[Bioclusters] mpiblast w/ SGE problem?

Iddo Friedberg idoerg at gmail.com
Thu Oct 18 16:08:10 EDT 2007


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

#$ -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





I. Friedberg

"The only problem with troubleshooting is that
sometimes trouble shoots back."

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