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: $TMPDIR/machines 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. -Chris 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