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/
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 software applications guide.
An example PBS job submission script named gmsh_job.sh
is provided below. It requests 1 CPU, 2 GiB memory, and 8 GiB local disk on a compute node on Gadi from the normal
queue 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 in our queue structure guide.
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/` # 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