You're using Apple's broken compiler. However this might actually be a regression since it used to work to build static libraries with that compiler. You really should download GCC through Mac Ports or Fink, or use Clang which is already on your system.
Cody Sent from my iPhone On May 28, 2013, at 4:43 AM, lorenzo alessio botti <[email protected]> wrote: > Dear all, > compiling libMesh on my system I get the following error > > CXXLD getpot_parse-opt > Undefined symbols for architecture x86_64: > "Hilbert::coordsToIndex(CFixBitVec const*, int, int, CBigBitVec&)", > referenced from: > Hilbert::HilbertIndices (anonymous > namespace)::get_hilbert_index<libMesh::Elem>(libMesh::Elem const*, > libMesh::MeshTools::BoundingBox const&)in > libmesh_opt.a(libmesh_opt_la-mesh_communication_global_indices.o) > Hilbert::HilbertIndices (anonymous > namespace)::get_hilbert_index<libMesh::Node>(libMesh::Node const*, > libMesh::MeshTools::BoundingBox const&)in > libmesh_opt.a(libmesh_opt_la-mesh_communication_global_indices.o) > (anonymous namespace)::get_hilbert_index(libMesh::Point const&, > libMesh::MeshTools::BoundingBox const&)in > libmesh_opt.a(libmesh_opt_la-mesh_communication_global_indices.o) > ld: symbol(s) not found for architecture x86_64 > collect2: ld returned 1 exit status > make[1]: *** [getpot_parse-opt] Error 1 > make: *** [all-recursive] Error 1 > > Any idea? > It works if I configure with --disable-libHilbert > > This is the configure output > > > digihabia:libmesh-0.9.1 ihabia$ ./configure > --prefix=/Users/ihabia/src2/libmesh-0.9.1/libmesh_build/ > --with-methods="opt" --enable-static --disable-shared > --with-mpi=/usr/local/ --disable-fortran --disable-second --disable-amr > --------------------------------------------- > ----------- Configuring libMesh ------------- > --------------------------------------------- > checking build system type... x86_64-apple-darwin11.4.2 > checking host system type... x86_64-apple-darwin11.4.2 > checking target system type... x86_64-apple-darwin11.4.2 > 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... yes > checking for style of include used by make... GNU > 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 mpicxx accepts -g... yes > checking dependency style of mpicxx... gcc3 > <<< C++ compiler is gcc-4.2 >>> > <<< C++ compiler is built by Apple >>> > checking whether we are using the GNU C compiler... yes > checking whether mpicc accepts -g... yes > checking for mpicc option to accept ISO C89... none needed > checking dependency style of mpicc... gcc3 >>>> Disabling Fortran language support per user request <<< > << Disabling GLIBCXX debugging on Darwin >>> > <<< Configuring libMesh with methods "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 mpicc... > /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld > checking if the linker > (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) is GNU ld... no > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm > checking the name lister (/usr/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-darwin11.4.2 file names to > x86_64-apple-darwin11.4.2 format... func_convert_file_noop > checking how to convert x86_64-apple-darwin11.4.2 file names to toolchain > format... func_convert_file_noop > checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/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 /usr/bin/nm output from mpicc 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... mpicc -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 mpicc supports -fno-rtti -fno-exceptions... no > checking for mpicc option to produce PIC... -fno-common -DPIC > checking if mpicc PIC flag -fno-common -DPIC works... yes > checking if mpicc static flag -static works... no > checking if mpicc supports -c -o file.o... yes > checking if mpicc supports -c -o file.o... (cached) yes > checking whether the mpicc linker > (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports > shared libraries... yes > checking dynamic linker characteristics... darwin11.4.2 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... no > checking whether to build static libraries... yes > checking how to run the C++ preprocessor... mpicxx -E > checking for ld used by mpicxx... > /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld > checking if the linker > (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) is GNU ld... no > checking whether the mpicxx linker > (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports > shared libraries... yes > checking for mpicxx option to produce PIC... -fno-common -DPIC > checking if mpicxx PIC flag -fno-common -DPIC works... yes > checking if mpicxx static flag -static works... no > checking if mpicxx supports -c -o file.o... yes > checking if mpicxx supports -c -o file.o... (cached) yes > checking whether the mpicxx linker > (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports > shared libraries... yes > checking dynamic linker characteristics... darwin11.4.2 dyld > checking how to hardcode library paths into programs... immediate > checking Major version... 0 > checking Minor version... 9 > checking Point version... 1 > checking whether ln -s works... yes > checking for a sed that does not truncate output... (cached) /usr/bin/sed > checking for perl... /usr/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 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 >>> > 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... yes > <<< Using external boost installation >>> > checking /Users/ihabia/src2/petsc-3.3-p7//include/petscversion.h > usability... yes > checking /Users/ihabia/src2/petsc-3.3-p7//include/petscversion.h > presence... yes > checking for /Users/ihabia/src2/petsc-3.3-p7//include/petscversion.h... yes > <<< Configuring library with MPI from PETSC config >>> > <<< Configuring library with PETSc version 3.3.0 support >>> > checking /usr/lib/slepc/include/slepcversion.h usability... no > checking /usr/lib/slepc/include/slepcversion.h presence... no > checking for /usr/lib/slepc/include/slepcversion.h... no > <<< Invalid "$SLEPC_DIR" detected (slepcversion.h not found). SLEPc > disabled. >>> > checking /arch-darwin-c-opt/include/slepcconf.h usability... no > checking /arch-darwin-c-opt/include/slepcconf.h presence... no > checking for /arch-darwin-c-opt/include/slepcconf.h... no > 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 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... none > checking X11/Intrinsic.h usability... yes > checking X11/Intrinsic.h presence... yes > checking for X11/Intrinsic.h... yes > <<< Configuring library with Tecplot TecIO support >>> > <<< Configuring library with Metis support >>> > <<< 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 /usr/include/Eigen/Eigen usability... no > checking /usr/include/Eigen/Eigen presence... no > checking for /usr/include/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 /usr/include/glpk.h usability... no > checking /usr/include/glpk.h presence... no > checking for /usr/include/glpk.h... no > GLPK header files not found! > <<< 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 Nemesis version v5.22 support >>> > <<< Configuring library with libHilbert support >>> >>>> Disabling fparser optimization on darwin11.4.2 <<< > 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: 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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 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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/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/Makefile > config.status: creating include/libmesh_config.h.tmp > config.status: include/libmesh_config.h.tmp is unchanged > 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: include/libmesh_config.h is unchanged > config.status: executing depfiles commands > config.status: executing libtool commands > === configuring in contrib/netcdf/v4 > (/Users/ihabia/src2/libmesh-0.9.1/contrib/netcdf/v4) > configure: running /bin/sh ./configure --disable-option-checking > '--prefix=/Users/ihabia/src2/libmesh-0.9.1/libmesh_build' > '--with-methods=opt' '--enable-static' '--disable-shared' > '--with-mpi=/usr/local/' '--disable-fortran' '--disable-second' > '--disable-amr' 'CXX=mpicxx' 'CC=mpicc' > 'PETSC_DIR=/Users/ihabia/src2/petsc-3.3-p7/' 'PETSC_ARCH=arch-darwin-c-opt' > '--disable-netcdf-4' '--disable-testsets' 'CXX=mpicxx' 'CC=mpicc' 'F77=no' > 'FC=no' 'CPPFLAGS= ' 'LIBS= ' --cache-file=/dev/null --srcdir=. > configure: netCDF 4.2.1.1 > checking build system type... x86_64-apple-darwin11.4.2 > checking host system type... x86_64-apple-darwin11.4.2 > checking target system type... x86_64-apple-darwin11.4.2 > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... ./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... mpicc > 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 mpicc accepts -g... yes > checking for mpicc option to accept ISO C89... none needed > checking dependency style of mpicc... 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) mpicc > checking whether we are using the GNU C compiler... (cached) yes > checking whether mpicc accepts -g... (cached) yes > checking for mpicc option to accept ISO C89... (cached) none needed > checking dependency style of mpicc... (cached) gcc3 > checking whether mpicc 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 mpicc... > /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld > checking if the linker > (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) is GNU ld... no > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm > checking the name lister (/usr/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-darwin11.4.2 file names to > x86_64-apple-darwin11.4.2 format... func_convert_file_noop > checking how to convert x86_64-apple-darwin11.4.2 file names to toolchain > format... func_convert_file_noop > checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/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 /usr/bin/nm output from mpicc 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... mpicc -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 mpicc supports -fno-rtti -fno-exceptions... no > checking for mpicc option to produce PIC... -fno-common -DPIC > checking if mpicc PIC flag -fno-common -DPIC works... yes > checking if mpicc static flag -static works... no > checking if mpicc supports -c -o file.o... yes > checking if mpicc supports -c -o file.o... (cached) yes > checking whether the mpicc linker > (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports > shared libraries... yes > checking dynamic linker characteristics... darwin11.4.2 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... no > checking whether to build static libraries... yes > configure: finding other utilities > checking for doxygen... no > configure: WARNING: Doxygen not found - documentation will not be built > 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... mpicc -g -O2 > checking type mpicc... mpicc is hashed (/usr/local/bin/mpicc) > checking CXX... mpicxx > checking CXXFLAGS... > checking type mpicxx... mpicxx is /usr/local/bin/mpicxx > checking FC... no > checking FFLAGS... > ./configure: line 14294: type: no: not found > checking type no... > checking F90... unset > checking AR... ar > checking AR_FLAGS... cru > checking type ar... ar is hashed (/usr/bin/ar) > checking NM... /usr/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 no mpicxx > 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-0.9.1 > > C++ compiler type.................. : gcc4.2 > C++ compiler....................... : mpicxx > C compiler......................... : mpicc > Fortran compiler................... : no > Build Methods...................... : opt > > 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/ihabia/src2/libmesh-0.9.1/libmesh_build > Build user......................... : ihabia > Build host......................... : digihabia.local > Build architecture................. : x86_64-apple-darwin11.4.2 > Git revision....................... : external > > Library Features: > adaptive mesh refinement......... : 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... : no > 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............................. : no > 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 > sfcurves......................... : yes > slepc............................ : no > tbb.............................. : no > c++ threads...................... : no > c++ rtti ........................ : yes > tecio............................ : yes > tecplot...(vendor binaries)...... : no > tetgen........................... : yes > triangle......................... : yes > trilinos......................... : no > vtk.............................. : no > > libmesh_optional_INCLUDES........ : > -I/Users/ihabia/src2/petsc-3.3-p7/include > -I/Users/ihabia/src2/petsc-3.3-p7/arch-darwin-c-opt/include > -I/usr/local/include > > libmesh_optional_LIBS............ : -lz > -L/Users/ihabia/src2/petsc-3.3-p7//arch-darwin-c-opt/lib > -L/Users/ihabia/src2/petsc-3.3-p7/arch-darwin-c-opt/lib -lpetsc -lpthread > -lf2clapack -lf2cblas -ldl > > ------------------------------------------------------------------------------- > Configure complete, now type 'make' and then 'make install'. > > --------------------------------------------- > --------- Done Configuring libMesh ---------- > --------------------------------------------- > > Thanks. > Lorenzo > ------------------------------------------------------------------------------ > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may > _______________________________________________ > Libmesh-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/libmesh-users ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
