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Overview

Ferret is an interactive computer visualisation and analysis environment designed to meet the needs of oceanographers and meteorologists analysing large and complex gridded data sets. It offers a Mathematica-like approach to analysis. New variables can be defined interactively as mathematical expressions involving data set variables and calculations may be applied over arbitrarily shaped regions.

More information: https://ferret.pmel.noaa.gov/Ferret/

Usage

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

$ module avail ferret

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

$ module load ferret/7.6.0

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 ferret_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 ferret/7.6.0

# 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 Ferret application
ferret [Options]

Use ferret --help command after loading the module to see all the ferret command's Options. For ferret documentation: https://ferret.pmel.noaa.gov/Ferret/documentation/ferret-documentation

To run the job you would use the PBS command:

$ qsub ferret_job.sh