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Overview

Gmsh is a three-dimensional finite element mesh generator with a build-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities.

Gmsh is built around four modules: geometry, mesh, solver and post-processing. All geometrical, mesh, solver and post-processing instructions are prescribed either interactively using the graphical user interface (GUI) or in text files using Gmsh's own scripting language. Interactive actions generate language bits in the input files, and vice versa.

More information: https://gmsh.info/

Usage

You can check the versions installed in Gadi with a module query:

$ module avail gmsh

We normally recommend using the latest version available and always recommend to specify the version number with the module command:

$ module load gmsh/4.4.1

For more details on using modules see our modules help guide at https://opus.nci.org.au/display/Help/Environment+Modules.

An example PBS job submission script named gmsh_job.sh is provided below. It requests 1 CPU core, 2 GiB memory, and 8 GiB local disk on a compute node on Gadi from the normal queue for its exclusive access for 30 minutes against the project a00. It also requests the system to enter the working directory once the job is started. This script should be saved in the working directory from which the analysis will be done. To change the number of CPU cores, memory, or jobfs required, simply modify the appropriate PBS resource requests at the top of this file according to the information available at https://opus.nci.org.au/display/Help/Queue+Structure. Note that if your application does not work in parallel, setting the number of CPU cores to 1 and changing the memory and jobfs accordingly is required to prevent the compute resource waste.

#!/bin/bash

#PBS -P a00
#PBS -q normal
#PBS -l ncpus=1
#PBS -l mem=2GB
#PBS -l jobfs=8GB
#PBS -l walltime=00:30:00
#PBS -l wd

# Load module, always specify version number.
module load gmsh/4.4.1

# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`. Details on:
# https://opus.nci.org.au/display/Help/PBS+Directives+Explained

# Run Gmsh application
gmsh [Options]

Use gmsh --help command after loading the module to see all the gmsh command's Options. For Gmsh documentation: https://gmsh.info/doc/texinfo/gmsh.html

To run the job you would use the PBS command:

$ qsub gmsh_job.sh