{lang}[iimkl/2025b] SciPy-bundle v2025.07 by branfosj · Pull Request #23826 · easybuilders/easybuild-easyconfigs

branfosj · 2025-09-09T10:01:53Z

(created using eb --new-pr)

Requires fix in make RPATH wrapper script not add RPATH (linking) flags when -c flag specified easybuild-framework#4981

…numpy-2.3.2_fix_selected_kind_for_ifort.patch

github-actions · 2025-09-09T10:02:30Z

Updated software `SciPy-bundle-2025.07-iimkl-2025b.eb`

Diff against SciPy-bundle-2025.07-gfbf-2025b.eb

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-gfbf-2025b.eb

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-gfbf-2025b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb
index 1393e4562b..c8b268cfbd 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-gfbf-2025b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb
@@ -6,8 +6,13 @@ version = '2025.07'
 homepage = 'https://python.org/'
 description = "Bundle of Python packages for scientific software"
 
-toolchain = {'name': 'gfbf', 'version': '2025b'}
-toolchainopts = {'pic': True, 'lowopt': True}
+toolchain = {'name': 'iimkl', 'version': '2025b'}
+toolchainopts = {'pic': True, 'lowopt': True, 'strict': True,
+                 # '-fveclib=none' to avoid 'undefined symbol: pow8_h' in numpy
+                 # see https://github.com/numpy/numpy/issues/27111
+                 # '-mllvm -disable-hir-backward-temp-dependencies-resolver' to avoid AVX2 failure in numpy build
+                 # see https://github.com/numpy/numpy/issues/29679
+                 'extra_cflags': '-fveclib=none -mllvm -disable-hir-backward-temp-dependencies-resolver'}
 
 builddependencies = [
     ('hypothesis', '6.136.6'),
@@ -30,11 +35,14 @@ dependencies = [
 # order is important!
 exts_list = [
     ('numpy', '2.3.2', {
-        'patches': ['numpy-1.22.3_disable-broken-override-test.patch'],
+        'patches': ['numpy-1.22.3_disable-broken-override-test.patch',
+                    'numpy-2.3.2_fix_selected_kind_for_ifort.patch'],
         'checksums': [
             {'numpy-2.3.2.tar.gz': 'e0486a11ec30cdecb53f184d496d1c6a20786c81e55e41640270130056f8ee48'},
             {'numpy-1.22.3_disable-broken-override-test.patch':
              '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+            {'numpy-2.3.2_fix_selected_kind_for_ifort.patch':
+             '765cd11029acb97729d072171b3c9919bb0b09e6e0ea5134fd3d779de23f1a03'},
         ],
     }),
     ('ply', '3.11', {
@@ -61,6 +69,7 @@ exts_list = [
             'scipy-1.16.0_relax-tests-broken-neoverse-v1.patch',
             'scipy-1.16.0_remove-float16-differentiate-test.patch',
             'scipy-1.16.1_bump-orth-memory-efficiency-tolerance.patch',
+            'scipy-1.16.1_relax-tolerance.patch',
         ],
         'checksums': [
             {'scipy-1.16.1.tar.gz': '44c76f9e8b6e8e488a586190ab38016e4ed2f8a038af7cd3defa903c0a2238b3'},
@@ -73,6 +82,7 @@ exts_list = [
              'f857fc1e941c196285f2e871e803cf463fc59c040dd2955deda1dd277d4b00db'},
             {'scipy-1.16.1_bump-orth-memory-efficiency-tolerance.patch':
              '1eb58b162d04cbf957979897966bfcf318f05a2bdbb61f0b47c0b3881910b354'},
+            {'scipy-1.16.1_relax-tolerance.patch': 'd78b91cd896951cea39f194a64e9f88bb696f2cb805915b34c9021dd186e3de3'},
         ],
     }),
     ('numexpr', '2.11.0', {

Diff against SciPy-bundle-2025.06-gfbf-2025a.eb

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.06-gfbf-2025a.eb

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.06-gfbf-2025a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb
index 7d46aabb71..c8b268cfbd 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.06-gfbf-2025a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb
@@ -1,42 +1,48 @@
 easyblock = 'PythonBundle'
 
 name = 'SciPy-bundle'
-version = '2025.06'
+version = '2025.07'
 
 homepage = 'https://python.org/'
 description = "Bundle of Python packages for scientific software"
 
-toolchain = {'name': 'gfbf', 'version': '2025a'}
-toolchainopts = {'pic': True, 'lowopt': True}
+toolchain = {'name': 'iimkl', 'version': '2025b'}
+toolchainopts = {'pic': True, 'lowopt': True, 'strict': True,
+                 # '-fveclib=none' to avoid 'undefined symbol: pow8_h' in numpy
+                 # see https://github.com/numpy/numpy/issues/27111
+                 # '-mllvm -disable-hir-backward-temp-dependencies-resolver' to avoid AVX2 failure in numpy build
+                 # see https://github.com/numpy/numpy/issues/29679
+                 'extra_cflags': '-fveclib=none -mllvm -disable-hir-backward-temp-dependencies-resolver'}
 
 builddependencies = [
-    ('hypothesis', '6.133.2'),
+    ('hypothesis', '6.136.6'),
     ('UnZip', '6.0'),
     # scipy >= 1.9.0 uses Meson/Ninja
-    ('Meson', '1.6.1'),
+    ('Meson', '1.8.2'),
     ('meson-python', '0.18.0'),
-    ('Ninja', '1.12.1'),
-    ('pkgconf', '2.3.0'),  # required by scipy
-    ('Cython', '3.1.1'),  # required by numpy and scipy
-    ('pybind11', '2.13.6'),  # required by scipy
+    ('Ninja', '1.13.0'),
+    ('pkgconf', '2.4.3'),  # required by scipy
+    ('Cython', '3.1.2'),  # required by numpy and scipy
+    ('pybind11', '3.0.0'),  # required by scipy
     ('spin', '0.14'),  # required for testing numpy
 ]
 
 dependencies = [
-    ('Python', '3.13.1'),
-    ('Python-bundle-PyPI', '2025.04'),
+    ('Python', '3.13.5'),
+    ('Python-bundle-PyPI', '2025.07'),
 ]
 
 # order is important!
 exts_list = [
-    ('numpy', '2.3.1', {
-        'patches': [
-            'numpy-1.22.3_disable-broken-override-test.patch',
-        ],
+    ('numpy', '2.3.2', {
+        'patches': ['numpy-1.22.3_disable-broken-override-test.patch',
+                    'numpy-2.3.2_fix_selected_kind_for_ifort.patch'],
         'checksums': [
-            {'numpy-2.3.1.tar.gz': '1ec9ae20a4226da374362cca3c62cd753faf2f951440b0e3b98e93c235441d2b'},
+            {'numpy-2.3.2.tar.gz': 'e0486a11ec30cdecb53f184d496d1c6a20786c81e55e41640270130056f8ee48'},
             {'numpy-1.22.3_disable-broken-override-test.patch':
              '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+            {'numpy-2.3.2_fix_selected_kind_for_ifort.patch':
+             '765cd11029acb97729d072171b3c9919bb0b09e6e0ea5134fd3d779de23f1a03'},
         ],
     }),
     ('ply', '3.11', {
@@ -54,7 +60,7 @@ exts_list = [
     ('versioneer', '0.29', {
         'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
     }),
-    ('scipy', '1.16.0', {
+    ('scipy', '1.16.1', {
         'enable_slow_tests': True,
         'ignore_test_result': False,
         'patches': [
@@ -62,9 +68,11 @@ exts_list = [
             'scipy-1.16.0_skip-tests-broken-grace.patch',
             'scipy-1.16.0_relax-tests-broken-neoverse-v1.patch',
             'scipy-1.16.0_remove-float16-differentiate-test.patch',
+            'scipy-1.16.1_bump-orth-memory-efficiency-tolerance.patch',
+            'scipy-1.16.1_relax-tolerance.patch',
         ],
         'checksums': [
-            {'scipy-1.16.0.tar.gz': 'b5ef54021e832869c8cfb03bc3bf20366cbcd426e02a58e8a58d7584dfbb8f62'},
+            {'scipy-1.16.1.tar.gz': '44c76f9e8b6e8e488a586190ab38016e4ed2f8a038af7cd3defa903c0a2238b3'},
             {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
             {'scipy-1.16.0_skip-tests-broken-grace.patch':
              '33885518a572f843a0edeb7a58aa938202aae70267f6de1ce60acef97f393126'},
@@ -72,12 +80,15 @@ exts_list = [
              'a72d794b95dc437c03b323f86392b264c7ecfdbfa19e3bc01fba8d5d3ab2f21a'},
             {'scipy-1.16.0_remove-float16-differentiate-test.patch':
              'f857fc1e941c196285f2e871e803cf463fc59c040dd2955deda1dd277d4b00db'},
+            {'scipy-1.16.1_bump-orth-memory-efficiency-tolerance.patch':
+             '1eb58b162d04cbf957979897966bfcf318f05a2bdbb61f0b47c0b3881910b354'},
+            {'scipy-1.16.1_relax-tolerance.patch': 'd78b91cd896951cea39f194a64e9f88bb696f2cb805915b34c9021dd186e3de3'},
         ],
     }),
     ('numexpr', '2.11.0', {
-        'checksums': ['75b2c01a4eda2e7c357bc67a3f5c3dd76506c15b5fd4dc42845ef2e182181bad'],
         # workaround for: ValueError: invalid pyproject.toml config: project.license
         'preinstallopts': "sed -i '/^license =/d' pyproject.toml && ",
+        'checksums': ['75b2c01a4eda2e7c357bc67a3f5c3dd76506c15b5fd4dc42845ef2e182181bad'],
     }),
     ('bottleneck', '1.5.0', {
         'checksums': ['c860242cf20e69d5aab2ec3c5d6c8c2a15f19e4b25b28b8fca2c2a12cefae9d8'],
@@ -85,9 +96,9 @@ exts_list = [
     ('tzdata', '2025.2', {
         'checksums': ['b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9'],
     }),
-    ('pandas', '2.3.0', {
+    ('pandas', '2.3.1', {
         'preinstallopts': "export PANDAS_CI=0 && ",
-        'checksums': ['34600ab34ebf1131a7613a260a61dbe8b62c188ec0ea4c296da7c9a06b004133'],
+        'checksums': ['0a95b9ac964fe83ce317827f80304d37388ea77616b1425f0ae41c9d2d0d7bb2'],
     }),
     ('mpmath', '1.3.0', {
         'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],

Diff against SciPy-bundle-2024.06-foss-2023a-Python-2.7.18.eb

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.06-foss-2023a-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.06-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb
index ad784c9348..c8b268cfbd 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.06-foss-2023a-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb
@@ -1,72 +1,111 @@
 easyblock = 'PythonBundle'
 
 name = 'SciPy-bundle'
-version = '2024.06'
-versionsuffix = '-Python-%(pyver)s'
+version = '2025.07'
 
 homepage = 'https://python.org/'
 description = "Bundle of Python packages for scientific software"
 
-toolchain = {'name': 'foss', 'version': '2023a'}
-toolchainopts = {'pic': True, 'lowopt': True}
+toolchain = {'name': 'iimkl', 'version': '2025b'}
+toolchainopts = {'pic': True, 'lowopt': True, 'strict': True,
+                 # '-fveclib=none' to avoid 'undefined symbol: pow8_h' in numpy
+                 # see https://github.com/numpy/numpy/issues/27111
+                 # '-mllvm -disable-hir-backward-temp-dependencies-resolver' to avoid AVX2 failure in numpy build
+                 # see https://github.com/numpy/numpy/issues/29679
+                 'extra_cflags': '-fveclib=none -mllvm -disable-hir-backward-temp-dependencies-resolver'}
 
 builddependencies = [
-    ('hypothesis', '4.57.1', versionsuffix),
+    ('hypothesis', '6.136.6'),
     ('UnZip', '6.0'),
-    ('pybind11', '2.9.2', versionsuffix),  # required by scipy
+    # scipy >= 1.9.0 uses Meson/Ninja
+    ('Meson', '1.8.2'),
+    ('meson-python', '0.18.0'),
+    ('Ninja', '1.13.0'),
+    ('pkgconf', '2.4.3'),  # required by scipy
+    ('Cython', '3.1.2'),  # required by numpy and scipy
+    ('pybind11', '3.0.0'),  # required by scipy
+    ('spin', '0.14'),  # required for testing numpy
 ]
 
 dependencies = [
-    ('Python', '2.7.18'),
-    ('numpy', '1.16.6', versionsuffix)
+    ('Python', '3.13.5'),
+    ('Python-bundle-PyPI', '2025.07'),
 ]
 
 # order is important!
 exts_list = [
+    ('numpy', '2.3.2', {
+        'patches': ['numpy-1.22.3_disable-broken-override-test.patch',
+                    'numpy-2.3.2_fix_selected_kind_for_ifort.patch'],
+        'checksums': [
+            {'numpy-2.3.2.tar.gz': 'e0486a11ec30cdecb53f184d496d1c6a20786c81e55e41640270130056f8ee48'},
+            {'numpy-1.22.3_disable-broken-override-test.patch':
+             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+            {'numpy-2.3.2_fix_selected_kind_for_ifort.patch':
+             '765cd11029acb97729d072171b3c9919bb0b09e6e0ea5134fd3d779de23f1a03'},
+        ],
+    }),
     ('ply', '3.11', {
         'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
     }),
-    ('gast', '0.5.5', {
-        'checksums': ['5f4ae749ba7199034b6912af98f05b4058d6d48fc2f065037b241be819a22924'],
+    ('gast', '0.6.0', {
+        'checksums': ['88fc5300d32c7ac6ca7b515310862f71e6fdf2c029bbec7c66c0f5dd47b6b1fb'],
     }),
-    ('beniget', '0.4.1', {
-        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    ('beniget', '0.4.2.post1', {
+        'checksums': ['a0258537e65e7e14ec33a86802f865a667f949bb6c73646d55e42f7c45a052ae'],
     }),
-    ('scipy', '1.2.3', {
-        'patches': ['scipy-1.2.3_fix_nan_problem_in_vi.patch'],
-        'prebuildopts': 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ',
-        'checksums': [
-            'ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57',  # scipy-1.2.3.tar.gz
-            # scipy-1.2.3_fix_nan_problem_in_vi.patch
-            '0513c5d0491a3f062ed024b6aa7b382706e8c42b3a3fdd26ff7a4d305ac9a30d',
-        ],
+    ('pythran', '0.18.0', {
+        'checksums': ['5c003e8cbedf6dbb68c2869c49fc110ce8b5e8982993078a4a819f1dadc4fc6a'],
     }),
-    ('mpi4py', '3.1.6', {
-        'checksums': ['c8fa625e0f92b082ef955bfb52f19fa6691d29273d7d71135d295aa143dee6cb'],
+    ('versioneer', '0.29', {
+        'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
     }),
-    ('numexpr', '2.7.3', {
-        'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'],
+    ('scipy', '1.16.1', {
+        'enable_slow_tests': True,
+        'ignore_test_result': False,
+        'patches': [
+            'scipy-1.11.1_disable-tests.patch',
+            'scipy-1.16.0_skip-tests-broken-grace.patch',
+            'scipy-1.16.0_relax-tests-broken-neoverse-v1.patch',
+            'scipy-1.16.0_remove-float16-differentiate-test.patch',
+            'scipy-1.16.1_bump-orth-memory-efficiency-tolerance.patch',
+            'scipy-1.16.1_relax-tolerance.patch',
+        ],
+        'checksums': [
+            {'scipy-1.16.1.tar.gz': '44c76f9e8b6e8e488a586190ab38016e4ed2f8a038af7cd3defa903c0a2238b3'},
+            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
+            {'scipy-1.16.0_skip-tests-broken-grace.patch':
+             '33885518a572f843a0edeb7a58aa938202aae70267f6de1ce60acef97f393126'},
+            {'scipy-1.16.0_relax-tests-broken-neoverse-v1.patch':
+             'a72d794b95dc437c03b323f86392b264c7ecfdbfa19e3bc01fba8d5d3ab2f21a'},
+            {'scipy-1.16.0_remove-float16-differentiate-test.patch':
+             'f857fc1e941c196285f2e871e803cf463fc59c040dd2955deda1dd277d4b00db'},
+            {'scipy-1.16.1_bump-orth-memory-efficiency-tolerance.patch':
+             '1eb58b162d04cbf957979897966bfcf318f05a2bdbb61f0b47c0b3881910b354'},
+            {'scipy-1.16.1_relax-tolerance.patch': 'd78b91cd896951cea39f194a64e9f88bb696f2cb805915b34c9021dd186e3de3'},
+        ],
     }),
-    ('Bottleneck', '1.3.2', {
-        'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'],
+    ('numexpr', '2.11.0', {
+        # workaround for: ValueError: invalid pyproject.toml config: project.license
+        'preinstallopts': "sed -i '/^license =/d' pyproject.toml && ",
+        'checksums': ['75b2c01a4eda2e7c357bc67a3f5c3dd76506c15b5fd4dc42845ef2e182181bad'],
     }),
-    ('python_dateutil', '2.9.0.post0', {
-        'modulename': 'dateutil',
-        'source_tmpl': SOURCE_WHL,
-        'checksums': ['a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427'],
+    ('bottleneck', '1.5.0', {
+        'checksums': ['c860242cf20e69d5aab2ec3c5d6c8c2a15f19e4b25b28b8fca2c2a12cefae9d8'],
     }),
-    ('pytz', '2025.1', {
-        'source_tmpl': SOURCE_WHL,
-        'checksums': ['89dd22dca55b46eac6eda23b2d72721bf1bdfef212645d81513ef5d03038de57'],
+    ('tzdata', '2025.2', {
+        'checksums': ['b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9'],
     }),
-    ('pandas', '0.24.2', {
-        'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'],
+    ('pandas', '2.3.1', {
+        'preinstallopts': "export PANDAS_CI=0 && ",
+        'checksums': ['0a95b9ac964fe83ce317827f80304d37388ea77616b1425f0ae41c9d2d0d7bb2'],
     }),
     ('mpmath', '1.3.0', {
         'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
     }),
-    ('deap', '1.3.1', {
-        'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'],
+    ('deap', '1.4.3', {
+        'modulename': 'deap.base',
+        'checksums': ['7c97088fb05835bdc255bec475cb0e778de2b43e44cbefbf2bcd655aeec865fd'],
     }),
 ]

branfosj · 2025-09-09T10:06:43Z

Test report by @branfosj
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/727c3d1f5ee2f2064c084ec08e822c6c for a full test report.

      [209/521] Compiling C object numpy/_core/libloops_arithmetic.dispatch.h_AVX2.a.p/meson-generated_loops_arithmetic.dispatch.c.o
      FAILED: [code=1] numpy/_core/libloops_arithmetic.dispatch.h_AVX2.a.p/meson-generated_loops_arithmetic.dispatch.c.o
      icx -Inumpy/_core/libloops_arithmetic.dispatch.h_AVX2.a.p -Inumpy/_core -I../numpy/_core -Inumpy/_core/include -I../numpy/_core/include -I../numpy/_core/src/common -I../numpy/_core/src/multiarray -I../numpy/_core/src/npymath -I../numpy/_core/src/umath -I../numpy/_core/src/highway -I/rds/projects/2017/branfosj-rse/easybuild/EL8-ice/software/Python/3.13.5-GCCcore-14.3.0/include/python3.13 -I/rds/projects/2017/branfosj-rse/easybuild/EL8-ice/software/imkl/2025.2.0/mkl/2025.2/include -I/dev/shm/branfosj/build-up-EL8/SciPybundle/2025.07/iimkl-2025b/numpy/numpy-2.3.2/.mesonpy-auxqthy2/meson_cpu -fdiagnostics-color=always -DNDEBUG -Wall -Winvalid-pch -std=c11 -O3 -fno-strict-aliasing -msse -msse2 -msse3 -O1 -xHost -fp-speculation=strict -fp-model strict -fPIC -fveclib=none -fPIC -DNPY_INTERNAL_BUILD -DHAVE_NPY_CONFIG_H -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -O3 -DNPY_HAVE_SSE2 -DNPY_HAVE_SSE -DNPY_HAVE_SSE3 -DNPY_HAVE_SSSE3 -DNPY_HAVE_SSE41 -DNPY_HAVE_POPCNT -DNPY_HAVE_SSE42 -DNPY_HAVE_AVX -DNPY_HAVE_F16C -DNPY_HAVE_FMA3 -DNPY_HAVE_AVX2 -msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -maes -mpclmul -mbmi -mbmi2 -DNPY_MTARGETS_CURRENT=AVX2 -MD -MQ numpy/_core/libloops_arithmetic.dispatch.h_AVX2.a.p/meson-generated_loops_arithmetic.dispatch.c.o -MF numpy/_core/libloops_arithmetic.dispatch.h_AVX2.a.p/meson-generated_loops_arithmetic.dispatch.c.o.d -o numpy/_core/libloops_arithmetic.dispatch.h_AVX2.a.p/meson-generated_loops_arithmetic.dispatch.c.o -c numpy/_core/libloops_arithmetic.dispatch.h_AVX2.a.p/loops_arithmetic.dispatch.c
      PLEASE append the compiler options "-save-temps -v", rebuild the application to get the full command which is failing and submit a bug report to https://software.intel.com/en-us/support/priority-support which includes the failing command, input files for the command and the crash backtrace (if any).
      Stack dump:
      0.  Program arguments: /rds/projects/2017/branfosj-rse/easybuild/EL8-ice/software/intel-compilers/2025.2.0/compiler/2025.2/bin/compiler/clang @/dev/shm/branfosj/tmp-up-EL8/eb-t8ncmems/icx1476426627HG5X7I/icxargKSA90e
      1.  <eof> parser at end of file
      2.  Optimizer
      3.  Running pass "function(pragma-omp-simd-if,inject-tli-mappings,hir-ssa-deconstruction,hir-temp-cleanup,hir-normalize-casts,hir-propagate-casted-iv,hir-loop-concatenation,hir-pm-symbolic-tripcount-completeunroll,hir-array-transpose,hir-conditional-temp-sinking,hir-loop-peeling,hir-early-opt-predicate,hir-lmm,hir-store-result-into-temp-array,hir-aos-to-soa,hir-backward-temp-dependencies-resolver,hir-runtime-dd,hir-mv-const-ub,hir-sinking-for-perfect-loopnest,hir-non-zero-sinking-for-perfect-loopnest,hir-pragma-loop-blocking,hir-loop-distribute-loopnest,hir-loop-interchange,hir-generate-mkl-call,hir-loop-blocking,hir-undo-sinking-for-perfect-loopnest,hir-dead-store-elimination,hir-minmax-recognition,hir-identity-matrix-idiom-recognition,hir-lower-small-memset-memcpy,hir-pre-vec-complete-unroll,hir-cond-ldst-motion,hir-dead-store-elimination,hir-memory-reduction-sinking,hir-lmm,hir-min-max-blob-to-select,hir-last-value-computation,hir-loop-reroll,hir-loop-collapse,hir-loop-fusion,hir-dead-store-elimination,hir-loop-independent-scalar-repl,hir-opt-var-predicate,hir-temp-array-transpose,hir-loop-distribute-memrec,hir-loop-reversal,hir-loop-rematerialize,hir-multi-exit-loop-reroll,hir-idiom,hir-if-reversal,hir-unroll-and-jam,hir-mv-variable-stride,hir-opt-predicate,hir-special-opt-predicate,hir-lmm,hir-memory-reduction-sinking,hir-loop-independent-scalar-repl,hir-vec-dir-insert,hir-vplan-vec,hir-vplan-vec,hir-post-vec-complete-unroll,hir-general-unroll,hir-scalarrepl-array,hir-nontemporal-marking,hir-prefetching,hir-cg,vpo-cfg-restructuring,vpo-rename-operands,simplifycfg<bonus-inst-threshold=1;no-forward-switch-cond;no-switch-range-to-icmp;no-switch-to-lookup;keep-loops;no-hoist-common-insts;no-hoist-loads-stores-with-cond-faulting;no-sink-common-insts;speculate-blocks;simplify-cond-branch;no-invalidate-anders-res;no-speculate-unpredictables>,lower-subscript,sroa<modify-cfg>,nary-reassociate,gvn<>,sroa<modify-cfg>,simplifycfg<bonus-inst-threshold=1;no-forward-switch-cond;no-switch-range-to-icmp;no-switch-to-lookup;keep-loops;no-hoist-common-insts;no-hoist-loads-stores-with-cond-faulting;no-sink-common-insts;speculate-blocks;simplify-cond-branch;no-invalidate-anders-res;no-speculate-unpredictables>,instcombine<max-iterations=1;no-verify-fixpoint>,loop-carried-cse,dse,addsub-reassoc,vpo-restore-operands,loop-simplify,lower-switch,loop(loop-simplifycfg),vpo-cfg-restructuring)" on module "numpy/_core/libloops_arithmetic.dispatch.h_AVX2.a.p/loops_arithmetic.dispatch.c"
      4.  Running pass "hir-backward-temp-dependencies-resolver" on function "simd_divide_by_scalar_contig_s64"
      icx: error #10105: /rds/projects/2017/branfosj-rse/easybuild/EL8-ice/software/intel-compilers/2025.2.0/compiler/2025.2/bin/compiler/clang: core dumped
      icx: warning #10102: unknown signal(8130576)
      icx: error #10106: Fatal error in /rds/projects/2017/branfosj-rse/easybuild/EL8-ice/software/intel-compilers/2025.2.0/compiler/2025.2/bin/compiler/clang, terminated by unknown
      [210/521] Compiling C object numpy/_core/libloops_arithmetic.dispatch.h_SSE41.a.p/meson-generated_loops_arithmetic.dispatch.c.o
      [211/521] Compiling C++ object numpy/_core/libx86_simd_qsort_16bit.dispatch.h_AVX512_ICL.a.p/src_npysort_x86_simd_qsort_16bit.dispatch.cpp.o
      [212/521] Compiling C object numpy/_core/libloops_comparison.dispatch.h_baseline.a.p/meson-generated_loops_comparison.dispatch.c.o
      [213/521] Compiling C++ object numpy/_core/libx86_simd_argsort.dispatch.h_AVX512_SKX.a.p/src_npysort_x86_simd_argsort.dispatch.cpp.o
      [214/521] Compiling C++ object numpy/_core/libx86_simd_argsort.dispatch.h_AVX2.a.p/src_npysort_x86_simd_argsort.dispatch.cpp.o
      [215/521] Compiling C++ object numpy/_core/libx86_simd_qsort.dispatch.h_AVX512_SKX.a.p/src_npysort_x86_simd_qsort.dispatch.cpp.o
      [216/521] Compiling C++ object numpy/_core/libx86_simd_qsort.dispatch.h_AVX2.a.p/src_npysort_x86_simd_qsort.dispatch.cpp.o
      ninja: build stopped: subcommand failed.
      [end of output]

branfosj · 2025-09-09T10:06:56Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-09-09T10:10:17Z

@branfosj: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=23826 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23826 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7890

Test results coming soon (I hope)...

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2025-09-09T10:15:52Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/f6396a49607615b8cf678dff0f7c6ff8 for a full test report.

Thyre · 2025-09-09T10:39:30Z

Test report by @Thyre
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
ZAM054 - Linux Zorin OS 17, x86_64, 12th Gen Intel(R) Core(TM) i7-1260P, 1 x NVIDIA NVIDIA GeForce MX550, 580.65.06, Python 3.10.12
See https://gist.github.com/Thyre/dca8ce93cd16628c0bab217c83356a1a for a full test report.

Thyre · 2025-09-09T10:41:28Z

Reported to Intel via support ticket 06682863
Also comes up in NumPy repo, e.g. numpy/numpy#29679 (comment)

branfosj · 2025-09-09T11:42:00Z

Test report by @branfosj
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bear-pg0210u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8480CL (sapphirerapids), Python 3.6.8
See https://gist.github.com/branfosj/6c95b37a550d01648a7a4b6326e69f3c for a full test report.

branfosj · 2025-09-09T11:44:24Z

Test report by @branfosj
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/f3c10d48f857d0bb95f7b2509ee32ba3 for a full test report.

branfosj · 2025-09-09T11:58:29Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0208u17a - Linux RHEL 8.10, x86_64, AMD EPYC 9554 64-Core Processor (zen4), Python 3.6.8
See https://gist.github.com/branfosj/08c57f09f47230ce8a3cff48246d885a for a full test report.

branfosj · 2025-09-09T13:01:50Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-09-09T13:10:12Z

@branfosj: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=23826 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23826 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7893

Test results coming soon (I hope)...

Details

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2025-09-09T13:13:27Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/a08d0938d35eee239f5681cc709cdca4 for a full test report.

branfosj · 2025-09-09T16:23:54Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0201u03a - Linux RHEL 8.10, x86_64, INTEL(R) XEON(R) PLATINUM 8570 (sapphirerapids), Python 3.6.8
See https://gist.github.com/branfosj/bfbad3c09c99682f3a5929f738649137 for a full test report.

branfosj · 2025-09-09T16:28:47Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0210u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8480CL (sapphirerapids), Python 3.6.8
See https://gist.github.com/branfosj/813e41447dd9feb8a3c6c4cbf3030d39 for a full test report.

branfosj · 2025-09-09T16:35:43Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/37656fcb6ee9b482aaca980566b58461 for a full test report.

branfosj · 2025-09-09T16:37:08Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0208u17a - Linux RHEL 8.10, x86_64, AMD EPYC 9554 64-Core Processor (zen4), Python 3.6.8
See https://gist.github.com/branfosj/617f2a7823e641ea6b0cc3b07369ddef for a full test report.

Thyre · 2025-09-09T18:34:24Z

Test report by @Thyre
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor (zen4), 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: 6.16.5-arch1-1), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: 6.16.5-arch1-1), Python 3.13.7
See https://gist.github.com/Thyre/cf97fe98b7fde5d25a5d1f9c9fe9b6dd for a full test report.

Thyre · 2025-09-09T18:38:04Z

Hmm, is my test failure and the one of boegelbot maybe caused by still using core-avx2 as the optarch?

Thyre · 2025-09-10T07:14:34Z

@branfosj From the support ticket I filed:

The recommended workaround for now is to disable this particular pass by adding '-mllvm -disable-hir-backward-temp-dependencies-resolver'.

branfosj · 2025-09-10T08:07:43Z

@branfosj From the support ticket I filed:

The recommended workaround for now is to disable this particular pass by adding '-mllvm -disable-hir-backward-temp-dependencies-resolver'.

I've added that and removed the patch. We might want to target it more than this, but it will be good to check that it works.

branfosj · 2025-09-10T08:07:48Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-09-10T08:10:13Z

@branfosj: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=23826 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23826 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7912

Test results coming soon (I hope)...

Details

- notification for comment with ID 3273812990 processed

Message to humans: this is just bookkeeping information for me,
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branfosj · 2025-09-10T09:05:13Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0210u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8480CL (sapphirerapids), Python 3.6.8
See https://gist.github.com/branfosj/c5ab98d1efab3635fac67388282bacaa for a full test report.

boegelbot · 2025-09-10T09:05:50Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/73464f01c5658b4d0413a55eb889ce6f for a full test report.

Thyre · 2025-09-10T09:45:30Z

Test report by @Thyre
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
Linux - Linux Arch Linux UNKNOWN, x86_64, AMD Ryzen 7 7800X3D 8-Core Processor (zen4), 1 x AMD Navi 48 [Radeon RX 9070/9070 XT/9070 GRE] (device id: 0x7550, gfx: gfx1201, driver: 6.16.5-arch1-1), 1 x AMD Raphael (device id: 0x164e, gfx: gfx1036, driver: 6.16.5-arch1-1), Python 3.13.7
See https://gist.github.com/Thyre/93841b84d5cdc3535def986bc6334062 for a full test report.

schiotz · 2025-09-10T09:48:59Z

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2025.07-iimkl-2025b.eb

 toolchain = {'name': 'iimkl', 'version': '2025b'}
 toolchainopts = {'pic': True, 'lowopt': True, 'strict': True,
+                 # '-fveclib=none' to avoid 'undefined symbol: pow8_h' in numpy
+                 # see https://github.com/numpy/numpy/issues/27111


-fveclib=none may cost significant performance. Have you tried linking with -lsvml instead (small vector math library)?
(untested, it may not work...)

@branfosj Thoughts on this suggestion?

I've not found where we can set this that prevents the build failure.

Getting it to work is far more important than element-wise exponentials being a bit faster!

branfosj · 2025-09-10T09:57:54Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0201u03a - Linux RHEL 8.10, x86_64, INTEL(R) XEON(R) PLATINUM 8570 (sapphirerapids), Python 3.6.8
See https://gist.github.com/branfosj/7297785440adfb4da15bfb3abc09a4c1 for a full test report.

branfosj · 2025-09-10T10:11:23Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/95f902e19159a76322f0e11884293896 for a full test report.

branfosj · 2025-09-10T10:12:10Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0208u17a - Linux RHEL 8.10, x86_64, AMD EPYC 9554 64-Core Processor (zen4), Python 3.6.8
See https://gist.github.com/branfosj/96e63baf1327074fc6e83c3cf37daff9 for a full test report.

boegel · 2025-09-10T11:27:47Z

Test report by @boegel
FAILED
Build succeeded for 3 out of 4 (1 easyconfigs in total)
node3590.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/1d8ea313f0c45bbe03755a3db4909dbc for a full test report.

Thyre · 2025-09-10T11:33:47Z

Test report by @boegel
FAILED
Build succeeded for 3 out of 4 (1 easyconfigs in total)
node3590.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/1d8ea313f0c45bbe03755a3db4909dbc for a full test report.

We require the framework fixes for the rpath wrapper, otherwise Meson fails to detect lots of features unfortunately.
I think that commit used is a bit too old for that (Tue Aug 19 17:50:45 2025 +0200)

boegel · 2025-09-10T14:34:01Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3590.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/1ed33253a98d9f48320c32aa39eaaf2a for a full test report.

boegel

lgtm

boegel · 2025-09-23T18:07:53Z

Going in, thanks @branfosj!

adding easyconfigs: SciPy-bundle-2025.07-iimkl-2025b.eb and patches: …

4d23126

…numpy-2.3.2_fix_selected_kind_for_ifort.patch

branfosj added the update label Sep 9, 2025

branfosj marked this pull request as draft September 9, 2025 10:03

Thyre added the 2025b issues & PRs related to 2025b common toolchains label Sep 9, 2025

add patch to avoid building AVX2 version of loops_arithmetic

6346b09

relax tolerance

aba2ad5

disable compiler feature and remove patch

c378451

branfosj marked this pull request as ready for review September 10, 2025 09:10

add comments to explain added flags

13f4bdb

schiotz reviewed Sep 10, 2025

View reviewed changes

boegel added this to the next release (5.1.2) milestone Sep 10, 2025

boegel approved these changes Sep 10, 2025

View reviewed changes

boegel merged commit 29a59cb into easybuilders:develop Sep 23, 2025
8 checks passed

branfosj deleted the 20250909110146_new_pr_SciPy-bundle202507 branch September 23, 2025 18:35

boegel mentioned this pull request Sep 24, 2025

update numpy easyblock for SciPy-bundle v2024.05 w/ iimkl/2024a easybuilders/easybuild-easyblocks#3922

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Updated software `SciPy-bundle-2025.07-iimkl-2025b.eb`

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