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:
- https://support.pawsey.org.au/documentation/display/US/Supercomputing+Documentation
- https://support.pawsey.org.au/documentation/display/US/Compiling+on+Magnus+and+Galaxy
- Cheat sheet: https://support.pawsey.org.au/documentation/download/attachments/34017103/Magnus_Quick_Reference_Guide.pdf?version=1&modificationDate=1536029582214&api=v2
Option 1: MobaXterm
Option 2: Use ssh from a linux terminal
Naviagate to your group folder: cd $MYGROUP$ or cd /home/username/group/username
Git clone the code (suntans code and tutorial)
git clone https://github.com/ofringer/suntans.git
git checkout variable_coriolis
Use commands:
Set to the gnu programming environment: module swap PrgEnv-cray PrgEnv-gnu
module list list all currently loaded modules
module avail : list all available modules
Load netcdf: module load cray-netcdf
Follow the instructions in README.md. Also:
Change mpicc to cc in /Makefile.in
make
Replace Makefile with Makefile.pawsey i.e. cp 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=
Run make
Clone the tutorial...
Go to the iwaves_shelf example cd suntans_tutorial iwaves_shelf
Edit the Makefile:
- Replace
mpiccwithcc - 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...
Use a singularity (docker-like) container -- see the iwaves_shelf/python_singularity script