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PYTHONPATH set by spack is broken on Fedora 37 #33923

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#40773
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PYTHONPATH set by spack is broken on Fedora 37#33923
#40773
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alalazoadamjstewart
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bugSomething isn't workingtriageThe issue needs to be prioritized
@balay

Description

@balay
balay
opened on Nov 15, 2022

Steps to reproduce

  • setup system python in ~/.spack/packages.yaml
  python:
    buildable: False
    externals:
    - spec: [email protected]%[email protected]
      prefix: /usr
  • spack install py-numpy

Error message

balay@pj01 spack.orig]$ eval `./bin/spack load --sh   py-numpy`
[balay@pj01 spack.orig]$ python3 -c "import numpy; print(numpy.__file__)"
/usr/lib64/python3.11/site-packages/numpy/__init__.py
[balay@pj01 spack.orig]$ ./bin/spack find -p py-numpy
-- linux-fedora37-skylake / [email protected] --------------------------
[email protected]  /home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh
==> 1 installed package
[balay@pj01 spack.orig]$ echo $PYTHONPATH
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-setuptools-59.4.0-rgac3zhrekwrzs4w4hcs3omsutc6n5cv/local/lib64/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-setuptools-59.4.0-rgac3zhrekwrzs4w4hcs3omsutc6n5cv/local/lib/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/local/lib64/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/local/lib/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-setuptools-59.4.0-rgac3zhrekwrzs4w4hcs3omsutc6n5cv/local/lib64/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-setuptools-59.4.0-rgac3zhrekwrzs4w4hcs3omsutc6n5cv/local/lib/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-cython-0.29.32-zhikpenzqk6klv425hhfkil2is7zvla3/local/lib64/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-cython-0.29.32-zhikpenzqk6klv425hhfkil2is7zvla3/local/lib/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-wheel-0.37.1-jra3r6z6soemlggorr7tgz2pzms5lsl4/local/lib64/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-wheel-0.37.1-jra3r6z6soemlggorr7tgz2pzms5lsl4/local/lib/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-setuptools-59.4.0-rgac3zhrekwrzs4w4hcs3omsutc6n5cv/local/lib64/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-setuptools-59.4.0-rgac3zhrekwrzs4w4hcs3omsutc6n5cv/local/lib/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-pip-22.2.2-gx5wdlrcl2pai3pvhucy4yw42g2rst6i/local/lib64/python3.11/site-packages:/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-pip-22.2.2-gx5wdlrcl2pai3pvhucy4yw42g2rst6i/local/lib/python3.11/site-packages
[balay@pj01 spack.orig]$ find /home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh -name *.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/core/_multiarray_tests.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/core/_operand_flag_tests.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/core/_rational_tests.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/core/_simd.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/core/_struct_ufunc_tests.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/core/_umath_tests.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/fft/_pocketfft_internal.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/linalg/_umath_linalg.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/linalg/lapack_lite.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/_bounded_integers.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/_common.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/_generator.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/_mt19937.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/_pcg64.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/_philox.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/_sfc64.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/bit_generator.cpython-311-x86_64-linux-gnu.so
/home/balay/spack.orig/opt/spack/linux-fedora37-skylake/gcc-12.2.1/py-numpy-1.23.4-27kw7ucbqregxz6khsa3jxenjhelzbqh/lib64/python3.11/site-packages/numpy/random/mtrand.cpython-311-x86_64-linux-gnu.so

Information on your system

[balay@pj01 spack.orig]$ ./bin/spack debug report
* **Spack:** 0.20.0.dev0 (0811f81a09bbe87274a9aae093245ff7d8a4af9c)
* **Python:** 3.11.0
* **Platform:** linux-fedora37-skylake
* **Concretizer:** clingo

General information

  • I have run spack debug report and reported the version of Spack/Python/Platform
  • I have searched the issues of this repo and believe this is not a duplicate
  • I have run the failing commands in debug mode and reported the output

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