Greenfield User Guide
Torque, an open source version of the Portable Batch System (PBS), controls all access to Greenfield's compute processors for both batch and interactive jobs.
To run a job on Greenfield, use the qsub command to submit a job script to the scheduler. A job script consists of PBS directives, comments and executable commands.
There are two queues on Greenfield: the batch queue and the debug queue. Interactive jobs can run in either queue and the method for doing so is discussed below.
The debug queue is used for debugging runs. It is not to be used for production runs. The maximum walltime for jobs in the debug queue is 30 minutes.
The batch queue is for all production runs. Jobs can use a maximum of 168 hours (7 days) of walltime.
You determine how much memory your job will be allocated through the value of your core request.
After you create your batch script, submit it to PBS with the qsub command.
Your batch output--your .o and .e files--is returned to the directory from which you issued the qsub command after your job finishes.
A form of interactive access is available on greenfield by using the -I option to qsub. For example, the command
qsub -I -l nodes=1:ppn=15 -l walltime=5:00 -q debug
requests interactive access to 15 cores for 5 minutes in the debug queue. Your qsub -I request will wait until it can be satisfied. If you want to cancel your request you should type ^C.
When you get your shell prompt back your interactive job is ready to start. At this point any commands you enter will be run as if you had entered them in a batch script. Stdin, stdout, and stderr are connected to your terminal. To run an MPI or hybrid program you must use the mpirun command just as you would in a batch script.
When you finish your interactive session type ^D. When you use qsub -I you are charged for the entire time you hold your processors whether you are computing or not. Thus, as soon as you are done executing commands you should type ^D.
X11 connections in interactive use
In order to use any X11 tool, you must also include -X on the qsub command line:
qsub -X -I -l nodes=1:ppn=15 -l walltime=5:00
This assumes that the DISPLAY variable is set. Two ways in which DISPLAY is automatically set for you are:
- Connecting to greenfield with ssh -X greenfield.psc.edu
- Enabling X11 tunneling in your Windows ssh tool
Monitoring and Killing Jobs
The qstat and pbsnodes commands provide information about jobs and queues. The qdel command is used to kill a job.
The qstat command requests the status of jobs or queues. Options include:
|-a||Displays the status of the queues, including running and queued jobs. For each job it shows the amount of walltime and the number of cores and processors requested. For running jobs it shows the amount of walltime the job has already used.|
|-s||Includes comments provided by the batch administrator or scheduler.|
|-f||Provides a full status display|
|-u username||Displays all running or queued jobs belonging to user username|
The pbsnodes -a command shows details about the nodes.
The qdel command is used to kill queued and running jobs. For example,
Give the jobid of the job you want to kill (here, 54) as the argument to
qdel. The jobid is displayed when the job is submitted. You can also find the jobid with
qstat -u username. If you cannot kill a job you want to kill send email to firstname.lastname@example.org.