[maker-devel] maker MPI

[Carson Holt]

LAMMPI is pretty much dead, even their website recommends using OpenMPI
instead.

For installing MAKER with OpenMPI you need to set a couple of
environmental variables before MAKER setup.

export OMPI_MCA_mpi_warn_on_fork  0
export LD_PRELOAD /software/openmpi-1.4.3/lib/libmpi.so:$LD_PRELOAD

These not only need to be set before compilation, but also before any run
(so add them to you ~/.bashrc or ~/.bash_profile or any module load
scripts thanks).  The LD_PRELOAD statement needs to be set for any program
using OpenMPI's shared libraries and not just MAKER, so it's normally a
good idea to have that set system wide for all users.  The detail can be
Found in the OpenMPI documentation.  Note sometimes system library updates
can break OpenMPI's shared libraries while not breaking OpenMPI itself, so
you might also need to recompile OpenMPI if it has broken shared libraries.

Thanks,
Carson


On 13-02-04 6:48 PM, "Kathryn E. Bushley"
<bushleyk at science.oregonstate.edu> wrote:

>Greetings,
>
>We are reinstalling maker after a system upgrade and having some
>issues with getting MPI version running.  One question, will maker
>only run in MPI-CH2 or will it also run in LAM-MPI?  When trying to
>run in MPI-CH2, we get this error:
>
>/local/cluster/mpich2-1.2.1p1/bin/mpdboot -f
>/home/bpp/bushleyk/MPI2/fungi0_machinefile.txt
>cd /pseudospace2/bushleyk/MAKER/Testrun;
>/local/cluster/mpich2-1.2.1p1/bin/mpiexec -machinefile
>/home/bpp/bushleyk/MPI2/fungi0_machinefile.txt -n 4
>'/local/cluster/MAKER_2.10/bin/mpi_maker'
>/usr/bin/perl: symbol lookup error:
>/local/cluster/MAKER_2.10/bin/../perl/lib/auto/Parallel/MPIcar/MPIcar.so:
> 
>undefined symbol: Perl_Tstack_sp_ptr
>/usr/bin/perl: symbol lookup error:
>/local/cluster/MAKER_2.10/bin/../perl/lib/auto/Parallel/MPIcar/MPIcar.so:
> 
>undefined symbol: Perl_Tstack_sp_ptr
>/usr/bin/perl: symbol lookup error:
>/local/cluster/MAKER_2.10/bin/../perl/lib/auto/Parallel/MPIcar/MPIcar.so:
> 
>undefined symbol: Perl_Tstack_sp_ptr
>/usr/bin/perl: symbol lookup error:
>/local/cluster/MAKER_2.10/bin/../perl/lib/auto/Parallel/MPIcar/MPIcar.so:
> 
>undefined symbol: Perl_Tstack_sp_ptr
>make: *** [maker] Error 127
>
>which maybe means it's not finding the right perl?
>
>
>When trying to run in LAM-MPI we get this error, was wondering what
>the MAKER/EVALUATOR is?
>
>ERROR: Cannot start process. MAKER/EVALUATOR already running
>with different settings in this same directory.
>
>
>FATAL ERROR
>running  repeat masker.
>#--------- command -------------#
>Widget::RepeatMasker:
>/local/cluster/spatafora/RepeatMasker/RepeatMasker
>/pseudospace2/bushleyk/MAKER/Testrun/dpp_contig.maker.output/dpp_contig_da
>tastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-50
>0-500.0.all.rb -species all -dir
>/pseudospace2/bushleyk/MAKER/Testrun/dpp_contig.maker.output/dpp_contig_da
>tastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa
>1
>#-------------------------------#
>--------------------------------------------------------------------------
>---
>It seems that [at least] one of the processes that was started with
>mpirun did not invoke MPI_INIT before quitting (it is possible that
>more than one process did not invoke MPI_INIT -- mpirun was only
>notified of the first one, which was on node n0).
>
>mpirun can *only* be used with MPI programs (i.e., programs that
>invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
>to run non-MPI programs over the lambooted nodes.
>--------------------------------------------------------------------------
>---
>Received SIGTERM
>make: *** [maker_new] Error 252
>
>
>
>
>
>
>
>
>Best,
>
>Kathryn
>
>
>"To err is human...to really foul up requires the root password."
>
>
>Kathryn E. Bushley
>Postdoctoral Researcher
>2082 Cordley Hall
>Department of Botany and Plant Pathology
>Oregon State University
>Corvallis, OR 97331
>office: (541) 737-5284
>cell: (541) 908-0116
>
>
>
>
>
>
>
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