Merge branch '2023.06-software.eessi.io' of github-trz:EESSI/software…

…-layer into debug-2023.06-software.eessi.io-PyTorch-2.1.2-foss-2023a
EESSI · Aug 8, 2024 · d12685a · d12685a
2 parents e207878 + 3db7ade
commit d12685a
Show file tree

Hide file tree

Showing 7 changed files with 103 additions and 0 deletions.
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
@@ -1,2 +1,7 @@
 easyconfigs:
   - BLAST+-2.14.0-gompi-2022b.eb
+  - BioPerl-1.7.8-GCCcore-12.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21136
+        from-commit: d8076ebaf8cb915762adebf88d385cc672b350dc
+  - gnuplot-5.4.6-GCCcore-12.2.0.eb 
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -27,4 +27,18 @@ easyconfigs:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
         from-commit: a92667fe32396bbd4106243658625f7ff2adcd68
   - amdahl-0.3.1-gompi-2023a.eb
+  - librosa-0.10.1-foss-2023a.eb
+  - xarray-2023.9.0-gfbf-2023a.eb
+  - SciTools-Iris-3.9.0-foss-2023a.eb
+  - OpenFOAM-v2312-foss-2023a.eb:
+      options:
+        # https://github.com/easybuilders/easybuild-easyblocks/pull/3388
+        include-easyblocks-from-commit: c8256a36e7062bc09f5ce30552a9de9827054c9e
+        # https://github.com/easybuilders/easybuild-easyconfigs/pull/20841
+        from-commit: f0e91e6e430ebf902f7788ebb47f0203dee60649
+  - BioPerl-1.7.8-GCCcore-12.3.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21136
+        from-commit: d8076ebaf8cb915762adebf88d385cc672b350dc
+  - grpcio-1.57.0-GCCcore-12.3.0.eb
   - PyTorch-bundle-2.1.2-foss-2023a.eb
diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240729-eb-4.9.2-Python-ctypes.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240729-eb-4.9.2-Python-ctypes.yml
@@ -0,0 +1,24 @@
+# 2024.07.29
+# 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-3.10.8-GCCcore-12.2.0:
+      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
diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240801-eb-4.9.2-Python-ctypes-zen4.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240801-eb-4.9.2-Python-ctypes-zen4.yml
@@ -0,0 +1,17 @@
+# 2024.08.01
+# 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 for
+# zen4 with EESSI.
+# 
+# See https://gitlab.com/eessi/support/-/issues/77
+easyconfigs:
+  - 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
diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -11,3 +11,14 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
         from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f
+  - Highway-1.0.4-GCCcore-12.3.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20942
+        from-commit: 524da37b903585cea5a9eeb4156d1c8d57636bd8
+  - librosa-0.10.1-foss-2023a.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb
+  - BioPerl-1.7.8-GCCcore-12.3.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21136
+        from-commit: d8076ebaf8cb915762adebf88d385cc672b350dc
+  - MODFLOW-6.4.4-foss-2023a.eb
diff --git a/eb_hooks.py b/eb_hooks.py
@@ -220,6 +220,19 @@ def parse_hook_fontconfig_add_fonts(ec, eprefix):
         raise EasyBuildError("fontconfig-specific hook triggered for non-fontconfig easyconfig?!")
 
 
+def parse_hook_grpcio_zlib(ec, ecprefix):
+    """Adjust preinstallopts to use ZLIB from compat layer."""
+    if ec.name == 'grpcio' and ec.version in ['1.57.0']:
+        exts_list = ec['exts_list']
+        original_preinstallopts = (exts_list[0][2])['preinstallopts']
+        original_option = "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True"
+        new_option = "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=False"
+        (exts_list[0][2])['preinstallopts'] = original_preinstallopts.replace(original_option, new_option, 1)
+        print_msg("Modified the easyconfig to use compat ZLIB with GRPC_PYTHON_BUILD_SYSTEM_ZLIB=False")
+    else:
+        raise EasyBuildError("grpcio-specific hook triggered for a non-grpcio easyconfig?!")
+
+
 def parse_hook_openblas_relax_lapack_tests_num_errors(ec, eprefix):
     """Relax number of failing numerical LAPACK tests for aarch64/neoverse_v1 CPU target for OpenBLAS < 0.3.23"""
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
@@ -767,6 +780,7 @@ def inject_gpu_property(ec):
     'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
+    'grpcio': parse_hook_grpcio_zlib,
     'LAMMPS': parse_hook_lammps_remove_deps_for_CI_aarch64,
     'CP2K': parse_hook_CP2K_remove_deps_for_aarch64,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,

diff --git a/init/eessi_archdetect.sh b/init/eessi_archdetect.sh
@@ -1,4 +1,22 @@
 #!/usr/bin/env bash
+
+# Confirm the current shell is Bash >= 4
+# (works for sh, bash, dash, zsh, ksh, but not fish, tcsh, elvish)
+if [ -n "$BASH_VERSION" ]; then
+    # Extract the major version numbers
+    bash_version=$(echo "$BASH_VERSION" | grep -oP '^\d+\.\d+')
+    major_version=$(echo "$bash_version" | cut -d. -f1)
+
+    # Check if the major version is 4 or higher
+    if [ "$major_version" -lt 4 ]; then
+        echo "Error: This script must be run with Bash >= 4, you have $BASH_VERSION." >&2
+        exit 1
+    fi
+else
+    echo "Error: This script must be run with Bash." >&2
+    exit 1
+fi
+
 VERSION="1.1.0"
 
 # default log level: only emit warnings or errors