#29131 closed defect (duplicate)

scipy build failure with system openblas

Reported by: mjo Owned by:
Priority: major Milestone: sage-duplicate/invalid/wontfix
Component: build Keywords:
Cc: embray, mkoeppe, dimpase, fbissey Merged in:
Authors: Reviewers:
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: Stopgaps:

Status badges

Description

I built a new (Gentoo) PC at work and tried to build a checkout of the develop branch today for the first time. It gets stuck on scipy:

Installing collected packages: scipy
  Created temporary directory: /tmp/pip-record-ndwbxtbu
  Running setup.py install for scipy: started
    Running command /home/mjo/src/sage.git/local/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-0nur8xhy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-ndwbxtbu/install-record.txt --single-version-externally-managed --root /home/mjo/src/sage.git/local/var/tmp/sage/build/scipy-1.2.0/inst --compile

    Note: if you need reliable uninstall behavior, then install
    with pip instead of using `setup.py install`:

      - `pip install .`       (from a git repo or downloaded source
                               release)
      - `pip install scipy`   (last SciPy release on PyPI)


    Running from scipy source directory.
    lapack_opt_info:
    lapack_mkl_info:
    Disabled lapack_mkl_info: (MKLROOT is None)
    Disabled lapack_mkl_info: (MKLROOT is None)
    customize UnixCCompiler
      libraries mkl_rt not found in []
      NOT AVAILABLE

    openblas_lapack_info:
    customize UnixCCompiler
    Disabled openblas_lapack_info: (OPENBLAS is None)
    customize UnixCCompiler
      libraries openblas not found in []
      NOT AVAILABLE

    openblas_clapack_info:
    customize UnixCCompiler
    Disabled openblas_clapack_info: (OPENBLAS is None)
    customize UnixCCompiler
      libraries openblas,lapack not found in []
      NOT AVAILABLE

    atlas_3_10_threads_info:
    Disabled atlas_3_10_threads_info: (PTATLAS is None)
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE

    atlas_3_10_info:
    Disabled atlas_3_10_info: (ATLAS is None)
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE

    atlas_threads_info:
    Disabled atlas_threads_info: (PTATLAS is None)
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
    Disabled atlas_info: (ATLAS is None)
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    accelerate_info:
      NOT AVAILABLE

    /home/mjo/src/sage.git/local/lib/python3.7/site-packages/numpy/distutils/system_info.py:636: UserWarning:
        Atlas (http://math-atlas.sourceforge.net/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [atlas]) or by setting
        the ATLAS environment variable.
      self.calc_info()
    lapack_info:
    customize UnixCCompiler
      libraries openblas not found in ['/home/mjo/src/sage.git/local/lib']
      NOT AVAILABLE

    /home/mjo/src/sage.git/local/lib/python3.7/site-packages/numpy/distutils/system_info.py:636: UserWarning:
        Lapack (http://www.netlib.org/lapack/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [lapack]) or by setting
        the LAPACK environment variable.
      self.calc_info()
    lapack_src_info:
      NOT AVAILABLE

    /home/mjo/src/sage.git/local/lib/python3.7/site-packages/numpy/distutils/system_info.py:636: UserWarning:
        Lapack (http://www.netlib.org/lapack/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [lapack_src]) or by setting
        the LAPACK_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-req-build-0nur8xhy/setup.py", line 492, in <module>
        setup_package()
      File "/tmp/pip-req-build-0nur8xhy/setup.py", line 488, in setup_package
        setup(**metadata)
      File "/home/mjo/src/sage.git/local/lib/python3.7/site-packages/numpy/distutils/core.py", line 137, in setup
        config = configuration()
      File "/tmp/pip-req-build-0nur8xhy/setup.py", line 395, in configuration
        raise NotFoundError(msg)
    numpy.distutils.system_info.NotFoundError: No lapack/blas resources found.
    Running setup.py install for scipy: finished with status 'error'
Cleaning up...
  Removing source in /tmp/pip-req-build-0nur8xhy
Removed build tracker '/tmp/pip-req-tracker-gwywnm72'
Command "/home/mjo/src/sage.git/local/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-0nur8xhy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-ndwbxtbu/install-record.txt --single-version-externally-managed --root /home/mjo/src/sage.git/local/var/tmp/sage/build/scipy-1.2.0/inst --compile" failed with error code 1 in /tmp/pip-req-build-0nur8xhy/
Exception information:
Traceback (most recent call last):
  File "/home/mjo/src/sage.git/local/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 143, in main
    status = self.run(options, args)
  File "/home/mjo/src/sage.git/local/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 366, in run
    use_user_site=options.use_user_site,
  File "/home/mjo/src/sage.git/local/lib/python3.7/site-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs
    **kwargs
  File "/home/mjo/src/sage.git/local/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 791, in install
    spinner=spinner,
  File "/home/mjo/src/sage.git/local/lib/python3.7/site-packages/pip/_internal/utils/misc.py", line 705, in call_subprocess
    % (command_desc, proc.returncode, cwd))
pip._internal.exceptions.InstallationError: Command "/home/mjo/src/sage.git/local/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-0nur8xhy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-record-ndwbxtbu/install-record.txt --single-version-externally-managed --root /home/mjo/src/sage.git/local/var/tmp/sage/build/scipy-1.2.0/inst --compile" failed with error code 1 in /tmp/pip-req-build-0nur8xhy/
Error: installing with pip3 failed
********************************************************************************
Error installing scipy-1.2.0
********************************************************************************

real    0m4.058s
user    0m2.699s
sys     0m0.456s
************************************************************************
Error installing package scipy-1.2.0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
  /home/mjo/src/sage.git/logs/pkgs/scipy-1.2.0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/mjo/src/sage.git/local/var/tmp/sage/build/scipy-1.2.0 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
  (cd '/home/mjo/src/sage.git/local/var/tmp/sage/build/scipy-1.2.0' && '/home/mjo/src/sage.git/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************

I cherry-picked the two site.cfg fixes (aea76abd8 and 040f6f3a602) for numpy just in case they were somehow related, but that didn't help. I'll start reverting suspicious commits but I figured I'd report it in case this is already familiar to someone.

Change History (4)

comment:2 Changed 14 months ago by mjo

  • Milestone changed from sage-9.1 to sage-duplicate/invalid/wontfix
  • Status changed from new to needs_review

Oof, thanks!

comment:3 Changed 14 months ago by mjo

  • Status changed from needs_review to positive_review

comment:4 Changed 14 months ago by chapoton

  • Resolution set to duplicate
  • Status changed from positive_review to closed
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