CORAL - simulation manager for NEMO - is a collaborative job submission script manager for NEMO

Charles Pelletier 316660af9a iscpl update 4 tahun lalu
archive 6a8837f120 Initial commit 7 tahun lalu
nemo 167f550ba0 Adding xios arch conf for zenobe 6 tahun lalu
templates 316660af9a iscpl update 4 tahun lalu
utils 66e490c8a3 Update bench figure 6 tahun lalu
zone 6a8837f120 Initial commit 7 tahun lalu
.gitignore 6a8837f120 Initial commit 7 tahun lalu
AUTHORS 6a8837f120 Initial commit 7 tahun lalu
BUGS 6a8837f120 Initial commit 7 tahun lalu
LICENSE 6fb1416ef8 Initial commit 7 tahun lalu
NEWS 6a8837f120 Initial commit 7 tahun lalu
README.md aa4a75ac02 Update 'README.md' 6 tahun lalu
TODO 6a8837f120 Initial commit 7 tahun lalu
coral 6a1a56da3f Cleaned Genius skeleton 5 tahun lalu
gener_perturb_nemo_restart.bash f1da60f28c Add bash script to generate perturbed initial conditions from NEMO restart 6 tahun lalu
setup-coral.sh 6a8837f120 Initial commit 7 tahun lalu

README.md

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://git@www.climate.be:3022/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 lemaitre3

Benchmarks

Lemaitre3

Blocking Switch = 2 x 576 cores & 1 x 768 cores

  • Compiler: intel-2016a
  • Flags: -O2 -i4 -r8 -fp-model precise -xHost
XIOS NEMO WTIME per YEAR #CORES MEM/CPU
2 22 133min17 24 3072
2 46 77min14 48 3072
2 140 44min20 142 3072
4 260 43min15 264 3584
4 520 36min09 524 3584
8 760 40min31 768 3584
8 1048 50min51 1056 3584
8 1912 53min49 1920 3584

Zenobe

  • Compiler: intel-2015b
  • Flags: -O2 -i4 -r8 -fp-model precise -xHost
XIOS NEMO WTIME per YEAR #CORES MEM/CPU
2 22 229min28 24 2625
2 46 146min 48 2625
2 140 58min29 142 2625
4 260 48min30 264 2625
4 520 34min54 524 2625
4 760 38min46 768 2625
8 1048 43min 1056 2625
8 1936 36min26 1944 2625

bench_nemo.jpeg

Acknowledgments

  • Thanks @dfr for initializing this project.

Contributors

License

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