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

…-layer into multiple_cvmfs_repos_eessi_container

.github/workflows/test-software.eessi.io.yml

@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   check_missing:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:

.github/workflows/test_eessi_container_script.yml

@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   eessi_container_script:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:

.github/workflows/test_licenses.yml

@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1

.github/workflows/tests.yml

@@ -5,10 +5,10 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10']
+        python: [3.7, 3.8, 3.9, '3.10']
       fail-fast: false
     steps:
     - name: checkout

.github/workflows/tests_archdetect.yml

@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         proc_cpuinfo:

.github/workflows/tests_init.yml

@@ -5,10 +5,10 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10']
+        python: [3.7, 3.8, 3.9, '3.10']
       fail-fast: false
     steps:
     - name: checkout

.github/workflows/tests_readme.yml

@@ -14,7 +14,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1

.github/workflows/tests_scripts.yml

@@ -28,7 +28,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
     - name: checkout
       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1

easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml

@@ -0,0 +1,5 @@
+easyconfigs:
+  - OpenMPI-4.1.5-GCC-12.3.0.eb
+  - foss-2023a.eb
+  - SciPy-bundle-2023.07-gfbf-2023a.eb
+  - ESPResSo-4.2.2-foss-2023a.eb

easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml

@@ -0,0 +1,6 @@
+easyconfigs:
+  - OpenBLAS-0.3.24-GCC-13.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20820
+        from-commit: 1fc885b35dacdeb2feef4af207a2daa2502bae08
+  - foss-2023b.eb

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml

@@ -0,0 +1,2 @@
+easyconfigs:
+  - BCFtools-1.18-GCC-12.3.0.eb

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml

@@ -0,0 +1,3 @@
+easyconfigs:
+  - IPython-8.17.2-GCCcore-13.2.0.eb
+  - dlb-3.4-gompi-2023b.eb

easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml

@@ -2,3 +2,4 @@ easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb
   - TensorFlow-2.13.0-foss-2023a.eb
   - R-4.3.2-gfbf-2023a.eb
+  - ParaView-5.11.2-foss-2023a.eb

eb_hooks.py

@@ -23,6 +23,7 @@
 CPU_TARGET_NEOVERSE_N1 = 'aarch64/neoverse_n1'
 CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1'
 CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic'
+CPU_TARGET_A64FX = 'aarch64/a64fx'
 
 EESSI_RPATH_OVERRIDE_ATTR = 'orig_rpath_override_dirs'
 
@@ -335,6 +336,24 @@ def pre_configure_hook(self, *args, **kwargs):
         PRE_CONFIGURE_HOOKS[self.name](self, *args, **kwargs)
 
 
+def pre_configure_hook_BLIS_a64fx(self, *args, **kwargs):
+    """
+    Pre-configure hook for BLIS when building for A64FX:
+    - add -DCACHE_SECTOR_SIZE_READONLY to $CFLAGS for BLIS 0.9.0, cfr. https://github.com/flame/blis/issues/800
+    """
+    if self.name == 'BLIS':
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if self.version == '0.9.0' and cpu_target == CPU_TARGET_A64FX:
+            # last argument of BLIS' configure command is configuration target (usually 'auto' for auto-detect),
+            # specifying of variables should be done before that
+            config_opts = self.cfg['configopts'].split(' ')
+            cflags_var = 'CFLAGS="$CFLAGS -DCACHE_SECTOR_SIZE_READONLY"'
+            config_target = config_opts[-1]
+            self.cfg['configopts'] = ' '.join(config_opts[:-1] + [cflags_var, config_target])
+    else:
+        raise EasyBuildError("BLIS-specific hook triggered for non-BLIS easyconfig?!")
+
+
 def pre_configure_hook_gromacs(self, *args, **kwargs):
     """
     Pre-configure hook for GROMACS:
@@ -469,20 +488,30 @@ def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs):
 def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
     """
     Pre-test hook for SciPy-bundle: skip failing tests for selected SciPy-bundle versions
-    In version 2021.10, 2 failing tests in scipy 1.6.3:
+    In version 2021.10 on neoverse_v1, 2 failing tests in scipy 1.6.3:
         FAILED optimize/tests/test_linprog.py::TestLinprogIPSparse::test_bug_6139 - A...
         FAILED optimize/tests/test_linprog.py::TestLinprogIPSparsePresolve::test_bug_6139
         = 2 failed, 30554 passed, 2064 skipped, 10992 deselected, 76 xfailed, 7 xpassed, 40 warnings in 380.27s (0:06:20) =
-    In versions 2023.02, 2023.07, and 2023.11, 2 failing tests in scipy (versions 1.10.1, 1.11.1, 1.11.4):
+    In versions 2023.02 + 2023.07 + 2023.11 on neoverse_v1, 2 failing tests in scipy (versions 1.10.1, 1.11.1, 1.11.4):
         FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris
         FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris_float32
         = 2 failed, 54409 passed, 3016 skipped, 223 xfailed, 13 xpassed, 10917 warnings in 892.04s (0:14:52) =
-    In previous versions we were not as strict yet on the numpy/SciPy tests
+    In version 2023.07 on a64fx, 4 failing tests in scipy 1.11.1:
+        FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparse::test_bug_6139
+        FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparsePresolve::test_bug_6139
+        FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris
+        FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris_float32
+        = 4 failed, 54407 passed, 3016 skipped, 223 xfailed, 13 xpassed, 10917 warnings in 6068.43s (1:41:08) =
+    (in previous versions we were not as strict yet on the numpy/SciPy tests)
     """
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-    scipy_bundle_versions = ('2021.10', '2023.02', '2023.07', '2023.11')
-    if self.name == 'SciPy-bundle' and self.version in scipy_bundle_versions and cpu_target == CPU_TARGET_NEOVERSE_V1:
-        self.cfg['testopts'] = "|| echo ignoring failing tests"
+    scipy_bundle_versions_nv1 = ('2021.10', '2023.02', '2023.07', '2023.11')
+    scipy_bundle_versions_a64fx = ('2023.07', '2023.11')
+    if self.name == 'SciPy-bundle':
+        if cpu_target == CPU_TARGET_NEOVERSE_V1 and self.version in scipy_bundle_versions_nv1:
+            self.cfg['testopts'] = "|| echo ignoring failing tests"
+        elif cpu_target == CPU_TARGET_A64FX and self.version in scipy_bundle_versions_a64fx:
+            self.cfg['testopts'] = "|| echo ignoring failing tests"
 
 def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs):
     """
@@ -680,12 +709,13 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
+    'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
+    'BLIS': pre_configure_hook_BLIS_a64fx,
     'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,
     'WRF': pre_configure_hook_wrf_aarch64,
-    'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
 }
 
 PRE_TEST_HOOKS = {

eessi-2023.06-known-issues.yml

@@ -1,3 +1,10 @@
+- aarch64/a64x:
+  - SciPy-bundle-2023.07-gfbf-2023a:
+    - issue: https://github.com/EESSI/software-layer/issues/318
+    - info: "4 failing tests (vs 54407 passed) in scipy test suite"
+  - SciPy-bundle-2023.11-gfbf-2023b:
+    - issue: https://github.com/EESSI/software-layer/issues/318
+    - info: "3 failing tests (vs 54875 passed) in scipy test suite"
 - aarch64/generic:
   - PyTorch-2.1.2-foss-2023a:
     - issue: https://github.com/EESSI/software-layer/issues/461