[Beowulf] perl with OpenMPI gotcha?

Michael Di Domenico mdidomenico4 at gmail.com
Mon Nov 23 14:12:39 UTC 2020

if you're referencing this module


which hasn't been updated since 2011, i would suspect there's
something wrong in the perl<->mpi library exchange that will prevent
this from working.

i have a vague recollection of trying this way back when and it barely
worked back then.

i can't suggest a solution though, i'm not sure i understand what
you're trying to do.

On Fri, Nov 20, 2020 at 4:43 PM David Mathog <mathog at caltech.edu> wrote:
> I'm hoping one of you has been to the end of this road already and can
> point out what is going wrong.
> I have some perl scripts which have been carried along for a couple of
> decades now which use PVM to start simple jobs on the compute nodes, wait
> for them to finish (listing jobs as they close out), and then cleans
> up.  Since this is the only thing which PVM is used for it seemed like it
> might be (way past) time to migrate that to MPI, specifically OpenMPI
> 4.0.1, which is what is on the cluster.
> There are apparently tricks required, either that, or the test script
> does not run on a single standalone machine, or perhaps OpenMPI is not
> configured right?
> There are already modules for OpenMPI and bioperl, and I decided to
> install Parallel::MPI::Simple into the latter, since it holds all the perl
> modules which were not installed with dnf on this CentOS 8 system.  Like so:
>    module load bioperl
>    module load OpenMPI
>    cd /usr/common/src/perl_modules
>    cpanm -l $ROOT_BIOPERL Parallel::MPI::Simple 2>&1 \
>      | tee install_perl_parallel_mpi_simple_2020_11_20.log
> (no errors or warnings).
> There is a little test program "ic.pl" which comes with Parallel::MPI::Simple,
> however just invoking it turns up that it cannot find Simple.so.  I have
> been down this road before with Perl and MPI with the "Maker" program -
> some libraries must be preloaded or they just will not be found by Perl.
> Once that is done all the missing library and symbol errors go away.  But it still does not run:
> LD_PRELOAD=/usr/common/modules/el8/x86_64/software/bioperl/1.7.7-CentOS-vanilla/lib/perl5/x86_64-linux-thread-multi/auto/Parallel/MPI/Simple/Simple.so:/opt/ompi401/lib/libmpi.so
> $ROOT_BIOPERL/lib/perl5/x86_64-linux-thread-multi/Parallel/MPI/ic.pl
> [poweredge:04423] *** An error occurred in MPI_Send
> [poweredge:04423] *** reported by process [603979777,0]
> [poweredge:04423] *** on communicator MPI_COMM_WORLD
> [poweredge:04423] *** MPI_ERR_RANK: invalid rank
> [poweredge:04423] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
> will now abort,
> [poweredge:04423] ***    and potentially your MPI job)
> Any idea what might be wrong here?
> Also, searching turned up very little information on using MPI with perl.
> (Lots on using MPI with other languages of course.)
> The Parallel::MPI::Simple module is itself almost a decade old.
> We have a batch manager but I would prefer not to use it in this case.
> Is there some library/method other than MPI which people typically use
> these days for this sort of compute cluster process control with Perl
> from the head node?
> Thanks,
> David Mathog
> _______________________________________________
> Beowulf mailing list, Beowulf at beowulf.org sponsored by Penguin Computing
> To change your subscription (digest mode or unsubscribe) visit https://beowulf.org/cgi-bin/mailman/listinfo/beowulf

More information about the Beowulf mailing list