Adding LAM DYNAMICO-only working configuration on JeanZay

LAM-dynamics/01_build.sh

+#!/bin/bash
+# This script downloads and builds XIOS and DYNAMICO in the current working directory.
+ARCH_NAME=X64_JEANZAY
+NUM_JOBS=8
+
+# Get the latest XIOS
+module load svn/1.9.7
+svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOS
+
+pushd XIOS/
+./make_xios --arch ${ARCH_NAME} --job ${NUM_JOBS}
+popd
+
+# Get the latest DYNAMICO (on trunk2master branch by default).
+git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git DYNAMICO
+
+pushd DYNAMICO/
+./make_icosa -arch ${ARCH_NAME} -parallel mpi -prod -with_xios -job ${NUM_JOBS}
+popd

LAM-dynamics/02_create_runs.sh

+#!/bin/bash
+# This input file must agree with the header https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico/-/blob/trunk2master/TEST_CASE/LAM_ERA5/ERA_062000.nc_header
+ERA5_PATH=/gpfsstore/rech/wuu/ump84rg/DATA/ERA5_062000.nc
+
+mkdir -p RUNS/LAM_CREATE_ETAT0_MPI40
+mkdir -p RUNS/LAM_RUN_MPI40
+
+DYNAMICO_PATH=../../DYNAMICO
+
+# Prepare the create etat0 run
+pushd RUNS/LAM_CREATE_ETAT0_MPI40
+cp ${DYNAMICO_PATH}/TEST_CASE/LAM_ERA5/CREATE_ETAT0/* .
+# Remove references to XIOS LMDZ defintions
+sed -i /LMDZ/d iodef.xml
+# Create symoblic links to built DYNAMICO
+ln -s ${DYNAMICO_PATH} build
+ln -s build/bin/icosa_gcm.exe gcm.exe
+# Prepare input files
+mkdir input/
+ln -s ${ERA5_PATH} input/
+ln -s ${ERA5_PATH} input/ERA5.nc
+# Prepare job script
+cp ../../jean-zay/job_interactive.sh .
+popd
+
+# Prepare the main run
+pushd RUNS/LAM_RUN_MPI40
+cp ${DYNAMICO_PATH}/TEST_CASE/LAM_ERA5/RUN/* .
+# Remove references to XIOS LMDZ defintions
+sed -i /LMDZ/d iodef.xml
+# Change the length of the RUN to 29 days, activate dynamico.nc
+sed -i 's/run_length=2592000/run_length=2505600/g' run_dynamico.def
+sed -i 's/enabled="false"/enabled="true"/g' file_def_dynamico.xml
+# Create symoblic links to built DYNAMICO
+ln -s ${DYNAMICO_PATH} build
+ln -s build/bin/icosa_gcm.exe gcm.exe
+# Prepare input files
+mkdir input/
+ln -s ${ERA5_PATH} input/
+ln -s ${ERA5_PATH} input/ERA5.nc
+# Prepare job script
+cp ../../jean-zay/job.sh .
+popd
\ No newline at end of file

LAM-dynamics/03_prepare_etat0.sh

+#!/bin/bash
+# Run interactive job to create etat0
+pushd RUNS/LAM_CREATE_ETAT0_MPI40/
+./job_interactive.sh
+popd
+
+# Copy generated etat0
+cp RUNS/LAM_CREATE_ETAT0_MPI40/netcdf/* RUNS/LAM_RUN_MPI40/input/
+
+pushd RUNS/LAM_RUN_MPI40/input/
+cp start0.nc start.nc
+popd
\ No newline at end of file

LAM-dynamics/README.md

+# LAM with DYNAMICO only
+
+This is an easy example how to run LAM+DYNAMICO on JeanZay without any physics.
+
+## Execution
+
+```sh
+# This will build DYNAMICO and XIOS
+./01_build.sh
+# This will prepare the RUNS (CREATE_ETAT0 and RUN)
+./02_create_runs.sh
+# This will create the ETAT0 for the main run
+./03_prepare_etat0.sh
+# Now, run the LAM!
+cd RUN/LAM_RUN_MPI40/
+sbatch job.sh
+# Check the results
+cd netcdf/
+ncview dynamico.nc
+```
\ No newline at end of file

LAM-dynamics/jean-zay/job.sh

+#!/bin/bash
+## Request name
+#SBATCH --job-name=DCMIP41_mpi
+## Number of tasks (=MPI processes) to use
+#SBATCH --ntasks=40
+## Number of OpenMP threads
+#SBATCH --cpus-per-task=1
+
+## QoS for short jobs
+#SBATCH --qos=qos_cpu-dev
+## Elapsed time limit HH:MM:SS
+#SBATCH --time=00:30:00
+
+# do not use hyperthreading
+#SBATCH --hint=nomultithread
+# standard outputs
+#SBATCH --output=DYNAMICO%j.out
+#SBATCH --error=DYNAMICO%j.out
+# Change computing group if needed !
+#SBATCH -A wuu@cpu
+
+export OMP_NUM_THREADS=1
+# OpenMP binding
+export OMP_PLACES=cores
+
+# stack
+export OMP_STACKSIZE=128M
+ulimit -s unlimited
+
+# move to submission directory
+cd ${SLURM_SUBMIT_DIR}
+
+# load the same modules as during compilation
+source build/arch.env
+module list
+
+# cleanup execution directory and run
+rm -rf gcm.log logs *.nc netcdf
+ln -s input/*.nc .
+date > gcm.log
+ulimit -s unlimited
+srun ./gcm.exe >> gcm.log
+date >> gcm.log
+
+# move output files to netcdf subdir
+mkdir -p netcdf
+cp gcm.log *.def netcdf
+mv *.nc netcdf
+
+# keep log files, source code and executable for debug
+mkdir -p logs
+cp *.xml logs
+cp -pr gcm.exe logs
+cp -pr build/src logs
+mv xios_client_*.err xios_client_*.out gcm.log logs
+

LAM-dynamics/jean-zay/job_interactive.sh

+#!/bin/bash
+export OMP_NUM_THREADS=1
+# OpenMP binding
+export OMP_PLACES=cores
+
+# stack
+export OMP_STACKSIZE=128M
+ulimit -s unlimited
+
+# load the same modules as during compilation
+source build/arch.env
+module list
+
+# cleanup execution directory and run
+rm -rf gcm.log logs *.nc netcdf
+ln -s input/*.nc .
+date > gcm.log
+ulimit -s unlimited
+./gcm.exe >> gcm.log
+date >> gcm.log
+
+# move output files to netcdf subdir
+mkdir -p netcdf
+cp gcm.log *.def netcdf
+mv *.nc netcdf
+
+# keep log files, source code and executable for debug
+mkdir -p logs
+cp *.xml logs
+cp -pr gcm.exe logs
+cp -pr build/src logs
+mv xios_client_*.err xios_client_*.out gcm.log logs