asked on

Looping a shell script

Hi,

I have a shell script (pipeline.sh) located in the following directory:

/fs/nas15/home/mqbpgsm4/permanalysis/bin

I would like to run 1000 instances of this script on a linux server by submitting it to a queue using Qsub 1000 times.

i.e:
qsub -b y (/directory/permanalysis/bin) -N perm1 sh pipeline.sh

I would like to loop it so that the job is submitted to server 1000 times:
i.e.

qsub -b y (/directory/permanalysis/bin) -N perm1 sh pipeline.sh
qsub -b y (/directory/permanalysis/bin) -N perm2 sh pipeline.sh
qsub -b y (/directory/permanalysis/bin) -N perm3 sh pipeline.sh
to
qsub -b y (/directory/permanalysis/bin) -N perm1000 sh pipeline.sh

Is this at all possible?

Thanks,

Stephen

Xizz

Hi Stephen,

You could try something like this:

#!/bin/bash
for ((i=1;i<=1000;i++));
do
   qsub -b y (/directory/permanalysis/bin) -N $i sh pipeline.sh
done

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Tintin

for i in $(seq 1 1000)
do
   qsub -b y (/directory/permanalysis/bin) -N $i sh pipeline.sh
done

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Peter Kwan

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StephenMcGowan

ASKER

Hi Guys,

Thanks for getting back to me.

Would I need to define the bin folder for the location of pipeline.sh?

i.e:

#define pipeline.sh location
$directory=~/fs/nas15/home/mqbpgsm4/permanalysis/bin

X=1
while [ $X -le 1000 ];
do
    eval "qsub -b y $directory -N perm$X sh pipeline.sh"
    X=`expr $X + 1`
done

Open in new window

Thanks,

Stephen

Xizz

Yes you could do that, otherwise place the script in the same folder.

StephenMcGowan

ASKER

Sorry,

Just to double check, would the attached file work ok?
I just want to double check this out before potentially submitting 1000 jobs to the server.

Thanks again,

Stephen
loopscript.sh