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 <mat...@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@beowulf.org sponsored by Penguin Computing > To change your subscription (digest mode or unsubscribe) visit > https://beowulf.org/cgi-bin/mailman/listinfo/beowulf _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscription (digest mode or unsubscribe) visit https://beowulf.org/cgi-bin/mailman/listinfo/beowulf
