Using LADiM at IMR

This chapter is specific to the Institute of Marine Research (IMR) and shows how to use LADiM on computing resources available to us.

Computer resources

The machines rhea, dedun, and demeter are available for running LADiM. Rhea and dedun are common resources at IMR with 32 cores each, while demeter is a smaller machine dedicated for LADiM and in particular the operational salmon lice simulations.

The machines have a data storage facility /gpfs/gpfs0. Forcing data for LADiM may be found under the /gpfs/gpfs0/osea/ROMS-archives directory.

Python environment

LADiM requires python 3.6 or higher. This is available with an (ana)conda python installation. First time issue the command:

/software/osea/anaconda/bin/conda init zsh

(substitute bash for zsh if this is your preferred shell). This modifies your .zshrc (of .bashrc) to use the correct python environment.

IMPORTANT. Add the following line to your .zshrc or .bashrc (preferably both):

export MKL_NUM_THREADS=1

This prevents the MKL (Intel’s Math Kernel Library) used by python from capturi ng all cores, effective blocking all other (including your own) activity at the machine. You may get a slight speed-up with 2 instead of 1.

Exit the shell and log in again. The modified configuration is common for all three machines.

Alternative LADiM versions

LADiM offers a high degree of flexibility by the yaml-configuration and the possibility of alternative gridforce and ibm modules. More flexibility is possible by editing the rest of the code. To not mess up the operational salmon lice runs, this has to be done in a separate git branch and used from a separate conda environment. For instance, to use the beta development branch issue the command:

conda activate beta

LADiM at fram

It is possible to use LADiM at the HPC resource fram at the national facility Sigma2. This is not recommended. We will have to pay for all processors at a compute node without the benefit of parallell computing.