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SciPy-bundle-2021.05-foss-2021a.eb cannot pass the numpy test #824

Open yanchenmochen opened 1 year ago

yanchenmochen commented 1 year ago

when I want to build the PETSc/3.15.1-foss-2021a, I ran into the issue which confused me very much time.

` export PYTHONPATH=/tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages:$PYTHONPATH && unset LDFLAGS && cd .. && /home/zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/bin/python -c "import sys; import numpy; sys.exit(not numpy.test(verbose=2))"

`

` ImportError while importing test module '/tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages/numpy/core/tests/test_dtype.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) /tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages/numpy/core/tests/test_dtype.py:4: in import ctypes zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/ctypes/init.py:8: in from ctypes import Union, Structure, Array E ImportError: libffi.so.7: cannot open shared object file: No such file or directory ____ ERROR collecting core/tests/testmultiarray.py ____ ImportError while importing test module '/tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages/numpy/core/tests/test_multiarray.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) /tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages/numpy/core/tests/test_multiarray.py:10: in import ctypes zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/ctypes/init.py:8: in from _ctypes import Union, Structure, Array E ImportError: libffi.so.7: cannot open shared object file: No such file or directory _ ERROR collecting core/tests/test_umathaccuracy.py ImportError while importing test module '/tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages/numpy/core/tests/test_umath_accuracy.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) /tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages/numpy/core/tests/test_umath_accuracy.py:6: in from ctypes import c_longlong, c_double, c_float, c_int, cast, pointer, POINTER zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/ctypes/init.py:8: in from ctypes import Union, Structure, Array E ImportError: libffi.so.7: cannot open shared object file: No such file or directory ____ ERROR collecting lib/tests/test_io.py __ ImportError while importing test module '/tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages/numpy/lib/tests/test_io.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) /tmp/eb-ar3jsp7p/tmpglh2ot_a/lib/python3.9/site-packages/numpy/lib/tests/test_io.py:17: in from ctypes import c_bool zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/ctypes/init.py:8: in from _ctypes import Union, Structure, Array E ImportError: libffi.so.7: cannot open shared object file: No such file or directory ======================================================================================== warnings summary ======================================================================================== zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/nose/importer.py:12 /home/zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses from imp import find_module, load_module, acquire_lock, release_lock

zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/_pytest/cacheprovider.py:428 /home/zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/_pytest/cacheprovider.py:428: PytestCacheWarning: cache could not write path /home/.pytest_cache/v/cache/nodeids config.cache.set("cache/nodeids", sorted(self.cached_nodeids))

zjlab/.local/easybuild/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/_pytest/cacheprovider.py:382 `

https://github.com/numpy/numpy/issues/16769

https://github.com/easybuilders/easybuild-easyconfigs/issues/11789

https://github.com/easybuilders/easybuild-easyconfigs/issues/13531

boegel commented 1 year ago

@yanchenmochen It looks like some files in the libffi dependency of your Python installation were removed? Can you check if reinstalling libffi-3.3-GCCcore-10.3.0.eb with eb --rebuild fixes the problem you're seeing?