Re: [Libmesh-users] metis and libmesh installed

[John P. <jwp...@gm...>]

On Thu, Sep 20, 2018 at 9:19 AM Mauro Cacace <ca...@gf...> wrote:

> Hi John,
>
> thanks for the quick reply.
>
> Please find attached the config.log.
>
> I will ask the IT admin for granting you access to the cluster.
>

Thanks.

In the meantime I can try and explain what we currently do to avoid this
issue. If you look at the value of the libmesh_optional_LIBS variable in
your config.log, you should see something like the following (newlines
added for readability):

-lglpk
-lz
-L/cluster/petsc/petsc-3.9.3/lib
-Wl,-rpath,/cluster/petsc/petsc-3.9.3/lib
-Wl,-rpath,/opt/intel/ipsxe_2017_update1/compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib/debug_mt
-L/opt/intel/ipsxe_2017_update1/compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib/debug_mt
-Wl,-rpath,/opt/intel/ipsxe_2017_update1/compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib
-L/opt/intel/ipsxe_2017_update1/compilers_and_libraries_2017.1.132/linux/mpi/intel64/lib
-Wl,-rpath,/opt/gcc/gcc-7.2.0/lib/gcc/x86_64-pc-linux-gnu/7.2.0
-L/opt/gcc/gcc-7.2.0/lib/gcc/x86_64-pc-linux-gnu/7.2.0
-Wl,-rpath,/opt/gcc/gcc-7.2.0/lib64
-L/opt/gcc/gcc-7.2.0/lib64
-Wl,-rpath,/opt/intel/ipsxe_2017_update1/impi/2017.1.132/intel64/lib
-L/opt/intel/ipsxe_2017_update1/impi/2017.1.132/intel64/lib
-Wl,-rpath,/opt/intel/ipsxe_2017_update1/ipp/lib/intel64
-L/opt/intel/ipsxe_2017_update1/ipp/lib/intel64
-Wl,-rpath,/opt/intel/ipsxe_2017_update1/tbb/lib/intel64/gcc4.1
-L/opt/intel/ipsxe_2017_update1/tbb/lib/intel64/gcc4.1
-Wl,-rpath,/opt/intel/ipsxe_2017_update1/mkl/lib/intel64
-L/opt/intel/ipsxe_2017_update1/mkl/lib/intel64
-Wl,-rpath,/opt/intel/ipsxe_2017_update1/mkl/interfaces/fftw3xf
-L/opt/intel/ipsxe_2017_update1/mkl/interfaces/fftw3xf
-Wl,-rpath,/opt/gcc/gcc-7.2.0/lib
-L/opt/gcc/gcc-7.2.0/lib
-Wl,-rpath,/opt/intel/mpi-rt/2017.0.0/intel64/lib/debug_mt
-Wl,-rpath,/opt/intel/mpi-rt/2017.0.0/intel64/lib
-lpetsc
-lcmumps
-ldmumps
-lsmumps
-lzmumps
-lmumps_common
-lpord
-lscalapack
-lsuperlu_dist
-lHYPRE
-lspai
-lflapack
-lfblas
-lhdf5hl_fortran
-lhdf5_fortran
-lhdf5_hl
-lhdf5
-lparmetis
-lmetis
-lX11
-lmpifort
-lmpi
-lmpigi
-lrt
-lpthread
-lgfortran
-lm
-lgcc_s
-lquadmath
-lstdc++
-ldl
-Wl,-rpath,/usr/local/lib
-L/usr/local/lib


As you can see, "-L/usr/local/lib" appears *last* in this list, and we
actually do this on purpose to avoid linking in system libraries that may
be in conflict with custom-built software. I was under the impression that
you link against the *first* -lmetis that you come across, and that should
be the one in -L/cluster/petsc/petsc-3.9.3/lib, which comes first in your
link line. This impression may be incorrect, however.

One final comment: the error message you posted comes during the linking of
the meshid-opt executable, so it is possible that there is a libmesh_opt.so
in your libmesh/build/.libs directory? If so, I would be curious what the
output of "ldd" on that shared library is.

-- 
John