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Instructions to run SUNTANS on Pawsey

Steps to go through:

  • Logging in to Pawsey
  • Loading modules
  • Compiling code
  • Submitting a job to the queue using slurm
  • Downloading data

General instructions for running on Pawsey (Magnus) are here:

Step 1) Logging in

Option 1: MobaXterm

Option 2: Use ssh from a linux terminal

ssh username@setonix.pawsey.org.au

Step 2) Download the source code and this tutorial

Naviagate to your software folder: cd $MYSOFTWARE

Git clone the code (suntans code and tutorial)

git clone https://github.com/ofringer/suntans.git

git checkout variable_coriolis

Step 3) Loading modules

Use commands:

Set to the gnu programming environment. This is default on setonix.

module list list all currently loaded modules

module avail : list all available modules

Load netcdf: module load netcdf-c/4.8.1

Download and build parmetis:

This installation is manual but you will learn how software packages are installed.

  • Download Parmetis: wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD/ParMetis-3.2.0.tar.gz
  • Download Parametis (backup): curl https://cloudstor.aarnet.edu.au/plus/s/Y9eVZuaKclvsY6W/download -o ParMetis-3.2.0.tar.gz
  • Untar the folder: tar -xvf ParMetis-3.2.0.tar.gz
  • Change directory to the folder: cd ParMetis-3.2.0
  • Change mpicc to cc in /Makefile.in
  • Compile the library: make
  • done.

Compiling suntans

  • Download theexamples: git clone https://github.com/mrayson/suntans_tutorial.git

  • Replace suntans/main/Makefile with iwaves_shelf/Makefile.pawsey i.e. cp <path-to-suntans-tutorial>/iwaves_shelf/Makefile.pawsey <path-to-suntans-code/main>/Makefile

  • Update Makefile.in to:

#MPIHOME=
PARMETISHOME=/your/path/to/ParMetis-3.2.0
TRIANGLEHOME=
#NETCDF4HOME=

  • Navigate to the iwaves_shelf test case folder

  • Update Makefile $SUNTANSHOME variable e.g. SUNTANSHOME='/home/mrayson/software/code/suntans/main

  • Run make

Run an example (no python)

Clone the tutorial...

Go to the iwaves_shelf example cd suntans_tutorial iwaves_shelf

Edit the Makefile:

  • Replace mpicc with cc
  • Set the SUNTANSHOME variable to the path where SUNTANS is located

Update iwaves_shelf_slurm.sh

  • Set the SUNTANSHOME variable

Run the example: sbatch iwaves_shelf_slurm.sh

Check the job is running: squeue -u mrayson

Check the status of the job: watch tail <name_of_log_file_in_slurm_script>

The job will fail because your python environment is not setup correctly...

Setting up python on Pawsey

Use a singularity (docker-like) container -- see the iwaves_shelf/python_singularity script