ecearth_patch

EC-Earth_patch

EC-Earth is a global coupled climate model. It is developed by a consortium of European research institutions. The goal of this project is to adapt this model for our needs in TECLIM: install, run management, etc.

Important Notes

YOU MUST HAVE YOUR ~/.ssh/id_rsa.pub FILE BEFORE STARTING TO WORK WITH GIT ON ZENOBE.

mv $HOME/.ssh/config $HOME/.ssh/config_old
cat config | sed -e 's/pbarriat/'$USER'/g' > $HOME/.ssh/config

[ ! -f ~/.ssh/id_rsa.pub ] && ssh-keygen -t rsa
ssh-copy-id -i ~/.ssh/id_rsa.pub gwceci.cism.ucl.ac.be

Install

First, clone the pbarriat/ecearth_patch repository:

mkdir ~/modeles
cd ~/modeles
mkdir ecearth
git clone ssh://regit/pbarriat/ecearth_patch.git

Now, update your shell startup script (~/.bashrc) to add ecearth globals variables to your environment.

For instance on Zenobe, you need to add:

configure_ecearth()
{
  if [ `hostname` != "frontal1" ]; then
    echo "First, we move to frontal1..."
    touch ~/.configure_ecearth
    ssh frontal1
  fi
  export EC_DEP=/projects/acad/ecearth/opt
  if [ -f $EC_DEP/modules.load ]; then
    source $EC_DEP/modules.load
  fi
  [[ -f ~/.configure_ecearth ]] && rm ~/.configure_ecearth
}
if [ `hostname` = "frontal1" ]; then
  [[ -f ~/.configure_ecearth ]] && configure_ecearth
fi
if [ `hostname` = "frontal3" ]; then
  PATH="/projects/acad/ecearth/opt/apps/lua/lua/bin:$PATH"
  . /projects/acad/ecearth/opt/lmod/lmod/init/profile
  ulimit -u 8192
  export OMP_NUM_THREADS=2
fi

Then, checkout the EC-Earth SVN repository. Four alternatives:

cd ecearth

svn co https://svn.ec-earth.org/ecearth3/tags/3.2.2 ecearth_3.2.2

svn co https://svn.ec-earth.org/ecearth3/tags/3.2.3 ecearth_3.2.3

svn co https://svn.ec-earth.org/ecearth3/branches/projects/primavera ecearth_primavera

svn co https://svn.ec-earth.org/ecearth3/trunk ecearth_trunk

Final step, go to the pbarriat/ecearth_patch repository and run the install.sh script:

cd ecearth_patch
./install.sh

Compile

Lemaitre3

• Go to ecearth sources and create all the Makefile's with lemaitre3 configuration:

cd ecearth_3.2.2/sources
./util/ec-conf/ec-conf -p lemaitre3-intelmpi config-build.xml

module purge
module load 2016a netCDF-Fortran/4.4.4-intel-2016a grib_api/1.16.0-intel-2016a openjpeg/1.5.2-intel-2016a

• Compile oasis3:

cd oasis3-mct/util/make_dir
make BUILD_ARCH=ecconf -f TopMakefileOasis3
cd ../../..

• Compile IFS:

cd ifs-36r4
./makeifs -j 4
cd ..

• Compile xios-2:

cd xios-2
./make_xios --prod --arch ecconf --use_oasis oasis3_mct --netcdf_lib netcdf4_par -j 4
cd ..

• Compile NEMO:

cd nemo-3.6/CONFIG
./makenemo -n ORCA1L75_LIM3 -m ecconf -j4
cd ../..

• Compile runoff-mapper:

cd runoff-mapper/src
make
cd ../..

Primavera context:

• Compile amip-forcing:

cd amip-forcing/src
make
cd ../..

• Configure ELPiN:

cd util/ELPiN
mkdir bathymetries
ln -s /scratch/ucl/elic/pbarriat/DATA/EC-EARTH/nemo/initial/ORCA1L75/bathy_meter.nc bathymetries/ece_bathy_meter_ORCA1.nc
ln -s /scratch/ucl/elic/pbarriat/DATA/EC-EARTH/nemo/initial/ORCA025L75/bathy_meter.nc bathymetries/ece_bathy_meter_ORCA025.nc
sed -i 's/ORCA025/ORCA1/g' src/namelist_mpp
./Configure
cd ../..

Zenobe

First, sign out of Zenobe and sign in again. Then, type configure_ecearth.

Compile the model:

1. Go to ~/modeles/ecearth_$tag/sources and:

   ./util/ec-conf/ec-conf -p zenobe-intelmpi config-build.xml
   

2. Go to ./oasis3-mct/util/make_dir and:

   make BUILD_ARCH=ecconf -f TopMakefileOasis3
   

3. Go to ./ifs-36r4 and:

   ./makeifs -j 4
   

4. Go to ./xios-2 and:

   ./make_xios --prod --arch ecconf --use_oasis oasis3_mct --netcdf_lib netcdf4_par -j 4
   

5. Go to ./nemo-3.6/CONFIG and:

   ./makenemo -n ORCA1L75_LIM3 -m ecconf -j4
   

6. Go to ./runoff-mapper/src and:

   make
   

Primavera context:

1. Go to ./amip-forcing/src and:

   make
   

2. Go to ./util/ELPiN and:

   mkdir bathymetries
   ln -s /SCRATCH/acad/ecearth/DATA/nemo/initial/ORCA1L75/bathy_meter.nc bathymetries/ece_bathy_meter_ORCA1.nc
   ln -s /SCRATCH/acad/ecearth/DATA/nemo/initial/ORCA025L75/bathy_meter.nc bathymetries/ece_bathy_meter_ORCA025.nc
   sed -i 's#"$min_num"#"${min_num/./,}"#g' ELPiNv2.cmd
   sed -i 's/ORCA025/ORCA1/g' src/namelist_mpp
   ./Configure
   

Run

Lemaitre3

cd ../runtime/classic
../../sources/util/ec-conf/ec-conf -p lemaitre3 config-run.xml
vi ece-ifs+nemo.sh
sbatch ece-ifs+nemo.sh

Zenobe

For a quick classical run test:

• Go to ~/modeles/ecearth_$tag/runtime/classic and:

  ../../sources/util/ec-conf/ec-conf -p zenobe config-run.xml
  

• Submit the script ece-ifs+nemo.sh to the PBS batch system:

  qsub ece-ifs+nemo.sh
  

Benchmarks

Lemaitre3

XIOS	NEMO	IFS	Runoff	WTIME per YEAR	#CORES
1	64	78	1	3h56	144
22	72	288	1		384
22	144	432	1		600

Zenobe

XIOS	NEMO	IFS	Runoff	WTIME per YEAR	#CORES
1	64	78	1	5h	144
22	72	288	1	3h15	384
22	144	432	1		600

Contributors

• ELIC members @pbarriat

License

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