I just upgraded to Ubuntu 14.04, and I now get the error below (related to netCDF) during configure. Any suggestions?
Thanks! David -------------------------------------------------------------------- ~/software/libmesh_build/opt_real$ /home/dknez/software/libmesh-src/configure --enable-everything --enable-slepc --with-metis=PETSc --with-subdomain-id-bytes=4 --with-boundary-id-bytes=4 --prefix=/home/dknez/software/libmesh_install/opt_real/libmesh --with-methods=opt --enable-shared --------------------------------------------- ----------- Configuring libMesh ------------- --------------------------------------------- checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1000' is supported by ustar format... yes checking whether GID '1000' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports nested variables... (cached) 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... mpicxx 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-4.8 >>> checking for mpicc... mpicc 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 whether mpicc understands -c and -o together... yes checking dependency style of mpicc... gcc3 checking for mpif90... mpif90 checking whether we are using the GNU Fortran compiler... yes checking whether mpif90 accepts -g... yes checking for mpif77... mpif77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether mpif77 accepts -g... yes <<< Configuring libMesh with methods "opt" >>> checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by mpicc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump 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... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from mpicc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no 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... -fPIC -DPIC checking if mpicc PIC flag -fPIC -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/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so 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... mpicxx -E checking for ld used by mpicxx... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for mpicxx option to produce PIC... -fPIC -DPIC checking if mpicxx PIC flag -fPIC -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/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so 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 mpif77 option to produce PIC... -fPIC checking if mpif77 PIC flag -fPIC works... yes checking if mpif77 static flag -static works... no checking if mpif77 supports -c -o file.o... yes checking if mpif77 supports -c -o file.o... (cached) yes checking whether the mpif77 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so 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 mpif90 option to produce PIC... -fPIC checking if mpif90 PIC flag -fPIC works... yes checking if mpif90 static flag -static works... no checking if mpif90 supports -c -o file.o... yes checking if mpif90 supports -c -o file.o... (cached) yes checking whether the mpif90 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking Major version... 1 checking Minor version... 0 checking Point version... 0 checking whether ln -s works... yes checking for a sed that does not truncate output... (cached) /bin/sed checking for perl... /usr/bin/perl checking for pkg-config... /usr/bin/pkg-config 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 ----- --------------------------------------------- <<< Configuring library with warnings >>> <<< Configuring library to disable libMesh::CommWorld >>> <<< Configuring library to require ``include "libmesh/etc.h"'' style >>> <<< Configuring library to keep names in libMesh namespace >>> configuring size of boundary_id... 4 configuring size of dof_id... 4 configuring size of processor_id... 2 configuring size of subdomain_id... 4 <<< Configuring library with unique id support >>> configuring size of unique_id... 8 <<< Configuring library with stack trace file support >>> <<< 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 with node constraints support >>> <<< Configuring library to use ghosted local vectors >>> <<< Configuring library to store node valence >>> <<< Configuring library with higher order p-FEM shapes >>> <<< Configuring library with infinite elements >>> <<< 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 with performance logging 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 for petscarch... no checking /include/petscversion.h usability... no checking /include/petscversion.h presence... no checking for /include/petscversion.h... no <<< PETSc disabled. Will try configuring MPI now... >>> note: MPI library path not given... trying prefix=/usr note: using /usr/lib/libmpi(.a/.so) checking for lam_show_version in -llam... no nm: /usr/lib/libmpi.so: no symbols nm: /usr/lib/libmpi.so.1: no symbols nm: /usr/lib/libmpi.so.1.0.8: no symbols checking for MPI_Init in -lmpi... yes Found valid MPI installlaion... note: using /usr/include/mpi/mpi.h checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes <<< SLEPc disabled. Please set your "$SLEPC_DIR" environment variable correctly to enable SLEPc. >>> 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 for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no 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 >>> <<< Testing X11 headers with -I/usr/include >>> checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking size of void *... (cached) 8 <<< Configuring library with Tecplot TecIO support >>> <<< 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 /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! checking hdf5.h usability... yes checking hdf5.h presence... yes checking for hdf5.h... yes checking for hdf5 - version >= 1.8.0... yes checking for H5Fopen in -lhdf5... yes <<< Configuring library with HDF5 support >>> <<< Configuring library with NetCDF version 4 support >>> <<< 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 >>> checking for a sed that does not truncate output... (cached) /bin/sed checking for bison... bison -y <<< Configuring library with fparser support (release version) >>> checking for cppunit-config... /usr/bin/cppunit-config checking for Cppunit - version >= 1.10.0... 1.13.1 <<< 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/miscellaneous/miscellaneous_ex10/Makefile config.status: creating examples/miscellaneous/miscellaneous_ex11/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 (/home/akselos/software/libmesh_build/opt_real/contrib/netcdf/v4) configure: running /bin/bash /home/akselos/software/libmesh-src/contrib/netcdf/v4/configure --disable-option-checking '--prefix=/home/akselos/software/libmesh_install/opt_real/libmesh' '--enable-everything' '--enable-slepc' '--with-metis=PETSc' '--with-subdomain-id-bytes=4' '--with-boundary-id-bytes=4' '--with-methods=opt' '--enable-shared' '--disable-testsets' 'CXX=mpicxx' 'CC=mpicc' 'F77=mpif77' 'FC=mpif90' 'CPPFLAGS= ' 'LIBS=-L/lib -lhdf5 -Wl,-rpath,/lib ' --cache-file=/dev/null --srcdir=/home/akselos/software/libmesh-src/contrib/netcdf/v4 configure: netCDF 4.3.1 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes /home/akselos/software/libmesh-src/contrib/netcdf/v4/configure: line 19941: syntax error: unexpected end of file configure: error: /home/akselos/software/libmesh-src/contrib/netcdf/v4/configure failed for contrib/netcdf/v4 ------------------------------------------------------------------------------ Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
