One thing to note is that one cannot use scratch on the m9000 – so jobs must be run in the user's home (or a sub-directory of home).

Your job script will look something like this¹⁾:

my_job.qsub

#! /bin/bash
#PBS -l select=1:ncpus=128:mpiprocs=128:jobtype=spark
#PBS -l place=free
#PBS -l walltime=06:00:00
#PBS -q spark
#PBS -o /export/home/username/blastjob/stdout.txt
#PBS -e /export/home/username/blastjob/stderr.txt
#PBS -M youremail@address.com
#PBS -m be
#PBS -N m9000_blast
 
# NOTE: Scratch doesn't exist on m9000 -- so run in your home, or a subdir of home
cd /export/home/username/blastjob
NP=`cat $PBS_NODEFILE | wc -l`
 
EXE="/opt/gridware/bioinformatics/m9000/ncbi-blast-2.2.24/bin/blastx"
ARGS="-db /opt/gridware/bioinformatics/db/blast/nr -query my_seqs.fasta -evalue 0.001 -num_alignments 20 -outfmt 5 -num_threads ${NP} > my_results.xml"
 
$EXE $ARGS

Of course one should set the parameters as required. (Setting a small evalue is recommended as is limiting the number of alignments). For blast2go users remember to set -outfmt to 5 for XML output. Note one should also select the correct EXEcutable and -db: blastx, blastn and blastp are available for the former, while nr and nt are available for the latter.

Finally submit your job using:

user@login01:~ $ msub my_job.msub