How to submit jobs on Combo
Contents
[hide]Queuing System
For the efficient use of the cluster, two Monitoring/Job Management software (PBS/Torque and Maui) have been installed.
After logging into to the cluster, the user is on the master node. When a program is run, it is also immediately run on the master. This is the "interactive mode", which is convenient for running simple commands like ls, vi, etc. or for editing/compiling a program. But, long computing jobs should be submitted through the queuing system. The submitted job will be in a queue waiting for its turn, then will be sent to one or more compute node(s), which the job will have dedicated access to until it finishes. Therefore, the job will run faster and the cluster will be more efficiently utilized.
Basic Commands
Some basic commands that every cluster user should know before they start running jobs on these system:
| Command | Description |
|---|---|
| qsub | To submit a job to the queuing system |
| qdel | To delete a job that has been submitted to the queuing system |
| qstat/showq | List all information about queues and jobs |
Sample PBS job scripts
PBS job script for Parallel OPENMPI
Submit Your Jobs
Submit your batch job from the frontend with the command
qsub [job_script]
You get the job_name and job_id assigned, which can be used with various command.
Monitor Your Jobs
To see the progress information of running jobs, the command showq(Maui) and qstat(Torque) can be used. Both commands give you a summary of the status of submitted jobs and queues They give slightly different types of information. qstat shows a list of all running and waiting jobs in the queue, sorted by job identifier.
Please note that sometimes it takes a minute for submitted job to showq up under showq.
Another difference is that qstat shows time used for running jobs, while showq displays time left until the job will be killed by the queue system. When a job has finished it will no longer appear in the qstat or showq output.
Besides, the web based cluster monitor Ganglia (available from http://combos.tk/ganglia) is a very helpful tools to monitor the compute-node loading/status.
To delete a running job, use
qdel [jobid]
Frequently Used PBS Command
PBS supplies a command line interface. This is used to submit, monitor, modify, and delete jobs. The following are some frequent used PBS user commands and their functions:
| Command | Description |
|---|---|
| qsub | Submit a job |
| qstat | List all information of queues and jobs |
| qdel | Delete a job |
| qhold | Hold a batch job to keep it from being scheduled for running |
| qmove | Move a job to a different queue or server |
| qmsg | Append a message to the output of an executing job |
| qrerun | Terminate an executing job and return it to a queue |
| qrls | Release a held job |
| qsig | Send a signal to an executing job |
Frequently Used qsub option
| Command | Description |
|---|---|
| qsub -l list | Set job resource list |
| qsub -N jobname | Set job name to jobname |
| qsub -q dest | Submit to queue dest |
The resource requested on command line has a high preference than the directive line in the script file. For an example, submit job by command
qsub -l nodes=2:ppn=4 [jobscript]
this job will run on 2 compute nodes with 4 processors each instead of what stated in the script file.
Frequently Used qstat option
| Command | Description |
|---|---|
| qstat -a | List all jobs |
| qstat -q | List all queues on the system |
| qstat -n | List |
| qstat -u userid | List all jobs owned by user userid |
| qstat -r | List all running jobs |
| qstat -f jobid | List all information known about specified job(jobid) |
Acknowledgement
With reference to: High Performance Cluster Computing Centre (HPCCC) at Hong Kong Baptist University, http://www.sci.hkbu.edu.hk/hpccc/index.php High Performace Computing Service (HPCS) at Cambridge, http://www.hpc.cam.ac.uk/
