Hi all,
I can build dolfin 1.4.0 just fine without petsc4py, but when I include it
it goes until ~98% and then craps out with the error below (truncated).
Any ideas? I'm using SWIG 2.12. CMake output (with command) attached.
Thanks!
In file included from
/soft/python/2.7.3/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1803:0,
from
/soft/python/2.7.3/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from
/soft/python/2.7.3/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:4035:
/soft/python/2.7.3/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by " "#defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject* _wrap_delete_HierarchicalMeshFunctionUInt(PyObject*,
PyObject*)’:
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9612:7:
error: inconsistent user-defined literal suffixes ‘argn’ and ‘type’ in
string literal
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9612:7:
error: unable to find string literal operator ‘operator"" argn’
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject* _wrap_HierarchicalMeshFunctionUInt_depth(PyObject*,
PyObject*)’:
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9658:7:
error: inconsistent user-defined literal suffixes ‘argn’ and ‘type’ in
string literal
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9658:7:
error: unable to find string literal operator ‘operator"" argn’
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject*
_wrap_HierarchicalMeshFunctionUInt_has_parent(PyObject*, PyObject*)’:
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9709:7:
error: inconsistent user-defined literal suffixes ‘argn’ and ‘type’ in
string literal
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9709:7:
error: unable to find string literal operator ‘operator"" argn’
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject*
_wrap_HierarchicalMeshFunctionUInt_has_child(PyObject*, PyObject*)’:
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9755:7:
error: inconsistent user-defined literal suffixes ‘argn’ and ‘type’ in
string literal
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9755:7:
error: unable to find string literal operator ‘operator"" argn’
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject*
_wrap_HierarchicalMeshFunctionUInt__parent__SWIG_0(PyObject*, int,
PyObject**)’:
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9799:7:
error: inconsistent user-defined literal suffixes ‘argn’ and ‘type’ in
string literal
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9799:7:
error: unable to find string literal operator ‘operator"" argn’
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject*
_wrap_HierarchicalMeshFunctionUInt__parent__SWIG_1(PyObject*, int,
PyObject**)’:
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9843:7:
error: inconsistent user-defined literal suffixes ‘argn’ and ‘type’ in
string literal
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9843:7:
error: unable to find string literal operator ‘operator"" argn’
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject*
_wrap_HierarchicalMeshFunctionUInt__child__SWIG_0(PyObject*, int,
PyObject**)’:
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9909:7:
error: inconsistent user-defined literal suffixes ‘argn’ and ‘type’ in
string literal
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9909:7:
error: unable to find string literal operator ‘operator"" argn’
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject*
_wrap_HierarchicalMeshFunctionUInt__child__SWIG_1(PyObject*, int,
PyObject**)’:
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9953:7:
error: inconsistent user-defined literal suffixes ‘argn’ and ‘type’ in
string literal
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:9953:7:
error: unable to find string literal operator ‘operator"" argn’
/home/mwelland/programs/dolfin-1.4.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ‘PyObject*
_wrap_HierarchicalMeshFunctionUInt__root_node__SWIG_0(PyObject*, int,
PyObject**)’:
cmake --prefix=/home/mwelland/fenics-14_petsc4Py
-DCMAKE_INSTALL_PREFIX=/home/mwelland/fenics-14_petsc4Py
-DDOLFIN_ENABLE_CGAL=OFF -DDOLFIN_ENABLE_UNIT_TESTS=OFF
-DDOLFIN_ENABLE_CHOLMOD=OFF -DDOLFIN_ENABLE_PETSC4PY=ON ..
-- The C compiler identification is GNU 4.7.2
-- The CXX compiler identification is GNU 4.7.2
-- Check for working C compiler: /software/mvapich2-gnu-psm-1.9.5/bin/mpicc
-- Check for working C compiler: /software/mvapich2-gnu-psm-1.9.5/bin/mpicc --
works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /software/mvapich2-gnu-psm-1.9.5/bin/mpicxx
-- Check for working CXX compiler: /software/mvapich2-gnu-psm-1.9.5/bin/mpicxx
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
fatal: Not a git repository (or any parent up to mount point /fusion/gpfs)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_STD_CPP11
-- Performing Test HAVE_STD_CPP11 - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler:
/software/mvapich2-gnu-psm-1.9.5/bin/mpif90
-- Check for working Fortran compiler:
/software/mvapich2-gnu-psm-1.9.5/bin/mpif90 -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /software/mvapich2-gnu-psm-1.9.5/bin/mpif90 supports
Fortran 90
-- Checking whether /software/mvapich2-gnu-psm-1.9.5/bin/mpif90 supports
Fortran 90 -- yes
-- 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 size_t
-- Check size of size_t - done
-- Found MPI_C:
/software/mvapich2-gnu-psm-1.9.5/lib/libmpich.so;/software/mvapich2-gnu-psm-1.9.5/lib/libopa.so;/software/mvapich2-gnu-psm-1.9.5/lib/libmpl.so;/usr/lib64/libpsm_infinipath.so;/usr/lib64/libm.so;/usr/lib64/libpthread.so
-- Found MPI_CXX:
/software/mvapich2-gnu-psm-1.9.5/lib/libmpichcxx.so;/software/mvapich2-gnu-psm-1.9.5/lib/libmpich.so;/software/mvapich2-gnu-psm-1.9.5/lib/libopa.so;/software/mvapich2-gnu-psm-1.9.5/lib/libmpl.so;/usr/lib64/libpsm_infinipath.so;/usr/lib64/libm.so;/usr/lib64/libpthread.so
-- Found MPI_Fortran:
/software/mvapich2-gnu-psm-1.9.5/lib/libmpichf90.so;/software/mvapich2-gnu-psm-1.9.5/lib/libmpich.so;/software/mvapich2-gnu-psm-1.9.5/lib/libopa.so;/software/mvapich2-gnu-psm-1.9.5/lib/libmpl.so;/usr/lib64/libpsm_infinipath.so;/usr/lib64/libm.so;/usr/lib64/libpthread.so
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Performing Test OPENMP_UINT_TEST_RUNS
-- Performing Test OPENMP_UINT_TEST_RUNS - Success
-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- thread
-- iostreams
-- UFC version: 1.4.0
-- Found Eigen3: /home/mwelland/local_gnu_sequential/include/eigen3 (Required
is at least version "3.0.0")
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6")
-- Found PythonInterp: /soft/python/2.7.3/bin/python2 (found suitable version
"2.7.3", minimum required is "2")
-- NumPy header version 1.9.0.dev-e3794e7 found
-- Found SWIG: /home/mwelland/local_gnu_sequential/bin/swig (found version
"2.0.12")
-- Checking for package 'PETSc'
-- PETSC_DIR is /home/mwelland/local_gnu_sequential
-- PETSC_ARCH is empty
-- Found petscconf.h
-- Include directory /usr/bin/include does not exist
-- Unable to find library gfortran
-- Performing test PETSC_TEST_RUNS - Success
-- Performing Test PETSC_CUSP_FOUND
-- Performing Test PETSC_CUSP_FOUND - Failed
-- PETSc configured without Cusp support
-- Found PETSc: /home/mwelland/local_gnu_sequential/lib/libpetsc.so (Required
is at least version "3.3")
-- Checking for package 'SLEPc'
-- SLEPC_DIR is SLEPC_DIR-NOTFOUND
-- SLEPc could not be found. Be sure to set SLEPC_DIR, PETSC_DIR, and
PETSC_ARCH. (missing: SLEPC_LIBRARIES SLEPC_DIR SLEPC_INCLUDE_DIRS
SLEPC_TEST_RUNS SLEPC_VERSION SLEPC_VERSION_OK) (Required is at least version
"3.3")
-- Checking for package 'PETSc4Py'
-- petsc4py version 3.4 found
-- Performing Test PARMETIS_TEST_RUNS
-- Performing Test PARMETIS_TEST_RUNS - Success
-- Found ParMETIS:
/home/mwelland/local_gnu_sequential/lib/libparmetis.so;/home/mwelland/local_gnu_sequential/lib/libmetis.so
(Required is at least version "4.0.2")
-- Checking for package 'SCOTCH-PT'
-- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing:
SCOTCH_LIBRARIES SCOTCH_TEST_RUNS)
-- Checking for package 'AMD'
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Performing Test UMFPACK_TEST_RUNS
-- Performing Test UMFPACK_TEST_RUNS - Success
-- Found HDF5:
/home/mwelland/local_gnu_sequential/lib/libhdf5.a;/soft/mkl/11.0.5.192/mkl/lib/intel64/libmkl_scalapack_lp64.so;/soft/mkl/11.0.5.192/mkl/lib/intel64/libmkl_intel_lp64.so;/soft/mkl/11.0.5.192/mkl/lib/intel64/libmkl_core.so;/soft/mkl/11.0.5.192/mkl/lib/intel64/libmkl_sequential.so;/soft/mkl/11.0.5.192/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so;/usr/lib64/libpthread.so;/usr/lib64/libm.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so
-- PASTIX_LIBRARIES
PASTIX_LIBRARY-NOTFOUND;/usr/lib64/librt.so;/usr/lib64/libm.so
-- A library with BLAS API found.
-- PaStiX could not be found. Be sure to set PASTIX_DIR. (missing:
PASTIX_INCLUDE_DIRS PASTIX_TEST_RUNS PASTIX_VERSION PASTIX_VERSION_OK)
-- Checking for Trilinos
-- Unable to find Trilinos (>= 11.0.0)
-- Trilinos could not be found
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Checking for package 'Sphinx'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE SPHINX_VERSION_OK)
(Required is at least version "1.1.0")
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /home/mwelland/local_gnu_sequential/bin/qmake (found version
"4.8.6")
-- Found VTK: /soft/vtk/5.6.0/lib/vtk-5.6 (found version "5.6")
--
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) PETSC4PY
-- (OK) UMFPACK
-- (OK) PARMETIS
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) HDF5
-- (OK) VTK
-- (OK) QT
--
-- The following optional packages were not enabled:
-- -------------------------------------------------
-- (--) CHOLMOD
-- (--) CGAL
--
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) SLEPC
-- (**) TRILINOS
-- (**) PASTIX
-- (**) SCOTCH
-- (**) SPHINX
--
makde--
-- Generating SWIG interface.
-- --------------------------
-- Found Qt4: /home/mwelland/local_gnu_sequential/bin/qmake (found version
"4.8.6")
-- Disabling generation of documentation because Sphinx is missing.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mwelland/programs/dolfin-1.4.0/build
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