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."