Skip to content

py-numpy: build fails when using preinstalled python [also has cython installed] #18520

@balay

Description

@balay

py-numpy build fails when using preinstalled python3.

System Cython is also installed - however this build is using spack dependencies for cython. Likely system cython is getting picked up instead of spack installed cython?

[balay@pj01 .spack]$ cat ~/.spack/packages.yaml
packages:
  python:
    externals:
    - spec: "[email protected]%[email protected]"
      prefix: /usr
[balay@pj01 .spack]$ python3 -c "import cython;print(cython.__version__)"
0.29.13
[balay@pj01 .spack]$ spack spec py-numpy
Input spec
--------------------------------
py-numpy

Concretized
--------------------------------
[email protected]%[email protected]+blas+lapack arch=linux-fedora31-skylake
    ^[email protected]%[email protected]~consistent_fpcsr~ilp64+pic+shared threads=none arch=linux-fedora31-skylake
    ^[email protected]%[email protected] arch=linux-fedora31-skylake
        ^[email protected]%[email protected] arch=linux-fedora31-skylake
            ^[email protected]%[email protected]+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87 arch=linux-fedora31-skylake

[balay@pj01 .spack]$ spack install py-numpy
==> Installing openblas
==> No binary for openblas found: installing from source
==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/04/0484d275f87e9b8641ff2eecaa9df2830cbe276ac79ad80494822721de6e1693.tar.gz
############################################################################################################################################################################################################ 100.0%
==> openblas: Executing phase: 'edit'
==> openblas: Executing phase: 'build'
==> openblas: Executing phase: 'install'
[+] /home/balay/spack/opt/spack/linux-fedora31-skylake/gcc-9.3.1/openblas-0.3.10-rjaatbkpaiylnv7k7osx64n2ylyytvxu
==> [email protected] : externally installed in /usr
[+] /usr
==> Installing py-setuptools
==> No binary for py-setuptools found: installing from source
==> Fetching https://pypi.io/packages/source/s/setuptools/setuptools-49.2.0.zip
############################################################################################################################################################################################################ 100.0%
==> py-setuptools: Executing phase: 'build'
==> py-setuptools: Executing phase: 'install'
[+] /home/balay/spack/opt/spack/linux-fedora31-skylake/gcc-9.3.1/py-setuptools-49.2.0-c6an5huaysuobc3k4ycsacw6edoxvjxh
==> Installing py-cython
==> No binary for py-cython found: installing from source
==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/e5/e57acb89bd55943c8d8bf813763d20b9099cc7165c0f16b707631a7654be9cad.tar.gz
############################################################################################################################################################################################################ 100.0%
==> py-cython: Executing phase: 'build'
==> py-cython: Executing phase: 'install'
[+] /home/balay/spack/opt/spack/linux-fedora31-skylake/gcc-9.3.1/py-cython-0.29.21-sues7uro5rryb2b63s3esw3zihz2iuyu
==> Installing py-numpy
==> No binary for py-numpy found: installing from source
==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/b8/b8456987b637232602ceb4d663cb34106f7eb780e247d51a260b84760fd8f491.zip
############################################################################################################################################################################################################ 100.0%
==> py-numpy: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 1:
    '/usr/bin/python3.7' '-s' 'setup.py' '--no-user-cfg' 'build'
See build log for details:
  /home/balay/spack-temp/stage/spack-stage-py-numpy-1.19.1-sknmujvto2tr3dqp5qbocpiwwb3k2qu4/spack-build-out.txt
[balay@pj01 .spack]$ spack debug report
* **Spack:** 0.15.4-853-f4d3a1a0c
* **Python:** 3.7.8
* **Platform:** linux-fedora31-skylake

Additional information

spack-build-out.txt
spack-build-env.txt

Metadata

Metadata

Assignees

Type

No type

Projects

No projects

Milestone

No milestone

Relationships

None yet

Development

No branches or pull requests

Issue actions