OMA error message
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Entering edit mode
4.2 years ago
ni • 0

Hi, I´m trying to run OMA in a cluster but I got two error:

1- "/home/username/OMA.2.1.1/bin/omadarwin: line 18: ulimit: stack size: cannot modify limit: Operation not permitted"
2- "ERROR: parallel setup must be called with positive integer values"


I just did a file.sh with:

 #!/bin/bash
export NR_PROCESSES=100


and then: qsub file.sh

Can someone help me with this?

Thanks!

oma ortholog • 1.4k views
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Entering edit mode
4.2 years ago

Hi I think these are two issues. I observed that on some SGE setups you need to set the environment variables outside the submission script, prior to calling the qsub command.

The problem about the stacksize is related to the cluster setup. You should try to set the stacksize to the maximal possible size, maybe 64000: ulimit -s 64000

Hope this will help.

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Entering edit mode
4.2 years ago
ni • 0

Hi, Thanks for your answer. I tried to set the environment variables inside the script using "export PATH=\$PATH:/home/username/OMA.2.1.1/OMA/bin" and I had the error that I described about the positive integer values and if I try outside the script it gives me "oma: command not found". This problem happens only with a script.sh, because if I try to run in the same cluster but without the script works well. Any idea to solve this?

Thanks!