[petsc-users] configure error with netcdf

[Matthew Knepley]

On Fri, Sep 7, 2012 at 6:41 PM, fdkong <fd.kong at siat.ac.cn> wrote:

> Hi all,
>
> There are anyone who know how to install netcdf with cross compile? I
> configured petsc with netcdf, but got error below:
>

Send externalpackages./netcdf*/config.log

  Thanks,

    Matt


>
> ===============================================================================
>              Configuring PETSc to compile on your system
>
>
> ===============================================================================
> ===============================================================================
>
>                                                    ***** WARNING: MPI_DIR
> found in enviornment variables - ignoring ******
>
>
>  ===============================================================================
>
>
>  ===============================================================================
>
>                                                              WARNING!
> Compiling PETSc with no debugging, this should
>
>                                                only be done for timing and
> production runs. All development should
>
>                      be done when configured using --with-debugging=1
>
>
> ===============================================================================
>
>
>  ===============================================================================
>
>                                                    Configuring NetCDF; this
> may take several minutes
>
>
>  ===============================================================================
>
>
>
>
>
> *******************************************************************************
>          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
> details):
>
> -------------------------------------------------------------------------------
> Error running make on NetCDF: Could not execute "cd
> /projects/fako9399/petsc-3.3-p3/externalpackages/netcdf-4.1.1 &&
> AR="/usr/bin/ar" ARFLAGS="cr"
> CC="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicc" CFLAGS="
> -fPIC  -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O
>  -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include
> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."
> CXX="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicxx"
> CXXFLAGS="  -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O
> -fPIC   -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include
> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."
> FC="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpif90" FCFLAGS="
> -fPIC  -Wno-unused-variable -O
> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include
> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."
> F90="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpif90"
> ./configure --prefix=/projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt
> --libdir=/projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt/lib
> --disable-dap --enable-shared":
> configure: netCDF 4.1.1
> checking build system type... x86_64-unknown-linux-gnu
> checking host 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... gawk
> checking whether make sets $(MAKE)... yes
> configure: checking user options
> checking whether CXX is set to ''... no
> checking whether FC is set to ''... no
> checking whether F90 is set to ''... no
> checking whether a NCIO_MINBLOCKSIZE was specified... 256
> checking whether udunits is to be built... no
> checking if fsync support is enabled... yes
> checking whether extra valgrind tests should be run... no
> checking whether libcf is to be built... 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 a location for the parallel-netcdf library was
> specified... no
> checking whether new netCDF-4 C++ API is to be built... no
> checking whether extra example tests should be run... no
> checking whether parallel IO tests should be run... no
> checking whether a location for the HDF5 library was specified...
> checking whether a location for the ZLIB library was specified...
> checking whether a location for the SZLIB library was specified...
> checking whether a location for the HDF4 library was specified...
> 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 a path for curl-config was specified... no
> checking whether a location for curl installation was specified... no
> configure: checking whether a location for curl-config is in PATH... yes
> checking whether DAP client is to be built... no
> checking whether dap remote testing should be enabled (default on)... no
> checking whether the time-consuming dap tests should be enabled (default
> off)... no
> checking whether a location for liboc was specified... no
> checking whether netCDF extra tests should be run (developers only)... no
> checking whether Fortran compiler(s) should be tested during configure...
> yes
> checking whether FFIO will be used... no
> checking whether to skip C++, F77, or F90 APIs if compiler is broken... yes
> checking whether only the C library is desired... no
> checking whether examples should be built... yes
> checking whether F77 API is desired... yes
> checking whether any Fortran API is desired... yes
> checking whether F90 API is desired... yes
> checking whether fortran type sizes should be checked... yes
> checking whether C API is desired... yes
> checking where to get netCDF C-only library for separate fortran
> libraries...
> checking whether CXX API is desired... yes
> checking whether v2 netCDF API should be built... yes
> checking whether the ncgen/ncdump should be built... yes
> 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... .
> checking whether a win32 DLL is desired... no
> checking whether separate fortran libs are desired... yes
> configure: finding C compiler
> 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... configure: error: in
> `/projects/fako9399/petsc-3.3-p3/externalpackages/netcdf-4.1.1':
> configure: error: cannot run C compiled programs.
> If you meant to cross compile, use `--host'.
> See `config.log' for more details.
>
> *******************************************************************************
>
> The configure script is:
>
>   ./configure --with-clanguage=cxx --with-shared-libraries=1
> --with-dynamic-loading=1 --download-f-blas-lapack=1 --with-mpi-dir=$MPI_DIR
> --known-mpi-shared-libraries=0 --with-batch=1  --download-parmetis=1
> --download-metis=1 --with-64-bit-indices=1 --download-netcdf=1
> --download-exodusii=1 --with-debugging=no  --download-ptscotch=1
>
> I also attached the file configure.log
>
> ------------------
> Fande Kong
> ShenZhen Institutes of Advanced Technology
> Chinese Academy of Sciences
>
>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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