Cheaha Quick Start (Deprecated)
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Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.
As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.
Thank you,
The Research Computing Team
Cheaha is a shared cluster computing environment for UAB researchers. A shared cluster environment uses a job scheduler to run tasks on the cluster to provide optimal resource sharing among users. Cheaha uses a job scheduling system call SGE to schedule and manage jobs. A user needs to tell SGE about resource requirements (e.g. CPU, memory) so that it can schedule jobs effectively. These resource requirements along with actual application code can be specified in a single file commonly referred as 'Job Script/File'. Following is a simple job script that prints job number and hostname.
#!/bin/bash # # Define the shell used by your compute job # #$ -S /bin/bash # # Tell the cluster to run in the current directory from where you submit the job # #$ -cwd # # Tell the scheduler only need 10 minutes # #$ -l h_rt=00:01:00,s_rt=0:00:55,vf=512M # # Set your email address and request notification when you job is complete or if it fails # #$ -M YOUR_EMAIL_ADDRESS #$ -m eas # # Tell the scheduler to use the environment from your current shell # #$ -V echo "The job $JOB_ID is running on $HOSTNAME"
Lines starting with '#$' have a special meaning in the SGE world. SGE specific configuration options are specified after the '#$' characters. SGE offers many configuration options but above mentioned options should be useful for basic job scripts. A job script is submitted to the cluster using SGE specific commands. There are many commands available, but following three commands are the most common:
- qsub - to submit job
- qdel - to delete job
- qstat - to view job status
We can submit above job script using qsub command:
$ qsub HelloCheaha.sh