I have compiled libmesh on mac osx 10.8 using packages from macports. My macports is in standard location /opt/local. PETSC and SLEPC are enabled by setting variables
$ echo $PETSC_DIR /opt/local/lib/petsc $ echo $SLEPC_DIR /opt/local/lib/petsc This is my configure VER=0.9.2.1 VTK=5.10 ./configure \ --prefix=$HOME/Applications/libmesh/install-$VER \ --enable-examples \ --enable-mpi \ --enable-perflog \ --disable-tecplot \ --enable-tecio \ --enable-nodeconstraint \ --enable-blocked-storage \ --disable-trilinos \ --with-glpk-include=/opt/local/include \ --with-glpk-lib=/opt/local/lib \ --with-hdf5=/opt/local \ --with-vtk-include=/opt/local/include/vtk-$VTK \ --with-vtk-lib=/opt/local/lib/vtk-$VTK \ --with-tbb=/opt/local \ CXX=openmpicxx CC=openmpicc FC=openmpif90 F77=openmpif90 \ CXXFLAGS=-I/usr/X11/include LDFLAGS=-L/usr/X11/lib On Wed, Sep 18, 2013 at 12:39 PM, Vera Franziska Loeser < [email protected]> wrote: > Hi, > > well, I had to set the PETSC_DIR and SLEPC_DIR. > export PETSC_DIR=/macports/lib/petsc > export SLEPC_DIR=/macports/lib/petsc > > And, as you said, now I have Problems with MPI. > At first I tried without MPI and got the following errors (so the same > configure command): > > Undefined symbols for architecture x86_64: > "MPI::Win::Free()", referenced from: > vtable for MPI::Win in getpot_parse_dbg-getpot_parse.o > "MPI::Comm::Comm()", referenced from: > MPI::Intracomm::Intracomm() in getpot_parse_dbg-getpot_parse.o > MPI::Intracomm::Intracomm(ompi_communicator_t*) in > getpot_parse_dbg-getpot_parse.o > "MPI::Datatype::Free()", referenced from: > vtable for MPI::Datatype in getpot_parse_dbg-getpot_parse.o > "_ompi_mpi_cxx_op_intercept", referenced from: > MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype > const&), bool) in getpot_parse_dbg-getpot_parse.o > ld: symbol(s) not found for architecture x86_64 > collect2: error: ld returned 1 exit status > make[1]: *** [getpot_parse-dbg] Error 1 > make[1]: *** Waiting for unfinished jobs.... > > Next I tried with the openmpi path (that openmpi that macports used to > install pets I think) and got the following errors by typing > ../configure --prefix=/Users/vera/Desktop/libmesh_root/installed > --with-glpk-include=/macports/include > --with-glpk-lib=/macports/lib > --with-eigen-include=/macports/include/eigen3/Eigen > --with-mpi-dir=/macports/lib/openmpi > --enable-petsc > --enable-slepc > > Undefined symbols for architecture x86_64: > "MPI::Win::Free()", referenced from: > vtable for MPI::Win in getpot_parse_opt-getpot_parse.o > "MPI::Comm::Comm()", referenced from: > MPI::Intracomm::Clone() const in getpot_parse_opt-getpot_parse.o > MPI::Graphcomm::Clone() const in getpot_parse_opt-getpot_parse.o > MPI::Cartcomm::Sub(bool const*) const in > getpot_parse_opt-getpot_parse.o > MPI::Intracomm::Create_graph(int, int const*, int const*, bool) > const in getpot_parse_opt-getpot_parse.o > MPI::Cartcomm::Clone() const in getpot_parse_opt-getpot_parse.o > MPI::Intercomm::Merge(bool) const in getpot_parse_opt-getpot_parse.o > MPI::Intracomm::Create(MPI::Group const&) const in > getpot_parse_opt-getpot_parse.o > ... > "MPI::Datatype::Free()", referenced from: > vtable for MPI::Datatype in getpot_parse_opt-getpot_parse.o > "_ompi_mpi_cxx_op_intercept", referenced from: > MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype > const&), bool) in getpot_parse_opt-getpot_parse.o > ld: symbol(s) not found for architecture x86_64 > collect2: error: ld returned 1 exit status > make[1]: *** [getpot_parse-opt] Error 1 > make: *** [all-recursive] Error 1 > > > > > Now my configuration looks like that: > > --------------------------------------------- > ----------- Configuring libMesh ------------- > --------------------------------------------- > checking build system type... x86_64-apple-darwin12.5.0 > checking host system type... x86_64-apple-darwin12.5.0 > checking target system type... x86_64-apple-darwin12.5.0 > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... ../build-aux/install-sh -c -d > checking for gawk... no > checking for mawk... no > checking for nawk... no > checking for awk... awk > checking whether make sets $(MAKE)... yes > checking how to create a ustar tar archive... gnutar > checking whether make supports nested variables... yes > checking whether to enable maintainer-specific portions of Makefiles... yes > checking for src/base/libmesh.C... no > <<< Configuring build directory for VPATH build >>> > checking for style of include used by make... GNU > checking for mpicxx... no > checking for mpiCC... no > checking for mpicc... no > checking for g++... g++ > checking whether the C++ compiler works... yes > checking for C++ compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C++ compiler... yes > checking whether g++ accepts -g... yes > checking dependency style of g++... gcc3 > <<< C++ compiler is gcc-4.8 >>> > checking for mpicc... no > checking for gcc... gcc > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking dependency style of gcc... gcc3 > checking for mpif90... no > checking for gfortran... gfortran > checking whether we are using the GNU Fortran compiler... yes > checking whether gfortran accepts -g... yes > checking for mpif77... no > checking for gfortran... gfortran > checking whether we are using the GNU Fortran 77 compiler... yes > checking whether gfortran accepts -g... yes > << Disabling GLIBCXX debugging on Darwin >>> > No build methods specified, defaulting to "dbg devel opt" > <<< Configuring libMesh with methods "dbg devel opt" >>> > checking how to print strings... printf > checking for a sed that does not truncate output... /usr/bin/sed > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for fgrep... /usr/bin/grep -F > checking for ld used by gcc... /macports/bin/ld > checking if the linker (/macports/bin/ld) is GNU ld... no > checking for BSD- or MS-compatible name lister (nm)... /macports/bin/nm > checking the name lister (/macports/bin/nm) interface... BSD nm > checking whether ln -s works... yes > checking the maximum length of command line arguments... 196608 > checking whether the shell understands some XSI constructs... yes > checking whether the shell understands "+="... yes > checking how to convert x86_64-apple-darwin12.5.0 file names to > x86_64-apple-darwin12.5.0 format... func_convert_file_noop > checking how to convert x86_64-apple-darwin12.5.0 file names to toolchain > format... func_convert_file_noop > checking for /macports/bin/ld option to reload object files... -r > checking for objdump... no > checking how to recognize dependent libraries... pass_all > checking for dlltool... no > checking how to associate runtime and link libraries... printf %s\n > checking for ar... ar > checking for archiver @FILE support... no > checking for strip... strip > checking for ranlib... ranlib > checking command to parse /macports/bin/nm output from gcc object... ok > checking for sysroot... no > checking for mt... no > checking if : is a manifest tool... no > checking for dsymutil... dsymutil > checking for nmedit... nmedit > checking for lipo... lipo > checking for otool... otool > checking for otool64... no > checking for -single_module linker flag... yes > checking for -exported_symbols_list linker flag... yes > checking for -force_load linker flag... yes > checking how to run the C preprocessor... gcc -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for dlfcn.h... yes > checking for objdir... .libs > checking if gcc supports -fno-rtti -fno-exceptions... no > checking for gcc option to produce PIC... -fno-common -DPIC > checking if gcc PIC flag -fno-common -DPIC works... yes > checking if gcc static flag -static works... no > checking if gcc supports -c -o file.o... yes > checking if gcc supports -c -o file.o... (cached) yes > checking whether the gcc linker (/macports/bin/ld) supports shared > libraries... yes > checking dynamic linker characteristics... darwin12.5.0 dyld > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... no > checking how to run the C++ preprocessor... g++ -E > checking for ld used by g++... /macports/bin/ld > checking if the linker (/macports/bin/ld) is GNU ld... no > checking whether the g++ linker (/macports/bin/ld) supports shared > libraries... yes > checking for g++ option to produce PIC... -fno-common -DPIC > checking if g++ PIC flag -fno-common -DPIC works... yes > checking if g++ static flag -static works... no > checking if g++ supports -c -o file.o... yes > checking if g++ supports -c -o file.o... (cached) yes > checking whether the g++ linker (/macports/bin/ld) supports shared > libraries... yes > checking dynamic linker characteristics... darwin12.5.0 dyld > checking how to hardcode library paths into programs... immediate > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... no > checking for gfortran option to produce PIC... -fno-common > checking if gfortran PIC flag -fno-common works... yes > checking if gfortran static flag -static works... no > checking if gfortran supports -c -o file.o... yes > checking if gfortran supports -c -o file.o... (cached) yes > checking whether the gfortran linker (/macports/bin/ld) supports shared > libraries... yes > checking dynamic linker characteristics... darwin12.5.0 dyld > checking how to hardcode library paths into programs... immediate > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... no > checking for gfortran option to produce PIC... -fno-common > checking if gfortran PIC flag -fno-common works... yes > checking if gfortran static flag -static works... no > checking if gfortran supports -c -o file.o... yes > checking if gfortran supports -c -o file.o... (cached) yes > checking whether the gfortran linker (/macports/bin/ld) supports shared > libraries... yes > checking dynamic linker characteristics... darwin12.5.0 dyld > checking how to hardcode library paths into programs... immediate > checking Major version... 0 > checking Minor version... 9 > checking Point version... 3 > checking whether ln -s works... yes > checking for a sed that does not truncate output... (cached) /usr/bin/sed > checking for perl... /macports/bin/perl > checking for pkg-config... no > checking whether the compiler implements namespaces... yes > --------------------------------------------- > ------- Configuring compiler features ------- > --------------------------------------------- > <<< Default floating point is double precision (double) >>> > checking for C/C++ restrict keyword... __restrict > <<< Configuring library with getpwuid >>> > <<< Configuring library with exception throwing support >>> > checking size of short int... 2 > checking size of int... 4 > checking size of unsigned int... 4 > checking size of long int... 8 > checking size of float... 4 > checking size of double... 8 > checking size of void *... 8 > checking size of function_pointer... 8 > checking whether the compiler supports Run-Time Type Identification... yes > checking getopt.h usability... yes > checking getopt.h presence... yes > checking for getopt.h... yes > checking csignal usability... yes > checking csignal presence... yes > checking for csignal... yes > checking sys/resource.h usability... yes > checking sys/resource.h presence... yes > checking for sys/resource.h... yes > checking whether the compiler has locale... yes > checking whether the compiler has stringstream... yes > checking fenv.h usability... yes > checking fenv.h presence... yes > checking for fenv.h... yes > checking xmmintrin.h usability... yes > checking xmmintrin.h presence... yes > checking for xmmintrin.h... yes > checking whether the compiler supports std::unordered_multimap... no > checking whether the compiler supports std::tr1::unordered_multimap... yes > checking whether the compiler supports std::unordered_map... no > checking whether the compiler supports std::tr1::unordered_map... yes > checking whether the compiler supports std::unordered_set... no > checking whether the compiler supports std::tr1::unordered_set... yes > checking for dlfcn.h... (cached) yes > checking whether the compiler supports GCC C++ ABI name demangling... yes > checking whether the c++ compiler supports glibc backtrace... yes > checking for OpenMP flag of C++ compiler... -fopenmp > <<< Configuring library with OpenMP support >>> > --------------------------------------------- > ----- Done configuring compiler features ---- > --------------------------------------------- > --------------------------------------------- > ----- Configuring core library features ----- > --------------------------------------------- > >>> WARNING: using a legacy option <<< > >>> Configuring library to enable a default libMesh::CommWorld <<< > <<< Configuring library to require ``include "libmesh/etc.h"'' style >>> > <<< Configuring library to keep names in libMesh namespace >>> > configuring size of boundary_id... 2 > configuring size of dof_id... 4 > configuring size of processor_id... 2 > configuring size of subdomain_id... 2 > <<< Configuring library with AMR support >>> > <<< Configuring library with variational smoother support >>> > <<< Configuring library with periodic BC support >>> > <<< Configuring library with Dirichlet constraint support >>> > <<< Configuring library to use ghosted local vectors >>> > <<< Configuring library with higher order p-FEM shapes >>> > <<< Configuring library with second derivatives >>> > checking rpc/rpc.h usability... yes > checking rpc/rpc.h presence... yes > checking for rpc/rpc.h... yes > checking for xdrstdio_create... yes > <<< Configuring library with XDR support >>> > <<< Configuring library with real number support >>> > <<< Configuring library with reference counting support >>> > <<< Configuring library example suite support >>> > --------------------------------------------- > -- Done configuring core library features --- > --------------------------------------------- > --------------------------------------------- > ----- Configuring for optional packages ----- > --------------------------------------------- > checking for boostlib >= 1.20.0... configure: We could not detect the > boost libraries (version 1.20 or higher). If you have a staged boost > library (still not installed) please specify $BOOST_ROOT in your > environment and do not give a PATH to --with-boost option. If you are sure > you have boost installed, then check your version number looking in > <boost/version.hpp>. See http://randspringer.de/boost for more > documentation. > <<< External boost installation *not* found... will try to configure for > libmesh's internal boost >>> > checking for boostlib >= 1.20.0... yes > <<< Using libmesh-provided boost in ./contrib >>> > checking /macports/lib/petsc/include/petscversion.h usability... yes > checking /macports/lib/petsc/include/petscversion.h presence... yes > checking for /macports/lib/petsc/include/petscversion.h... yes > <<< Configuring library with MPI from PETSC config >>> > <<< Configuring library with PETSc version 3.3.0 support >>> > checking /macports/lib/petsc/include/slepcversion.h usability... yes > checking /macports/lib/petsc/include/slepcversion.h presence... yes > checking for /macports/lib/petsc/include/slepcversion.h... yes > <<< Querying SLEPc configuration from > /macports/lib/petsc/conf/slepc_variables >>> > <<< Configuring library with SLEPc version 3.3.0 support >>> > checking /usr/include/tbb/task_scheduler_init.h usability... no > checking /usr/include/tbb/task_scheduler_init.h presence... no > checking for /usr/include/tbb/task_scheduler_init.h... no > checking whether pthreads work with -pthread... yes > checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE > checking if more special flags are required for pthreads... -D_THREAD_SAFE > checking for PTHREAD_PRIO_INHERIT... yes > <<< Configuring library with pthread support >>> > checking whether the compiler supports std::thread... no > checking whether TBB supports tbb::tbb_thread... no > <<< Configuring library with Laspack support >>> > <<< Configuring library with SFC support >>> > checking zlib.h usability... yes > checking zlib.h presence... yes > checking for zlib.h... yes > checking for gzopen in -lz... yes > <<< Configuring library with gzstreams support >>> > checking for bzip2... bzip2 > checking for bunzip2... bunzip2 > <<< Using bzip2/bunzip2 for writing/reading compressed .bz2 files >>> > checking for xz... xz > <<< Using xz for writing/reading compressed .xz files >>> > checking X11/Intrinsic.h usability... no > checking X11/Intrinsic.h presence... no > checking for X11/Intrinsic.h... no > <<< Configuring library with Metis support >>> > checking for thread local storage (TLS) class... __thread > <<< Configuring library with Parmetis support >>> > checking for doxygen... no > <<< Configuring library with Tetgen support >>> > <<< Configuring library with Triangle support >>> > <<< Configuring library with GMV support >>> > checking /vtkConfigure.h usability... no > checking /vtkConfigure.h presence... no > checking for /vtkConfigure.h... no > VTK header files not found! > checking /macports/include/eigen3/Eigen//Eigen/Eigen usability... no > checking /macports/include/eigen3/Eigen//Eigen/Eigen presence... no > checking for /macports/include/eigen3/Eigen//Eigen/Eigen... no > <<< external Eigen header files not found, using Eigen from ./contrib >>> > checking Eigen/Dense usability... yes > checking Eigen/Dense presence... yes > checking for Eigen/Dense... yes > checking Eigen/Sparse usability... yes > checking Eigen/Sparse presence... yes > checking for Eigen/Sparse... yes > checking for eigen - version >= 3.1.2... yes > <<< Configuring library with Eigen support >>> > checking /macports/include//glpk.h usability... yes > checking /macports/include//glpk.h presence... yes > checking for /macports/include//glpk.h... yes > <<< Configuring library with GLPK version 4.48 support >>> > checking for main in -lglpk... yes > <<< Configuring library with GLPK support >>> > checking hdf5.h usability... no > checking hdf5.h presence... no > checking for hdf5.h... no > checking for hdf5 - version >= 1.8.0... configure: optional HDF5 library > not found, or does not meet version requirements > <<< Configuring library with NetCDF version 4 support >>> > defining -DNOT_NETCDF4 for our Exodus build > <<< Configuring library with Exodus version v5.22 support >>> > <<< Configuring library with Exodus Fortran API >>> > <<< Configuring library with Nemesis version v5.22 support >>> > <<< Configuring library with libHilbert support >>> > >>> Disabling fparser optimization on darwin12.5.0 <<< > checking for a sed that does not truncate output... (cached) /usr/bin/sed > checking for bison... bison -y > <<< Configuring library with fparser support (release version) >>> > checking for cppunit-config... no > checking for Cppunit - version >= 1.10.0... no > <<< Configuring library with nanoflann KDtree support >>> > ---------------------------------------------- > --- Done configuring for optional packages --- > ---------------------------------------------- > removing duplicate include paths... > removing duplicate libraries... > checking for git... /usr/bin/git > checking that generated files are newer than configure... done > configure: creating ./config.status > config.status: creating Makefile > config.status: creating include/Makefile > config.status: creating include/libmesh/Makefile > config.status: creating contrib/Makefile > config.status: creating contrib/utils/Makefile > config.status: creating contrib/utils/Make.common > config.status: creating tests/Makefile > config.status: creating doc/Doxyfile > config.status: creating contrib/utils/libmesh.pc > config.status: creating contrib/utils/libmesh-opt.pc > config.status: creating contrib/utils/libmesh-dbg.pc > config.status: creating contrib/utils/libmesh-devel.pc > config.status: creating contrib/utils/libmesh-prof.pc > config.status: creating contrib/utils/libmesh-oprof.pc > config.status: creating contrib/bin/libmesh-config > config.status: creating contrib/bin/xda2mgf > config.status: creating contrib/bin/create_libmesh_release > config.status: creating doc/dot > config.status: creating contrib/boost/include/Makefile > config.status: creating contrib/laspack/Makefile > config.status: creating contrib/sfcurves/Makefile > config.status: creating contrib/gzstream/Makefile > config.status: creating contrib/tecplot/tecio/Makefile > config.status: creating contrib/tecplot/binary/Makefile > config.status: creating contrib/metis/Makefile > config.status: creating contrib/parmetis/Makefile > config.status: creating contrib/tetgen/Makefile > config.status: creating contrib/triangle/Makefile > config.status: creating contrib/gmv/Makefile > config.status: creating contrib/eigen/eigen/Makefile > config.status: creating contrib/netcdf/v3/Makefile > config.status: creating contrib/exodusii/v5.09/Makefile > config.status: creating contrib/exodusii/v5.22/exodus/Makefile > config.status: creating contrib/nemesis/v3.09/Makefile > config.status: creating contrib/nemesis/v5.22/nemesis/Makefile > config.status: creating contrib/libHilbert/Makefile > config.status: creating contrib/fparser/Makefile > config.status: creating contrib/fparser/extrasrc/Makefile > config.status: creating contrib/nanoflann/Makefile > config.status: creating examples/introduction/introduction_ex1/Makefile > config.status: creating examples/introduction/introduction_ex2/Makefile > config.status: creating examples/introduction/introduction_ex3/Makefile > config.status: creating examples/introduction/introduction_ex4/Makefile > config.status: creating examples/introduction/introduction_ex5/Makefile > config.status: creating examples/adaptivity/adaptivity_ex1/Makefile > config.status: creating examples/adaptivity/adaptivity_ex2/Makefile > config.status: creating examples/adaptivity/adaptivity_ex3/Makefile > config.status: creating examples/adaptivity/adaptivity_ex4/Makefile > config.status: creating examples/adaptivity/adaptivity_ex5/Makefile > config.status: creating examples/adjoints/adjoints_ex1/Makefile > config.status: creating examples/adjoints/adjoints_ex2/Makefile > config.status: creating examples/adjoints/adjoints_ex3/Makefile > config.status: creating examples/adjoints/adjoints_ex4/Makefile > config.status: creating examples/adjoints/adjoints_ex5/Makefile > config.status: creating examples/eigenproblems/eigenproblems_ex1/Makefile > config.status: creating examples/eigenproblems/eigenproblems_ex2/Makefile > config.status: creating examples/eigenproblems/eigenproblems_ex3/Makefile > config.status: creating examples/fem_system/fem_system_ex1/Makefile > config.status: creating examples/fem_system/fem_system_ex2/Makefile > config.status: creating > examples/solution_transfer/solution_transfer_ex1/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex1/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex2/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex3/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex4/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex5/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex6/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex7/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex8/Makefile > config.status: creating examples/miscellaneous/miscellaneous_ex9/Makefile > config.status: creating examples/subdomains/subdomains_ex1/Makefile > config.status: creating examples/subdomains/subdomains_ex2/Makefile > config.status: creating > examples/systems_of_equations/systems_of_equations_ex1/Makefile > config.status: creating > examples/systems_of_equations/systems_of_equations_ex2/Makefile > config.status: creating > examples/systems_of_equations/systems_of_equations_ex3/Makefile > config.status: creating > examples/systems_of_equations/systems_of_equations_ex4/Makefile > config.status: creating > examples/systems_of_equations/systems_of_equations_ex5/Makefile > config.status: creating > examples/systems_of_equations/systems_of_equations_ex6/Makefile > config.status: creating examples/reduced_basis/reduced_basis_ex1/Makefile > config.status: creating examples/reduced_basis/reduced_basis_ex2/Makefile > config.status: creating examples/reduced_basis/reduced_basis_ex3/Makefile > config.status: creating examples/reduced_basis/reduced_basis_ex4/Makefile > config.status: creating examples/reduced_basis/reduced_basis_ex5/Makefile > config.status: creating examples/reduced_basis/reduced_basis_ex6/Makefile > config.status: creating examples/reduced_basis/reduced_basis_ex7/Makefile > config.status: creating examples/transient/transient_ex1/Makefile > config.status: creating examples/transient/transient_ex2/Makefile > config.status: creating examples/vector_fe/vector_fe_ex1/Makefile > config.status: creating examples/vector_fe/vector_fe_ex2/Makefile > config.status: creating examples/vector_fe/vector_fe_ex3/Makefile > config.status: creating examples/vector_fe/vector_fe_ex4/Makefile > config.status: creating examples/Makefile > config.status: creating include/libmesh_config.h.tmp > config.status: executing include/libmesh_config.h commands > config.status: creating include/libmesh_config.h - prefix LIBMESH for > include/libmesh_config.h.tmp defines > config.status: executing depfiles commands > config.status: executing libtool commands > === configuring in contrib/netcdf/v4 > (/Users/vera/Desktop/libmesh_root/build/contrib/netcdf/v4) > configure: running /bin/sh ../../../../contrib/netcdf/v4/configure > --disable-option-checking > '--prefix=/Users/vera/Desktop/libmesh_root/installed' > '--with-glpk-include=/macports/include/' '--with-glpk-lib=/macports/lib' > '--with-eigen-include=/macports/include/eigen3/Eigen/' '--enable-petsc' > '--enable-slepc' 'PETSC_DIR=/macports/lib/petsc' > 'SLEPC_DIR=/macports/lib/petsc' '--disable-netcdf-4' '--disable-testsets' > 'CXX=g++' 'CC=gcc' 'F77=gfortran' 'FC=gfortran' 'CPPFLAGS= ' 'LIBS= ' > --cache-file=/dev/null --srcdir=../../../../contrib/netcdf/v4 > configure: netCDF 4.2.1.1 > checking build system type... x86_64-apple-darwin12.5.0 > checking host system type... x86_64-apple-darwin12.5.0 > checking target system type... x86_64-apple-darwin12.5.0 > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... > ../../../../contrib/netcdf/v4/install-sh -c -d > checking for gawk... no > checking for mawk... no > checking for nawk... no > checking for awk... awk > checking whether make sets $(MAKE)... yes > checking whether make supports nested variables... yes > configure: checking user options > checking whether a win32 DLL is desired... no > checking whether a NCIO_MINBLOCKSIZE was specified... 256 > checking if fsync support is enabled... yes > checking whether extra valgrind tests should be run... no > checking whether we should try to build netCDF-4... no > checking whether reading of HDF4 SD files is to be enabled... no > checking whether to fetch some sample HDF4 files from Unidata ftp site to > test HDF4 reading (requires wget)... no > checking whether parallel I/O for classic and 64-bit offset files using > parallel-netcdf is to be enabled... no > checking whether extra example tests should be run... no > checking whether parallel IO tests should be run... no > checking whether a default chunk size in bytes was specified... 4194304 > checking whether a maximum per-variable cache size for HDF5 was > specified... 67108864 > checking whether a number of chunks for the default per-variable cache was > specified... 10 > checking whether a default file cache size for HDF5 was specified... > 4194304 > checking whether a default file cache maximum number of elements for HDF5 > was specified... 1009 > checking whether a default cache preemption for HDF5 was specified... 0.75 > checking whether netCDF-4 logging is enabled... no > checking whether cdmremote client is to be built... no > checking whether DAP client is to be built... yes > checking for style of include used by make... GNU > checking for gcc... gcc > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking dependency style of gcc... gcc3 > checking for curl_easy_setopt in -lcurl... yes > checking for library containing curl_easy_setopt... -lcurl > checking whether dap remote testing should be enabled (default off)... no > checking whether netcdf4 group names should be enabled (default on)... yes > checking whether the time-consuming dap tests should be enabled (default > off)... no > checking whether netCDF extra tests should be run (developers only)... no > checking whether FFIO will be used... no > checking whether examples should be built... yes > checking whether v2 netCDF API should be built... yes > checking whether the ncgen/ncdump/nccopy should be built... yes > checking whether test should be built and run... no > checking whether large file (> 2GB) tests should be run... no > checking whether benchmaks should be run (experimental)... no > checking whether extreme numbers should be used in tests... yes > checking where to put large temp files if large file tests are run... . > configure: finding C compiler > checking for gcc... (cached) gcc > checking whether we are using the GNU C compiler... (cached) yes > checking whether gcc accepts -g... (cached) yes > checking for gcc option to accept ISO C89... (cached) none needed > checking dependency style of gcc... (cached) gcc3 > checking whether gcc and cc understand -c and -o together... yes > checking for an ANSI C-conforming const... yes > checking whether a CURLOPT_KEYPASSWD is defined... yes > configure: setting up libtool > checking how to print strings... printf > checking for a sed that does not truncate output... /usr/bin/sed > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for fgrep... /usr/bin/grep -F > checking for ld used by gcc... /macports/bin/ld > checking if the linker (/macports/bin/ld) is GNU ld... no > checking for BSD- or MS-compatible name lister (nm)... /macports/bin/nm > checking the name lister (/macports/bin/nm) interface... BSD nm > checking whether ln -s works... yes > checking the maximum length of command line arguments... 196608 > checking whether the shell understands some XSI constructs... yes > checking whether the shell understands "+="... yes > checking how to convert x86_64-apple-darwin12.5.0 file names to > x86_64-apple-darwin12.5.0 format... func_convert_file_noop > checking how to convert x86_64-apple-darwin12.5.0 file names to toolchain > format... func_convert_file_noop > checking for /macports/bin/ld option to reload object files... -r > checking for objdump... no > checking how to recognize dependent libraries... pass_all > checking for dlltool... no > checking how to associate runtime and link libraries... printf %s\n > checking for ar... ar > checking for archiver @FILE support... no > checking for strip... strip > checking for ranlib... ranlib > checking command to parse /macports/bin/nm output from gcc object... ok > checking for sysroot... no > checking for mt... no > checking if : is a manifest tool... no > checking for dsymutil... dsymutil > checking for nmedit... nmedit > checking for lipo... lipo > checking for otool... otool > checking for otool64... no > checking for -single_module linker flag... yes > checking for -exported_symbols_list linker flag... yes > checking for -force_load linker flag... yes > checking how to run the C preprocessor... gcc -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for dlfcn.h... yes > checking for objdir... .libs > checking if gcc supports -fno-rtti -fno-exceptions... no > checking for gcc option to produce PIC... -fno-common -DPIC > checking if gcc PIC flag -fno-common -DPIC works... yes > checking if gcc static flag -static works... no > checking if gcc supports -c -o file.o... yes > checking if gcc supports -c -o file.o... (cached) yes > checking whether the gcc linker (/macports/bin/ld) supports shared > libraries... yes > checking dynamic linker characteristics... darwin12.5.0 dyld > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... yes > configure: finding other utilities > checking for doxygen... no > checking for special C compiler options needed for large files... no > checking for _FILE_OFFSET_BITS value needed for large files... no > configure: displaying some results > checking CPPFLAGS... > checking CC CFLAGS... gcc -g -O2 > checking type gcc... gcc is hashed (/macports/bin/gcc) > checking CXX... g++ > checking CXXFLAGS... > checking type g++... g++ is /macports/bin/g++ > checking FC... gfortran > checking FFLAGS... > checking type gfortran... gfortran is /macports/bin/gfortran > checking F90... unset > checking AR... ar > checking AR_FLAGS... cru > checking type ar... ar is hashed (/macports/bin/ar) > checking NM... /macports/bin/nm > checking NMFLAGS... > configure: checking types, headers, and functions > checking for stdlib.h... (cached) yes > checking for sys/types.h... (cached) yes > checking sys/param.h usability... yes > checking sys/param.h presence... yes > checking for sys/param.h... yes > checking for dirent.h that defines DIR... yes > checking for library containing opendir... none required > checking for ANSI C header files... (cached) yes > checking for sys/wait.h that is POSIX.1 compatible... yes > checking whether time.h and sys/time.h may both be included... yes > checking locale.h usability... yes > checking locale.h presence... yes > checking for locale.h... yes > checking stdio.h usability... yes > checking stdio.h presence... yes > checking for stdio.h... yes > checking stdarg.h usability... yes > checking stdarg.h presence... yes > checking for stdarg.h... yes > checking errno.h usability... yes > checking errno.h presence... yes > checking for errno.h... yes > checking ctype.h usability... yes > checking ctype.h presence... yes > checking for ctype.h... yes > checking fcntl.h usability... yes > checking fcntl.h presence... yes > checking for fcntl.h... yes > checking malloc.h usability... no > checking malloc.h presence... no > checking for malloc.h... no > checking for stdlib.h... (cached) yes > checking for string.h... (cached) yes > checking for strings.h... (cached) yes > checking for unistd.h... (cached) yes > checking for sys/stat.h... (cached) yes > checking getopt.h usability... yes > checking getopt.h presence... yes > checking for getopt.h... yes > checking sys/time.h usability... yes > checking sys/time.h presence... yes > checking for sys/time.h... yes > checking for vprintf... yes > checking for _doprnt... no > checking sys/resource.h usability... yes > checking sys/resource.h presence... yes > checking for sys/resource.h... yes > checking for stdbool.h that conforms to C99... yes > checking for _Bool... yes > checking for strlcat... yes > checking for strerror... yes > checking for snprintf... yes > checking for strchr... yes > checking for strrchr... yes > checking for strcat... yes > checking for strcpy... yes > checking for strdup... yes > checking for strcasecmp... yes > checking for strtod... yes > checking for strtoll... yes > checking for strtoull... yes > checking for strstr... yes > checking for mkstemp... yes > checking for rand... yes > checking for getrlimit... yes > checking for gettimeofday... yes > checking for fsync... yes > checking for MPI_Comm_f2c... no > checking whether in-memory files are enabled... yes > checking for memmove... yes > checking for getpagesize... yes > checking for sysconf... yes > checking whether mmap is enabled for in-memory files... no > checking for stdlib.h... (cached) yes > checking for unistd.h... (cached) yes > checking for sys/param.h... (cached) yes > checking for getpagesize... (cached) yes > checking for working mmap... yes > checking for mremap... no > mmap function or mremap function is not available: disabling mmap > checking for size_t... yes > checking for working alloca.h... yes > checking for alloca... yes > checking whether isnan is declared... yes > checking whether isinf is declared... yes > checking whether isfinite is declared... yes > checking whether signbit is declared... yes > checking for struct stat.st_blksize... yes > checking for IEEE floating point format... yes > checking for size_t... (cached) yes > checking for off_t... yes > checking for ssize_t... yes > checking for ptrdiff_t... yes > checking for uchar... no > checking for longlong... no > checking whether char is unsigned... no > checking whether byte ordering is bigendian... no > checking size of short... 2 > checking size of int... 4 > checking size of long... 8 > checking size of long long... 8 > checking size of float... 4 > checking size of double... 8 > checking size of off_t... 8 > checking size of size_t... 8 > checking for library containing deflate... -lz > checking for floor in -lm... yes > checking what to call the output of the ftpbin target... > binary-netcdf-4.2.1.1_nc3.tar gfortran g++ > checking binary distribution directory... /home/ftp/pub/binary/dummy_system > checking value of LIBS... -lm -lz -lcurl > configure: generating header files and makefiles > checking that generated files are newer than configure... done > configure: creating ./config.status > config.status: creating Makefile > config.status: creating nc-config > config.status: creating netcdf.pc > config.status: creating include/Makefile > config.status: creating h5_test/Makefile > config.status: creating man4/Makefile > config.status: creating man4/images/Makefile > config.status: creating libsrc/Makefile > config.status: creating libsrc4/Makefile > config.status: creating nctest/Makefile > config.status: creating nc_test4/Makefile > config.status: creating nc_test/Makefile > config.status: creating ncdump/Makefile > config.status: creating ncgen3/Makefile > config.status: creating ncgen/Makefile > config.status: creating examples/Makefile > config.status: creating examples/C/Makefile > config.status: creating examples/CDL/Makefile > config.status: creating oc/Makefile > config.status: creating libdap2/Makefile > config.status: creating libcdmr/Makefile > config.status: creating librpc/Makefile > config.status: creating libdispatch/Makefile > config.status: creating liblib/Makefile > config.status: creating ncdump/cdl4/Makefile > config.status: creating ncdump/expected4/Makefile > config.status: creating ncdap_test/Makefile > config.status: creating ncdap_test/testdata3/Makefile > config.status: creating ncdap_test/expected3/Makefile > config.status: creating ncdap_test/expected4/Makefile > config.status: creating ncdap_test/expectremote3/Makefile > config.status: creating ncdap_test/expectremote4/Makefile > config.status: creating config.h > config.status: config.h is unchanged > config.status: executing depfiles commands > config.status: executing libtool commands > > ----------------------------------- SUMMARY > ----------------------------------- > > Package version.................... : libmesh-0.9.3-pre > > C++ compiler type.................. : gcc4.8 > C++ compiler....................... : g++ > C compiler......................... : gcc > Fortran compiler................... : gfortran > Build Methods...................... : dbg devel opt > > CPPFLAGS...(dbg)................... : -DDEBUG > CXXFLAGS...(dbg)................... : -O0 -felide-constructors -g -ansi > -pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat > -Wparentheses -Woverloaded-virtual -fopenmp > CFLAGS.....(dbg)................... : -g -Wimplicit -fopenmp > > CPPFLAGS...(devel)................. : > CXXFLAGS...(devel)................. : -O2 -felide-constructors -g -ansi > -pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat > -Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing > -Woverloaded-virtual -Wdisabled-optimization -fopenmp > CFLAGS.....(devel)................. : -O2 -g -Wimplicit -funroll-loops > -fstrict-aliasing -fopenmp > > CPPFLAGS...(opt)................... : -DNDEBUG > CXXFLAGS...(opt)................... : -O2 -felide-constructors > -funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp > CFLAGS.....(opt)................... : -O2 -funroll-loops -fstrict-aliasing > -fopenmp > > Install dir........................ : > /Users/vera/Desktop/libmesh_root/installed > Build user......................... : vera > Build host......................... : > veras-macbook.speedport_w723_v_typ_a_1_00_098 > Build architecture................. : x86_64-apple-darwin12.5.0 > Git revision....................... : > 1b400061e232bf80c88a2a6fdc2a784f2248dbad > > Library Features: > adaptive mesh refinement......... : yes > blocked matrix/vector storage.... : no > complex variables................ : no > example suite.................... : yes > ghosted vectors.................. : yes > high-order shape functions....... : yes > id size (boundaries)............. : 2 bytes > id size (dofs)................... : 4 bytes > id size (processors)............. : 2 bytes > id size (subdomains)............. : 2 bytes > infinite elements................ : no > Dirichlet constraints............ : yes > node constraints................. : no > parallel mesh.................... : no > performance logging.............. : no > periodic boundary conditions..... : yes > reference counting............... : yes > shape function 2nd derivatives... : yes > stack trace files................ : no > variational smoother............. : yes > xdr binary I/O................... : yes > providing libMesh::CommWorld..... : yes ***LEGACY FEATURE*** > > Optional Packages: > boost............................ : yes > cppunit.......................... : no > eigen............................ : yes > exodus........................... : yes > version....................... : v5.22 > fparser.......................... : yes > build from version............ : release > glpk............................. : yes > gmv.............................. : yes > gzstream......................... : yes > hdf5............................. : no > laspack.......................... : yes > libhilbert....................... : yes > metis............................ : yes > mpi.............................. : yes > nanoflann........................ : yes > nemesis.......................... : yes > version....................... : v5.22 > netcdf........................... : yes > version....................... : 4 > openmp........................... : yes > parmetis......................... : yes > petsc............................ : yes > version....................... : 3.3.0 > pthreads......................... : yes > sfcurves......................... : yes > slepc............................ : yes > tbb.............................. : no > c++ threads...................... : no > c++ rtti ........................ : yes > tecio............................ : no > tecplot...(vendor binaries)...... : no > tetgen........................... : yes > triangle......................... : yes > trilinos......................... : no > vtk.............................. : no > > libmesh_optional_INCLUDES........ : -I/macports/include -D_THREAD_SAFE > -pthread -I/macports/lib/petsc/include -I/macports/lib/petsc//include > -I/macports/include/openmpi -I../contrib/boost/include > > libmesh_optional_LIBS............ : -Wl,-rpath,/macports/lib > -L/macports/lib -lglpk -L/macports/lib/petsc//lib -lslepc > -L/macports/lib/petsc/lib > -L/macports/lib/gcc48/gcc/x86_64-apple-darwin12/4.8.1 -L/macports/lib/gcc48 > -lpetsc -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord > -lscalapack -lblacs -lparmetis -lmetis -lml -lptesmumps -lptscotch > -lptscotcherr -lpthread -lyaml -Wl,-framework -Wl,Accelerate -lhdf5_fortran > -lhdf5 -lhdf5hl_fortran -lhdf5_hl -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran > -lSystem -lgcc_ext.10.5 -lquadmath -lm -lz -ldl > > > ------------------------------------------------------------------------------- > Configure complete, now type 'make' and then 'make install'. > > --------------------------------------------- > --------- Done Configuring libMesh ---------- > --------------------------------------------- > > > > > Thanks for your help. > > Best, > Vera > > > On 09/17/13, John Peterson <[email protected]> wrote: > > > On Tue, Sep 17, 2013 at 1:25 AM, Vera Franziska Loeser < > > [email protected]> wrote: > > > > > Hi, > > > > > > I still try to install Libmesh on my Mac (OS X 10.8) but I am not able > to > > > enable slepc and pets so that the make checks are working. > > > I installed petsc and slepc via macports and my configure command is: > > > > > > ../configure --prefix=/Users/vera/Desktop/libmesh_root/installed > > > --with-glpk-include=/macports/include --with-glpk-lib=/macports/lib > > > --with-eigen-include=/macports/include/eigen3/Eigen --enable-petsc > > > --enable-slepc > > > > > > > > > I'd say this: > > > > checking for mpicxx... no > > > checking for mpiCC... no > > > checking for mpicc... no > > > > > > > is also a potential problem. You really want to have the MPI compiler > > scripts (they should be installed by the macports MPI) in your PATH when > > you configure libmesh, so that libmesh can get the right MPI includes and > > libraries, preferably the same ones that were used when PETSc and SLEPc > > were built. > > > > -- > > John > > > ------------------------------------------------------------------------------ > > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, > SharePoint > > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack > includes > > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > > > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > > _______________________________________________ > > Libmesh-users mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/libmesh-users > > > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, > SharePoint > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack > includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > _______________________________________________ > Libmesh-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/libmesh-users > ------------------------------------------------------------------------------ LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
