job-submission-and-execution.md

Job Submission and Execution

Job Submission

When allocating computational resources for the job, please specify

1. a suitable queue for your job (the default is qprod)
2. the number of computational nodes required
3. the number of cores per node required
4. the maximum wall time allocated to your calculation, note that jobs exceeding the maximum wall time will be killed
5. your Project ID
6. a Jobscript or interactive switch

!!! note Use the qsub command to submit your job to a queue for allocation of computational resources.

Submit the job using the qsub command:

$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript

The qsub command submits the job to the queue, i.e. the qsub command creates a request to the PBS Job manager for allocation of specified resources. The resources will be allocated when available, subject to the above described policies and constraints. After the resources are allocated, the jobscript or interactive shell is executed on the first of the allocated nodes.

!!! note PBS statement nodes (qsub -l nodes=nodespec) are not supported on the Anselm cluster.

Job Submission Examples

$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=16,walltime=03:00:00 ./myjob

In this example, we allocate 64 nodes, 16 cores per node, for 3 hours. We allocate these resources via the qprod queue, consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. The jobscript 'myjob' will be executed on the first node in the allocation.

$ qsub -q qexp -l select=4:ncpus=16 -I

In this example, we allocate 4 nodes, 16 cores per node, for 1 hour. We allocate these resources via the qexp queue. The resources will be available interactively.

$ qsub -A OPEN-0-0 -q qnvidia -l select=10:ncpus=16 ./myjob

In this example, we allocate 10 nvidia accelerated nodes, 16 cores per node, for 24 hours. We allocate these resources via the qnvidia queue. the jobscript 'myjob' will be executed on the first node in the allocation.

$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=16 ./myjob

In this example, we allocate 10 nodes, 16 cores per node, for 12 hours. We allocate these resources via the qfree queue. It is not required that the project OPEN-0-0 has any available resources left. Consumed resources are still accounted for. The jobscript myjob will be executed on the first node in the allocation.

All qsub options may be saved directly into the jobscript. In such cases, it is not necessary to specify any options for qsub.

$ qsub ./myjob