[petsc-users] configure error with netcdf

[Barry Smith]

   This is likely the same flex problem you say with ptscotch:

  ncgen.l:142: warning: passing argument 1 of ‘ncgerror’ discards qualifiers from pointer target type
ncgentab.o: In function `ignore':
ncgentab.c:(.text+0x1e2): undefined reference to `yyunput'
collect2: ld returned 1 exit status
make[2]: *** [ncgen3] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2


  netcdf.py would have to be modified in the same way as ptscotch.py was modified to do the right thing with flex

   Satish, do you know how to do it? Cause I sure don't.

   Barry



On Sep 8, 2012, at 10:35 AM, fdkong <fd.kong at siat.ac.cn> wrote:

> 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
> <config.zip><configure.zip>