Question: OMA error message
0
gravatar for ni
19 days ago by
ni0
ni0 wrote:

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       
../bin/oma /home/username/OMA.2.1.1/parameters.drw

and then: qsub file.sh

Can someone help me with this?

Thanks!

ortholog oma • 222 views
ADD COMMENTlink modified 11 days ago • written 19 days ago by ni0
0
gravatar for adrian.altenhoff
18 days ago by
Switzerland
adrian.altenhoff300 wrote:

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.

ADD COMMENTlink written 18 days ago by adrian.altenhoff300
0
gravatar for ni
11 days ago by
ni0
ni0 wrote:

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!

ADD COMMENTlink written 11 days ago by ni0
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