Installing py-matplotlib fails #6634
Description
Spack failed on a vanilla install of py-matplotliib. The build failed with the following message in the terminal:
==> Installing py-matplotlib
==> '/data/scott/projects/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/python-2.7.14-iforq4u7htoo6tmiir66l3mqpcdr2dfa/bin/python2.7' '-c' 'from distutils.sysconfig import get_config_var; print get_config_var('"'"'prefix'"'"')'
==> '/data/scott/projects/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/python-2.7.14-iforq4u7htoo6tmiir66l3mqpcdr2dfa/bin/python2.7' '-c' 'from distutils.sysconfig import get_config_var; print get_config_var('"'"'prefix'"'"')'
==> link /data/scott/projects/spack/var/spack/stage/py-matplotlib-2.0.2-wqkodrqwhu4bfecgpidikv3los5kurgk -> /tmp/scott/spack-stage/spack-stage-2LxOpQ
==> Using cached archive: /data/scott/projects/spack/var/spack/cache/py-matplotlib/py-matplotlib-2.0.2.tar.gz
==> Staging archive: /data/scott/projects/spack/var/spack/stage/py-matplotlib-2.0.2-wqkodrqwhu4bfecgpidikv3los5kurgk/matplotlib-2.0.2.tar.gz
==> '/bin/tar' '-xf' '/data/scott/projects/spack/var/spack/stage/py-matplotlib-2.0.2-wqkodrqwhu4bfecgpidikv3los5kurgk/matplotlib-2.0.2.tar.gz'
==> Created stage in /data/scott/projects/spack/var/spack/stage/py-matplotlib-2.0.2-wqkodrqwhu4bfecgpidikv3los5kurgk
==> No patches needed for py-matplotlib
==> Building py-matplotlib [PythonPackage]
==> WRITE LOCK: /data/scott/projects/spack/var/spack/stage/.lock[1196596153666456453:1] [Acquiring]
==> WRITE LOCK: /data/scott/projects/spack/var/spack/stage/.lock[1196596153666456453:1] [Acquired]
==> WRITE LOCK: /data/scott/projects/spack/opt/spack/.spack-db/prefix_lock[6488122333627063305:1] [Acquiring]
==> WRITE LOCK: /data/scott/projects/spack/opt/spack/.spack-db/prefix_lock[6488122333627063305:1] [Acquired]
==> Executing phase: 'build'
==> WRITE LOCK: /data/scott/projects/spack/opt/spack/.spack-db/prefix_lock[6488122333627063305:1] [Released]
==> WRITE LOCK: /data/scott/projects/spack/var/spack/stage/.lock[1196596153666456453:1] [Released]
==> Error: ProcessError: Command exited with status 1:
'/data/scott/projects/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/python-2.7.14-iforq4u7htoo6tmiir66l3mqpcdr2dfa/bin/python2.7' 'setup.py' '--no-user-cfg' 'build'
See build log for details:
/data/scott/projects/spack/var/spack/stage/py-matplotlib-2.0.2-wqkodrqwhu4bfecgpidikv3los5kurgk/matplotlib-2.0.2/spack-build.out
Traceback (most recent call last):
File "/data/scott/projects/spack/lib/spack/spack/build_environment.py", line 662, in child_process
return_value = function()
File "/data/scott/projects/spack/lib/spack/spack/package.py", line 1444, in build_process
phase(self.spec, self.prefix)
File "/data/scott/projects/spack/lib/spack/spack/package.py", line 114, in phase_wrapper
phase(spec, prefix)
File "/data/scott/projects/spack/lib/spack/spack/build_systems/python.py", line 167, in build
self.setup_py('build', *args)
File "/data/scott/projects/spack/lib/spack/spack/build_systems/python.py", line 135, in setup_py
self.python(setup, '--no-user-cfg', *args, **kwargs)
File "/data/scott/projects/spack/lib/spack/spack/build_systems/python.py", line 129, in python
inspect.getmodule(self).python(*args, **kwargs)
File "/data/scott/projects/spack/lib/spack/spack/util/executable.py", line 183, in __call__
proc.returncode, cmd_line)
ProcessError: Command exited with status 1:
'/data/scott/projects/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/python-2.7.14-iforq4u7htoo6tmiir66l3mqpcdr2dfa/bin/python2.7' 'setup.py' '--no-user-cfg' 'build'Here is the build output file from the failed matplotlib build
Looking in there, I notice that at the bottom there is a stack trace which ends with the lines:
...
File "/data/scott/projects/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/py-numpy-1.13.3-rhfri2h44q37ud7dwavxvaatj2a7cbk5/lib/python2.7/site-packages/numpy/core/__init__.py", line 26, in <module>
raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed. Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control). Otherwise reinstall numpy.
Original error was: /usr/local/lib/libmkl_intel_thread.so: undefined symbol: omp_in_parallelSo I have also attached the build log from that numpy build, though I didn't see anything obvious in there that indicated any real kind of failure.
Steps to reproduce the issue
$ spack -d install py-matplotlibInformation on your system
This happened on Ubuntu 16.04, with no custom packages or modules yaml files. Please let me know if more system information is needed.