Supported combinations are - either DOLFIN 1.4.0 + PETSc 3.3,3.4 - or DOLFIN dev + PETSc 3.3,3.4,3.5,dev
You can install FEniCS dev version by setting STABLE_BUILD=false in dorsal.cfg. Jan On Tue, 04 Nov 2014 10:52:40 +0100 Serge Van Criekingen <[email protected]> wrote: > Hello, > > I recently updated my PETSc install to the 3.5.2 version, and tried > to recompile FEniCS after this. > Everything goes right up to the building phase, where I run into > errors, the first one being this one: > > > [ 28%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/la/PETScKrylovSolver.cpp.o > > > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp: > > In member function ‘void > dolfin::PETScKrylovSolver::set_petsc_operators()’: > > > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp: > > 528:62: erreur: ‘SAME_PRECONDITIONER’ was not declared in this > > scope ierr = KSPSetOperators(_ksp, _matA->mat(), _matP->mat(), > SAME_PRECONDITIONER); > > The full dorsal output can be found below. > I would greatly appreciate a hint on what is the best way to go over > this problem. > Thank you very much, > Serge > > --------------------- > > > ./dorsal.sh FEniCS/platforms/supported/opensuse11.3.platform > Found configuration for project FEniCS. > Skipping parmetis-4.0.2 > Skipping SuiteSparse-4.0.2 > Skipping scotch_6.0.0_esmumps > Skipping ScientificPython-2.8 > Skipping fiat-1.4.0 > Skipping ufl-1.4.0 > Skipping ffc-1.4.0 > Skipping instant-1.4.0 > Fetching dolfin-1.4.0 > Verifying dolfin-1.4.0 > dolfin-1.4.0.tar.gz: OK > Unpacking dolfin-1.4.0 > Building dolfin-1.4.0 > -- The C compiler identification is GNU 4.9.1 > -- The CXX compiler identification is GNU 4.9.1 > -- Check for working C compiler: /home/zatopek/gcc/MyInstall/bin/gcc > -- Check for working C compiler: /home/zatopek/gcc/MyInstall/bin/gcc > -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working CXX compiler: /home/zatopek/gcc/MyInstall/bin/g++ > -- Check for working CXX > compiler: /home/zatopek/gcc/MyInstall/bin/g++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > fatal: Not a git repository (or any parent up to mount point /home) > 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: > /home/zatopek/gcc/MyInstall/bin/gfortran > -- Check for working Fortran compiler: > /home/zatopek/gcc/MyInstall/bin/gfortran -- works > -- Detecting Fortran compiler ABI info > -- Detecting Fortran compiler ABI info - done > -- Checking whether /home/zatopek/gcc/MyInstall/bin/gfortran supports > Fortran 90 > -- Checking whether /home/zatopek/gcc/MyInstall/bin/gfortran 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: > /opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so > -- Found MPI_CXX: > /opt/openmpi/lib/libmpi_cxx.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so > -- Found MPI_Fortran: > /opt/openmpi/lib/libmpi_f90.so;/opt/openmpi/lib/libmpi_f77.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.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: 1.56.0 > -- Found the following Boost libraries: > -- filesystem > -- program_options > -- system > -- thread > -- iostreams > -- UFC version: 1.4.0 > -- Found Eigen3: /home/zatopek/Eigen3/eigen-eigen-1306d75b4a21 > (Required is at least version "3.0.0") > -- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6") > -- Found PythonInterp: /home/zatopek/Python/MyInstall/bin/python > (found suitable version "2.7.8", minimum required is "2") > -- NumPy header version 1.8.1 found > -- Found SWIG: /home/zatopek/swig-2.0.12/MyInstall/bin/swig (found > version "2.0.12") > -- Checking for package 'PETSc' > -- PETSC_DIR is /home/zatopek/PETSc/petsc-3.5.2-opt > -- PETSC_ARCH is arch-linux2-c-opt > -- Found petscconf.h > -- Include directory /home/zatopek/PETSc/petsc-3.5.2/include does not > exist -- Include directory > /home/zatopek/PETSc/petsc-3.5.2/arch-linux2-c-opt/include does not > exist -- 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/zatopek/PETSc/petsc-3.5.2-opt/arch-linux2-c-opt/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 3.5 found > -- Performing Test PARMETIS_TEST_RUNS > -- Performing Test PARMETIS_TEST_RUNS - Success > -- Found ParMETIS: > /home/zatopek/FenicsProject/MyInstall/lib/libparmetis.so;/home/zatopek/FenicsProject/MyInstall/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: > /home/zatopek/FenicsProject/MyInstall/lib/libptscotch.a;/home/zatopek/FenicsProject/MyInstall/lib/libscotch.a;/home/zatopek/FenicsProject/MyInstall/lib/libptscotcherr.a > -- 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' > -- 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: > /usr/lib64/libhdf5.so;/usr/lib64/libpthread.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so > -- HDF5 has been found, but is missing parallel support. It will not > be enabled. > -- 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 > -- Checking for package 'CGAL' > -- Performing Test CGAL_TEST_RUNS > -- Performing Test CGAL_TEST_RUNS - Failed > -- CGAL could not be found. Be sure to set CGAL_DIR (missing: > CGAL_TEST_RUNS) (Required is at least version "4.1") > -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7") > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.23") > -- checking for module 'cppunit' > -- package 'cppunit' not found > -- CPPUNIT could not be found. Be sure to set CPPUNIT_DIR. (missing: > CPPUNIT_LIBRARIES CPPUNIT_INCLUDE_DIRS) > -- Checking for package 'Sphinx' > -- Found Sphinx: /home/zatopek/Sphinx/MyInstall/bin/sphinx-build > (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 "4.6.3") > -- Found VTK: /home/zatopek/VTK/MyInstall/lib/cmake/vtk-6.1 (found > version "6.1") > -- > -- The following optional packages were found: > -- ------------------------------------------- > -- (OK) OPENMP > -- (OK) MPI > -- (OK) PETSC > -- (OK) PETSC4PY > -- (OK) UMFPACK > -- (OK) CHOLMOD > -- (OK) SCOTCH > -- (OK) PARMETIS > -- (OK) ZLIB > -- (OK) PYTHON > -- (OK) SPHINX > -- (OK) VTK > -- (OK) QT > -- > -- The following optional packages were not found: > -- ----------------------------------------------- > -- (**) SLEPC > -- (**) TRILINOS > -- (**) PASTIX > -- (**) CGAL > -- (**) HDF5 > -- > -- > -- Generating SWIG interface. > -- -------------------------- > -- Found Qt4: /usr/bin/qmake (found version "4.6.3") > -- Enabling generation of documentation. > -- Initializing sphinx projects > -- Enabling generation of html-documentation > -- Configuring done > -- Generating done > CMake Warning: > Manually-specified variables were not used by the project: > > CGAL_DISABLE_ROUNDING_MATH_CHECK > > > -- Build files have been written to: > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > make: entrant dans le répertoire « > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > » > make[1]: entrant dans le répertoire « > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > » > make[2]: entrant dans le répertoire « > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > » > Scanning dependencies of target dolfin > make[2]: quittant le répertoire « > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > » > make[2]: entrant dans le répertoire « > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > » > [ 1%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/PolyhedronUtils.cpp.o > [ 1%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/UnitTetrahedronMesh.cpp.o > [ 1%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/ImplicitDomainMeshGenerator.cpp.o > [ 2%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/CSGOperators.cpp.o > [ 2%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/GeometryToCGALConverter.cpp.o > [ 2%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/BoxMesh.cpp.o > [ 2%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/CSGCGALMeshGenerator3D.cpp.o > [ 3%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/EllipseMesh.cpp.o > [ 3%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/CSGGeometry.cpp.o > [ 3%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/CSGPrimitives2D.cpp.o > [ 5%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/RectangleMesh.cpp.o > [ 5%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/CSGGeometries3D.cpp.o > [ 5%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/UnitTriangleMesh.cpp.o > [ 6%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/IntervalMesh.cpp.o > [ 6%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/EllipsoidMesh.cpp.o > [ 6%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/CSGMeshGenerator.cpp.o > [ 6%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/generation/Triangulate.cpp.o > [ 7%] Building CXX object 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/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp: > > In member function ‘void > dolfin::PETScKrylovSolver::set_petsc_operators()’: > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:528:62: > > erreur: ‘SAME_PRECONDITIONER’ was not declared in this scope > ierr = KSPSetOperators(_ksp, _matA->mat(), _matP->mat(), > SAME_PRECONDITIONER); > ^ > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:533:82: > > erreur: too many arguments to function ‘PetscErrorCode > KSPSetOperators(KSP, Mat, Mat)’ > ierr = KSPSetOperators(_ksp, _matA->mat(), _matP->mat(), > SAME_NONZERO_PATTERN); > ^ > In file included from > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScUserPreconditioner.h:29:0, > from > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:39: > /home/zatopek/PETSc/MyInstall/include/petscksp.h:260:29: note: > declared here PETSC_EXTERN PetscErrorCode > KSPSetOperators(KSP,Mat,Mat); ^ > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:539:53: > > erreur: too many arguments to function ‘PetscErrorCode > KSPSetOperators(KSP, Mat, Mat)’ > DIFFERENT_NONZERO_PATTERN); > ^ > In file included from > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScUserPreconditioner.h:29:0, > from > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:39: > /home/zatopek/PETSc/MyInstall/include/petscksp.h:260:29: note: > declared here PETSC_EXTERN PetscErrorCode > KSPSetOperators(KSP,Mat,Mat); ^ > make[2]: *** > [dolfin/CMakeFiles/dolfin.dir/la/PETScKrylovSolver.cpp.o] Erreur 1 > make[2]: quittant le répertoire « > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > » > make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Erreur 2 > make[1]: quittant le répertoire « > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > » > make: *** [all] Erreur 2 > make: quittant le répertoire « > /home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir > » > Failure with exit status: 2 > Exit message: There was a problem building dolfin-1.4.0. > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
