🌊 CROCO-Lengau-UCT 🌊

This repository provides scripts, configuration files, and documentation for running CROCO on Lengau using Intel Compilers and MPI, supporting ocean modelling research at UCT. CROCO on GPUs: https://croco-ocean.gitlabpages.inria.fr/croco_doc/model/model.parallel.html#run-with-gpu and GPU able release https://gitlab.inria.fr/croco-ocean/croco/-/releases

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📅 Last Update: 11 March 2025
👨‍💻 Author: Mthetho Vuyo Sovara
📝 Developer Notes

Example usage:

Clone the repo and try the example:

git clone https://github.com/msovara/croco-chpc-uct-egs.git
cd msovara/examples
./download.sh

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🛠️ Developer Guide

The main dependencies are:

• MPI (Intel)
• zlib
• curl
• HDF5 (parallel enabled)
• netCDF-C (parallel enabled)
• netCDF-Fortran

🚀 Script 1: download.sh

This script handles downloading and extracting all dependencies and CROCO source code.

🛠️ Script 2: build.sh

This script handles building and installing all dependencies and CROCO.

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📋 User Notes

The CROCO model has been installed in the /home/apps/chpc/earth directory where earth system science applications on LENGAU are typically installed. To use CROCO, you must first load the CROCO module and Matlab (for pre-processing) into your shell environment:

module avail 2>&1 | grep -i croco
module load chpc/earth/croco/2.0.1
module avail 2>&1 | grep -i matlab
module load chpc/math/matlab/R2020a

🖥️ Script 3: lengau_jobscript

Example PBS Job Script for Running CROCO on Lengau

🛠️ Job Variations:

1. For a small test run:

#PBS -N croco_test
#PBS -l walltime=01:00:00
#PBS -l select=1:ncpus=24:mpiprocs=24
#PBS -q debug

2. For a large production run:

#PBS -N croco_production
#PBS -l walltime=48:00:00
#PBS -l select=8:ncpus=24:mpiprocs=24
#PBS -q large

3. For a high-resolution run with OpenMP (Not applicable here):

#PBS -N croco_highres
#PBS -l walltime=24:00:00
#PBS -l select=4:ncpus=24:mpiprocs=12:ompthreads=2

Additional Options:

1. To restart from a previous run:

# Copy restart files
cp /path/to/previous/run/restart*.nc .

# Modify croco.in to use restart files
sed -i 's/NRREC.*=.*0/NRREC = 1/' croco.in

# Run CROCO
mpirun -np $PBS_NP croco croco.in > $OUTDIR/croco.log 2>&1

2. To run multiple simulations in sequence:

# Run first simulation
mpirun -np $PBS_NP croco croco_sim1.in > $OUTDIR/croco_sim1.log 2>&1

# Run second simulation
mpirun -np $PBS_NP croco croco_sim2.in > $OUTDIR/croco_sim2.log 2>&1

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📋 Load performance tools

module load chpc/perf/vtune

# Run with performance monitoring
mpirun -np $PBS_NP amplxe-cl -collect hotspots -result-dir=$OUTDIR/vtune_results -- croco croco.in