[Beowulf] perl with OpenMPI gotcha?

[Jonathan Engwall]

After looking for ic.pl and not finding it, I clicked on it. You see it in
hypertext. Again found nothing. Everyone seems to agree the code is a
decade old. Perhaps it is an api call to nothing and should be ignored.
Can you find the test program or compile without it? It may be non
existant.
Jonathan Engwall

On Mon, Nov 23, 2020, 6:13 AM Michael Di Domenico <mdidomenico4 at gmail.com>
wrote:

> if you're referencing this module
>
> https://metacpan.org/changes/distribution/Parallel-MPI-Simple
>
> 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
> >
> >
> >
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