Merge branch '2023.06-software.eessi.io' of gh-nessi:EESSI/software-l…

…ayer into eessi-2023.06-netCDF/4.9.2-gompi/2023b

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml

@@ -0,0 +1,2 @@
+easyconfigs:
+  - SciPy-bundle-2023.02-gfbf-2022b.eb

eb_hooks.py

@@ -367,31 +367,28 @@ def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
         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 2023.07 and 2023.11, 2 failing tests in scipy 1.11.1 and 1.11.4:
+    In versions 2023.02, 2023.07, and 2023.11, 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
     """
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-    if self.name == 'SciPy-bundle' and self.version in ['2021.10', '2023.07', '2023.11'] and cpu_target == CPU_TARGET_NEOVERSE_V1:
+    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"
 
 
 def pre_single_extension_hook(ext, *args, **kwargs):
-    """Main pre-configure hook: trigger custom functions based on software name."""
+    """Main pre-extension: trigger custom functions based on software name."""
     if ext.name in PRE_SINGLE_EXTENSION_HOOKS:
         PRE_SINGLE_EXTENSION_HOOKS[ext.name](ext, *args, **kwargs)
 
 
-def pre_single_extension_testthat(ext, *args, **kwargs):
-    """
-    Pre-extension hook for testthat R package, to fix build on top of recent glibc.
-    """
-    if ext.name == 'testthat' and LooseVersion(ext.version) < LooseVersion('3.1.0'):
-        # use constant value instead of SIGSTKSZ for stack size,
-        # cfr. https://github.com/r-lib/testthat/issues/1373 + https://github.com/r-lib/testthat/pull/1403
-        ext.cfg['preinstallopts'] = "sed -i 's/SIGSTKSZ/32768/g' inst/include/testthat/vendor/catch.h && "
+def post_single_extension_hook(ext, *args, **kwargs):
+    """Main post-extension hook: trigger custom functions based on software name."""
+    if ext.name in POST_SINGLE_EXTENSION_HOOKS:
+        POST_SINGLE_EXTENSION_HOOKS[ext.name](ext, *args, **kwargs)
 
 
 def pre_single_extension_isoband(ext, *args, **kwargs):
@@ -404,6 +401,39 @@ def pre_single_extension_isoband(ext, *args, **kwargs):
         ext.cfg['preinstallopts'] = "sed -i 's/SIGSTKSZ/32768/g' src/testthat/vendor/catch.h && "
 
 
+def pre_single_extension_numpy(ext, *args, **kwargs):
+    """
+    Pre-extension hook for numpy, to change -march=native to -march=armv8.4-a for numpy 1.24.2
+    when building for aarch64/neoverse_v1 CPU target.
+    """
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    if ext.name == 'numpy' and ext.version == '1.24.2' and cpu_target == CPU_TARGET_NEOVERSE_V1:
+        # note: this hook is called before build environment is set up (by calling toolchain.prepare()),
+        # so environment variables like $CFLAGS are not defined yet
+        # unsure which of these actually matter for numpy, so changing all of them
+        ext.orig_optarch = build_option('optarch')
+        update_build_option('optarch', 'march=armv8.4-a')
+
+
+def post_single_extension_numpy(ext, *args, **kwargs):
+    """
+    Post-extension hook for numpy, to reset 'optarch' build option.
+    """
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    if ext.name == 'numpy' and ext.version == '1.24.2' and cpu_target == CPU_TARGET_NEOVERSE_V1:
+        update_build_option('optarch', ext.orig_optarch)
+
+
+def pre_single_extension_testthat(ext, *args, **kwargs):
+    """
+    Pre-extension hook for testthat R package, to fix build on top of recent glibc.
+    """
+    if ext.name == 'testthat' and LooseVersion(ext.version) < LooseVersion('3.1.0'):
+        # use constant value instead of SIGSTKSZ for stack size,
+        # cfr. https://github.com/r-lib/testthat/issues/1373 + https://github.com/r-lib/testthat/pull/1403
+        ext.cfg['preinstallopts'] = "sed -i 's/SIGSTKSZ/32768/g' inst/include/testthat/vendor/catch.h && "
+
+
 def post_sanitycheck_hook(self, *args, **kwargs):
     """Main post-sanity-check hook: trigger custom functions based on software name."""
     if self.name in POST_SANITYCHECK_HOOKS:
@@ -531,9 +561,14 @@ def inject_gpu_property(ec):
 
 PRE_SINGLE_EXTENSION_HOOKS = {
     'isoband': pre_single_extension_isoband,
+    'numpy': pre_single_extension_numpy,
     'testthat': pre_single_extension_testthat,
 }
 
+POST_SINGLE_EXTENSION_HOOKS = {
+    'numpy': post_single_extension_numpy,
+}
+
 POST_SANITYCHECK_HOOKS = {
     'CUDA': post_sanitycheck_cuda,
 }