Question: Tunnel qsub commands
1
gravatar for manuel.pasieka
20 months ago by
manuel.pasieka30 wrote:

Hi,

I have a cluster/system configuration where the node running galaxy has no direct way to submit jobs onto a cluster (running PBSPro), but has ssh access to another node that does.

I hoped to be able to tunnel the qsub and qstat calls made by galaxy to the other node, by replacing the qsub and qstat commands on the galaxy node by a simple wrapper scrippt of the form

#!/bin/bash
ssh cluser_node "qsub $@"

This seems to work by using qsub by hand, but I get strange errors about drmma initialization problems

Does Galaxy need more? than qsub and qstat?

thx, Manuel

ssh tunnel • 678 views
ADD COMMENTlink modified 20 months ago by Nate Coraor3.2k • written 20 months ago by manuel.pasieka30
3
gravatar for Nate Coraor
20 months ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:

Hi Manuel,

I'd suggest you take a look at the CLI job runner. It is documented in job_conf.xml.sample_advanced and is designed to do exactly what you're looking to do here.

ADD COMMENTlink written 20 months ago by Nate Coraor3.2k

Thank you, I am currently investigating this option.

ADD REPLYlink written 20 months ago by manuel.pasieka30

Hello Nate. Thank you for your reply. I can now confirm that using the CLI job runner would be a valid solution. Only that the job plugin is currently only available for the Torque interface and is not working for PBSPro out of the box. I am currently writing a port of the job plugin for PBSPro.

ADD REPLYlink modified 20 months ago • written 20 months ago by manuel.pasieka30
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