Altering jobs that are in the queue

Wed 15 August 2012 by Dr. Dirk Colbry

Blog post edited by Anonymous - "Migration of unmigrated content due to installation of a new plugin"

Recently a user came by my office to complain that his jobs where not running in the queue. This is a reasonable complainte because many of our nodes are being drained to reboot and avoid the 208 day bug. Fortunately this user had a lot of single threaded jobs that could run on the gfx10 nodes. To run on these nodes the user needs to change the jobs to add the feature=gbe option (Gigabyte either-net). First I tried the following command:

qalter -l feature=gbe $PBS_JOBID

Unfortunately,the qalter command modifies jobs in the resource manager but the job is waiting on the scheduler. I had hoped that the scheduler would talk to the resouce manager and update the properties but this did not happen. After talking with others in the office we found the command to alter jobs in the scheduler:

 mjobctl -m feature=gbe $PBS_JOBID

This worked great and propagated all changes to the resource manager. I wrote a quick script to change all nodes currently pending in the queue to accept add this change:

#!/bin/bash -l
for job in `qselect -s Q -u $USER`;
     echo mjobctl -m feature=gbe $job
     mjobctl -m feature=gbe $job

I added a qalter_all_gbe command to powertools to help users do the same thing on the hpcc.

  • Dirk

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Blogpost migrated from ICER Wiki using custom python script. Comment on errors below.