-*- mode: compilation; default-directory: "/project/6002183/lavery/fenics/dolfin.19_03_23/python/" -*- Compilation started at Sun Mar 24 11:37:30 pip3 -vvv install . Created temporary directory: /tmp/pip-ephem-wheel-cache-8wx3xhfd Created temporary directory: /tmp/pip-req-tracker-kd9rpz2j Created requirements tracker '/tmp/pip-req-tracker-kd9rpz2j' Created temporary directory: /tmp/pip-install-ogbqg9si Looking in links: /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic Processing /project/6002183/lavery/fenics/dolfin.19_03_23/python Created temporary directory: /tmp/pip-req-build-pct5ubbb Added file:///project/6002183/lavery/fenics/dolfin.19_03_23/python to build tracker '/tmp/pip-req-tracker-kd9rpz2j' Running setup.py (path:/tmp/pip-req-build-pct5ubbb/setup.py) egg_info for package from file:///project/6002183/lavery/fenics/dolfin.19_03_23/python Running command python setup.py egg_info running egg_info creating pip-egg-info/fenics_dolfin.egg-info writing pip-egg-info/fenics_dolfin.egg-info/PKG-INFO writing dependency_links to pip-egg-info/fenics_dolfin.egg-info/dependency_links.txt writing requirements to pip-egg-info/fenics_dolfin.egg-info/requires.txt writing top-level names to pip-egg-info/fenics_dolfin.egg-info/top_level.txt writing manifest file 'pip-egg-info/fenics_dolfin.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/fenics_dolfin.egg-info/SOURCES.txt' writing manifest file 'pip-egg-info/fenics_dolfin.egg-info/SOURCES.txt' Source in /tmp/pip-req-build-pct5ubbb has version 2018.2.0.dev0, which satisfies requirement fenics-dolfin==2018.2.0.dev0 from file:///project/6002183/lavery/fenics/dolfin.19_03_23/python Removed fenics-dolfin==2018.2.0.dev0 from file:///project/6002183/lavery/fenics/dolfin.19_03_23/python from build tracker '/tmp/pip-req-tracker-kd9rpz2j' Requirement already satisfied: numpy in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from fenics-dolfin==2018.2.0.dev0) (1.16.2) Requirement already satisfied: pkgconfig in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from fenics-dolfin==2018.2.0.dev0) (1.4.0) Requirement already satisfied: pybind11==2.2.4 in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from fenics-dolfin==2018.2.0.dev0) (2.2.4) Requirement already satisfied: fenics-ffc<2018.3,>=2018.2.0.dev0 in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from fenics-dolfin==2018.2.0.dev0) (2018.2.0.dev0) Requirement already satisfied: fenics-ufl<2018.3,>=2018.2.0.dev0 in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from fenics-dolfin==2018.2.0.dev0) (2018.2.0.dev0) Requirement already satisfied: fenics-dijitso<2018.3,>=2018.2.0.dev0 in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from fenics-dolfin==2018.2.0.dev0) (2018.2.0.dev0) Requirement already satisfied: fenics-fiat<2018.3,>=2018.2.0.dev0 in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from fenics-ffc<2018.3,>=2018.2.0.dev0->fenics-dolfin==2018.2.0.dev0) (2018.2.0.dev0) Requirement already satisfied: sympy in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from fenics-fiat<2018.3,>=2018.2.0.dev0->fenics-ffc<2018.3,>=2018.2.0.dev0->fenics-dolfin==2018.2.0.dev0) (1.3) Requirement already satisfied: mpmath>=0.19 in /project/6002183/lavery/FENICS/lib/python3.7/site-packages (from sympy->fenics-fiat<2018.3,>=2018.2.0.dev0->fenics-ffc<2018.3,>=2018.2.0.dev0->fenics-dolfin==2018.2.0.dev0) (1.1.0) Could not parse version from link: file:///project/6002183/lavery/fenics/dolfin.19_03_23/python Building wheels for collected packages: fenics-dolfin Created temporary directory: /tmp/pip-wheel-j9v9ucsc Running setup.py bdist_wheel for fenics-dolfin ... [?25l Destination directory: /tmp/pip-wheel-j9v9ucsc Running command /home/lavery/projects/def-bingalls/lavery/FENICS/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-pct5ubbb/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-j9v9ucsc --python-tag cp37 running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/dolfin copying dolfin/__init__.py -> build/lib.linux-x86_64-3.7/dolfin creating build/lib.linux-x86_64-3.7/dolfin/common copying dolfin/common/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/common copying dolfin/common/timer.py -> build/lib.linux-x86_64-3.7/dolfin/common copying dolfin/common/plotting.py -> build/lib.linux-x86_64-3.7/dolfin/common creating build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/functionspace.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/specialfunctions.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/multimeshfunction.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/argument.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/jit.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/multimeshfunctionspace.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/function.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/expression.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/constant.py -> build/lib.linux-x86_64-3.7/dolfin/function creating build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/solvers.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/problem.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/errorcontrolgenerator.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/interpolation.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/form.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/projection.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/norms.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/assembling.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/adaptivesolving.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/formmanipulations.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/multimeshdirichletbc.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/dirichletbc.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/solving.py -> build/lib.linux-x86_64-3.7/dolfin/fem creating build/lib.linux-x86_64-3.7/dolfin/la copying dolfin/la/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/la copying dolfin/la/solver.py -> build/lib.linux-x86_64-3.7/dolfin/la creating build/lib.linux-x86_64-3.7/dolfin/io copying dolfin/io/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/io creating build/lib.linux-x86_64-3.7/dolfin/jit copying dolfin/jit/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/jit copying dolfin/jit/jit.py -> build/lib.linux-x86_64-3.7/dolfin/jit copying dolfin/jit/pybind11jit.py -> build/lib.linux-x86_64-3.7/dolfin/jit creating build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/svgtools.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/meshvaluecollection.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/ufl_util.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/ale.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/meshfunction.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/subdomain.py -> build/lib.linux-x86_64-3.7/dolfin/mesh creating build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/multistagesolvers.py -> build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/multistagescheme.py -> build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/factorize.py -> build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/rushlarsenschemes.py -> build/lib.linux-x86_64-3.7/dolfin/multistage creating build/lib.linux-x86_64-3.7/dolfin/parameter copying dolfin/parameter/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/parameter creating build/lib.linux-x86_64-3.7/dolfin_utils creating build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert copying dolfin_utils/meshconvert/__init__.py -> build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert copying dolfin_utils/meshconvert/abaqus.py -> build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert copying dolfin_utils/meshconvert/xml_writer.py -> build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert copying dolfin_utils/meshconvert/meshconvert.py -> build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert creating build/lib.linux-x86_64-3.7/dolfin_utils/test copying dolfin_utils/test/skips.py -> build/lib.linux-x86_64-3.7/dolfin_utils/test copying dolfin_utils/test/paths.py -> build/lib.linux-x86_64-3.7/dolfin_utils/test copying dolfin_utils/test/__init__.py -> build/lib.linux-x86_64-3.7/dolfin_utils/test copying dolfin_utils/test/fixtures.py -> build/lib.linux-x86_64-3.7/dolfin_utils/test creating build/lib.linux-x86_64-3.7/fenics copying fenics/__init__.py -> build/lib.linux-x86_64-3.7/fenics running build_ext -- The C compiler identification is GNU 7.3.0 -- The CXX compiler identification is GNU 7.3.0 -- Check for working C compiler: /cvmfs/soft.computecanada.ca/custom/bin/cc -- Check for working C compiler: /cvmfs/soft.computecanada.ca/custom/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-7.3.0/bin/c++ -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-7.3.0/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PythonInterp: /home/lavery/projects/def-bingalls/lavery/FENICS/bin/python (found version "3.7") -- Found PythonLibs: /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/libpython3.7m.so -- Performing Test HAS_CPP14_FLAG -- Performing Test HAS_CPP14_FLAG - Success -- Found PkgConfig: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/pkg-config (found version "0.29") -- Checking for one of the modules 'craypetsc_real;PETSc' -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of PetscInt -- Check size of PetscInt - done -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- LTO enabled -- Checking for package 'PETSc4Py' -- petsc4py version 3.10.1 found -- Found PETSc4py: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/petsc4py/include -- Found MPI4PY: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include -- Configuring done CMake Warning at /home/lavery/FENICS/share/cmake/pybind11/pybind11Tools.cmake:131 (add_library): Cannot generate a safe linker search path for target cpp because files in some directories may conflict with libraries in implicit directories: link library [libhdf5.so] in /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2018.3/openmpi3.1/hdf5-mpi/1.10.3/lib may be hidden by files in: /lib64 Some of these libraries may not be found correctly. Call Stack (most recent call first): CMakeLists.txt:34 (pybind11_add_module) -- Generating done -- Build files have been written to: /tmp/pip-req-build-pct5ubbb/build/temp.linux-x86_64-3.7 Scanning dependencies of target cpp [ 4%] Building CXX object CMakeFiles/cpp.dir/src/dolfin.cpp.o [ 9%] Building CXX object CMakeFiles/cpp.dir/src/parameter.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/fem.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/function.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/generation.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/adaptivity.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/geometry.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/common.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/ale.cpp.o [ 71%] Building CXX object CMakeFiles/cpp.dir/src/graph.cpp.o [ 71%] Building CXX object CMakeFiles/cpp.dir/src/ts.cpp.o [ 71%] Building CXX object CMakeFiles/cpp.dir/src/mesh.cpp.o [ 71%] Building CXX object CMakeFiles/cpp.dir/src/multistage.cpp.o [ 71%] Building CXX object CMakeFiles/cpp.dir/src/log.cpp.o [ 71%] Building CXX object CMakeFiles/cpp.dir/src/math.cpp.o [ 76%] Building CXX object CMakeFiles/cpp.dir/src/io.cpp.o [ 85%] Building CXX object CMakeFiles/cpp.dir/src/nls.cpp.o [ 85%] Building CXX object CMakeFiles/cpp.dir/src/refinement.cpp.o [ 90%] Building CXX object CMakeFiles/cpp.dir/src/MPICommWrapper.cpp.o [ 95%] Building CXX object CMakeFiles/cpp.dir/src/la.cpp.o In file included from /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.h:14:0, from /tmp/pip-req-build-pct5ubbb/src/mpi_casters.h:28, from /tmp/pip-req-build-pct5ubbb/src/casters.h:26, from /tmp/pip-req-build-pct5ubbb/src/la.cpp:29: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h: In function ‘int import_mpi4py__MPI()’: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:261:113: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Status = __Pyx_ImportType("mpi4py.MPI", "Status", sizeof(struct PyMPIStatusObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Status) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:262:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Datatype = __Pyx_ImportType("mpi4py.MPI", "Datatype", sizeof(struct PyMPIDatatypeObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Datatype) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:263:116: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Request = __Pyx_ImportType("mpi4py.MPI", "Request", sizeof(struct PyMPIRequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Request) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:264:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Prequest = __Pyx_ImportType("mpi4py.MPI", "Prequest", sizeof(struct PyMPIPrequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Prequest) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:265:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Grequest = __Pyx_ImportType("mpi4py.MPI", "Grequest", sizeof(struct PyMPIGrequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Grequest) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:266:116: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Message = __Pyx_ImportType("mpi4py.MPI", "Message", sizeof(struct PyMPIMessageObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Message) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:267:101: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Op = __Pyx_ImportType("mpi4py.MPI", "Op", sizeof(struct PyMPIOpObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Op) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:268:110: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Group = __Pyx_ImportType("mpi4py.MPI", "Group", sizeof(struct PyMPIGroupObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Group) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:269:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Info = __Pyx_ImportType("mpi4py.MPI", "Info", sizeof(struct PyMPIInfoObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Info) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:270:125: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Errhandler = __Pyx_ImportType("mpi4py.MPI", "Errhandler", sizeof(struct PyMPIErrhandlerObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Errhandler) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:271:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Comm = __Pyx_ImportType("mpi4py.MPI", "Comm", sizeof(struct PyMPICommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Comm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:272:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Intracomm = __Pyx_ImportType("mpi4py.MPI", "Intracomm", sizeof(struct PyMPIIntracommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Intracomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:273:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Topocomm = __Pyx_ImportType("mpi4py.MPI", "Topocomm", sizeof(struct PyMPITopocommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Topocomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:274:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Cartcomm = __Pyx_ImportType("mpi4py.MPI", "Cartcomm", sizeof(struct PyMPICartcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Cartcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:275:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Graphcomm = __Pyx_ImportType("mpi4py.MPI", "Graphcomm", sizeof(struct PyMPIGraphcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Graphcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:276:134: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Distgraphcomm = __Pyx_ImportType("mpi4py.MPI", "Distgraphcomm", sizeof(struct PyMPIDistgraphcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Distgraphcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:277:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Intercomm = __Pyx_ImportType("mpi4py.MPI", "Intercomm", sizeof(struct PyMPIIntercommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Intercomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:278:104: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Win = __Pyx_ImportType("mpi4py.MPI", "Win", sizeof(struct PyMPIWinObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Win) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:279:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_File = __Pyx_ImportType("mpi4py.MPI", "File", sizeof(struct PyMPIFileObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_File) goto bad; ^ In file included from /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.h:14:0, from /tmp/pip-req-build-pct5ubbb/src/mpi_casters.h:28, from /tmp/pip-req-build-pct5ubbb/src/casters.h:26, from /tmp/pip-req-build-pct5ubbb/src/fem.cpp:70: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h: In function ‘int import_mpi4py__MPI()’: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:261:113: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Status = __Pyx_ImportType("mpi4py.MPI", "Status", sizeof(struct PyMPIStatusObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Status) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:262:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Datatype = __Pyx_ImportType("mpi4py.MPI", "Datatype", sizeof(struct PyMPIDatatypeObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Datatype) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:263:116: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Request = __Pyx_ImportType("mpi4py.MPI", "Request", sizeof(struct PyMPIRequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Request) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:264:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Prequest = __Pyx_ImportType("mpi4py.MPI", "Prequest", sizeof(struct PyMPIPrequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Prequest) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:265:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Grequest = __Pyx_ImportType("mpi4py.MPI", "Grequest", sizeof(struct PyMPIGrequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Grequest) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:266:116: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Message = __Pyx_ImportType("mpi4py.MPI", "Message", sizeof(struct PyMPIMessageObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Message) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:267:101: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Op = __Pyx_ImportType("mpi4py.MPI", "Op", sizeof(struct PyMPIOpObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Op) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:268:110: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Group = __Pyx_ImportType("mpi4py.MPI", "Group", sizeof(struct PyMPIGroupObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Group) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:269:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Info = __Pyx_ImportType("mpi4py.MPI", "Info", sizeof(struct PyMPIInfoObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Info) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:270:125: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Errhandler = __Pyx_ImportType("mpi4py.MPI", "Errhandler", sizeof(struct PyMPIErrhandlerObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Errhandler) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:271:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Comm = __Pyx_ImportType("mpi4py.MPI", "Comm", sizeof(struct PyMPICommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Comm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:272:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Intracomm = __Pyx_ImportType("mpi4py.MPI", "Intracomm", sizeof(struct PyMPIIntracommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Intracomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:273:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Topocomm = __Pyx_ImportType("mpi4py.MPI", "Topocomm", sizeof(struct PyMPITopocommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Topocomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:274:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Cartcomm = __Pyx_ImportType("mpi4py.MPI", "Cartcomm", sizeof(struct PyMPICartcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Cartcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:275:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Graphcomm = __Pyx_ImportType("mpi4py.MPI", "Graphcomm", sizeof(struct PyMPIGraphcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Graphcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:276:134: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Distgraphcomm = __Pyx_ImportType("mpi4py.MPI", "Distgraphcomm", sizeof(struct PyMPIDistgraphcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Distgraphcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:277:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Intercomm = __Pyx_ImportType("mpi4py.MPI", "Intercomm", sizeof(struct PyMPIIntercommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Intercomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:278:104: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Win = __Pyx_ImportType("mpi4py.MPI", "Win", sizeof(struct PyMPIWinObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Win) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:279:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_File = __Pyx_ImportType("mpi4py.MPI", "File", sizeof(struct PyMPIFileObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_File) goto bad; ^ In file included from /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/petsc4py/include/petsc4py/petsc4py.h:9:0, from /tmp/pip-req-build-pct5ubbb/src/petsc_casters.h:33, from /tmp/pip-req-build-pct5ubbb/src/casters.h:27, from /tmp/pip-req-build-pct5ubbb/src/nls.cpp:37: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/petsc4py/include/petsc4py/petsc4py.PETSc_api.h:208:22: warning: ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ used but never defined static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, const char *class_name, size_t size, enum __Pyx_ImportType_CheckSize check_size); ^~~~~~~~~~~~~~~~ gmake[2]: *** [CMakeFiles/cpp.dir/src/fem.cpp.o] Error 1 gmake[2]: *** Waiting for unfinished jobs.... gmake[2]: *** [CMakeFiles/cpp.dir/src/la.cpp.o] Error 1 gmake[1]: *** [CMakeFiles/cpp.dir/all] Error 2 gmake: *** [all] Error 2 Traceback (most recent call last): File "", line 1, in File "/tmp/pip-req-build-pct5ubbb/setup.py", line 100, in zip_safe=False) File "/home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup return distutils.core.setup(**attrs) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 192, in run self.run_command('build') File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-req-build-pct5ubbb/setup.py", line 47, in run self.build_extension(ext) File "/tmp/pip-req-build-pct5ubbb/setup.py", line 76, in build_extension subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp, env=env) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/subprocess.py", line 328, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j31']' returned non-zero exit status 2. error  Failed building wheel for fenics-dolfin [?25h Running setup.py clean for fenics-dolfin Running command /home/lavery/projects/def-bingalls/lavery/FENICS/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-pct5ubbb/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all running clean removing 'build/temp.linux-x86_64-3.7' (and everything under it) removing 'build/lib.linux-x86_64-3.7' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it removing 'build' Failed to build fenics-dolfin Installing collected packages: fenics-dolfin Created temporary directory: /tmp/pip-record-lw0_jpxx Running setup.py install for fenics-dolfin ... [?25l Running command /home/lavery/projects/def-bingalls/lavery/FENICS/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-pct5ubbb/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-lw0_jpxx/install-record.txt --single-version-externally-managed --compile --install-headers /home/lavery/projects/def-bingalls/lavery/FENICS/include/site/python3.7/fenics-dolfin running install running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/dolfin copying dolfin/__init__.py -> build/lib.linux-x86_64-3.7/dolfin creating build/lib.linux-x86_64-3.7/dolfin/common copying dolfin/common/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/common copying dolfin/common/timer.py -> build/lib.linux-x86_64-3.7/dolfin/common copying dolfin/common/plotting.py -> build/lib.linux-x86_64-3.7/dolfin/common creating build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/functionspace.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/specialfunctions.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/multimeshfunction.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/argument.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/jit.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/multimeshfunctionspace.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/function.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/expression.py -> build/lib.linux-x86_64-3.7/dolfin/function copying dolfin/function/constant.py -> build/lib.linux-x86_64-3.7/dolfin/function creating build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/solvers.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/problem.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/errorcontrolgenerator.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/interpolation.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/form.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/projection.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/norms.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/assembling.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/adaptivesolving.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/formmanipulations.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/multimeshdirichletbc.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/dirichletbc.py -> build/lib.linux-x86_64-3.7/dolfin/fem copying dolfin/fem/solving.py -> build/lib.linux-x86_64-3.7/dolfin/fem creating build/lib.linux-x86_64-3.7/dolfin/la copying dolfin/la/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/la copying dolfin/la/solver.py -> build/lib.linux-x86_64-3.7/dolfin/la creating build/lib.linux-x86_64-3.7/dolfin/io copying dolfin/io/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/io creating build/lib.linux-x86_64-3.7/dolfin/jit copying dolfin/jit/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/jit copying dolfin/jit/jit.py -> build/lib.linux-x86_64-3.7/dolfin/jit copying dolfin/jit/pybind11jit.py -> build/lib.linux-x86_64-3.7/dolfin/jit creating build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/svgtools.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/meshvaluecollection.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/ufl_util.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/ale.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/meshfunction.py -> build/lib.linux-x86_64-3.7/dolfin/mesh copying dolfin/mesh/subdomain.py -> build/lib.linux-x86_64-3.7/dolfin/mesh creating build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/multistagesolvers.py -> build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/multistagescheme.py -> build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/factorize.py -> build/lib.linux-x86_64-3.7/dolfin/multistage copying dolfin/multistage/rushlarsenschemes.py -> build/lib.linux-x86_64-3.7/dolfin/multistage creating build/lib.linux-x86_64-3.7/dolfin/parameter copying dolfin/parameter/__init__.py -> build/lib.linux-x86_64-3.7/dolfin/parameter creating build/lib.linux-x86_64-3.7/dolfin_utils creating build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert copying dolfin_utils/meshconvert/__init__.py -> build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert copying dolfin_utils/meshconvert/abaqus.py -> build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert copying dolfin_utils/meshconvert/xml_writer.py -> build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert copying dolfin_utils/meshconvert/meshconvert.py -> build/lib.linux-x86_64-3.7/dolfin_utils/meshconvert creating build/lib.linux-x86_64-3.7/dolfin_utils/test copying dolfin_utils/test/skips.py -> build/lib.linux-x86_64-3.7/dolfin_utils/test copying dolfin_utils/test/paths.py -> build/lib.linux-x86_64-3.7/dolfin_utils/test copying dolfin_utils/test/__init__.py -> build/lib.linux-x86_64-3.7/dolfin_utils/test copying dolfin_utils/test/fixtures.py -> build/lib.linux-x86_64-3.7/dolfin_utils/test creating build/lib.linux-x86_64-3.7/fenics copying fenics/__init__.py -> build/lib.linux-x86_64-3.7/fenics running build_ext -- The C compiler identification is GNU 7.3.0 -- The CXX compiler identification is GNU 7.3.0 -- Check for working C compiler: /cvmfs/soft.computecanada.ca/custom/bin/cc -- Check for working C compiler: /cvmfs/soft.computecanada.ca/custom/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-7.3.0/bin/c++ -- Check for working CXX compiler: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-7.3.0/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PythonInterp: /home/lavery/projects/def-bingalls/lavery/FENICS/bin/python (found version "3.7") -- Found PythonLibs: /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/libpython3.7m.so -- Performing Test HAS_CPP14_FLAG -- Performing Test HAS_CPP14_FLAG - Success -- Found PkgConfig: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/pkg-config (found version "0.29") -- Checking for one of the modules 'craypetsc_real;PETSc' -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of PetscInt -- Check size of PetscInt - done -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- LTO enabled -- Checking for package 'PETSc4Py' -- petsc4py version 3.10.1 found -- Found PETSc4py: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/petsc4py/include -- Found MPI4PY: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include -- Configuring done CMake Warning at /home/lavery/FENICS/share/cmake/pybind11/pybind11Tools.cmake:131 (add_library): Cannot generate a safe linker search path for target cpp because files in some directories may conflict with libraries in implicit directories: link library [libhdf5.so] in /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/MPI/intel2018.3/openmpi3.1/hdf5-mpi/1.10.3/lib may be hidden by files in: /lib64 Some of these libraries may not be found correctly. Call Stack (most recent call first): CMakeLists.txt:34 (pybind11_add_module) -- Generating done -- Build files have been written to: /tmp/pip-req-build-pct5ubbb/build/temp.linux-x86_64-3.7 Scanning dependencies of target cpp [ 4%] Building CXX object CMakeFiles/cpp.dir/src/dolfin.cpp.o [ 9%] Building CXX object CMakeFiles/cpp.dir/src/parameter.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/fem.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/common.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/geometry.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/ale.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/function.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/generation.cpp.o [ 42%] Building CXX object CMakeFiles/cpp.dir/src/adaptivity.cpp.o [ 76%] Building CXX object CMakeFiles/cpp.dir/src/io.cpp.o [ 76%] Building CXX object CMakeFiles/cpp.dir/src/math.cpp.o [ 76%] Building CXX object CMakeFiles/cpp.dir/src/graph.cpp.o [ 76%] Building CXX object CMakeFiles/cpp.dir/src/multistage.cpp.o [ 76%] Building CXX object CMakeFiles/cpp.dir/src/log.cpp.o [ 76%] Building CXX object CMakeFiles/cpp.dir/src/mesh.cpp.o [ 76%] Building CXX object CMakeFiles/cpp.dir/src/ts.cpp.o [ 80%] Building CXX object CMakeFiles/cpp.dir/src/refinement.cpp.o [ 85%] Building CXX object CMakeFiles/cpp.dir/src/la.cpp.o [ 90%] Building CXX object CMakeFiles/cpp.dir/src/MPICommWrapper.cpp.o [ 95%] Building CXX object CMakeFiles/cpp.dir/src/nls.cpp.o In file included from /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.h:14:0, from /tmp/pip-req-build-pct5ubbb/src/mpi_casters.h:28, from /tmp/pip-req-build-pct5ubbb/src/casters.h:26, from /tmp/pip-req-build-pct5ubbb/src/la.cpp:29: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h: In function ‘int import_mpi4py__MPI()’: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:261:113: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Status = __Pyx_ImportType("mpi4py.MPI", "Status", sizeof(struct PyMPIStatusObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Status) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:262:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Datatype = __Pyx_ImportType("mpi4py.MPI", "Datatype", sizeof(struct PyMPIDatatypeObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Datatype) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:263:116: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Request = __Pyx_ImportType("mpi4py.MPI", "Request", sizeof(struct PyMPIRequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Request) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:264:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Prequest = __Pyx_ImportType("mpi4py.MPI", "Prequest", sizeof(struct PyMPIPrequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Prequest) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:265:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Grequest = __Pyx_ImportType("mpi4py.MPI", "Grequest", sizeof(struct PyMPIGrequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Grequest) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:266:116: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Message = __Pyx_ImportType("mpi4py.MPI", "Message", sizeof(struct PyMPIMessageObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Message) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:267:101: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Op = __Pyx_ImportType("mpi4py.MPI", "Op", sizeof(struct PyMPIOpObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Op) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:268:110: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Group = __Pyx_ImportType("mpi4py.MPI", "Group", sizeof(struct PyMPIGroupObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Group) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:269:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Info = __Pyx_ImportType("mpi4py.MPI", "Info", sizeof(struct PyMPIInfoObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Info) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:270:125: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Errhandler = __Pyx_ImportType("mpi4py.MPI", "Errhandler", sizeof(struct PyMPIErrhandlerObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Errhandler) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:271:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Comm = __Pyx_ImportType("mpi4py.MPI", "Comm", sizeof(struct PyMPICommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Comm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:272:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Intracomm = __Pyx_ImportType("mpi4py.MPI", "Intracomm", sizeof(struct PyMPIIntracommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Intracomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:273:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Topocomm = __Pyx_ImportType("mpi4py.MPI", "Topocomm", sizeof(struct PyMPITopocommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Topocomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:274:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Cartcomm = __Pyx_ImportType("mpi4py.MPI", "Cartcomm", sizeof(struct PyMPICartcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Cartcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:275:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Graphcomm = __Pyx_ImportType("mpi4py.MPI", "Graphcomm", sizeof(struct PyMPIGraphcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Graphcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:276:134: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Distgraphcomm = __Pyx_ImportType("mpi4py.MPI", "Distgraphcomm", sizeof(struct PyMPIDistgraphcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Distgraphcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:277:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Intercomm = __Pyx_ImportType("mpi4py.MPI", "Intercomm", sizeof(struct PyMPIIntercommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Intercomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:278:104: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Win = __Pyx_ImportType("mpi4py.MPI", "Win", sizeof(struct PyMPIWinObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Win) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:279:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_File = __Pyx_ImportType("mpi4py.MPI", "File", sizeof(struct PyMPIFileObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_File) goto bad; ^ In file included from /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.h:14:0, from /tmp/pip-req-build-pct5ubbb/src/mpi_casters.h:28, from /tmp/pip-req-build-pct5ubbb/src/casters.h:26, from /tmp/pip-req-build-pct5ubbb/src/fem.cpp:70: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h: In function ‘int import_mpi4py__MPI()’: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:261:113: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Status = __Pyx_ImportType("mpi4py.MPI", "Status", sizeof(struct PyMPIStatusObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Status) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:262:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Datatype = __Pyx_ImportType("mpi4py.MPI", "Datatype", sizeof(struct PyMPIDatatypeObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Datatype) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:263:116: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Request = __Pyx_ImportType("mpi4py.MPI", "Request", sizeof(struct PyMPIRequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Request) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:264:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Prequest = __Pyx_ImportType("mpi4py.MPI", "Prequest", sizeof(struct PyMPIPrequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Prequest) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:265:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Grequest = __Pyx_ImportType("mpi4py.MPI", "Grequest", sizeof(struct PyMPIGrequestObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Grequest) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:266:116: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Message = __Pyx_ImportType("mpi4py.MPI", "Message", sizeof(struct PyMPIMessageObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Message) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:267:101: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Op = __Pyx_ImportType("mpi4py.MPI", "Op", sizeof(struct PyMPIOpObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Op) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:268:110: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Group = __Pyx_ImportType("mpi4py.MPI", "Group", sizeof(struct PyMPIGroupObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Group) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:269:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Info = __Pyx_ImportType("mpi4py.MPI", "Info", sizeof(struct PyMPIInfoObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Info) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:270:125: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Errhandler = __Pyx_ImportType("mpi4py.MPI", "Errhandler", sizeof(struct PyMPIErrhandlerObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Errhandler) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:271:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Comm = __Pyx_ImportType("mpi4py.MPI", "Comm", sizeof(struct PyMPICommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Comm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:272:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Intracomm = __Pyx_ImportType("mpi4py.MPI", "Intracomm", sizeof(struct PyMPIIntracommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Intracomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:273:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Topocomm = __Pyx_ImportType("mpi4py.MPI", "Topocomm", sizeof(struct PyMPITopocommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Topocomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:274:119: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Cartcomm = __Pyx_ImportType("mpi4py.MPI", "Cartcomm", sizeof(struct PyMPICartcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Cartcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:275:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Graphcomm = __Pyx_ImportType("mpi4py.MPI", "Graphcomm", sizeof(struct PyMPIGraphcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Graphcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:276:134: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Distgraphcomm = __Pyx_ImportType("mpi4py.MPI", "Distgraphcomm", sizeof(struct PyMPIDistgraphcommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Distgraphcomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:277:122: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Intercomm = __Pyx_ImportType("mpi4py.MPI", "Intercomm", sizeof(struct PyMPIIntercommObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Intercomm) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:278:104: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_Win = __Pyx_ImportType("mpi4py.MPI", "Win", sizeof(struct PyMPIWinObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_Win) goto bad; ^ /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h:279:107: error: cannot convert ‘const char*’ to ‘PyObject* {aka _object*}’ for argument ‘1’ to ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ __pyx_ptype_6mpi4py_3MPI_File = __Pyx_ImportType("mpi4py.MPI", "File", sizeof(struct PyMPIFileObject), 1); if (!__pyx_ptype_6mpi4py_3MPI_File) goto bad; ^ In file included from /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/petsc4py/include/petsc4py/petsc4py.h:9:0, from /tmp/pip-req-build-pct5ubbb/src/petsc_casters.h:33, from /tmp/pip-req-build-pct5ubbb/src/casters.h:27, from /tmp/pip-req-build-pct5ubbb/src/nls.cpp:37: /home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/petsc4py/include/petsc4py/petsc4py.PETSc_api.h:208:22: warning: ‘PyTypeObject* __Pyx_ImportType(PyObject*, const char*, const char*, size_t, __Pyx_ImportType_CheckSize)’ used but never defined static PyTypeObject *__Pyx_ImportType(PyObject* module, const char *module_name, const char *class_name, size_t size, enum __Pyx_ImportType_CheckSize check_size); ^~~~~~~~~~~~~~~~ gmake[2]: *** [CMakeFiles/cpp.dir/src/fem.cpp.o] Error 1 gmake[2]: *** Waiting for unfinished jobs.... gmake[2]: *** [CMakeFiles/cpp.dir/src/la.cpp.o] Error 1 gmake[1]: *** [CMakeFiles/cpp.dir/all] Error 2 gmake: *** [all] Error 2 Traceback (most recent call last): File "", line 1, in File "/tmp/pip-req-build-pct5ubbb/setup.py", line 100, in zip_safe=False) File "/home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup return distutils.core.setup(**attrs) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run return orig.install.run(self) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/command/install.py", line 545, in run self.run_command('build') File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/pip-req-build-pct5ubbb/setup.py", line 47, in run self.build_extension(ext) File "/tmp/pip-req-build-pct5ubbb/setup.py", line 76, in build_extension subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp, env=env) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.0/lib/python3.7/subprocess.py", line 328, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j31']' returned non-zero exit status 2. error [?25hCleaning up... Removing source in /tmp/pip-req-build-pct5ubbb Removed build tracker '/tmp/pip-req-tracker-kd9rpz2j' Command "/home/lavery/projects/def-bingalls/lavery/FENICS/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-pct5ubbb/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-lw0_jpxx/install-record.txt --single-version-externally-managed --compile --install-headers /home/lavery/projects/def-bingalls/lavery/FENICS/include/site/python3.7/fenics-dolfin" failed with error code 1 in /tmp/pip-req-build-pct5ubbb/ Exception information: Traceback (most recent call last): File "/home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 143, in main status = self.run(options, args) File "/home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 366, in run use_user_site=options.use_user_site, File "/home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs **kwargs File "/home/lavery/projects/def-bingalls/lavery/FENICS/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 791, in install spinner=spinner, File "/home/lavery/projects/def-bingalls/lavery/FENICS/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/lavery/projects/def-bingalls/lavery/FENICS/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-pct5ubbb/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-lw0_jpxx/install-record.txt --single-version-externally-managed --compile --install-headers /home/lavery/projects/def-bingalls/lavery/FENICS/include/site/python3.7/fenics-dolfin" failed with error code 1 in /tmp/pip-req-build-pct5ubbb/ Compilation exited abnormally with code 1 at Sun Mar 24 11:38:41