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Question: Tunnel qsub commands
1
gravatar for manuel.pasieka
22 months ago by
manuel.pasieka • 30
manuel.pasieka • 30 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 • 746 views
ADD COMMENT • link •
modified 22 months ago by Nate Coraor ♦ 3.2k • written 22 months ago by manuel.pasieka • 30
3
gravatar for Nate Coraor
22 months ago by
Nate Coraor ♦ 3.2k
United States
Nate Coraor ♦ 3.2k 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 COMMENT • link written 22 months ago by Nate Coraor ♦ 3.2k

Thank you, I am currently investigating this option.

ADD REPLY • link written 22 months ago by manuel.pasieka • 30

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 REPLY • link modified 22 months ago • written 22 months ago by manuel.pasieka • 30
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