[petsc-users] configure error with netcdf

fdkong fd.kong at siat.ac.cn
Sat Sep 8 10:35:29 CDT 2012 

Thank you Matt. I added MPI shared libraries to my LD_LIBRARY_PATH. The error disappeared. But other errors happened. Please find the attached files!
 

 




------------------ Original ------------------
From:  "knepley"<knepley at gmail.com>;
Date:  Sat, Sep 8, 2012 12:30 PM
To:  "fdkong"<fd.kong at siat.ac.cn>; 
Cc:  "petsc-users"<petsc-users at mcs.anl.gov>; 
Subject:  Re: configure error with netcdf



On Fri, Sep 7, 2012 at 11:28 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


I attached the file config.log. 
 

Your MPI shared libraries are not in your LD_LIBRARY_PATH


configure:5252: checking whether we are cross compiling
 configure:5260: /curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicc -o conftest  -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.   conftest.c  >&5
 configure:5264: $? = 0
configure:5271: ./conftest
 ./conftest: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory
 configure:5275: $? = 127

 
   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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