[petsc-users] oddities with MPI

[Lukas van de Wiel]

Hi guys,

apparently the newer systems need libnl installed, which has 'end' and
potentially other things needed by openmpi.

sudo apt-get install libnl-3-dev

will fix it in Debian.

Best wishes
Lukas

On 11/27/17, Lukas van de Wiel <lukas.drinkt.thee at gmail.com> wrote:
> Good day!
>
> configuring PETSc 3.8.2 gives a spot of a bother with the openMPI bit
> and I wondered if other PETSc users experienced the same issue.
> Although PETSc does not appear to be to blame for this, this mailing
> list seemed a logical place to mention it in the hope that somebody
> may already have found a trivial solution. Otherwise I will just dig
> deeper:
>
> My standard configure script:
>
>
> ./configure  \
> COPTFLAGS='-O3 -march=native -mtune=native' \
> CXXOPTFLAGS='-O3 -march=native -mtune=native' \
> FOPTFLAGS='-O3 -march=native -mtune=native' \
> --with-debugging=0 \
> --with-x=0 \
> --with-ssl=0 \
> --with-shared-libraries=0 \
> --download-metis \
> --download-parmetis \
> --download-fblaslapack \
> --download-scalapack \
> --download-openmpi \
> --download-mumps \
> --download-hypre \
> --download-ptscotch
>
> which works perfectly on our compute cluster, which runs Slackware
> Linux 13.37.0, from 2011... and mpif90 wrapping to GCC 4.5.2. I
> know... don't ask...
>
> However, on more modern machines, such a Debian 9 machine I test with,
> and a Mac OS X machine from one of our users, all with contemporary
> GCC versions, give issues when compiling the openmpi part:
>
> /usr/bin/ld: ../../../oshmem/.libs/liboshmem.a(memheap_base_static.o):
> undefined reference to symbol '_end'
> //usr/lib/x86_64-linux-gnu/libnl-route-3.so.200: error adding symbols:
> DSO missing from command line
>
> (see attached the full configure.log from one of the Debian 9 machines)
>
> I would expect that our archaic Slackware cluster has trouble
> compiling recent PETSc version, and the newer machines would
> experience less problems, but exactly the opposite is true.
>
> Has anybody run into similar issues?
>
> Best wishes
>
> Lukas
>