[Bioclusters] mpiblast w/ SGE problem?

[Wilfred Li]

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."
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