SGE Jobs

• Introduction
• Listing of all jobs
• Deletion of jobs
• Clearing error status
• Altering the priority of the job

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 [email protected]
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

• -cj Clears the error state of the specified jobs(s).
• -cq  Clears the error state of the specified queue(s).
• -d  Disables the queue(s), i.e. no further jobs are dispatched to disabled queues while jobs already executing in these queues are allowed to finish.
• -e  Enables the queue(s).
• -f  Force the modification action for the queue despite the apparent current state of the queue. For example if a queue appears to be suspended but the job execution seems to be continuing the manager/operator can force a suspend operation which will send a SIGSTOP to the jobs. In any case, the queue or job status will be set even if the ge_execd(8) controlling the queues/jobs cannot be reached. Requires manager/operator privileges.
• -help  Prints a listing of all options.
• -rj If applied to running jobs, reschedules the jobs. Requires root or manager privileges.
• -rq  If applied to queues, reschedules all jobs currently running in this queue. Requires root or manager privileges.
• -sj  If applied to running jobs, suspends the jobs. If a job is both suspended explicitly and via suspension of its queue, a following unsuspend of the queue will not release the suspension state on the job.
• -sq  If applied to queues, suspends the queues and any jobs which might be active.
• -usj  If applied to jobs, unsuspends the jobs. If a job is both suspended explicitly and via suspension of its queue, a following unsuspend of the queue will not release the suspension state on the job.
• -usq  If applied to queues, unsuspends the queues and any jobs which might be active.

Altering the priority of the job

qalter -- Change Job Priority

NEWS CONTENTS

• 20170507 : Monitoring and Controlling Jobs ( biowiki.org )
• 20140919 : Bug in Univa Grid engine ( Sep 19, 2014 )

Old News ;-)

[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:

• qstat: Displays list of all jobs with no queue status information.
• qstat -u hpc1***: Displays list of all jobs belonging to user hpc1***
• qstat -f: gives full information about jobs and queues.
• qstat -j [job_id]: Gives the reason why the pending job (if any) is not being scheduled.

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:

• Modify a job: As a user, you have certain rights that apply exclusively to your jobs. The Grid Engine command line used is qmod. Check the man pages for the options that you are allowed to use.

• Suspend/(or Resume) a job: This uses the UNIX kill command, and applies only to running jobs, in practice you type

  qmod -s/(or-r)job_id (where job_id is given by qstat or qsub).

• Delete a job: You can delete a job that is running or spooled in the queue by using the qdel command like this

  qdel job_id (where job_id is given by qstat or qsub).

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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Last modified: March 12, 2019