Coral

Coral - simulation manager for NEMO

Purpose

Coral is a collaborative job submission script manager for the NEMO (Nucleus for European Modelling of the Ocean) modeling framework Documentation. With Coral, you can use and re-use job submission scripts designed and tested by your colleagues. You can ammend them in an easy way, and generate a submission script tailored to your needs. Then, you can share your script with your colleages.

Overview

• Run 'coral -h' to get a list of Coral commands, and 'coral <command> -h' to get help for a specific <command>
• Please see the Documentation for common usages and change log.
• Having trouble? Get help with Troubleshooting

Features

Once Nemo and Coral are properly installed, you can create a working submission script in three commands:

• coral init: initiate a set of configuration files (with working default values on the cluster) for the experiment features, data location, restart options, etc.
• coral build: create a submission script from the configuration files
• coral submit: submit the job, with options to run tests locally, ignore automatic job resubmission, restart from scratch, etc.
  

At each stage, you can act manually to adapt the workflow to your liking.

Once the job is submitted, you can simply run 'coral status' in the run directory to get an overview of what is happening. No need to look for job ids, or output files.

Requirements

NEMO & XIOS source code: see How to get NEMO from scratch

Install

Clone the Coral repository (for instance in the EXTERNAL directory of your NEMO install)

cd $HOME/modeles/nemo/3.6/EXTERNAL
git clone ssh://egit/TECLIM/Coral.git coral

and update your shell startup script to source the 'setup-coral.sh' file to add 'coral' to your PATH variable.

configure_nemo()
{
  [...]
  source $HOME/modeles/nemo/3.6/EXTERNAL/coral/setup-coral.sh
}

Getting started

NEMO & XIOS must be compiled: see How to compile NEMO

Create a NEMO config experiment

cd $HOME/modeles/nemo/3.6/CONFIG
# Create new experiment
./makenemo -n ORCA1_LIM3_REF -d "OPA_SRC LIM_SRC_3" -m myARCHfile -j0
# Check your CPP keys
vi ORCA1_LIM3_REF/cpp_ORCA1_LIM3_REF.fcm
# Compile
./makenemo -n ORCA1_LIM3_REF -m myARCHfile -j4

Create a Coral instance

cd ORCA1_LIM3_REF
mkdir CORAL00
cd CORAL00
coral -h
coral init -h
coral list
coral init elic_gnu

Benchmarks

Lemaitre3

Blocking Switch = 576 cores

XIOS	NEMO	WTIME per YEAR	#CORES	MEM/CPU
2	140		142	3072
2	260		262	3072
4	260	43 min	264	4096
4	520	36 min	524	3072
8	520	36 min	528	4096
8	520	37 min	528	3072
12	1040	35 min	1052	3072
16	1040	35 min	1056	3072
16	1856	32 min	1872	3072

Acknowledgments

• Thanks @dfr for initializing this project.

Contributors

• @dfr, @pbarriat.

License

This project is under the Creative Commons CC0 1.0 Universal License. See the LICENSE file for the full license text.