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 <[email protected]>
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
>
>
>
