Fail to install mpi4py

[Former user]

Hi all,

I am trying to install the developer version, and mpi4py fails to build with this output.

[mpi4py] Building mpi4py/onhjcgixciet, follow log with:
[mpi4py]   tail -f /opt/fenics/tmp/mpi4py-onhjcgixciet-3/_hashdist/build.log
[mpi4py] running: ['git', 'rev-list', '-n1', '--quiet', u'd5da39a2e334e585b97e83928995cca917610129']
[mpi4py] running: ['git', 'rev-list', '-n1', '--quiet', u'd5da39a2e334e585b97e83928995cca917610129']
[mpi4py] running: ['git', 'rev-list', '-n1', '--quiet', u'd5da39a2e334e585b97e83928995cca917610129']
[mpi4py] running: ['git', 'rev-list', '-n1', '--quiet', u'd5da39a2e334e585b97e83928995cca917610129']
[mpi4py] running: ['git', 'branch', u'tempmark/d5da39a2e334e585b97e83928995cca917610129', u'd5da39a2e334e585b97e83928995cca917610129']
[mpi4py] running: ['git', 'init']
[mpi4py] running: ['git', 'fetch', u'/opt/fenics/src/git/mpi4py', u'tempmark/d5da39a2e334e585b97e83928995cca917610129']
[mpi4py] running: ['git', 'checkout', u'd5da39a2e334e585b97e83928995cca917610129']
[mpi4py] running: ['git', 'branch', '-D', u'tempmark/d5da39a2e334e585b97e83928995cca917610129']
[mpi4py] running [u'/bin/bash', '_hashdist/build.sh']
[mpi4py] environment:
[mpi4py]   {'ARTIFACT': u'/opt/fenics/bld/mpi4py/onhjcgixciet',
[mpi4py]    'BASH': u'/bin/bash',
[mpi4py]    'BUILD': u'/opt/fenics/tmp/mpi4py-onhjcgixciet-3',
[mpi4py]    u'CYTHON_DIR': u'/opt/fenics/bld/cython/djlwbx2b5ndw',
[mpi4py]    u'CYTHON_ID': u'cython/djlwbx2b5ndwepu3nmpjdbprjhvxcu2j',
[mpi4py]    'HASHDIST_CPU_COUNT': '1',
[mpi4py]    'HDIST_CONFIG': '{"gc_roots":"/opt/fenics/gcroots","build_stores":[{"dir":"/opt/fenics/bld"}],"source_caches":[{"dir":"/opt/fenics/src"}],"cache":"/opt/fenics/cache","build_temp":"/opt/fenics/tmp"}',
[mpi4py]    'HDIST_IMPORT': u'cython/djlwbx2b5ndwepu3nmpjdbprjhvxcu2j mpi/gmkx3ftk3tz2q6qreifxplulowzcim5h numpy/yomfqy26t6kiaravxiqw4qsgv2vmbipi patchelf/k3rloj265ogtl4dmmmbmyt34dnffryka python/vocgqpztn6ne3pwxfogalqgbimemjhch',
[mpi4py]    'HDIST_IMPORT_PATHS': u'/opt/fenics/bld/cython/djlwbx2b5ndw:/opt/fenics/bld/mpi/gmkx3ftk3tz2:/opt/fenics/bld/numpy/yomfqy26t6ki:/opt/fenics/bld/patchelf/k3rloj265ogt:/opt/fenics/bld/python/vocgqpztn6ne',
[mpi4py]    'HDIST_VIRTUALS': '',
[mpi4py]    'MPICC': u'/opt/fenics/bld/mpi/gmkx3ftk3tz2/bin/mpicc',
[mpi4py]    'MPICXX': u'/opt/fenics/bld/mpi/gmkx3ftk3tz2/bin/mpic++',
[mpi4py]    'MPIEXEC': u'/opt/fenics/bld/mpi/gmkx3ftk3tz2/bin/mpiexec',
[mpi4py]    'MPIF77': u'/opt/fenics/bld/mpi/gmkx3ftk3tz2/bin/mpif77',
[mpi4py]    'MPIF90': u'/opt/fenics/bld/mpi/gmkx3ftk3tz2/bin/mpif90',
[mpi4py]    u'MPI_DIR': u'/opt/fenics/bld/mpi/gmkx3ftk3tz2',
[mpi4py]    u'MPI_ID': u'mpi/gmkx3ftk3tz2q6qreifxplulowzcim5h',
[mpi4py]    u'NUMPY_DIR': u'/opt/fenics/bld/numpy/yomfqy26t6ki',
[mpi4py]    u'NUMPY_ID': u'numpy/yomfqy26t6kiaravxiqw4qsgv2vmbipi',
[mpi4py]    'PATCHELF': u'/opt/fenics/bld/patchelf/k3rloj265ogt/bin/patchelf',
[mpi4py]    u'PATCHELF_DIR': u'/opt/fenics/bld/patchelf/k3rloj265ogt',
[mpi4py]    u'PATCHELF_ID': u'patchelf/k3rloj265ogtl4dmmmbmyt34dnffryka',
[mpi4py]    'PATH': u'/opt/fenics/bld/mpi/gmkx3ftk3tz2/bin:/opt/fenics/bld/cython/djlwbx2b5ndw/bin:/usr/bin:/bin',
[mpi4py]    'PKG_CONFIG_PATH': u'/opt/fenics/bld/mpi/gmkx3ftk3tz2/lib/pkgconfig',
[mpi4py]    'PWD': u'/opt/fenics/tmp/mpi4py-onhjcgixciet-3',
[mpi4py]    'PYTHON': u'/opt/fenics/bld/python/vocgqpztn6ne/bin/python',
[mpi4py]    'PYTHONPATH': u'/opt/fenics/bld/numpy/yomfqy26t6ki/lib/python2.7/site-packages:/opt/fenics/bld/cython/djlwbx2b5ndw/lib/python2.7/site-packages',
[mpi4py]    u'PYTHON_DIR': u'/opt/fenics/bld/python/vocgqpztn6ne',
[mpi4py]    u'PYTHON_ID': u'python/vocgqpztn6ne3pwxfogalqgbimemjhch'}
[mpi4py] running install
[mpi4py] running build
[mpi4py] running build_src
[mpi4py] ********************************************************************************
[mpi4py] 
[mpi4py]  You need to generate C source files with Cython!!
[mpi4py]  Download and install Cython <http://www.cython.org>
[mpi4py] 
[mpi4py] ********************************************************************************
[mpi4py] error: requires Cython>=0.15
[mpi4py|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status 1
[mpi4py|ERROR] command failed (code=1); raising
Command exited with non-zero status 127

I shall mention that cython was previously compiled by the build system during the process.

The build system used to work just fine a week ago, I wonder if the problem is upstream...

[Former user]

Using host-cython in the hashdist profile makes it work, so I guess I just walked into https://github.com/hashdist/hashstack/issues/583

Or even without the host-cython but simply installing cython in debian. It looks like the build system can't recognise its own compiled cython.

[Jan Blechta]

This is not DOLFIN issue. You may try reporting to fenics-developer-tools or rather directly to hashstack. According to my experience there is a bug (not reported) in https://github.com/hashdist/hashstack/blob/master/pkgs/cython.yaml, it should use setuptools rather than distutils, which causes that cython build ends up in a wrong dir.

[Former user]

Roger that, thanks!