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I'm using unix server (OS: centos5) and I'm using several clusters.

Some clusters have 8 cores, other are 24 cores and etc.

I execute jobs using this command.

qsub -q cluster_name -d $PWD Program_name

To efficiently use clusters, I'm using OPENMP for parallelization.

Problem is, in most times, my program use only 3 cores at the same time.

It means, I'm wasting computational power a lot.

When I use my PC (Ubuntu) not clusters,

I maximize efficiency, by using in the following way.

OPEN TERMINAL
export OPM_NUM_THREAD=A
./program_name

However, I don't know how to apply this method to the clusters.

Therefore, I want to use clusters in the following way. 

./Execute.sh

And Execute.sh is,

SET_NUMBER_OF_CORE_FOR_PROGRAM1
qsub -q cluster_name -d $PWD Program_name1&
SET_NUMBER_OF_CORE_FOR_PROGRAM2
qsub -q cluster_name -d $PWD Program_name2&
...
SET_NUMBER_OF_CORE_FOR_PROGRAMn
qsub -q cluster_name -d $PWD Program_namen&

at least I hope I can set same number of core for all programs.

If you know how to do this, please let me know.

Thank you for reading,

user2268721.

user2268721
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  • From [this](http://manuals.bioinformatics.ucr.edu/home/hpc) it seems you can specify the number of cores to be used... – Stark07 Dec 30 '14 at 05:40
  • Search for "Example: Requesting A Single Node with 8 Processors" in that page. I cross checked in the qsub man page, and that option is indeed available. – Stark07 Dec 30 '14 at 05:41

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