dolfin compilation fails with the latest trilinos

[JaroslavHron]

When compiling dolfin with older trilinos version, the compilation of dolfin is fine. For example using:

  trilinos:
    sources:
    - key: tar.bz2:uqktsqkffhdfsbjgbm567y5o4ty52eav
      url: http://trilinos.org/oldsite/download/files/trilinos-11.12.1-Source.tar.bz2

However when building dolfin with the latest hashstack trilinos package (=11.14.2) it fails with following result:

[dolfin] Building dolfin/gwvhxkfco64y, follow log with:
[dolfin]   tail -f /usr/local/pkg/HASH/tmp/dolfin-gwvhxkfco64y-1/build.log
[dolfin] running [u'/bin/bash', '_hashdist/build.sh']
[dolfin] environment:
[dolfin]   {'ARTIFACT': u'/usr/local/pkg/HASH/bld/dolfin/gwvhxkfco64y',
[dolfin]    'BASH': u'/bin/bash',
[dolfin]    u'BLAS_DIR': u'/usr/local/pkg/HASH/bld/blas/zok3lp3r7qrt',
[dolfin]    u'BLAS_ID': u'blas/zok3lp3r7qrt3wvvcttmnfbsd2kpere7',
[dolfin]    'BLAS_LDFLAGS': u'-Wl,-rpath,/usr/local/pkg/HASH/bld/sympy/o45yrlj5g2r7/lib -L/usr/local/pkg/HASH/bld/sympy/o45yrlj5g2r7/lib -lopenblas',
[dolfin]    u'BOOST_DIR': u'/usr/local/pkg/HASH/bld/boost/egqui4dm4vu6',
[dolfin]    u'BOOST_ID': u'boost/egqui4dm4vu6n4nqgtkiptmc52g75km7',
[dolfin]    'BOOST_MULTITHREADED': u'OFF',
[dolfin]    'BUILD': u'/usr/local/pkg/HASH/tmp/dolfin-gwvhxkfco64y-1',
[dolfin]    u'BZIP2_DIR': u'/usr/local/pkg/HASH/bld/bzip2/ngefwc5sfpdg',
[dolfin]    u'BZIP2_ID': u'bzip2/ngefwc5sfpdgvyu4a2sl6xlxz7pxz4yy',
[dolfin]    'CMAKE': u'cmake',
[dolfin]    u'CMAKE_DIR': u'/usr/local/pkg/HASH/bld/cmake/lbhoxj57mnvh',
[dolfin]    u'CMAKE_ID': u'cmake/lbhoxj57mnvh5jldorx2amwzir3r5z4b',
[dolfin]    u'EIGEN_DIR': u'/usr/local/pkg/HASH/bld/eigen/u4xobwnar3zk',
[dolfin]    u'EIGEN_ID': u'eigen/u4xobwnar3zkmypn3yb3qyhyicfzynue',
[dolfin]    u'FFC_DIR': u'/usr/local/pkg/HASH/bld/ffc/zsv5oh2g4sni',
[dolfin]    u'FFC_ID': u'ffc/zsv5oh2g4snima6pzb3anpy3l7l2fang',
[dolfin]    u'FIAT_DIR': u'/usr/local/pkg/HASH/bld/fiat/hsh7hxovgeja',
[dolfin]    u'FIAT_ID': u'fiat/hsh7hxovgeja7a7pdb3pfdn2vicp6zl4',
[dolfin]    'HASHDIST_CPU_COUNT': '8',
[dolfin]    u'HDF5_DIR': u'/usr/local/pkg/HASH/bld/hdf5/vbga5cccztxw',
[dolfin]    u'HDF5_ID': u'hdf5/vbga5cccztxwnwd7poh2l6kkbz3mflar',
[dolfin]    'HDF5_ROOT': u'/usr/local/pkg/HASH/bld/hdf5/vbga5cccztxw',
[dolfin]    'HDIST_CONFIG': '{"gc_roots":"/usr/local/pkg/HASH/gcroots","build_stores":[{"dir":"/usr/local/pkg/HASH/bld"}],"source_caches":[{"dir":"/usr/local/pkg/HASH/src"}],"cache":"/usr/local/pkg/HASH/cache","build_temp":"/usr/local/pkg/HASH/tmp"}',
[dolfin]    'HDIST_IMPORT': u'blas/zok3lp3r7qrt3wvvcttmnfbsd2kpere7 boost/egqui4dm4vu6n4nqgtkiptmc52g75km7 bzip2/ngefwc5sfpdgvyu4a2sl6xlxz7pxz4yy cmake/lbhoxj57mnvh5jldorx2amwzir3r5z4b eigen/u4xobwnar3zkmypn3yb3qyhyicfzynue ffc/zsv5oh2g4snima6pzb3anpy3l7l2fang fiat/hsh7hxovgeja7a7pdb3pfdn2vicp6zl4 hdf5/vbga5cccztxwnwd7poh2l6kkbz3mflar instant/oepnpnjjrw34k2z362zdfspvgrpm2ct7 libxml2/kuq3i64fa7wke5tep5icqnpudmydtzmr mpi/jrk6uiczudlaefwdkha2n7rxzurqwlzv numpy/bmi6e74etkc7atu27yahrvd4e7ikmjvc openblas/hllfjuqmc2tpqwhdl6on7vidh2jugzex patchelf/niejoubs6wcbq4s4nfic4ufuqqejc4p7 petsc/ig6wxqzwdxg5col3sp7cxededhrus56b petsc4py/afgtrx633dlz7rljv7jpg3u2ymlg4we3 pkg-config/satmw7zew7c2iuseoajzctg57hgubgjb ply/3esifydnrzk67ia7ahv7gtaya7b3x3rh python/vocgqpztn6ne3pwxfogalqgbimemjhch scotch/krys4gxnhwywonnnej4qpe7dz2vxrrjz six/3rc476cmjsuolgsogq5ruyaymxyiah4t slepc/lqm2c3fgph5rsdpnzh3lyteiglrzsqh5 slepc4py/ekinctogpgorblz3c7ol4q42dlass6eh suitesparse/katz65n7jkwdkse7mf3d5jvad3cexi5k swig/od6fcep573jhoc3az5fy5k635zvmymmb sympy/o45yrlj5g2r7idhjvrdzv2hgt2sq3mld trilinos/z3e34b2b26xpxxha22eu5vmzf2w7xawb ufl/6flobzd44jhcnbb3aq22yhdohbe3u6ry vtk/yf2qdlojmddki57jd44tp4o7c5n75w4j zlib/bhnxhnpzd62fuzvxfx7thetufhpm2c3z',
[dolfin]    'HDIST_IMPORT_PATHS': u'/usr/local/pkg/HASH/bld/blas/zok3lp3r7qrt:/usr/local/pkg/HASH/bld/boost/egqui4dm4vu6:/usr/local/pkg/HASH/bld/bzip2/ngefwc5sfpdg:/usr/local/pkg/HASH/bld/cmake/lbhoxj57mnvh:/usr/local/pkg/HASH/bld/eigen/u4xobwnar3zk:/usr/local/pkg/HASH/bld/ffc/zsv5oh2g4sni:/usr/local/pkg/HASH/bld/fiat/hsh7hxovgeja:/usr/local/pkg/HASH/bld/hdf5/vbga5cccztxw:/usr/local/pkg/HASH/bld/instant/oepnpnjjrw34:/usr/local/pkg/HASH/bld/libxml2/kuq3i64fa7wk:/usr/local/pkg/HASH/bld/mpi/jrk6uiczudla:/usr/local/pkg/HASH/bld/numpy/bmi6e74etkc7:/usr/local/pkg/HASH/bld/openblas/hllfjuqmc2tp:/usr/local/pkg/HASH/bld/patchelf/niejoubs6wcb:/usr/local/pkg/HASH/bld/petsc/ig6wxqzwdxg5:/usr/local/pkg/HASH/bld/petsc4py/afgtrx633dlz:/usr/local/pkg/HASH/bld/pkg-config/satmw7zew7c2:/usr/local/pkg/HASH/bld/ply/3esifydnrzk6:/usr/local/pkg/HASH/bld/python/vocgqpztn6ne:/usr/local/pkg/HASH/bld/scotch/krys4gxnhwyw:/usr/local/pkg/HASH/bld/six/3rc476cmjsuo:/usr/local/pkg/HASH/bld/slepc/lqm2c3fgph5r:/usr/local/pkg/HASH/bld/slepc4py/ekinctogpgor:/usr/local/pkg/HASH/bld/suitesparse/katz65n7jkwd:/usr/local/pkg/HASH/bld/swig/od6fcep573jh:/usr/local/pkg/HASH/bld/sympy/o45yrlj5g2r7:/usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp:/usr/local/pkg/HASH/bld/ufl/6flobzd44jhc:/usr/local/pkg/HASH/bld/vtk/yf2qdlojmddk:/usr/local/pkg/HASH/bld/zlib/bhnxhnpzd62f',
[dolfin]    'HDIST_VIRTUALS': '',
[dolfin]    u'INSTANT_DIR': u'/usr/local/pkg/HASH/bld/instant/oepnpnjjrw34',
[dolfin]    u'INSTANT_ID': u'instant/oepnpnjjrw34k2z362zdfspvgrpm2ct7',
[dolfin]    'LAPACK_LDFLAGS': u'-Wl,-rpath,/usr/local/pkg/HASH/bld/sympy/o45yrlj5g2r7/lib -L/usr/local/pkg/HASH/bld/sympy/o45yrlj5g2r7/lib -lopenblas',
[dolfin]    u'LIBXML2_DIR': u'/usr/local/pkg/HASH/bld/libxml2/kuq3i64fa7wk',
[dolfin]    u'LIBXML2_ID': u'libxml2/kuq3i64fa7wke5tep5icqnpudmydtzmr',
[dolfin]    'MPICC': u'mpicc',
[dolfin]    'MPICXX': u'mpicxx',
[dolfin]    'MPIEXEC': u'mpirun',
[dolfin]    'MPIF77': u'mpif77',
[dolfin]    'MPIF90': u'mpif90',
[dolfin]    u'MPI_DIR': u'/usr/local/pkg/HASH/bld/mpi/jrk6uiczudla',
[dolfin]    u'MPI_ID': u'mpi/jrk6uiczudlaefwdkha2n7rxzurqwlzv',
[dolfin]    u'NUMPY_DIR': u'/usr/local/pkg/HASH/bld/numpy/bmi6e74etkc7',
[dolfin]    u'NUMPY_ID': u'numpy/bmi6e74etkc7atu27yahrvd4e7ikmjvc',
[dolfin]    u'OPENBLAS_DIR': u'/usr/local/pkg/HASH/bld/sympy/o45yrlj5g2r7',
[dolfin]    u'OPENBLAS_ID': u'openblas/hllfjuqmc2tpqwhdl6on7vidh2jugzex',
[dolfin]    'PATCHELF': u'/usr/local/pkg/HASH/bld/patchelf/niejoubs6wcb/bin/patchelf',
[dolfin]    u'PATCHELF_DIR': u'/usr/local/pkg/HASH/bld/patchelf/niejoubs6wcb',
[dolfin]    u'PATCHELF_ID': u'patchelf/niejoubs6wcbq4s4nfic4ufuqqejc4p7',
[dolfin]    'PATH': u'/usr/local/pkg/HASH/bld/swig/od6fcep573jh/bin:/usr/local/pkg/HASH/bld/hdf5/vbga5cccztxw/bin:/usr/local/pkg/HASH/bld/ffc/zsv5oh2g4sni/bin:/usr/bin:/bin',
[dolfin]    u'PETSC4PY_DIR': u'/usr/local/pkg/HASH/bld/petsc4py/afgtrx633dlz',
[dolfin]    u'PETSC4PY_ID': u'petsc4py/afgtrx633dlz7rljv7jpg3u2ymlg4we3',
[dolfin]    u'PETSC_DIR': u'/usr/local/pkg/HASH/bld/petsc/ig6wxqzwdxg5',
[dolfin]    u'PETSC_ID': u'petsc/ig6wxqzwdxg5col3sp7cxededhrus56b',
[dolfin]    u'PKG_CONFIG_DIR': u'/usr/local/pkg/HASH/bld/pkg-config/satmw7zew7c2',
[dolfin]    'PKG_CONFIG_EXECUTABLE': u'',
[dolfin]    u'PKG_CONFIG_ID': u'pkg-config/satmw7zew7c2iuseoajzctg57hgubgjb',
[dolfin]    u'PLY_DIR': u'/usr/local/pkg/HASH/bld/ply/3esifydnrzk6',
[dolfin]    u'PLY_ID': u'ply/3esifydnrzk67ia7ahv7gtaya7b3x3rh',
[dolfin]    'PWD': u'/usr/local/pkg/HASH/tmp/dolfin-gwvhxkfco64y-1',
[dolfin]    'PYTHON': u'/usr/local/pkg/HASH/bld/python/vocgqpztn6ne/bin/python',
[dolfin]    'PYTHONPATH': u'/usr/local/pkg/HASH/bld/vtk/yf2qdlojmddk/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/ufl/6flobzd44jhc/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/slepc4py/ekinctogpgor/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/six/3rc476cmjsuo/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/ply/3esifydnrzk6/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/petsc4py/afgtrx633dlz/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/instant/oepnpnjjrw34/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/fiat/hsh7hxovgeja/lib/python2.7/site-packages:/usr/local/pkg/HASH/bld/ffc/zsv5oh2g4sni/lib/python2.7/site-packages',
[dolfin]    u'PYTHON_DIR': u'/usr/local/pkg/HASH/bld/python/vocgqpztn6ne',
[dolfin]    u'PYTHON_ID': u'python/vocgqpztn6ne3pwxfogalqgbimemjhch',
[dolfin]    u'SCOTCH_DIR': u'/usr/local/pkg/HASH/bld/scotch/krys4gxnhwyw',
[dolfin]    u'SCOTCH_ID': u'scotch/krys4gxnhwywonnnej4qpe7dz2vxrrjz',
[dolfin]    u'SIX_DIR': u'/usr/local/pkg/HASH/bld/six/3rc476cmjsuo',
[dolfin]    u'SIX_ID': u'six/3rc476cmjsuolgsogq5ruyaymxyiah4t',
[dolfin]    u'SLEPC4PY_DIR': u'/usr/local/pkg/HASH/bld/slepc4py/ekinctogpgor',
[dolfin]    u'SLEPC4PY_ID': u'slepc4py/ekinctogpgorblz3c7ol4q42dlass6eh',
[dolfin]    u'SLEPC_DIR': u'/usr/local/pkg/HASH/bld/slepc/lqm2c3fgph5r',
[dolfin]    u'SLEPC_ID': u'slepc/lqm2c3fgph5rsdpnzh3lyteiglrzsqh5',
[dolfin]    u'SUITESPARSE_DIR': u'/usr/local/pkg/HASH/bld/suitesparse/katz65n7jkwd',
[dolfin]    u'SUITESPARSE_ID': u'suitesparse/katz65n7jkwdkse7mf3d5jvad3cexi5k',
[dolfin]    u'SWIG_DIR': u'/usr/local/pkg/HASH/bld/swig/od6fcep573jh',
[dolfin]    'SWIG_EXECUTABLE': u'/usr/local/pkg/HASH/bld/swig/od6fcep573jh/bin/swig',
[dolfin]    u'SWIG_ID': u'swig/od6fcep573jhoc3az5fy5k635zvmymmb',
[dolfin]    u'SYMPY_DIR': u'/usr/local/pkg/HASH/bld/sympy/o45yrlj5g2r7',
[dolfin]    u'SYMPY_ID': u'sympy/o45yrlj5g2r7idhjvrdzv2hgt2sq3mld',
[dolfin]    u'TRILINOS_DIR': u'/usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp',
[dolfin]    u'TRILINOS_ID': u'trilinos/z3e34b2b26xpxxha22eu5vmzf2w7xawb',
[dolfin]    u'UFL_DIR': u'/usr/local/pkg/HASH/bld/ufl/6flobzd44jhc',
[dolfin]    u'UFL_ID': u'ufl/6flobzd44jhcnbb3aq22yhdohbe3u6ry',
[dolfin]    u'VTK_DIR': u'/usr/local/pkg/HASH/bld/vtk/yf2qdlojmddk',
[dolfin]    u'VTK_ID': u'vtk/yf2qdlojmddki57jd44tp4o7c5n75w4j',
[dolfin]    u'ZLIB_DIR': u'/usr/local/pkg/HASH/bld/zlib/bhnxhnpzd62f',
[dolfin]    u'ZLIB_ID': u'zlib/bhnxhnpzd62fuzvxfx7thetufhpm2c3z'}
[dolfin] patching file cmake/modules/FindAMD.cmake
[dolfin] patching file cmake/modules/FindBLASHeader.cmake
[dolfin] patching file cmake/modules/FindCHOLMOD.cmake
[dolfin] patching file cmake/modules/FindCppUnit.cmake
[dolfin] patching file cmake/modules/FindEigen3.cmake
[dolfin] patching file cmake/modules/FindMPI.cmake
[dolfin] patching file cmake/modules/FindPETSc.cmake
[dolfin] patching file cmake/modules/FindParMETIS.cmake
[dolfin] patching file cmake/modules/FindSCOTCH.cmake
[dolfin] patching file cmake/modules/FindSLEPc.cmake
[dolfin] Hunk #1 succeeded at 75 (offset 3 lines).
[dolfin] patching file cmake/modules/FindUMFPACK.cmake
[dolfin] Loading modules:
[dolfin] 
[dolfin] Currently Loaded Modules:
[dolfin]   1) openmpi/1.8.3-gnu
[dolfin] 
[dolfin] 
[dolfin] 
[dolfin] -- The C compiler identification is GNU 4.8.2
[dolfin] -- The CXX compiler identification is GNU 4.8.2
[dolfin] -- Check for working C compiler: /usr/bin/cc
[dolfin] -- Check for working C compiler: /usr/bin/cc -- works
[dolfin] -- Detecting C compiler ABI info
[dolfin] -- Detecting C compiler ABI info - done
[dolfin] -- Check for working CXX compiler: /usr/bin/c++
[dolfin] -- Check for working CXX compiler: /usr/bin/c++ -- works
[dolfin] -- Detecting CXX compiler ABI info
[dolfin] -- Detecting CXX compiler ABI info - done
[dolfin] fatal: Not a git repository (or any of the parent directories): .git
[dolfin] -- Performing Test HAVE_PIPE
[dolfin] -- Performing Test HAVE_PIPE - Success
[dolfin] -- Performing Test HAVE_PEDANTIC
[dolfin] -- Performing Test HAVE_PEDANTIC - Success
[dolfin] -- Performing Test HAVE_STD_CPP11
[dolfin] -- Performing Test HAVE_STD_CPP11 - Success
[dolfin] -- Performing Test HAVE_DEBUG
[dolfin] -- Performing Test HAVE_DEBUG - Success
[dolfin] -- Performing Test HAVE_O2_OPTIMISATION
[dolfin] -- Performing Test HAVE_O2_OPTIMISATION - Success
[dolfin] -- The Fortran compiler identification is GNU
[dolfin] -- Check for working Fortran compiler: /usr/bin/gfortran
[dolfin] -- Check for working Fortran compiler: /usr/bin/gfortran  -- works
[dolfin] -- Detecting Fortran compiler ABI info
[dolfin] -- Detecting Fortran compiler ABI info - done
[dolfin] -- Checking whether /usr/bin/gfortran supports Fortran 90
[dolfin] -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
[dolfin] -- Looking for sys/types.h
[dolfin] -- Looking for sys/types.h - found
[dolfin] -- Looking for stdint.h
[dolfin] -- Looking for stdint.h - found
[dolfin] -- Looking for stddef.h
[dolfin] -- Looking for stddef.h - found
[dolfin] -- Check size of size_t
[dolfin] -- Check size of size_t - done
[dolfin] -- Found MPI_C: /usr/local/pkg/openmpi/1.8.3/gnu/lib/libmpi.so  
[dolfin] -- Found MPI_CXX: /usr/local/pkg/openmpi/1.8.3/gnu/lib/libmpi_cxx.so;/usr/local/pkg/openmpi/1.8.3/gnu/lib/libmpi.so  
[dolfin] -- Found MPI_Fortran: /usr/local/pkg/openmpi/1.8.3/gnu/lib/libmpi_usempi.so;/usr/local/pkg/openmpi/1.8.3/gnu/lib/libmpi_mpifh.so;/usr/local/pkg/openmpi/1.8.3/gnu/lib/libmpi.so  
[dolfin] -- Try OpenMP C flag = [-fopenmp]
[dolfin] -- Performing Test OpenMP_FLAG_DETECTED
[dolfin] -- Performing Test OpenMP_FLAG_DETECTED - Success
[dolfin] -- Try OpenMP CXX flag = [-fopenmp]
[dolfin] -- Performing Test OpenMP_FLAG_DETECTED
[dolfin] -- Performing Test OpenMP_FLAG_DETECTED - Success
[dolfin] -- Found OpenMP: -fopenmp  
[dolfin] -- Performing Test OPENMP_UINT_TEST_RUNS
[dolfin] -- Performing Test OPENMP_UINT_TEST_RUNS - Success
[dolfin] -- Boost version: 1.55.0
[dolfin] -- Found the following Boost libraries:
[dolfin] --   filesystem
[dolfin] --   program_options
[dolfin] --   system
[dolfin] --   thread
[dolfin] --   iostreams
[dolfin] -- UFC version: 1.5.0
[dolfin] -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.1") 
[dolfin] -- Found PythonInterp: /usr/local/pkg/HASH/bld/python/vocgqpztn6ne/bin/python (found suitable version "2.7.6", minimum required is "2") 
[dolfin] -- NumPy header version 1.8.2 found
[dolfin] -- Found PY_ply: /usr/local/pkg/HASH/bld/ply/3esifydnrzk6/lib/python2.7/site-packages/ply  
[dolfin] -- Found SWIG: /usr/local/pkg/HASH/bld/swig/od6fcep573jh/bin/swig (found version "3.0.5") 
[dolfin] -- Checking for package 'PETSc'
[dolfin] -- PETSC_DIR is /usr/local/pkg/HASH/bld/petsc/ig6wxqzwdxg5
[dolfin] -- PETSC_ARCH is empty
[dolfin] -- Found petscconf.h
[dolfin] -- Performing test PETSC_TEST_RUNS - Success
[dolfin] -- Performing Test PETSC_CUSP_FOUND
[dolfin] -- Performing Test PETSC_CUSP_FOUND - Failed
[dolfin] -- PETSc configured without Cusp support
[dolfin] -- Check size of PetscInt
[dolfin] -- Check size of PetscInt - done
[dolfin] -- Found PETSc: /usr/local/pkg/HASH/bld/petsc/ig6wxqzwdxg5/lib/libpetsc.so (Required is at least version "3.3") 
[dolfin] -- Checking for package 'PETSc4Py'
[dolfin] -- petsc4py version 3.5 found
[dolfin] -- Found PETSc4py: /usr/local/pkg/HASH/bld/petsc4py/afgtrx633dlz/lib/python2.7/site-packages/petsc4py/include  
[dolfin] -- Checking for package 'SLEPc'
[dolfin] -- SLEPC_DIR is /usr/local/pkg/HASH/bld/slepc/lqm2c3fgph5r
[dolfin] -- Performing test SLEPC_TEST_RUNS - Success
[dolfin] -- Found SLEPc: /usr/local/pkg/HASH/bld/slepc/lqm2c3fgph5r/lib/libslepc.so (Required is at least version "3.3") 
[dolfin] -- Checking for package 'SLEPc4Py'
[dolfin] -- slepc4py version 3.5.1 found
[dolfin] -- Found SLEPc4py: /usr/local/pkg/HASH/bld/slepc4py/ekinctogpgor/lib/python2.7/site-packages/slepc4py/include (Required is at least version "3.5.1") 
[dolfin] -- Checking for package 'SCOTCH-PT'
[dolfin] -- Found SCOTCH (version 6.0.0)
[dolfin] -- Performing test SCOTCH_TEST_RUNS
[dolfin] -- Performing test SCOTCH_TEST_RUNS - Success
[dolfin] -- Found SCOTCH: /usr/local/pkg/HASH/bld/scotch/krys4gxnhwyw/lib/libptscotch.a;/usr/local/pkg/HASH/bld/scotch/krys4gxnhwyw/lib/libscotch.a;/usr/local/pkg/HASH/bld/scotch/krys4gxnhwyw/lib/libptscotcherr.a  
[dolfin] -- Checking for package 'AMD'
[dolfin] -- Looking for include file pthread.h
[dolfin] -- Looking for include file pthread.h - found
[dolfin] -- Looking for pthread_create
[dolfin] -- Looking for pthread_create - found
[dolfin] -- Found Threads: TRUE  
[dolfin] -- Checking for package 'UMFPACK'
[dolfin] -- Checking for package 'AMD'
[dolfin] -- Checking for package 'CHOLMOD'
[dolfin] -- Checking for package 'AMD'
[dolfin] -- A library with BLAS API found.
[dolfin] -- Performing Test PARMETIS_TEST_RUNS
[dolfin] -- Performing Test PARMETIS_TEST_RUNS - Success
[dolfin] -- Performing Test CHOLMOD_TEST_RUNS
[dolfin] -- Performing Test CHOLMOD_TEST_RUNS - Success
[dolfin] -- Performing Test UMFPACK_TEST_RUNS
[dolfin] -- Performing Test UMFPACK_TEST_RUNS - Success
[dolfin] -- Checking for package 'CHOLMOD'
[dolfin] -- Checking for package 'AMD'
[dolfin] -- A library with BLAS API found.
[dolfin] -- Found HDF5: /usr/local/pkg/HASH/bld/hdf5/vbga5cccztxw/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so  
[dolfin] -- Checking for Trilinos
[dolfin] CMake Error at /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/STK/STKConfig.cmake:143 (INCLUDE):
[dolfin]   include could not find load file:
[dolfin] 
[dolfin]     /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/STK/../STKDoc_tests/STKDoc_testsConfig.cmake
[dolfin] Call Stack (most recent call first):
[dolfin]   /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/PyTrilinos/PyTrilinosConfig.cmake:144 (INCLUDE)
[dolfin]   /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/Trilinos/TrilinosConfig.cmake:148 (include)
[dolfin]   CMakeLists.txt:503 (find_package)
[dolfin] 
[dolfin] 
[dolfin] CMake Error at /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/STK/STKConfig.cmake:144 (INCLUDE):
[dolfin]   include could not find load file:
[dolfin] 
[dolfin]     /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/STK/../STKUnit_tests/STKUnit_testsConfig.cmake
[dolfin] Call Stack (most recent call first):
[dolfin]   /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/PyTrilinos/PyTrilinosConfig.cmake:144 (INCLUDE)
[dolfin]   /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/Trilinos/TrilinosConfig.cmake:148 (include)
[dolfin]   CMakeLists.txt:503 (find_package)
[dolfin] 
[dolfin] 
[dolfin] CMake Error at /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/PyTrilinos/PyTrilinosConfig.cmake:145 (INCLUDE):
[dolfin]   include could not find load file:
[dolfin] 
[dolfin]     /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/PyTrilinos/../STKDoc_tests/STKDoc_testsConfig.cmake
[dolfin] Call Stack (most recent call first):
[dolfin]   /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/Trilinos/TrilinosConfig.cmake:148 (include)
[dolfin]   CMakeLists.txt:503 (find_package)
[dolfin] 
[dolfin] 
[dolfin] CMake Error at /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/PyTrilinos/PyTrilinosConfig.cmake:146 (INCLUDE):
[dolfin]   include could not find load file:
[dolfin] 
[dolfin]     /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/PyTrilinos/../STKUnit_tests/STKUnit_testsConfig.cmake
[dolfin] Call Stack (most recent call first):
[dolfin]   /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/Trilinos/TrilinosConfig.cmake:148 (include)
[dolfin]   CMakeLists.txt:503 (find_package)
[dolfin] 
[dolfin] 
[dolfin] CMake Error at /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/Trilinos/TrilinosConfig.cmake:151 (include):
[dolfin]   include could not find load file:
[dolfin] 
[dolfin]     /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/Trilinos/../STKDoc_tests/STKDoc_testsConfig.cmake
[dolfin] Call Stack (most recent call first):
[dolfin]   CMakeLists.txt:503 (find_package)
[dolfin] 
[dolfin] 
[dolfin] CMake Error at /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/Trilinos/TrilinosConfig.cmake:152 (include):
[dolfin]   include could not find load file:
[dolfin] 
[dolfin]     /usr/local/pkg/HASH/bld/trilinos/z3e34b2b26xp/lib/cmake/Trilinos/../STKUnit_tests/STKUnit_testsConfig.cmake
[dolfin] Call Stack (most recent call first):
[dolfin]   CMakeLists.txt:503 (find_package)
[dolfin] 
[dolfin] 
[dolfin] --   Trilinos version 11.14.2 found. Checking for components
[dolfin] --     Epetra found
[dolfin] --     Zoltan found
[dolfin] --     ML found
[dolfin] --     Ifpack found
[dolfin] --     Amesos found
[dolfin] --     Belos found
[dolfin] --   All necessary Trilinos components found. Trilinos will be enabled.
[dolfin] -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") 
[dolfin] -- Found VTK: /usr/local/pkg/HASH/bld/vtk/yf2qdlojmddk/lib/vtk-5.10 (found version "5.10")
[dolfin] -- 
[dolfin] -- The following optional packages were found:
[dolfin] -- -------------------------------------------
[dolfin] -- (OK) OPENMP
[dolfin] -- (OK) MPI
[dolfin] -- (OK) PETSC
[dolfin] -- (OK) PETSC4PY
[dolfin] -- (OK) SLEPC
[dolfin] -- (OK) SLEPC4PY
[dolfin] -- (OK) TRILINOS
[dolfin] -- (OK) UMFPACK
[dolfin] -- (OK) CHOLMOD
[dolfin] -- (OK) SCOTCH
[dolfin] -- (OK) PARMETIS
[dolfin] -- (OK) ZLIB
[dolfin] -- (OK) PYTHON
[dolfin] -- (OK) HDF5
[dolfin] -- (OK) VTK
[dolfin] -- 
[dolfin] -- The following optional packages were not enabled:
[dolfin] -- -------------------------------------------------
[dolfin] -- (--) PASTIX
[dolfin] -- (--) SPHINX
[dolfin] -- (--) QT
[dolfin] -- 
[dolfin] -- 
[dolfin] -- Generating SWIG interface.
[dolfin] -- --------------------------
[dolfin] -- Looking for Q_WS_X11
[dolfin] -- Looking for Q_WS_X11 - found
[dolfin] -- Looking for Q_WS_WIN
[dolfin] -- Looking for Q_WS_WIN - not found
[dolfin] -- Looking for Q_WS_QWS
[dolfin] -- Looking for Q_WS_QWS - not found
[dolfin] -- Looking for Q_WS_MAC
[dolfin] -- Looking for Q_WS_MAC - not found
[dolfin] -- Found Qt4: /usr/bin/qmake (found version "4.8.6") 
[dolfin] -- QT not found, or QT/VTK not enabled in DOLFIN. Not building demo_plot-qt
[dolfin] -- Configuring incomplete, errors occurred!
[dolfin] See also "/usr/local/pkg/HASH/tmp/dolfin-gwvhxkfco64y-1/_build/CMakeFiles/CMakeOutput.log".
[dolfin] See also "/usr/local/pkg/HASH/tmp/dolfin-gwvhxkfco64y-1/_build/CMakeFiles/CMakeError.log".
[dolfin|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status 1
[dolfin|ERROR] command failed (code=1); raising

[certik]

Can you post your profile that you use to trigger this failure? Let me try on my computer.

[JaroslavHron]

the used profiles are:
https://github.com/JaroslavHron/hashstack/blob/master/r0d0_fenics.yaml
together with
https://github.com/JaroslavHron/hashstack/blob/master/r0d0.yaml

[certik]

I see you use lots of stuff from the system, that I need to build from source on my RHEL6, I also use my own Hashdist compiled gcc to build this. So I am just using the r0d0_fenics profile, with my own gcc in PROLOGUE, i.e.:

extends:
- file: linux.yaml

parameters:
  debug: false
  PROLOGUE: |
    export PATH="/local/certik/bld/profile/bto56eplrk4v/bin:$PATH"; export CC=gcc CXX=g++ FC=gfortran

packages:
  launcher:

  mpi:
    use: openmpi
  blas:
    use: openblas
  lapack:
    use: openblas
  openblas:
    use_threads: false
  hypre:
    with_openblas: true
  hdf5:
  trilinos:
    sources:
    - key: tar.bz2:uqktsqkffhdfsbjgbm567y5o4ty52eav
      url: http://trilinos.org/oldsite/download/files/trilinos-11.12.1-Source.tar.bz2
  petsc:
    build_with: |
      openblas, trilinos
    download: |
      superlu, superlu_dist, hypre, scalapack, blacs, mumps, ml, metis, parmetis, scotch, suitesparse
    coptflags: -O2
    link: shared
    debug: false
  swig:
  boost:
    toolset: gcc
    address_model: 64
    build_with: python
  matplotlib:
  numpy:
  sympy:
  scipy:
  ffc:
  fiat:
  instant:
  ufl:
  uflacs:
  dolfin:
    build_with: |
      openblas, suitesparse, scotch, hdf5, petsc, petsc4py, trilinos, suitesparse, scotch, slepc, slepc4py, vtk, zlib
    with_find_path: true
  mpi4py:
  mshr:

I am using the latest Hashstack master (1ce0c7a). Building now.

[certik]

So this profile fails, as scipy can't find the openblas. I commented scipy out.

[certik]

Now PETSc failed:

2015/04/29 13:13:17 - INFO: [package:run_job] TESTING: checkESSL from config.packages.BlasLapack(/local/certik/tmp/petsc-rhvr7ynws5pa/config/BuildSystem/config/packages/BlasLapack.py:377)
2015/04/29 13:13:17 - INFO: [package:run_job] TESTING: checkPESSL from config.packages.BlasLapack(/local/certik/tmp/petsc-rhvr7ynws5pa/config/BuildSystem/config/packages/BlasLapack.py:389)
2015/04/29 13:13:17 - INFO: [package:run_job] TESTING: checkMKL from config.packages.BlasLapack(/local/certik/tmp/petsc-rhvr7ynws5pa/config/BuildSystem/config/packages/BlasLapack.py:383)
2015/04/29 13:13:17 - INFO: [package:run_job] TESTING: checkMissing from config.packages.BlasLapack(/local/certik/tmp/petsc-rhvr7ynws5pa/config/BuildSystem/config/packages/BlasLapack.py:402)
2015/04/29 13:13:18 - INFO: [package:run_job] TESTING: checklsame from config.packages.BlasLapack(/local/certik/tmp/petsc-rhvr7ynws5pa/config/BuildSystem/config/packages/BlasLapack.py:415)
2015/04/29 13:13:18 - INFO: [package:run_job] TESTING: alternateConfigureLibrary from PETSc.packages.pARMS(/local/certik/tmp/petsc-rhvr7ynws5pa/config/BuildSystem/config/package.py:574)
2015/04/29 13:13:18 - INFO: [package:run_job] TESTING: configureLibrary from PETSc.packages.SuperLU(/local/certik/tmp/petsc-rhvr7ynws5pa/config/BuildSystem/config/package.py:516)
2015/04/29 13:13:18 - INFO: [package:run_job]                       ===============================================================================
2015/04/29 13:13:18 - INFO: [package:run_job]                           Trying to download http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz for SUPERLU
2015/04/29 13:13:18 - INFO: [package:run_job]                       ===============================================================================
2015/04/29 13:14:21 - INFO: [package:run_job]                     
2015/04/29 13:14:21 - INFO: [package:run_job] *******************************************************************************
2015/04/29 13:14:21 - INFO: [package:run_job]          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
2015/04/29 13:14:21 - INFO: [package:run_job] -------------------------------------------------------------------------------
2015/04/29 13:14:21 - INFO: [package:run_job] Unable to download package SuperLU from: http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz
2015/04/29 13:14:21 - INFO: [package:run_job] * If URL specified manually - perhaps there is a typo?
2015/04/29 13:14:21 - INFO: [package:run_job] * If your network is disconnected - please reconnect and rerun ./configure
2015/04/29 13:14:21 - INFO: [package:run_job] * Or perhaps you have a firewall blocking the download
2015/04/29 13:14:21 - INFO: [package:run_job] * Alternatively, you can download the above URL manually, to /yourselectedlocation/superlu_4.3.tar.gz
2015/04/29 13:14:21 - INFO: [package:run_job]   and use the configure option:
2015/04/29 13:14:21 - INFO: [package:run_job]   --download-superlu=/yourselectedlocation/superlu_4.3.tar.gz
2015/04/29 13:14:21 - INFO: [package:run_job] *******************************************************************************
2015/04/29 13:14:21 - INFO: [package:run_job] 
2015/04/29 13:14:21 - ERROR: [package:run_job] Command '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status 1
2015/04/29 13:14:21 - ERROR: [package:run_job] command failed (code=1); raising

I've always been against PETSc downloading its own files, precisely for problems like this one. All dependencies should be installed using Hashdist, then we have full control over them, and we just point them to PETSc.

cc @ahmadia

[JaroslavHron]

Thanks for the testing.

Here is a fix for the "scipy can't find openblas" problem - #733 and similar for numpy - #734

And here #732 is a fix for hypre which fails at tests with openblas.

Concerning the PETSc - superlu can be skipped...
As far as I know the PETSc developers recommend to use these downloads since for most of the packages they maintain their own versions at https://bitbucket.org/petsc

[certik]

We should perhaps install those packages from https://bitbucket.org/petsc, but we should install them using Hashdist, not let them download from the build script. The build script must work without internet access.