On Sun, Sep 9, 2012 at 12:31 AM, Satish Balay <span dir="ltr"><<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
> ncgentab.c:(.text+0x1e2): undefined reference to `yyunput'<br>
<br>
I don't know whats going on here. I don't see lex/flex invoked.<br></blockquote><div><br></div><div>lex is invoked right above. Barry did not paste it.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Perhaps you can try the attached patch and see if it works. Its<br>
attempting to use the latest netcdf tarball.<br>
<br>
cd config/BuidSystem<br>
patch -Np1 < netcdf.patch<br>
<br>
Matt - If the changes look ok - I can push to petsc-dev<br>
<br>
- update to 4.2.1.1 tarball<br>
- remove configEnv. all configure options should be passed via command-line.<br>
- also remove make.inc. Its never used.<br>
- Add in --disable-hdf4 --disable-netcdf-4 to get rid of hdf5 errors<br>
- libnetcdf_c++.a not created by the new version? remove it from liblist<br>
<br>
exodusii.py also has some issues. Its makefiles are relying on<br>
PETSC_DIR/PETSC_ARCH env variable to be set by user - for obtaining<br>
ntcdf location, install-dir for 'make install' etc..<br></blockquote><div><br></div><div>Will look.</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Satish<br>
<br>
On Sat, 8 Sep 2012, Barry Smith wrote:<br>
<br>
><br>
> This is likely the same flex problem you say with ptscotch:<br>
><br>
> ncgen.l:142: warning: passing argument 1 of ‘ncgerror’ discards qualifiers from pointer target type<br>
> ncgentab.o: In function `ignore':<br>
> ncgentab.c:(.text+0x1e2): undefined reference to `yyunput'<br>
> collect2: ld returned 1 exit status<br>
> make[2]: *** [ncgen3] Error 1<br>
> make[1]: *** [all-recursive] Error 1<br>
> make: *** [all] Error 2<br>
><br>
><br>
> netcdf.py would have to be modified in the same way as ptscotch.py was modified to do the right thing with flex<br>
><br>
> Satish, do you know how to do it? Cause I sure don't.<br>
><br>
> Barry<br>
><br>
><br>
><br>
> On Sep 8, 2012, at 10:35 AM, fdkong <<a href="mailto:fd.kong@siat.ac.cn">fd.kong@siat.ac.cn</a>> wrote:<br>
><br>
> > 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!<br>
> ><br>
> ><br>
> ><br>
> > ------------------ Original ------------------<br>
> > From: "knepley"<<a href="mailto:knepley@gmail.com">knepley@gmail.com</a>>;<br>
> > Date: Sat, Sep 8, 2012 12:30 PM<br>
> > To: "fdkong"<<a href="mailto:fd.kong@siat.ac.cn">fd.kong@siat.ac.cn</a>>;<br>
> > Cc: "petsc-users"<<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>>;<br>
> > Subject: Re: configure error with netcdf<br>
> ><br>
> > On Fri, Sep 7, 2012 at 11:28 PM, fdkong <<a href="mailto:fd.kong@siat.ac.cn">fd.kong@siat.ac.cn</a>> wrote:<br>
> > >> Hi all,<br>
> > >><br>
> > >> There are anyone who know how to install netcdf with cross compile? I<br>
> > >> configured petsc with netcdf, but got error below:<br>
> > >><br>
> ><br>
> > >Send externalpackages./netcdf*/config.log<br>
> ><br>
> > > Thanks,<br>
> ><br>
> > > Matt<br>
> ><br>
> > I attached the file config.log.<br>
> ><br>
> > Your MPI shared libraries are not in your LD_LIBRARY_PATH<br>
> ><br>
> > configure:5252: checking whether we are cross compiling<br>
> > 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<br>
> > configure:5264: $? = 0<br>
> > configure:5271: ./conftest<br>
> > ./conftest: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory<br>
> > configure:5275: $? = 127<br>
> ><br>
> > Matt<br>
> > >><br>
> > >> >===========================================================================>====<br>
> > >> Configuring PETSc to compile on your system<br>
> > >><br>
> > >><br>
> > >> >===========================================================================>====<br>
> > > >===========================================================================>====<br>
> > >><br>
> > >> ***** WARNING: MPI_DIR<br>
> > >> found in enviornment variables - ignoring ******<br>
> > >>><br>
> > >><br>
> > >> >===========================================================================>====<br>
> > >><br>
> > >><br>
> > >> ===============================================================================<br>
> > >><br>
> > >> WARNING!<br>
> > >> Compiling PETSc with no debugging, this should<br>
> > >><br>
> > >> only be done for timing and<br>
> > >> production runs. All development should<br>
> > >><br>
> > >> be done when configured using --with-debugging=1<br>
> > ><br>
> > ><br>
> > > ===============================================================================<br>
> > >><br>
> > >><br>
> > >> ===============================================================================<br>
> > >><br>
> > >> Configuring NetCDF; this<br>
> > >> may take several minutes<br>
> > >><br>
> > >><br>
> > >> ===============================================================================<br>
> > >><br>
> > >><br>
> > >><br>
> > >><br>
> > >><br>
> > >> *******************************************************************************<br>
> > >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for<br>
> > >> details):<br>
> > >><br>
> > >> -------------------------------------------------------------------------------<br>
> > >> Error running make on NetCDF: Could not execute "cd<br>
> > >> /projects/fako9399/petsc-3.3-p3/externalpackages/netcdf-4.1.1 &&<br>
> > >> AR="/usr/bin/ar" ARFLAGS="cr"<br>
> > >> CC="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicc" CFLAGS="<br>
> > >> -fPIC -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O<br>
> > >> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include<br>
> > >> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."<br>
> > >> CXX="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicxx"<br>
> > >> CXXFLAGS=" -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O<br>
> > >> -fPIC -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include<br>
> > >> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."<br>
> > >> FC="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpif90" FCFLAGS="<br>
> > >> -fPIC -Wno-unused-variable -O<br>
> > >> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include<br>
> > >> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."<br>
> > >> F90="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpif90"<br>
> > >> ./configure --prefix=/projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt<br>
> > >> --libdir=/projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt/lib<br>
> > >> --disable-dap --enable-shared":<br>
> > >> configure: netCDF 4.1.1<br>
> > >> checking build system type... x86_64-unknown-linux-gnu<br>
> > >> checking host system type... x86_64-unknown-linux-gnu<br>
> > >> checking for a BSD-compatible install... /usr/bin/install -c<br>
> > >> checking whether build environment is sane... yes<br>
> > >> checking for a thread-safe mkdir -p... /bin/mkdir -p<br>
> > >> checking for gawk... gawk<br>
> > >> checking whether make sets $(MAKE)... yes<br>
> > >> configure: checking user options<br>
> > > >checking whether CXX is set to ''... no<br>
> > >> checking whether FC is set to ''... no<br>
> > >> checking whether F90 is set to ''... no<br>
> > >> checking whether a NCIO_MINBLOCKSIZE was specified... 256<br>
> > >> checking whether udunits is to be built... no<br>
> > > >checking if fsync support is enabled... yes<br>
> > >> checking whether extra valgrind tests should be run... no<br>
> > >> checking whether libcf is to be built... no<br>
> > >> checking whether reading of HDF4 SD files is to be enabled... no<br>
> > >> checking whether to fetch some sample HDF4 files from Unidata ftp site to<br>
> > > >test HDF4 reading (requires wget)... no<br>
> > >> checking whether parallel I/O for classic and 64-bit offset files using<br>
> > >> parallel-netcdf is to be enabled... no<br>
> > > >checking whether a location for the parallel-netcdf library was<br>
> > >> specified... no<br>
> > >> checking whether new netCDF-4 C++ API is to be built... no<br>
> > > >checking whether extra example tests should be run... no<br>
> > > >checking whether parallel IO tests should be run... no<br>
> > > >checking whether a location for the HDF5 library was specified...<br>
> > >> checking whether a location for the ZLIB library was specified...<br>
> > >> checking whether a location for the SZLIB library was specified...<br>
> > >> checking whether a location for the HDF4 library was specified...<br>
> > >> checking whether a default chunk size in bytes was specified... 4194304<br>
> > > >checking whether a maximum per-variable cache size for HDF5 was<br>
> > > >specified... 67108864<br>
> > > >checking whether a number of chunks for the default per-variable cache was<br>
> > >> specified... 10<br>
> > >> checking whether a default file cache size for HDF5 was specified...<br>
> > > >4194304<br>
> > > >checking whether a default file cache maximum number of elements for HDF5<br>
> > > >was specified... 1009<br>
> > > >checking whether a default cache preemption for HDF5 was specified... 0.75<br>
> > > >checking whether netCDF-4 logging is enabled... no<br>
> > > >checking whether a path for curl-config was specified... no<br>
> > > >checking whether a location for curl installation was specified... no<br>
> > > >configure: checking whether a location for curl-config is in PATH... yes<br>
> > > >checking whether DAP client is to be built... no<br>
> > > >checking whether dap remote testing should be enabled (default on)... no<br>
> > > >checking whether the time-consuming dap tests should be enabled (default<br>
> > > >off)... no<br>
> > > >checking whether a location for liboc was specified... no<br>
> > >> checking whether netCDF extra tests should be run (developers only)... no<br>
> > > >checking whether Fortran compiler(s) should be tested during configure...<br>
> > > >yes<br>
> > > >checking whether FFIO will be used... no<br>
> > > >checking whether to skip C++, F77, or F90 APIs if compiler is broken... yes<br>
> > > >checking whether only the C library is desired... no<br>
> > >> checking whether examples should be built... yes<br>
> > >> checking whether F77 API is desired... yes<br>
> > > >checking whether any Fortran API is desired... yes<br>
> > > >checking whether F90 API is desired... yes<br>
> > > >checking whether fortran type sizes should be checked... yes<br>
> > >> checking whether C API is desired... yes<br>
> > >> checking where to get netCDF C-only library for separate fortran<br>
> > >> libraries...<br>
> > > >checking whether CXX API is desired... yes<br>
> > > >checking whether v2 netCDF API should be built... yes<br>
> > > >checking whether the ncgen/ncdump should be built... yes<br>
> > >> checking whether large file (> 2GB) tests should be run... no<br>
> > > >checking whether benchmaks should be run (experimental)... no<br>
> > >> checking whether extreme numbers should be used in tests... yes<br>
> > > >checking where to put large temp files if large file tests are run... .<br>
> > > >checking whether a win32 DLL is desired... no<br>
> > > >checking whether separate fortran libs are desired... yes<br>
> > >> configure: finding C compiler<br>
> > > >checking whether the C compiler works... yes<br>
> > >> checking for C compiler default output file name... a.out<br>
> > > >checking for suffix of executables...<br>
> > > >checking whether we are cross compiling... configure: error: in<br>
> > >> `/projects/fako9399/petsc-3.3-p3/externalpackages/netcdf-4.1.1':<br>
> > > >configure: error: cannot run C compiled programs.<br>
> > > >If you meant to cross compile, use `--host'.<br>
> > > >See `config.log' for more details.<br>
> > >><br>
> > >> *******************************************************************************<br>
> > >><br>
> > > >The configure script is:<br>
> > >><br>
> > > > ./configure --with-clanguage=cxx --with-shared-libraries=1<br>
> > >> --with-dynamic-loading=1 --download-f-blas-lapack=1 --with-mpi-dir=$MPI_DIR<br>
> > >> --known-mpi-shared-libraries=0 --with-batch=1 --download-parmetis=1<br>
> > > >--download-metis=1 --with-64-bit-indices=1 --download-netcdf=1<br>
> > > >--download-exodusii=1 --with-debugging=no --download-ptscotch=1<br>
> > >><br>
> > >> I also attached the file configure.log<br>
> > >><br>
> > > >------------------<br>
> > > >Fande Kong<br>
> > >> ShenZhen Institutes of Advanced Technology<br>
> > > >Chinese Academy of Sciences<br>
> > >><br>
> > >><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
> > -- Norbert Wiener<br>
> > <config.zip><configure.zip><br>
><br>
> </blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<br>