To run a job on the UTM HPC cluster, you will need to set up a Portable Batch System (PBS) file. This PBS file defines the commands and cluster resources used for the job. A PBS file is a simple text file that can be easily edited with a UNIX editor, such as vi or pico command.>
In order to use the HPC compute nodes, you must first log into one of the head nodes, portal utmgrid, and submit a PBS job.
a. The qsub command is used to submit a job to the PBS queue and to request additional resources.
b. The qstat command is used to check on the status of a job already in the PBS queue.
To simplify submitting a job, you can create a PBS script and use the qsub and qstat commands to interact with the PBS queue.
To set the parameters for your job, you can create a control file that contains the commands to be executed. Typically, this is in the form of a PBS script. This script is then submitted to PBS using the qsub command.
Here is a sample PBS file, named pbs-script, followed by an explanation of each line of the file.
#PBS -N lammps
#PBS -l nodes=1:ppn=2
#PBS -l walltime=00:10:00
#PBS -M firstname.lastname@example.org
#PBS -m abc
mpirun -np 2 [LAMMPS executable] [filename input] [filename output]
To submit your job as stated below
|qsub -q hpc pbs-script|
|qsub -q bigmem pbs-script|
|qsub -q qamar pbs-script|
Please note that QAMAR HPC only have 4 cpu’s so if u are using this cluster please make sure in the script, you state “ppn=4” to make sure your job can run.
To check on the status of your job, you will use the qstat command. The command
|qstat –u [your username]|
will show you the current status of all your submitted jobs.