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Contents Bulletin Scripting in shell and Perl Network troubleshooting History Humor

SGE Jobs

News Grid Engine Recommended Links SGE Troubleshooting Job stuck in the queue problem Job or Queue Reported in Error State E Monitoring and Controlling Jobs
Why Won't My Jobs Run ? Job Post Mortem Queue states Starting and Killing SGE Daemons Monitoring Queues Queue instance in AU state Viewing SGE Job Output
qmod qdel qalter -- Change Job Priority Submitting parallel OpenMPI jobs SGE Submit Scripts SGE preventing oversubscription in two queues for the same hosts Excluding SGE queue from scheduling
qsub  qstat Enabling schedd_job_info Execution hosts SGE hostgroups SGE Resource Quota Sets sge_conf
Monitoring Queues and Jobs Starting and Killing SGE Daemons SGE cheat sheet Tips History Humor Etc

Introduction

qalter -w v <jobid>      This command enlists the reasons why a job is not dispatchable in principle.

Listing of all jobs

qstat -u '*'

Deletion of jobs

Sometimes we want to delete a job before its running. For this you can use the

      qdel job_id

command.

      qdel 903

The example deletes the job number 903.

      qdel -f 903

Clearing error status

To clear error status of the job you can use qmod

Command qmod enables users classified as owners (see queue_conf(5) for details) to modify the state of Grid Engine queues for his/her machine as well as the state of his/her own jobs. This command send a signal to a running job :

qmod -sj | -usf | -cd  # suspend | unsuspend | clear error

A manager/operator or root can execute qmod for any queue and job in a cluster but only from administrative hosts. Find additional information concerning wc_queue_list and wc_job_list in sge_types(1).

To disable queue use qmod -d Q. To enable back the queue, you can use qmod -e Q.

For example

qmod -e all.q@node23    # enable node23 in queue all.q (-d == disable)
> qmod -sj 1277
santaklaus - suspended job 1277
> qmod -usj 1277
santaklaus - unsuspended job 1277
# qmod -e comp-pvfs-*
Queue "comp-pvfs-0-0.q" has been enabled by root@frontend-0.local
root - queue "comp-pvfs-0-1.q" is already enabled
root - queue "comp-pvfs-0-2.q" is already enabled
[root@frontend-0 root]# qstat -f
queuename            qtype used/tot. load_avg arch      states
----------------------------------------------------------------------------
comp-pvfs-0-0.q      BIP   0/2       0.10     glinux      
----------------------------------------------------------------------------
comp-pvfs-0-1.q      BIP   0/2       0.58     glinux     
----------------------------------------------------------------------------
comp-pvfs-0-2.q      BIP   0/2       0.02     glinux     
----------------------------------------------------------------------------
frontend-0.q         BIP   0/2       0.01     glinux

For more information in using SGE, please refer to the SGE documentation and the man pages.

General syntax

qmod  [  options  ] [  wc_job_range_list  |  wc_queue_list ] 

Options

Altering the priority of the job

qalter -- Change Job Priority


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[May 07, 2017] Monitoring and Controlling Jobs

biowiki.org

After submitting your job to Grid Engine you may track its status by using either the qstat command, the GUI interface QMON, or by email.

Monitoring with qstat

The qstat command provides the status of all jobs and queues in the cluster. The most useful options are:

You can refer to the man pages for a complete description of all the options of the qstat command.

Monitoring Jobs by Electronic Mail

Another way to monitor your jobs is to make Grid Engine notify you by email on status of the job.

In your batch script or from the command line use the -m option to request that an email should be send and -M option to precise the email address where this should be sent. This will look like:

#$ -M myaddress@work
#$ -m beas

Where the (-m) option can select after which events you want to receive your email. In particular you can select to be notified at the beginning/end of the job, or when the job is aborted/suspended (see the sample script lines above).

And from the command line you can use the same options (for example):

qsub -M myaddress@work -m be job.sh

How do I control my jobs

Based on the status of the job displayed, you can control the job by the following actions:

Monitoring and controlling with QMON

You can also use the GUI QMON, which gives a convenient window dialog specifically designed for monitoring and controlling jobs, and the buttons are self explanatory.


For further information, see the SGE User's Guide ( PDF, HTML).


[Sep 19, 2014] Bug in Univa Grid engine

There are some differences between Univa and Sun Grid Engine 6.2u7 queue structure:

You can't directly import a queue from Oracle grid engine to Univa grid engine. The structure of the queue is slightly different.



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