Merge branch 'main' of github.com:EESSI/software-layer into rebuild_gromacs

Author: bedroge

easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2022b.yml

@@ -35,3 +35,24 @@ easyconfigs:
 #  - HarfBuzz-5.3.1-GCCcore-12.2.0.eb
 ##  - Qt5-5.15.7-GCCcore-12.2.0.eb
 ##  - QuantumESPRESSO-7.2-foss-2022b.eb
+# Apps originaly added from gracehopper on https://github.com/EESSI/software-layer/pull/1031
+  - MUMPS-5.6.1-foss-2022b-metis.eb 
+  # - GL2PS-1.4.2-GCCcore-12.2.0.eb 
+  # - GST-plugins-base-1.22.1-GCC-12.2.0.eb
+  # - wxWidgets-3.2.2.1-GCC-12.2.0.eb
+  - Archive-Zip-1.68-GCCcore-12.2.0.eb
+  - jemalloc-5.3.0-GCCcore-12.2.0.eb
+  - Judy-1.0.5-GCCcore-12.2.0.eb
+  - libaio-0.3.113-GCCcore-12.2.0.eb
+  - Z3-4.12.2-GCCcore-12.2.0.eb
+  - tbb-2021.10.0-GCCcore-12.2.0.eb
+  # - dask-2023.7.1-foss-2022b.eb
+  # - netcdf4-python-1.6.3-foss-2022b.eb
+  - Ruby-3.2.2-GCCcore-12.2.0.eb
+# originally built with EB 4.9.2; PR 21526 and PR 3467 included since EB 5.0.0, thus need to use *from-commit
+  # - ROOT-6.26.10-foss-2022b.eb:
+  #     options:
+  #      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21526
+  #      from-commit: 6cbfbd7d7a55dc7243f46d0beea510278f4718df
+  #      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3467
+  #      include-easyblocks-from-commit: c3aebe1f133d064a228c5d6c282e898b83d74601

easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml

@@ -298,3 +298,8 @@ easyconfigs:
   - Valgrind-3.21.0-gompi-2023a.eb
   - OrthoFinder-2.5.5-foss-2023a.eb
   - BWA-0.7.18-GCCcore-12.3.0.eb
+  - lit-18.1.2-GCCcore-12.3.0.eb
+      # needed due to changed/new dependencies for R-bundle-CRAN-2023.12-foss-2023a.eb
+      # without any from-commit this will use a version from April 6, 2024
+      # https://github.com/easybuilders/easybuild-easyconfigs/blob/88f6f9c7439c535e62461e6e71b1961c7be118b8/easybuild/easyconfigs/l/lit/lit-18.1.2-GCCcore-12.3.0.eb
+      # EB 5.0.0 has a few changes to that

easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023b.yml

@@ -107,7 +107,7 @@ easyconfigs:
 #      options:
 #        from-pr: 20792
   - Valgrind-3.23.0-gompi-2023b.eb
-  # recipes taken from https://github.com/EESSI/software-layer/pull/996
+# recipes taken from https://github.com/EESSI/software-layer/pull/996
   - lit-18.1.7-GCCcore-13.2.0.eb:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20902
@@ -116,4 +116,68 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22469
         from-commit: fc22841fef99cbb2a221c18029b15e692e78c27c
-
+  - PDT-3.25.2-GCCcore-13.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22523
+        from-commit: 0044f08898e12cfd31177bfce0747ef2172226d1
+# from here on easyconfigs were originally built with EB 4.9.3
+# originally built with EB 4.9.3, PR 21436 was merged into develop before EB
+# 4.9.4 was released, but maybe it wasn't included in EB 4.9.4, to be on the safe
+# side we just use the commit, PR 3569 was targetting Sapphire Rapids, so likely
+# that is not needed here, however we keep it to stay in sync with what was used
+# for Sapphire Rapids
+  - LAMMPS-29Aug2024-foss-2023b-kokkos.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21436
+        from-commit: 9dc24e57880a8adb06ae10557c5315e66671a533
+        # see https://github.com/easybuilders/easybuild-easyblocks/pull/3569
+        include-easyblocks-from-commit: 362b4679193612e04abe336fa041e2a34d183991
+# included for gracehopper on https://github.com/EESSI/software-layer/pull/993
+  - SIONlib-1.7.7-GCCcore-13.2.0-tools.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21752
+        # NOTE, commit is the last one before the merge commit for PR 21752
+        from-commit: 6b8b53493a1188a5baa56a133574daac239730e7
+  - Score-P-8.4-gompi-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyblocks/pull/3496
+        # NOTE, commit is the last one before the merge commit for PR 3496
+        include-easyblocks-from-commit: 60633b0acfd41a0732992d9e16800dae71a056eb
+  - Cython-3.0.10-GCCcore-13.2.0.eb
+  - Mustache-1.3.3-foss-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21783
+        # NOTE, commit is the last one before the merge commit for PR 21783
+        from-commit: 5fa3db9eb36f91cba3fbf351549f8ba2849abc33
+  - GDRCopy-2.4-GCCcore-13.2.0.eb
+#  - GROMACS-2024.4-foss-2023b.eb:
+#      options:
+#        # https://github.com/easybuilders/easybuild-easyconfigs/pull/21851
+#        # NOTE, below commit is the merge commit for PR 21851
+#        from-commit: f0fa64b440deaf5fb0a6d26ff1bb3e9f36626c8a
+# Disable Gromacs build, there is an error with a test that require a further analysis
+  - SlurmViewer-1.0.1-GCCcore-13.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21899
+        # NOTE, below commit is the merge commit for PR 21899
+        from-commit: 0bdeb23c9ea5a3caefd353ecd936919424c1bba4
+  - wxWidgets-3.2.6-GCC-13.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21915
+        # NOTE, below commit is the merge commit for PR 21915
+        from-commit: 58f16c0caf8c5494c68e9eda8cbf19e9145d3cfa
+  - DP3-6.2-foss-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21765
+        # NOTE, below commit is the merge commit for PR 21765
+        from-commit: c7e4bfe1a57cf9781ce346ba8ae9081644408c23
+  - WSClean-3.5-foss-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21765
+        # NOTE, below commit is the merge commit for PR 21765
+        from-commit: c7e4bfe1a57cf9781ce346ba8ae9081644408c23
+  - EveryBeam-0.6.1-foss-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21765
+        # NOTE, below commit is the merge commit for PR 21765
+        from-commit: c7e4bfe1a57cf9781ce346ba8ae9081644408c23

easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-5.1.1-2023b.yml

@@ -0,0 +1,2 @@
+easyconfigs:
+  - MLflow-2.18.0-gfbf-2023b.eb

easystacks/software.eessi.io/2023.06/accel/nvidia/rebuilds/20250828-eb-5.1.1-rebuild-ESPResSo-for-cuda-sanity-check.yml

@@ -0,0 +1,12 @@
+# We'll rebuild all CUDA software, for various reasons
+# 1. We now have a proper CUDA sanity check, and if anything was 'wrong' with our current CUDA installs, we'd like
+# to know about it
+# 2. The PR implementing a CI to check for differences between officially supported CUDA Compute Capabilities shows
+# that there are a lot of missing installations https://github.com/EESSI/software-layer/pull/1087 . A rebuild PR like
+# this will have the convenient side effect of filling all those holes
+easyconfigs:
+  - ESPResSo-4.2.2-foss-2023a-CUDA-12.1.1.eb:
+      options:
+        # need an additional patch to build for the right CUDA architecture,
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/23795
+        from-commit: f3940e57527848706505b846ac4f2fce86fd5def

easystacks/software.eessi.io/2023.06/accel/nvidia/rebuilds/20250828-eb-5.1.1-rebuild-UCX-UCC-OSU-for-cuda-sanity-check.yml

@@ -0,0 +1,13 @@
+# We'll rebuild all CUDA software, for various reasons
+# 1. We now have a proper CUDA sanity check, and if anything was 'wrong' with our current CUDA installs, we'd like
+# to know about it
+# 2. The PR implementing a CI to check for differences between officially supported CUDA Compute Capabilities shows
+# that there are a lot of missing installations https://github.com/EESSI/software-layer/pull/1087 . A rebuild PR like
+# this will have the convenient side effect of filling all those holes
+easyconfigs:
+  - UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.4.0.eb
+  - NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb:
+      options:
+         cuda-sanity-check-accept-missing-ptx: True 
+  - UCC-CUDA-1.2.0-GCCcore-13.2.0-CUDA-12.4.0.eb
+  - OSU-Micro-Benchmarks-7.5-gompi-2023b-CUDA-12.4.0.eb

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-001-system.yml

@@ -2,3 +2,5 @@ easyconfigs:
   - Java-11.0.27.eb
   - Java-17.0.15.eb
   - Java-21.0.7.eb
+  - Trimmomatic-0.39-Java-11.eb
+  - FastQC-0.12.1-Java-11.eb

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-2023a.yml

@@ -10,3 +10,10 @@ easyconfigs:
         # See https://github.com/easybuilders/easybuild-easyconfigs/pull/22932
         from-commit: 3211d34eb16ff31b8de3dfef55ecaaf1ec205c6f
   - MrBayes-3.2.7-gompi-2023a.eb
+  - Flye-2.9.3-GCC-12.3.0.eb
+  - websockify-0.13.0-gfbf-2023a.eb:
+      options:
+        # See https://github.com/easybuilders/easybuild-easyconfigs/pull/23596
+        from-commit: daa610c5b3aaf43b80779805d85f13a1d5a8734e
+  - MLflow-2.10.2-gfbf-2023a.eb
+  - Salmon-1.10.3-GCC-12.3.0.eb

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-2023b.yml

@@ -1,3 +1,10 @@
 easyconfigs:
   - openCARP-17.0-foss-2023b.eb
   - libheif-1.19.5-GCCcore-13.2.0.eb
+  - Subread-2.1.1-GCC-13.2.0.eb
+  - Flye-2.9.4-GCC-13.2.0.eb
+  - MLflow-2.18.0-gfbf-2023b.eb
+  - snakemake-8.28.0-foss-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22371
+        from-commit: 29f82e43229663c22f0c76cb3fc7b6dd5c407cd7

easystacks/software.eessi.io/2023.06/rebuilds/20250912-eb-4.9.2-Python-ctypes-a64fx.yml

@@ -0,0 +1,20 @@
+# 2025.09.12
+# Python ctypes relies on LD_LIBRARY_PATH and doesn't respect rpath linking. There is a workaround
+# for the EasyBuild context in https://github.com/easybuilders/easybuild-easyblocks/pull/3352.
+#
+# This rebuild ensures this fix is available for all Python versions shipped with EESSI.
+# 
+# See https://gitlab.com/eessi/support/-/issues/77
+easyconfigs:
+  - Python-3.10.8-GCCcore-12.2.0-bare:
+      options:
+        # See https://github.com/easybuilders/easybuild-easyblocks/pull/3352
+        include-easyblocks-from-commit: 1ee17c0f7726c69e97442f53c65c5f041d65c94f
+  - Python-3.11.3-GCCcore-12.3.0:
+      options:
+        # See https://github.com/easybuilders/easybuild-easyblocks/pull/3352
+        include-easyblocks-from-commit: 1ee17c0f7726c69e97442f53c65c5f041d65c94f
+  - Python-3.11.5-GCCcore-13.2.0:
+      options:
+        # See https://github.com/easybuilders/easybuild-easyblocks/pull/3352
+        include-easyblocks-from-commit: 1ee17c0f7726c69e97442f53c65c5f041d65c94f