University of Pretoria
Operational / Internal Site

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

computing:hpcc:comsol [2015/10/12 15:15] (current)
Line 1: Line 1:
 +====== COMSOL simulations with SLURM ======
 +
 +A total of 10 COMSOL CKL and 2 COMSOL FNL licenses are available for use on the
 +cluster.
 +
 +Below are SLURM templates for various types of COMSOL simulations.
 +** Please use the smallest feasible values for the simulation so that our
 +cluster usage can be optimised. ** COMSOL is also available in a limited
 +interactive mode (see bottom of page).
 +
 +Note: In the templates, there are various parameters you should change to
 +reflect your simulation requirements. These parameters are indicated with
 +''<​CHANGETHIS>''​ tag. For example:
 +
 +<​code>​
 +#SBATCH --mail-user=<​CHANGETHIS>​
 +</​code>​
 +
 +===== Moderate size multi-CPU COMSOL simulation: 1 CKL license =====
 +
 +This template is suitable for large simulations that require more memory than
 +is available on desktop computers and would typically run more than an hour on
 +a lab computer. A single task is defined that will be allocated 4 CPU cores.
 +
 +Typically values for ''​--mem-per-cpu''​ are 2000 (for 2G) or 4000 (for 4G) for
 +larger simulations.
 +
 +<file bash comsol.slurm>​
 +#!/bin/bash
 +#SBATCH --output=<​CHANGETHIS>​.log
 +#SBATCH --job-name=<​CHANGETHIS>​
 +#SBATCH --cpus-per-task=4
 +#SBATCH --mem-per-cpu=<​CHANGETHIS>​
 +#SBATCH --licenses=comsolckl:​1
 +#SBATCH --time=<​CHANGETHIS>​
 +#SBATCH --mail-type=END
 +#SBATCH --mail-user=<​CHANGETHIS>​
 +
 +# Run COMSOL model simulation
 +MODEL=<​CHANGETHIS>​
 +srun comsol batch -inputfile $MODEL.mph -outputfile $MODEL\_out.mph -np 4 -ckl
 +</​file>​
 +
 +===== Maximum size multi-CPU COMSOL simulation: 1 CKL license =====
 +
 +This template, for a model with name ''​comsol_max'',​ is suitable for very large
 +simulations that would require days to run on a desktop computer. A single
 +task is defined that will be allocated 12 CPU cores.
 +
 +Typically values for ''​--mem-per-cpu''​ are 2000 (for 2G) or 2500 (for 2.5) for
 +larger simulations.
 +
 +<file bash comsol_max.slurm>​
 +#!/bin/bash
 +#SBATCH --output=<​CHANGETHIS>​.log
 +#SBATCH --job-name=<​CHANGETHIS>​
 +#SBATCH --cpus-per-task=12
 +#SBATCH --mem-per-cpu=<​CHANGETHIS>​
 +#SBATCH --licenses=comsolckl:​1
 +#SBATCH --time=<​CHANGETHIS>​
 +#SBATCH --mail-type=END
 +#SBATCH --mail-user=<​CHANGETHIS>​
 +
 +# Run COMSOL model simulation
 +MODEL=<​CHANGETHIS>​
 +srun comsol batch -inputfile $MODEL.mph -outputfile $MODEL\_out.mph -np 12 -ckl
 +</​file>​
 +
 +===== Maximum size multi-CPU COMSOL simulation: 1 FNL license =====
 +
 +This template, for a model with name ''​comsol_fnl'',​ is suitable for very large
 +simulations that would require days to run on a desktop computer. A single
 +task is defined that will be allocated 12 CPU cores.
 +
 +Typically values for ''​--mem-per-cpu''​ are 2000 (for 2G) or 2500 (for 2.5) for
 +larger simulations.
 +
 +<file bash comsol_fnl.slurm>​
 +#!/bin/bash
 +#SBATCH --output=<​CHANGETHIS>​.log
 +#SBATCH --job-name=<​CHANGETHIS>​
 +#SBATCH --cpus-per-task=12
 +#SBATCH --mem-per-cpu=<​CHANGETHIS>​
 +#SBATCH --licenses=comsolfnl:​1
 +#SBATCH --time=<​CHANGETHIS>​
 +#SBATCH --mail-type=END
 +#SBATCH --mail-user=<​CHANGETHIS>​
 +
 +# Run COMSOL model simulation
 +MODEL=<​CHANGETHIS>​
 +srun comsol batch -inputfile $MODEL.mph -outputfile $MODEL\_out.mph -np 12
 +</​file>​
 +
 +===== Interactive COMSOL: 1 CKL license =====
 +
 +For the creation of large models it is sometime necessary to run COMSOL in
 +interactive mode on the cluster. To do so, simply run **''​comsol''​** after
 +logging in on the head node. This will start a single CPU session with 12GB of
 +memory with the COMSOL CKL license. Note that it will take about 30 to 50
 +seconds for the session to be allocated on the cluster and for COMSOL to start.
 +Note furthermore that the session has a hard time limit of 4 hours and will
 +also terminate after 20 minutes of inactivity.
 +
 +** Do not use the interactive session for simulations. **
 +
 +For the X11 graphics to be handled correctly, this assumes you have a X11
 +server installed on your computer and that you logged in with X11 forwarding
 +enabled.