[Bioclusters] mpiblast w/ SGE problem?

[Iddo Friedberg]

I tried with an without specifying the machine file (i.e. I also did a
-machinefile $TMPDIR/machines. No go.

The manual didn't really help either...

On 10/18/07, Wilfred Li <wilfred at sdsc.edu> wrote:
>
> http://www.rocksclusters.org/roll-documentation/bio/4.3/mpiblast_usage.h
> tml here is the rocks documentation. Like Chris mentioned, you don't
> need to specify the machine file, which probably only has one node
> listed?
>
> Regards,
>
> Wilfred
>
>         -----Original Message-----
>         From: bioclusters-bounces+wilfred=sdsc.edu at bioinformatics.org
>         [mailto:bioclusters-bounces+wilfred=sdsc.edu at bioinformatics.org]
> On
>         Behalf Of Iddo Friedberg
>         Sent: Thursday, October 18, 2007 1:08 PM
>         To: bioclusters at bioinformatics.org
>         Subject: [Bioclusters] mpiblast w/ SGE problem?
>
>         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
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>



-- 

I. Friedberg

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