I've tried to install fenics using dorsal. To make PETSc 3.4.2 work with fenics I've set STABLE_BUILD=false in dorsal.cfg as indicated by http://fenicsproject.org/qa/1769/problem-installation-using-dorsal. Installation seems to work fine: Trilinos seems to work but not PETSc. Even if petsc library was build, when I try to use PETS, it is not available as linear algebra backend within the fenics environment and looking to the dolfing-config.cmake petsc library is not linked.
Looking at the dorsal_configure_log in src/dolfin/ -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Performing Test HAVE_PIPE -- Performing Test HAVE_PIPE - Success -- Performing Test HAVE_PEDANTIC -- Performing Test HAVE_PEDANTIC - Success -- Performing Test HAVE_STD -- Performing Test HAVE_STD - 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: /usr/bin/gfortran -- Check for working Fortran compiler: /usr/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes -- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-linux-gnu/libnsl.so;/usr/lib/i386-linux-gnu/libutil.so;/usr/lib/i386-linux-gnu/libm.so;/usr/lib/i386-linux-gnu/libdl.so -- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-linux-gnu/libnsl.so;/usr/lib/i386-linux-gnu/libutil.so;/usr/lib/i386-linux-gnu/libm.so;/usr/lib/i386-linux-gnu/libdl.so -- Found MPI_Fortran: /usr/lib/openmpi/lib/libmpi_f90.so;/usr/lib/openmpi/lib/libmpi_f77.so;/usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-linux-gnu/libnsl.so;/usr/lib/i386-linux-gnu/libutil.so;/usr/lib/i386-linux-gnu/libm.so;/usr/lib/i386-linux-gnu/libdl.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: 1.46.1 -- Found the following Boost libraries: -- filesystem -- program_options -- system -- thread -- iostreams -- mpi -- serialization -- UFC version: 2.2.0+ -- Found Eigen3: /usr/include/eigen3 (Required is at least version "3.0.0") -- Found LibXml2: /usr/lib/i386-linux-gnu/libxml2.so -- Found PythonInterp: /usr/bin/python (found suitable version "2.7.3", required is "2") -- NumPy header version 1.6.1 found -- Found SWIG: /usr/bin/swig2.0 (found version "2.0.4") -- Checking for package 'PETSc' -- PETSC_DIR is /home/mcarini/Research/Software/FEniCS -- PETSC_ARCH is empty -- Found petscconf.h -- Performing test PETSC_TEST_RUNS - Failed -- Performing test PETSC_TEST_3RD_PARTY_LIBS_RUNS - Failed -- Performing Test PETSC_CUSP_FOUND -- Performing Test PETSC_CUSP_FOUND - Failed -- PETSc configured without Cusp support -- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. (missing: PETSC_TEST_RUNS) (Required is at least version "3.2") -- Performing Test PARMETIS_TEST_RUNS -- Performing Test PARMETIS_TEST_RUNS - Success -- Found ParMETIS: /home/mcarini/Research/Software/FEniCS/lib/libparmetis.so;/home/mcarini/Research/Software/FEniCS/lib/libmetis.so (Required is at least version "4.0.2") -- Checking for package 'SCOTCH-PT' -- Found SCOTCH (version 6.0.0) -- Performing test SCOTCH_TEST_RUNS -- Performing test SCOTCH_TEST_RUNS - Success -- Found SCOTCH: /usr/lib/libptscotch.so;/usr/lib/libscotch.so;/usr/lib/libptscotcherr.so -- Checking for package 'AMD' -- Looking for Fortran dgemm -- Looking for Fortran dgemm - found -- Looking for include files CMAKE_HAVE_PTHREAD_H -- Looking for include files CMAKE_HAVE_PTHREAD_H - found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Checking for package 'UMFPACK' -- Checking for package 'AMD' -- Checking for package 'CHOLMOD' -- Checking for package 'AMD' -- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Performing Test CHOLMOD_TEST_RUNS -- Performing Test CHOLMOD_TEST_RUNS - Success -- Performing Test UMFPACK_TEST_RUNS -- Performing Test UMFPACK_TEST_RUNS - Success -- Checking for package 'CHOLMOD' -- Checking for package 'AMD' -- A library with BLAS API found. -- Found HDF5: debug;/usr/lib/libhdf5.so;optimized;/usr/lib/libhdf5.so -- PASTIX_LIBRARIES /home/mcarini/Research/Software/FEniCS/lib/libpastix.a;/usr/lib/i386-linux-gnu/librt.so;/usr/lib/i386-linux-gnu/libm.so -- A library with BLAS API found. -- Performing Test PASTIX_TEST_RUNS -- Performing Test PASTIX_TEST_RUNS - Success -- PaStiX could not be found. Be sure to set PASTIX_DIR. (missing: PASTIX_VERSION_OK) -- Checking for Trilinos -- Trilinos version 11.4.1 found. Checking for components -- Epetra found -- Zoltan found -- ML found -- Ifpack found -- Amesos found -- All necessary Trilinos components found. Trilinos will be enabled. -- Checking for package 'CGAL' -- Performing Test CGAL_TEST_RUNS -- Performing Test CGAL_TEST_RUNS - Success -- Found CGAL: /home/mcarini/Research/Software/FEniCS/lib/libCGAL.so;/usr/lib/libboost_thread-mt.so;pthread;/usr/lib/libboost_system-mt.so;/usr/lib/i386-linux-gnu/libgmp.so;/usr/lib/i386-linux-gnu/libmpfr.so (Required is at least version "4.1") -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.2.3.4") -- checking for module 'cppunit' -- found cppunit, version 1.12.1 -- Found CPPUNIT: /usr/lib/libcppunit.so -- 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: /usr/bin/qmake (found version "4.8.1") -- Found VTK: /usr/lib/vtk-5.8 (found version "5.8") -- -- The following optional packages were found: -- ------------------------------------------- -- (OK) OPENMP -- (OK) MPI -- (OK) TRILINOS -- (OK) UMFPACK -- (OK) CHOLMOD -- (OK) SCOTCH -- (OK) PARMETIS -- (OK) CGAL -- (OK) ZLIB -- (OK) PYTHON -- (OK) HDF5 -- (OK) VTK -- (OK) QT -- -- The following optional packages were not found: -- ----------------------------------------------- -- (**) PETSC -- (**) PETSC4PY -- (**) SLEPC -- (**) TAO -- (**) PASTIX -- (**) SPHINX -- -- QVTK not found, disabling QT for plotting -- -- Generating SWIG interface. -- -------------------------- -- -- Generating form files in demo, test, bench and dolfin directories. May take some time... -- ---------------------------------------------------------------------------------------- -- -- Generating CMakeLists.txt files in demo, test and bench directories -- ------------------------------------------------------------------- -- -- Download demo and test data. May take some time... -- -------------------------------------------------- -- -- Copying demo and test data to build directory. -- ---------------------------------------------- -- Found Qt4: /usr/bin/qmake (found version "4.8.1") -- QT not found, or QT/VTK not enabled in DOLFIN. Not building demo_plot-qt -- Disabling generation of documentation because Sphinx is missing. -- Configuring done The environmet variable PETSC_ARCH is unset and I found that in "fenics-project-dorsal-f2c6a9148cdd/FEniCS/packages/petsc.package" : NAME=petsc-3.4.2 SOURCE=http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/ PACKING=.tar.gz BUILDCHAIN=custom CONFOPTS="COPTFLAGS=-O2 --with-debugging=0 --with-shared-libraries=1 --with-clanguage=cxx --with-c-support=1" for external_pkg in umfpack hypre mumps scalapack blacs ptscotch scotch metis parmetis pastix; do CONFOPTS="${CONFOPTS} --download-${external_pkg}=1" done if [ "${TRILINOS_DIR}" ]; then CONFOPTS="${CONFOPTS} --with-ml=1 --with-ml-lib=${TRILINOS_DIR}/lib/libml.so --with-ml-include=${TRILINOS_DIR}/include/trilinos" fi if [ "${CUDA_DIR}" ] && [ "${CUSP_DIR}" ]; then CONFOPTS="${CONFOPTS} --with-cuda=1 --with-cuda-dir=${CUDA_DIR} --with-cusp=1 --with-cusp-dir=${CUSP_DIR} --with-thrust=1 --with-thrust-dir=${CUDA_DIR}/include" fi package_specific_build () { ./configure --prefix=${INSTALL_PATH} ${CONFOPTS} make PETSC_DIR=${PWD} PETSC_ARCH=${PETSC_ARCH} all make PETSC_DIR=${PWD} PETSC_ARCH=${PETSC_ARCH} install } package_specific_register () { export PETSC_DIR=${INSTALL_PATH} unset PETSC_ARCH } PETSC_ARCH is unset as well as in petsccore.package Also PASTIX_VERSION_OK is unset What I have to do ? Should I modify the environment variable and redo the installation from scratch? Thank you
_______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
