[petsc-users] configure error with netcdf

Sun Sep 9 07:55:45 CDT 2012

On Sun, Sep 9, 2012 at 12:31 AM, Satish Balay <balay at mcs.anl.gov> wrote:

> > ncgentab.c:(.text+0x1e2): undefined reference to `yyunput'
>
> I don't know whats going on here. I don't see lex/flex invoked.
>

lex is invoked right above. Barry did not paste it.

> Perhaps you can try the attached patch and see if it works. Its
> attempting to use the latest netcdf tarball.
>
> cd config/BuidSystem
> patch -Np1 < netcdf.patch
>
> Matt - If the changes look ok - I can push to petsc-dev
>
> - update to 4.2.1.1 tarball
> - remove configEnv. all configure options should be passed via
> command-line.
> - also remove make.inc. Its never used.
> - Add in --disable-hdf4 --disable-netcdf-4 to get rid of hdf5 errors
> - libnetcdf_c++.a not created by the new version? remove it from liblist
>
> exodusii.py also has some issues. Its makefiles are relying on
> PETSC_DIR/PETSC_ARCH env variable to be set by user - for obtaining
> ntcdf location, install-dir for 'make install' etc..
>

Will look.

   Matt

> Satish
>
> On Sat, 8 Sep 2012, Barry Smith wrote:
>
> >
> >    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>
> >
> >

-- 
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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