Qsub
Qsub is the command used to submit jobs to the cluster. Users are permitted to use up to 350 cores and 1TB of memory at a time. Beyond that your work will queue until your running jobs have completed. Resource reservations are strictly enforced. Your jobs will not be able to grow beyond the CPU and memory reserved for your job.
Additional submit script examples are available on Acropolis in the directory /share/qsub_examples
This is a basic job submission script:
#!/bin/bash
#PBS -N TestJob
#PBS -l nodes=1:ppn=10,mem=10gb
#PBS -j oecd $PBS_O_WORKDIR
# execute program
/PathTo/Program.sh
The #PBS lines are options sent to the job scheduler. -N sets the job name -l sets number of nodes, processors per node(ppn), and 10GB of memory. -e and -o set the output of standard output and error. Run “man qsub” for more options.
Save this example as a script and submit it to the scheduler by running “qsub MyScript.sh”.
Job arrays
A job array can be used to submit a set of jobs to the scheduler. The following example would run a group of programs in the /PathTo/ directory called Program1.sh through Program20.sh.
#!/bin/bash
#PBS -N TestJobArray
#PBS -l nodes=1:ppn=10,mem=10gb
#PBS -j oe
#PBS -t 1-20cd $PBS_O_WORKDIR
# execute program
/PathTo/Program${PBS_ARRAYID}.sh