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Re: parallel + blast + LSF


From: Giuseppe Aprea
Subject: Re: parallel + blast + LSF
Date: Wed, 15 Apr 2015 17:35:11 +0200

Hi Martin,

I am not sure I understand. As far as I can see, things work exactly the opposite way: you have an LSF script which launches GNU Parallel on some hosts provided by LSF. Something like:

-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
#!/bin/bash

#BSUB -J gnuParallel_blast_test      # Name of the job.
#BSUB -o %J.out                              # Appends std output to file %J.out. (%J is the Job ID)
#BSUB -e %J.err                               # Appends std error to file %J.err.
#BSUB -q large                                 # Queue name.
#BSUB -n 30                                      # Number of CPUs.

module load 4.8.3/ncbi/12.0.0
module load 4.8.3/parallel/20150122

SLOTS=`cat ${LSB_DJOB_HOSTFILE} |wc -l`

SERVER=""

for i in `cat ${LSB_DJOB_HOSTFILE}| sort`
do
echo "/afs/enea.it/software/bin/blaunch.sh ${i}" >> servers
done 

cat absolute_path_to_sequences.fasta | parallel --no-notice -vv -j ${SLOTS} --slf servers --plain --recstart '>' -N 1 --pipe blastp -evalue 1e-05 -outfmt 6 -db absolute_path_to_db_file -query - -out absolute_path_to_result_file_{%}
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------

LSF is the one which gives you the execution hosts so if you are launching bsub from GNU parallel how do you know how to set the --slf option?


g



On Wed, Apr 15, 2015 at 4:24 PM, Martin d'Anjou <address@hidden> wrote:
On 15-04-15 09:34 AM, Giuseppe Aprea wrote:
Hi all,

I would like to ask you, please, some help in using parallel with blast alignment software.


I am trying to use GNU parallel v. 20150122 with blast for a very large sequences alignment. I am using Parallel on a cluster which uses LSF as queue system.

Hello Giuseppe,

I am an avid LSF user, and I want to use GNU Parallel to dispatch jobs to LSF. Could you please explain a little bit to me how GNU Parallel works with LSF? I do not see it in the on-line tutorials. For example, I would like to understand how to pass "bsub" options like -oo, -q queue_name, etc. to LSF from GNU Parallel.

Thanks,
Martin




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