Computational Cluster Programs
Commonly-Used SGE Commands
This page lists some of the more frequently used Sun Grid Engine commands. It does not list all of the options for each command. The man command can be used to see the detailed description of any of these commands. For example, to see a detailed description of the qsub command, enter:
man qsub
List of Commands:
qsub Submit a Job qstat Determine the Status of a Job qhost Display Node Information qdel Cancel a Job qhold Place a hold on a queued job to prevent it from running qrls Release a job held with qhold qmon An X-Windows interface to SGE commands
Use the qsub Command to Submit a Job
The qsub command is used to submit jobs to SGE. The syntax of the qsub command is:
qsub [-cwd] [-v SOME_VAR] [-o path] [-e path] [-M mail_address] [-m mail_options] [-l resources] script
Where:
- -cwd
- Directs SGE to run the job in the same directory from which you submitted it. Alternatively, you can specify this flag in the SGE command file for the job.
- -v SOME_VAR
- Passes environment variable SOME_VAR to the job. Alternatively, you can specify this flag in the SGE command file for the job.
- -o path
- Redirects stdout from the SGE script. The default is your home directory. Specify /dev/null to disgard SGE messages. Alternatively, you can specify this flag in the SGE command file for the job.
- -e path
- Redirects stderr from the SGE script. The default is your home directory. Specify /dev/null to disgard SGE error messages. Alternatively, you can specify this flag in the SGE command file for the job.
- -M mail_address
- where mail_address is user's email address. It is always login_id@mail on Hoffman2.
- -m mail_options
- Specifies the circumstances under which mail is to be sent to the job owner defined by -M option. For example options "bea" mean mail is sent at the begining, end, and at abort time (if it happens) of the job. Option "n" means no mail will be sent.
- -l resources
- Specifies a list of resouces required for your job, for example memory and time per core:
-l h_data=1024M,h_rt=24:00:00
- script
- Either the SGE command file or the script that starts up your job.
The qsub command line switches and options can also be used as active comments or embedded directives in an SGE command file that you submit with the qsub command. Advantages of this approach are: you have a record of what options were used to run your job; you can easily resubmit jobs; and you can use one command file as the basis for creating other similar command files. For example, if the file myjob.cmd contains:
#!/bin/csh
/path/to/executable
and the qsub command used to submit it is:
qsub -cwd -o path -M login_id@mail -m bea -l h_data=1024M,h_rt=24:00:00 myjob.cmd
then the same result could be achieved by adding the following lines to the myjob.cmd file before the /path/to/executable line:
#$ -cwd
#$ -o path
#$ -M login_id@mail
#$ -m bea
#$ -l h_data=1024M,h_rt=24:00:00
and submitting the myjob.cmd script with:
qsub myjob.cmd
After submitting a job with qsub, SGE will respond with something like:
Your job 624556 ("myjob.cmd") has been submitted
where 624556 is the job number assigned by SGE to your job.
Use the qstat Command to Determine the Status of a Job
The qstat command displays information about the jobs in the SGE queues, both running and waiting to run. The syntax of the qstat command is:
qstat [-f] [-j job_number] [-U login_id] [-u login_id]
where:
- (qstat alone with no arguments)
- Displays a list of all running and waiting jobs.
- -f
- Displays summary information on each queue as well as the job list.
- -j job_number
- Displays the status of the job whose job number is job_number
- -U login_id
- Displays a list of running and waiting jobs for those queues which login_id can access. Or use the groupjobs script for this information; enter groupjobs -help for usage information.
- -u login_id
- Displays a list of login_id 's running and waiting jobs. Or use the myjobs script for this information for your own login_id.
Use the qhost Command to Display Node Information
The qhost command displays information about compute nodes: their architectures, number of processors, load, etc. The syntax of the qhost command is:
qhost [-j] [-q]
where:
- (qhost alone with no arguments)
- Displays a table of information about the compute nodes.
- -j
- Adds information about the specific jobs that are running on each compute node.
- -q
- Shows the queues each compute node accepts.
Use the qdel Command to Cancel a Job
The qdel command is used to cancel a job either while it is waiting to execute or while it is running. The syntax of the qdel command is:
qdel job_number
If a running job does not get cancelled right away, enter:
qdel -f job_number
to force it to be cancelled. Jobs in the "dr" state (disabled running) cannot be cancelled by the job owner. They must be cancelled by a system administrator. "dr" state jobs usually indicate a system hardware problem.
Additional SGE Commands
October 2009
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