[petsc-users] 3.5.1 fail with mumps

[Satish Balay]

On Sun, 3 Aug 2014, Pascal Paschos wrote:

> Hi,
> 
> I've already seen a thread where someone recently was trying to build with mumps and was failing at test.
> The recommendation that seemed to have worked for that user, at least on this point, was
> a fresh install and shared libraries off. Well, I am having the same problem with 3.5.1 with the same error message he was getting.
> The build can not interpret symbols in some mumps and parmetis references.
> Whether shared libraries is set to 0 or 1 is irrelevant, at least in my case. The problem persists.
> The error messages are in the bottom of this post.
> And yes, all packages are there, otherwise petsc would not build in the first place. It fails a test with an error message that is
> typical of the build missing some include files that it expects to have present.
> Without mumps - metis & parmetis - the install is fine and tests complete fine.
> So, I guess I am wondering if the developers have any more insight to spare...
> Thanks.
> 
> Here is my configure:
> 
> ./configure --prefix=/software/petsc/3.5.1.1  \
> 
> --with-blas-lib=/software/lapack/3.5.0/lib/libblas.so --with-lapack-lib=/software/lapack/3.5.0/liblapack.so \
> 
> --with-hdf5=1 --with-hdf5-dir=/software/hdf5/1.8.10 \
> 
> --with-valgrind=1 --with-valgrind-dir=/software/valgrind/3.8.1 \
> 
> --with-boost=1 --with-boost-dir=/software/boost/1.41.0 \
> 
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 \
> 
> --with-debugging=1 \
> 
> --download-fftw=yes \
> 
> --download-scalapack=yes  \
> 
> --download-mumps=yes \
> 
> --download-parmetis=yes \
> 
> --download-metis=yes \
> 
> --CFLAGS="-I/usr/include -I/usr/include/openssl" \
> 
> --LDFLAGS=" -L/usr/lib64" \
> 
> --LDLIBS=" -lcrypto -lssl" \
> 
> --with-shared-libraries=0
> 
> 
> I found it necessary to pass references to libssl to the linker because otherwise the make is then complaining with an SSL related issue, that it can not find some include file.
> 

you can remove the ssl related options - and use --with-ssl=0

Satish

> 
> 
> make PETSC_DIR=/software/petsc/3.5.1.1 test
> 
> Running test examples to verify correct installation
> 
> Using PETSC_DIR=/software/petsc/3.5.1.1 and PETSC_ARCH=arch-linux2-c-debug
> 
> *******************Error detected during compile or link!*******************
> 
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> 
> /software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/snes/examples/tutorials ex19
> 
> *********************************************************************************
> 
> *********************W-a-r-n-i-n-g*************************
> 
> Your PETSC_DIR may not match the directory you are in
> 
> PETSC_DIR  /software/petsc/3.5.1.1 Current directory /software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/snes/examples/tutorials
> 
> Ignore this if you are running make test
> 
> ******************************************************
> 
> mpicc -o ex19.o -c -I/usr/include -I/usr/include/openssl -g3 -O0   -I/software/petsc/3.5.1.1/include -I/software/petsc/3.5.1.1/include -I/software/valgrind/3.8.1/include -I/software/hdf5/1.8.10/include -I/software/boost/1.41.0/include -I/software/mpi/openmpi-1.6.3-gcc-4.6.3-trq4/include    `pwd`/ex19.c
> 
> mpicc -I/usr/include -I/usr/include/openssl -g3 -O0  -o ex19  ex19.o -L/software/petsc/3.5.1.1/lib  -lpetsc -Wl,-rpath,/software/petsc/3.5.1.1/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -Wl,-rpath,/software/lapack/3.5.0 -L/software/lapack/3.5.0 -llapack -Wl,-rpath,/software/lapack/3.5.0/lib -L/software/lapack/3.5.0/lib -lblas -lparmetis -lmetis -lX11 -lssl -lcrypto -lpthread -lfftw3_mpi -lfftw3 -Wl,-rpath,/software/hdf5/1.8.10/lib -L/software/hdf5/1.8.10/lib -lhdf5_fortran -lhdf5_hl -lhdf5 -L/software/mpi/openmpi-1.6.3-gcc-4.6.3-trq4/lib64 -L/hpc/software/gcc/4.6.3-rhel6/lib/gcc/x86_64-unknown-linux-gnu/4.6.3 -L/hpc/software/gcc/4.6.3-rhel6/lib/gcc -L/hpc/software/gcc/4.6.3-rhel6/lib64 -L/hpc/software/gcc/4.6.3-rhel6/lib -lmpi_f90 -lmpi_f77 -lgfortran -lm -lgfortran -lm -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpi_cxx -lstdc++ -ldl -lmpi -lnuma -lrt -lnsl -lutil -lgcc_s -lpthread -ldl
> 
> /software/petsc/3.5.1.1/lib/libpetsc.a(baij.o): In function `MatCreate_SeqBAIJ':
> 
> /hpc/software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/mat/impls/baij/seq/baij.c:3006: undefined reference to `MatGetFactor_baij_mumps's'
> 
> /software/petsc/3.5.1.1/lib/libpetsc.a(mpibaij.o): In function `MatCreate_MPIBAIJ':
> 
> /hpc/software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/mat/impls/baij/mpi/mpibaij.c:3049: undefined reference to `MatGetFactor_baij_mumps'
> 
> /software/petsc/3.5.1.1/lib/libpetsc.a(sbaij.o): In function `MatCreate_SeqSBAIJ':
> 
> /hpc/software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/mat/impls/sbaij/seq/sbaij.c:1966: undefined reference to `MatGetFactor_sbaij_mumps'
> 
> /software/petsc/3.5.1.1/lib/libpetsc.a(mpisbaij.o): In function `MatCreate_MPISBAIJ':
> 
> /hpc/software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/mat/impls/sbaij/mpi/mpisbaij.c:1803: undefined reference to `MatGetFactor_sbaij_mumps'
> 
> /software/petsc/3.5.1.1/lib/libpetsc.a(aij.o): In function `MatCreate_SeqAIJ':
> 
> /hpc/software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/mat/impls/aij/seq/aij.c:4136: undefined reference to `MatGetFactor_aij_mumps'
> 
> /software/petsc/3.5.1.1/lib/libpetsc.a(mpiaij.o): In function `MatCreate_MPIAIJ':
> 
> /hpc/software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/mat/impls/aij/mpi/mpiaij.c:5578: undefined reference to `MatGetFactor_aij_mumps'
> 
> /software/petsc/3.5.1.1/lib/libpetsc.a(spartition.o): In function `MatPartitioningRegisterAll':
> 
> /hpc/software/sources/builds/petsc-3.5.1_PP/petsc-debug/petsc-3.5.1/src/mat/partition/spartition.c:45: undefined reference to `MatPartitioningCreate_Parmetis'
> 
> 
>