[Bioclusters] mpiblast w/ SGE problem?

Chris Dagdigian dag at sonsorol.org
Thu Oct 18 17:26:37 EDT 2007

The biggest problem I see in that job script is that you are pointing  
mpiblast at a manually generated MPI machines file rather than the  
custom one that would get created by the pe_starter method in your  
parallel environment.

When the SGE scheduler creates your custom machines file (telling  
mpiblast where to place the tasks) the location is here:


So your mpirun command would have to contain:

mpirun -np $NSLOTS -machinefile $TMPDIR/machines <rest of command ..>

There is no point integrating a MPI app into Grid Engine unless the  
Grid Engine scheduler gets to pick which machines get the parallel  
task(s) :)

I also don't see a "#$ -pe <parallel environment>" request within the  
SGE job script; were you requesting one via the qsub command?

The other thing to look out for is the format of the machines file  
that SGE creates -- it may or may not include the fully qualified  
domain name and it may or may not be in the exact format that your  
particular MPI installation expects. You can control the format of  
the machines file by just looking at the source code for the script  
that is being run as the pe_starter method within the configuration  
of your parallel environment.


On Oct 18, 2007, at 4:08 PM, Iddo Friedberg wrote:

> hi,
> I am trying to run mpiblast on a ROCKS cluster using SGE. mpiblast  
> seems to
> be running well, but all slots are being run on a single node for some
> reason! Can anyone help? Full disclosure: newbie to mpi, mpiblast,  
> and SGE.
> Here is the command line I use:
> % qsub -pe mpich 10 mpiblast_sge.sh
> And here is the  shell script mpiblast_sge.sh
> ----------------------------------------------------------------------
> #!/bin/bash
> #$ -cwd
> #$ -j y
> #$ -S /bin/bash
> export MPI_DIR=/opt/mpich/gnu/
> # export BLASTDB=/share/bio/ncbi/db/
> export BLASTDB=/home/thumper1/users/idoerg/databases/STRING
> export BLASTMAT=/opt/Bio/ncbi/data
> export THOME=/home/thumper1/users/idoerg
> export P4_GLOBMEMSIZE=256000000
> $MPI_DIR/bin/mpirun -np $NSLOTS -machinefile
> /home/thumper1/users/idoerg/tmp/machines /opt/Bio/mpiblast/bin/ 
> mpiblast -d
> protein.sequences.v7.0.fa \
>         -i $THOME/databases/STRING/top_c60_test_1000.tfa -m 7 -p  
> blastp -o
> $THOME/databases/STRING/top_c60_test_1000.blast.xml
> ---------------------------------------------------------------------- 
> ---------------------------------------------------
> Thanks,
> Iddo
> -- 
> I. Friedberg
> "The only problem with troubleshooting is that
> sometimes trouble shoots back."
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

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