Hi all friends,
I am trying to run Interproscan (interproscan-5.14-53.0) on the cluster for searching a protein sequence file against Pfam and ProDom databases. Our cluster is SGE, so I specified it in the "properties file" based on the manual of the program. Also, I changed the number of CPU from 2 (default) to 10 in the properties file. I submitted the program via the below script:
#!/bin/bash
#$ -S /bin/bash
#$ -N run_in
#$ -q ltime.q
#$ -cwd
#$ -o output_in.dat
#$ -j no
#$ -pe mpi 27
#$ -v OMP_NUM_THREADS=$NSLOTS
cd /home/seta/software/interproscan-5.14-53.0
./interproscan.sh -mode cluster -clusterrunid i567 -i prot_seq.pep -t p -o prot_out.xmxl -f xml -appl Pfam, ProDom -goterms -iprlookup
But when I checked the job, it sounds that defined CPU numbers (10 in the properties file or 27 in the script) is not used by the program. I'm very concerned about the running time. Please kindly tell me how I can reduce the time and run the job as fast as possible?
Thank you in advance