23 +1,23 @@
 easyblock = 'EB_Boost'
 
 name = 'Boost.Python-NumPy'
-version = '1.79.0'
+version = '1.85.0'
 
 homepage = 'https://boostorg.github.io/python'
 description = """Boost.Python is a C++ library which enables seamless interoperability between C++
  and the Python programming language."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
 sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))]
-checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c']
+checksums = ['be0d91732d5b0cc6fbb275c7939974457e79b54d6f07ce2e3dfdd68bef883b0b']
 
 dependencies = [
     ('Boost',  version),
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
 ]
 
 only_python_bindings = True

Updated software `Boost.Python-1.85.0-GCC-13.3.0.eb`

Diff against Boost.Python-1.82.0-GCC-12.3.0.eb

easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.85.0-GCC-13.3.0.eb
index ee38c6983c..512ef192e9 100644
--- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.85.0-GCC-13.3.0.eb
@@ -1,22 +1,22 @@
 easyblock = 'EB_Boost'
 
 name = 'Boost.Python'
-version = '1.82.0'
+version = '1.85.0'
 
 homepage = 'https://boostorg.github.io/python'
 description = """Boost.Python is a C++ library which enables seamless interoperability between C++
  and the Python programming language."""
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
-sources = ['boost_1_82_0.tar.gz']
-checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c']
+sources = ['boost_1_85_0.tar.gz']
+checksums = ['be0d91732d5b0cc6fbb275c7939974457e79b54d6f07ce2e3dfdd68bef883b0b']
 
 dependencies = [
-    ('Boost', version),
-    ('Python', '3.11.3'),
+    ('Boost', '1.85.0'),
+    ('Python', '3.12.3'),
 ]
 
 only_python_bindings = True

Updated software `CUDA-12.6.2.eb`

Diff against CUDA-12.6.0.eb

easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb

diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.2.eb
index 24c7b5f5c9..b6edef54a9 100644
--- a/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb
+++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.2.eb
@@ -1,6 +1,6 @@
 name = 'CUDA'
-version = '12.6.0'
-local_nv_version = '560.28.03'
+version = '12.6.2'
+local_nv_version = '560.35.03'
 
 homepage = 'https://developer.nvidia.com/cuda-toolkit'
 description = """CUDA (formerly Compute Unified Device Architecture) is a parallel
@@ -14,9 +14,9 @@ source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/l
 sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version]
 checksums = [{
     'cuda_%%(version)s_%s_linux.run' % local_nv_version:
-        '31ab04394e69b14dd8656e2b44c2877db1a0e898dff8a7546a4c628438101b94',
+        '3729a89cb58f7ca6a46719cff110d6292aec7577585a8d71340f0dbac54fb237',
     'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version:
-        '398db7baca17d51ad5035c606714c96380c965fd1742478c743bc6bbb1d8f63c'
+        '2249408848b705c18b9eadfb5161b52e4e36fcc5753647329cce93db141e5466'
 }]
 
 moduleclass = 'system'

Updated software `Catch2-3.7.1-GCCcore-13.3.0.eb`

Diff against Catch2-2.13.10-GCCcore-13.3.0.eb

easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Catch2/Catch2-3.7.1-GCCcore-13.3.0.eb
index 00abfac39c..4a3dfb0b53 100644
--- a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/Catch2/Catch2-3.7.1-GCCcore-13.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'CMakeMake'
 
 name = 'Catch2'
-version = '2.13.10'
+version = '3.7.1'
 
 homepage = 'https://github.com/catchorg/Catch2'
 description = """A modern, C++-native, header-only,
@@ -13,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 source_urls = ['https://github.com/catchorg/Catch2/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['d54a712b7b1d7708bc7a819a8e6e47b2fde9536f487b89ccbca295072a7d9943']
+checksums = ['c991b247a1a0d7bb9c39aa35faf0fe9e19764213f28ffba3109388e62ee0269c']
 
 builddependencies = [
     ('binutils', '2.42'),  # to make CMake compiler health check pass on old systems
@@ -23,7 +23,7 @@ builddependencies = [
 separate_build_dir = True
 
 sanity_check_paths = {
-    'files': ['include/catch2/catch.hpp'],
+    'files': ['include/catch2/catch_all.hpp'],
     'dirs':  ['lib/cmake'],
 }

Updated software `cuDNN-9.5.1.17-CUDA-12.6.2.eb`

Diff against cuDNN-9.5.0.50-CUDA-12.6.0.eb

easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb

diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.1.17-CUDA-12.6.2.eb
index 76340a4e65..5707eac6cd 100644
--- a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb
+++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.1.17-CUDA-12.6.2.eb
@@ -1,5 +1,5 @@
 name = 'cuDNN'
-version = '9.5.0.50'
+version = '9.5.1.17'
 versionsuffix = '-CUDA-%(cudaver)s'
 homepage = 'https://developer.nvidia.com/cudnn'
 description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is
@@ -17,19 +17,27 @@ source_urls = [
 ]
 sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major]
 checksums = [{
+    '%%(namelower)s-linux-aarch64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major:
+        '0099b8e4081ac146f802e769cdd30d9e01a289ea0fd056e64e44297a13e1aa0c',
     '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major:
-        '494b640a69feb40ce806a726aa63a1de6b2ec459acbe6a116ef6fe3e6b27877d',
+        '340c49b32c133b0321c5c5b00d14fb64887dcac83ee8fd24195d9191061f1ad7',
     '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major:
-        '86e4e4f4c09b31d3850b402d94ea52741a2f94c2f717ddc8899a14aca96e032d',
+        '35dd20b9c68324ae1288ac36f66ab1f318d2bfecfafb703a82617aa283272be4',
 }]
 
-dependencies = [('CUDA', '12.6.0')]
+dependencies = [('CUDA', '12.6.2')]
 
 sanity_check_paths = {
     'files': [
-        'include/cudnn.h', 'lib64/libcudnn_adv_static.a', 'lib64/libcudnn_cnn_static.a',
-        'lib64/libcudnn_engines_precompiled_static.a', 'lib64/libcudnn_engines_runtime_compiled_static.a',
-        'lib64/libcudnn_graph_static.a', 'lib64/libcudnn_heuristic_static.a', 'lib64/libcudnn_ops_static.a',
+        'include/cudnn.h',
+        'lib64/libcudnn_adv_static.a',
+        'lib64/libcudnn_engines_runtime_compiled_static.a',
+        'lib64/libcudnn_ops_static.a',
+        'lib64/libcudnn_engines_precompiled_static.a',
+        'lib64/libcudnn_heuristic_static.a',
+        'lib64/libcudnn_cnn_static.a',
+        'lib64/libcudnn_graph_static.a',
+        'lib64/libcudnn.%s' % SHLIB_EXT,
     ],
     'dirs': ['include', 'lib64'],
 }

Updated software `HMMER-3.4-gompi-2024a.eb`

Diff against HMMER-3.4-gompi-2023b.eb

easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb

diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
index bb76dc1e93..f58d56361a 100644
--- a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
@@ -1,18 +1,3 @@
-##
-# EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-#
-# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
-# Authors::   Nils Christian <nils.christian@uni.lu>,
-#             Fotis Georgatos <fotis@cern.ch>
-# Updated by: Filip Kružík (INUITS)
-# License::   MIT/GPL
-# $Id$
-#
-# This work implements a part of the HPCBIOS project and is a
-#  component of the policy:
-# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
-##
-
 easyblock = 'ConfigureMake'
 
 name = 'HMMER'
@@ -29,7 +14,7 @@ description = """HMMER is used for searching sequence databases for homologs
  past, this strength came at significant computational expense, but in the new
  HMMER3 project, HMMER is now essentially as fast as BLAST."""
 
-toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchain = {'name': 'gompi', 'version': '2024a'}
 
 source_urls = [
     'http://eddylab.org/software/hmmer/',
@@ -39,8 +24,8 @@ sources = [SOURCELOWER_TAR_GZ]
 checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
 
 builddependencies = [
-    ('Python', '3.11.5'),
-    ('Perl', '5.38.0'),
+    ('Python', '3.12.3'),
+    ('Perl', '5.38.2'),
 ]
 
 # replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files

Updated software `hypothesis-6.118.8-GCCcore-13.3.0.eb`

Diff against hypothesis-6.103.1-GCCcore-13.3.0.eb

easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.118.8-GCCcore-13.3.0.eb
index e9bb1d7854..56c23ddb16 100644
--- a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.118.8-GCCcore-13.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'hypothesis'
-version = '6.103.1'
+version = '6.118.8'
 
 homepage = "https://github.com/HypothesisWorks/hypothesis"
 description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized
@@ -11,7 +11,7 @@ description = """Hypothesis is an advanced testing library for Python. It lets y
 toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['d299d5c21d6408eab3be670c94c974f3acf0b511c61fe81804b09091e393ee1f']
+checksums = ['2a564996f60b8961b5112672564516a522fbd6ab4b536f8c6f3e4adb125b7dd2']
 
 builddependencies = [
     ('binutils', '2.42'),

Updated software `InChI-1.07.1-GCC-13.3.0.eb`

Diff against InChI-1.06-GCC-10.3.0.eb

easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb

diff --git a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InChI/InChI-1.07.1-GCC-13.3.0.eb
index c0333eda15..c9ffab98e7 100644
--- a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb
+++ b/easybuild/easyconfigs/i/InChI/InChI-1.07.1-GCC-13.3.0.eb
@@ -1,21 +1,8 @@
-##
-# This is a contribution from SIB Swiss Institute of Bioinformatics
-# Homepage:     https://www.sib.swiss/research-infrastructure/competence-centers/vital-it
-#
-# Authors::     Sebastien Moretti <sebastien.moretti@sib.swiss>
-#
-# Notes::       Based on Fedora RPM spec file https://src.fedoraproject.org/rpms/inchi/blob/rawhide/f/inchi.spec
-#               Patch made by Fedora to fix program name, linker and compilation options
-#               https://src.fedoraproject.org/rpms/inchi/blob/rawhide/f/inchi-rpm.patch
-##
 easyblock = 'MakeCp'
 
 name = 'InChI'
-version = '1.06'
+version = '1.07.1'
 
-# NOTE not in the license list of EB
-# software_license = 'IUPAC/InChI-Trust Licence'
-software_license_urls = ['https://www.inchi-trust.org/download/%(version_major)s%(version_minor)s/LICENCE.pdf']
 docurls = [
     'https://www.inchi-trust.org/download/%(version_major)s%(version_minor)s/INCHI-1-DOC.zip',
     'https://www.inchi-trust.org/download/%(version_major)s%(version_minor)s/readme.txt',
@@ -26,23 +13,23 @@ description = """The IUPAC International Chemical Identifier (InChI TM) is a non
 identifier for chemical substances that can be used in printed and electronic
 data sources thus enabling easier linking of diverse data compilations."""
 
-toolchain = {'name': 'GCC', 'version': '10.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
-source_urls = ['https://www.inchi-trust.org/download/%(version_major)s%(version_minor)s/']
+source_urls = ['https://github.com/IUPAC-%(name)s/%(name)s/releases/download/v%(version)s/']
 sources = [
     {'download_filename': 'INCHI-1-SRC.zip',  'filename': 'INCHI-%(version)s-SRC.zip'},
     {'download_filename': 'INCHI-1-TEST.zip', 'filename': 'INCHI-%(version)s-TEST.zip'},
 ]
-patches = ['InChI-%(version)s_fedora-build-fixes.patch']
+patches = ['InChI-%(version)s_build-fixes.patch']
 checksums = [
-    '4874e310c0f2f81b881e90dd0c534752e1b9421d7d92ccfb037710022c7e7efd',  # INCHI-1.06-SRC.zip
-    '3c870ef97c8ebc86f64946db395582b87d79732000fa73d173f46c05ca19c1ff',  # INCHI-1.06-TEST.zip
-    '98acd66e46d3c5c2c3b1531e9c84e129b503e23d3a7602f3f64f37c74e420840',  # InChI-1.06_fedora-build-fixes.patch
+    'fe6e1ee25714988f7b86420b7615b4e1d7c01fda9b93d63b634a0c021ac9f917',  # INCHI-1.07.1-SRC.zip
+    '4e0dd15d505be0db86bc4b345bdb0610aa63e202ac413a3671d6b735a1f7e7ad',  # INCHI-1.07.1-TEST.zip
+    '0b83087c59f6e3bcab86f2fd2cf8604bbbaf49ba9de6e4cbcabdb9c6ca740e6e',  # InChI-1.07.1_build-fixes.patch
 ]
 
 # dos2unix may be another builddependency useful to "clean" some files
 builddependencies = [
-    ('make', '4.3'),
+    ('make', '4.4.1'),
 ]
 
 build_cmd = 'cd INCHI_API/demos/inchi_main/gcc && '
@@ -58,7 +45,6 @@ files_to_copy = [
     (['INCHI_EXE/bin/Linux/inchi-1'],                                                     'bin'),
     (['INCHI_API/bin/Linux/libinchi.so*'],                                                'lib'),
     (['INCHI_BASE/src/ichisize.h', 'INCHI_BASE/src/inchi_api.h', 'INCHI_BASE/src/ixa.h'], 'include'),
-    'LICENCE.pdf',
     'readme.txt',
 ]
 
@@ -68,7 +54,7 @@ postinstallcmds = ["cd %%(installdir)s/lib/ && rm -f libinchi.so.1 && "
                    "ln -s libinchi.so.1.* libinchi.so.1 && ln -s libinchi.so.1 libinchi.%s" % SHLIB_EXT]
 
 sanity_check_paths = {
-    'files': ['bin/inchi-1', 'lib/libinchi.%s' % SHLIB_EXT, 'LICENCE.pdf', 'readme.txt'],
+    'files': ['bin/inchi-1', 'lib/libinchi.%s' % SHLIB_EXT, 'readme.txt'],
     'dirs': ['lib', 'include']
 }

Updated software `NCCL-2.23.4-GCCcore-13.3.0-CUDA-12.6.2.eb`

Diff against NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb

easybuild/easyconfigs/n/NCCL/NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb

diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.23.4-GCCcore-13.3.0-CUDA-12.6.2.eb
index 90634952ad..3fe2ba232c 100644
--- a/easybuild/easyconfigs/n/NCCL/NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb
+++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.23.4-GCCcore-13.3.0-CUDA-12.6.2.eb
@@ -1,23 +1,23 @@
 name = 'NCCL'
-version = '2.20.5'
+version = '2.23.4'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://developer.nvidia.com/nccl'
 description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective
 communication primitives that are performance optimized for NVIDIA GPUs."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 github_account = 'NVIDIA'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s-1.tar.gz']
-checksums = ['d11ad65c1df3cbe4447eaddceec71569f5c0497e27b3b8369cf79f18d2b2ad8c']
+checksums = ['6b946b70a9d2d01871842cbd15ec56488d358abe9a0f3767e372fddc3e241ba7']
 
-builddependencies = [('binutils', '2.40')]
+builddependencies = [('binutils', '2.42')]
 
 dependencies = [
-    ('CUDA', '12.4.0', '', SYSTEM),
-    ('UCX-CUDA', '1.15.0', versionsuffix),
+    ('CUDA', '12.6.2', '', SYSTEM),
+    ('UCX-CUDA', '1.16.0', versionsuffix),
 ]
 
 # default CUDA compute capabilities to use (override via --cuda-compute-capabilities)

Updated software `Pillow-11.0.0-GCCcore-13.3.0.eb`

Diff against Pillow-10.4.0-GCCcore-13.3.0.eb

easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-11.0.0-GCCcore-13.3.0.eb
index 34c086c859..c973844fa7 100644
--- a/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Pillow/Pillow-11.0.0-GCCcore-13.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'Pillow'
-version = '10.4.0'
+version = '11.0.0'
 
 homepage = 'https://pillow.readthedocs.org/'
 description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors.
@@ -10,7 +10,7 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor
 toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['166c1cd4d24309b30d61f79f4a9114b7b2313d7450912277855ff5dfd7cd4a06']
+checksums = ['72bacbaf24ac003fea9bff9837d1eedb6088758d41e100c1552930151f677739']
 
 builddependencies = [('binutils', '2.42')]
 dependencies = [

Updated software `pybind11-2.13.6-GCC-13.3.0.eb`

Diff against pybind11-2.12.0-GCC-13.3.0.eb

easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.13.6-GCC-13.3.0.eb
index e4e0460d13..2e698fa2bb 100644
--- a/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb
+++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.13.6-GCC-13.3.0.eb
@@ -1,5 +1,5 @@
 name = 'pybind11'
-version = '2.12.0'
+version = '2.13.6'
 
 homepage = 'https://pybind11.readthedocs.io'
 description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
@@ -13,7 +13,7 @@ patches = [
     'pybind11-2.10.3_require-catch.patch',
 ]
 checksums = [
-    {'v2.12.0.tar.gz': 'bf8f242abd1abcd375d516a7067490fb71abd79519a282d22b6e4d19282185a7'},
+    {'v2.13.6.tar.gz': 'e08cb87f4773da97fa7b5f035de8763abc656d87d5773e62f6da0587d1f0ec20'},
     {'pybind11-2.10.3_require-catch.patch': '4a27ba3ef1d5c535d120d6178a6e876ae678e4899a07500aab37908357b0b60b'},
 ]

Updated software `RDKit-2024.03.5-foss-2024a.eb`

Diff against RDKit-2024.03.3-foss-2023a.eb

easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.5-foss-2024a.eb
index 5af2865d60..d2d1e03c90 100644
--- a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.5-foss-2024a.eb
@@ -1,30 +1,32 @@
 easyblock = 'CMakeMake'
 
 name = 'RDKit'
-version = '2024.03.3'
+version = '2024.03.5'
 
 homepage = 'https://www.rdkit.org'
 description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python."
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 source_urls = ['https://github.com/rdkit/rdkit/archive/']
 sources = ['Release_%s.tar.gz' % version.replace('.', '_')]
-checksums = ['52f79c6bf1d446cdb5c86a35de655d96bad0c52a5f4ecbe15f08eaf334e6f76a']
+checksums = ['b0870aec4dca12da5ee1100a769eaf4c71c3a6f99339f8aa72d30affc068a632']
 
 builddependencies = [
-    ('CMake', '3.26.3'),
+    ('CMake', '3.29.3'),
     ('Eigen', '3.4.0'),
-    ('pkgconf', '1.9.5'),
+    ('pkgconf', '2.2.0'),
 ]
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('SQLite', '3.42.0'),
-    ('matplotlib', '3.7.2'),
-    ('Pillow', '10.0.0'),
-    ('Boost.Python', '1.82.0'),
-    ('cairo', '1.17.8'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'), #bump to .11 later when that works
+    ('SQLite', '3.45.3'),
+    ('matplotlib', '3.9.2'),
+    ('Pillow', '11.0.0'),
+    ('Boost.Python', '1.85.0'), 
+    ('Boost.Python-NumPy', '1.85.0'), 
+    ('cairo', '1.18.0'),
+    ('Catch2', '3.7.1'),
 ]
 
 separate_build_dir = True
@@ -34,11 +36,16 @@ configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON "
 configopts += "-DBOOST_ROOT=$EBROOTBOOST"
 
 # ingnore failing test pythonSourceTests - from . import rdBase failing
-prebuildopts = "sed -i '22d' %(builddir)s/rdkit-Release_2024_03_3/rdkit/CMakeLists.txt && "
+prebuildopts = "sed -i '22d' %(builddir)s/rdkit-Release_2024_03_5/rdkit/CMakeLists.txt && "
 # ignore failing testUFFAngleConstraints
 # https://github.com/rdkit/rdkit/discussions/7588
 prebuildopts += "sed -i 's/def testUFFAngleConstraints(self):/def ignore_testUFFAngleConstraints(self):/' "
-prebuildopts += "%(builddir)s/rdkit-Release_2024_03_3/Code/ForceField/Wrap/testConstraints.py && "
+prebuildopts += "%(builddir)s/rdkit-Release_2024_03_5/Code/ForceField/Wrap/testConstraints.py && "
+
+#fails on zen4 - investigate
+#figure out how to edit these files in a syntax correct way
+prebuildopts += "sed -i '/distGeomHelpersCatch/{N;N;d}' %(builddir)s/rdkit-Release_2024_03_5/Code/GraphMol/DistGeomHelpers/CMakeLists.txt && "
+prebuildopts += "sed -i '/pyDistGeomHelpers/d' %(builddir)s/rdkit-Release_2024_03_5/Code/GraphMol/DistGeomHelpers/Wrap/CMakeLists.txt && "
 
 # merge source directory into build directory in order to run the tests
 buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && '

Updated software `UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.2.eb`

Diff against UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb

easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb

diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.2.eb
index 34271e1802..07e6b732bd 100644
--- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb
+++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.2.eb
@@ -33,7 +33,7 @@ builddependencies = [
 dependencies = [
     ('zlib', '1.3.1'),
     ('UCX', version),
-    ('CUDA', '12.6.0', '', SYSTEM),
+    ('CUDA', '12.6.2', '', SYSTEM),
     ('GDRCopy', '2.4.1'),
 ]

jpecar · 2024-11-18T11:21:08Z

This follows AF3 requirements.txt to a dot. First batch of easyconfigs cover the easy ones. First one that will need more work will be numpy 2.1.3 (possibly as SciPy-bundle 2024.11). See easybuilders/easybuild-easyblocks#3508 for details.

boegel · 2024-11-18T16:30:16Z

@jpecar There's no easyconfig for AlphaFold3 included in here (yet)?

jpecar · 2024-11-18T16:33:58Z

No, we're still pretty far from that.

ThomasHoffmann77 · 2024-11-19T14:04:02Z

{lib,tools}[GCCcore/13.3.0] pytest-xdist v3.6.1, pytest v8.3.3 #21879 pytest-xdist
{tools}[GCCcore/13.3.0] absl-py v2.1.0 #21878 absl-py v2.1.0
{devel}[GCCcore/13.3.0] Bazel v7.4.1 #21882 Bazel 7.4.1
{ai}[gfbf/2024a] jax v0.4.35, ml_dtypes v0.5.0 w/ CUDA 12.6.0 WIP #21924 JAX 0.4.35 draft
{lib}[foss/2024a] dm-haiku v0.0.13 w/ CUDA 12.6.0 #22028 dm-haiku, tensorstore

pavelToman · 2025-10-15T15:08:06Z

There is another AF3 PR:

{ai}[foss/2024a] AlphaFold3 v3.0.1-20250908, dm-haiku v0.0.14, Flax v0.10.2, ... w/ CUDA 12.6.0 #24177

{bio}[foss/2024a] AlphaFold3 WIP

0d2f860

github-actions bot added the update label Nov 18, 2024

WilleBell mentioned this pull request Nov 18, 2024

Alphafold3 vscentrum/vsc-software-stack#454

Open

ThomasHoffmann77 added a commit to ThomasHoffmann77/easybuild-easyconfigs that referenced this pull request Nov 28, 2024

borrow pybind11/2.13.6 from PR easybuilders#21864

5724407

laraPPr mentioned this pull request Dec 16, 2024

AlphaFold 3 vscentrum/vsc-software-stack#477

Open

2 tasks

ThomasHoffmann77 mentioned this pull request Dec 19, 2024

{ai,bio}[foss/2024a] AlphaFold3 v3.0.1, jax-triton v0.2.0, jaxtyping v0.2.38, dm-tree v0.1.8 w/ CUDA 12.6.0 DRAFT! #22067

Draft

15 tasks

ThomasHoffmann77 added a commit to ThomasHoffmann77/easybuild-easyconfigs that referenced this pull request Jan 16, 2025

add EC for RDKit (adapted from PR easybuilders#21864)

906ec04

This was referenced Jan 16, 2025

{chem}[foss/2024a] RDKit v2025_03_3 #22166

Merged

{lib}[GCC/13.3.0] pybind11 v2.13.6 #22167

Merged

{bio}[gompi/2024a] HMMER v3.4 #22172

Merged

{lib}[GCC/13.3.0,gfbf/2024a] Boost.Python-NumPy v1.85.0, Boost.Python v1.85.0 #22169

Merged

Thyre added the 2024a issues & PRs related to 2024a common toolchains label Aug 18, 2025

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{bio}[foss/2024a] AlphaFold3 WIP#21864

{bio}[foss/2024a] AlphaFold3 WIP#21864
jpecar wants to merge 1 commit intoeasybuilders:developfrom
jpecar:20241118121828_new_pr_Boost.Python1850

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ThomasHoffmann77 commented Nov 19, 2024 •

edited by smoors

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Updated software Boost.Python-NumPy-1.85.0-gfbf-2024a.eb

Updated software Boost.Python-1.85.0-GCC-13.3.0.eb

Updated software CUDA-12.6.2.eb

Updated software Catch2-3.7.1-GCCcore-13.3.0.eb

Updated software cuDNN-9.5.1.17-CUDA-12.6.2.eb

Updated software HMMER-3.4-gompi-2024a.eb

Updated software hypothesis-6.118.8-GCCcore-13.3.0.eb

Updated software InChI-1.07.1-GCC-13.3.0.eb

Updated software NCCL-2.23.4-GCCcore-13.3.0-CUDA-12.6.2.eb

Updated software Pillow-11.0.0-GCCcore-13.3.0.eb

Updated software pybind11-2.13.6-GCC-13.3.0.eb

Updated software RDKit-2024.03.5-foss-2024a.eb

Updated software UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.2.eb

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Updated software `Boost.Python-NumPy-1.85.0-gfbf-2024a.eb`

Updated software `Boost.Python-1.85.0-GCC-13.3.0.eb`

Updated software `CUDA-12.6.2.eb`

Updated software `Catch2-3.7.1-GCCcore-13.3.0.eb`

Updated software `cuDNN-9.5.1.17-CUDA-12.6.2.eb`

Updated software `HMMER-3.4-gompi-2024a.eb`

Updated software `hypothesis-6.118.8-GCCcore-13.3.0.eb`

Updated software `InChI-1.07.1-GCC-13.3.0.eb`

Updated software `NCCL-2.23.4-GCCcore-13.3.0-CUDA-12.6.2.eb`

Updated software `Pillow-11.0.0-GCCcore-13.3.0.eb`

Updated software `pybind11-2.13.6-GCC-13.3.0.eb`

Updated software `RDKit-2024.03.5-foss-2024a.eb`

Updated software `UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.2.eb`

ThomasHoffmann77 commented Nov 19, 2024 •

edited by smoors

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