Difference between revisions of "Installing Mars mesoscale model on spirit"

Revision as of 17:24, 23 January 2023

Set up environment

Add this in your ~/.bashrc then source the file

module purge
module load intel/2021.4.0
module load intel-mkl/2020.4.304
module load openmpi/4.0.7
module load hdf5/1.10.7-mpi
module load netcdf-fortran/4.5.3-mpi
module load netcdf-c/4.7.4-mpi
declare -x WHERE_MPI=/net/nfs/tools/u20/22.3/PrgEnv/intel/linux-ubuntu20.04-zen2/openmpi/4.0.7-intel-2021.4.0-43fdcnab3ydwu7ycrplnzlp6xieusuz7/bin/
declare -x NETCDF=/scratchu/spiga/les_mars_project_spirit/netcdf_hacks/SPIRIT
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

Do not forget to declare the local directory in PATH by adding this to your ~/.bashrc

declare -x PATH=./:$PATH

It is necessary to unlimit the stacksize to avoit unwanted segmentation faults by adding this to your ~/.bashrc

ulimit -s unlimited

In the end, source the .bashrc file!

Set up the installer

Go to your 'data' directory (cd /homedata/_MY_LOGIN_ or cd /data/_MY_LOGIN_) and download the installer with the following command

svn co https://svn.lmd.jussieu.fr/Planeto/trunk/MESOSCALE/LMD_MM_MARS/SIMU

Make sure the installer can be executed

chmod 755 SIMU/meso_install.sh

Make a link (e.g. where you are, in the parent directory of /data) to the main script in this SIMU directory

ln -sf SIMU/meso_install.sh .

Run the installer with a simple display of possible options

./meso_install.sh -h

Install the code

Update to the latest version of installer

cd SIMU
svn update
chmod 755 meso_install.sh
cd ..

Run the installer by providing a name for your specific directory

./meso_install.sh -n DESCRIBE_YOUR_RESEARCH_PROJECT

Special case: In case you do not have a gitlab account, ask for an archive (tar.gz) of the code. Let us assume the name is git-trunk-mesoscale-compile-run-spirit.tar.gz and the file is in the current directory (for instance in /homedata/_MY_LOGIN_) then run the installer with the following command

./meso_install.sh -n DESCRIBE_YOUR_RESEARCH_PROJECT -a git-trunk-mesoscale-compile-run-spirit

Weird! fcm is not working interactively. It only works if being declared in the environment file by adding

declare -x PATH=/homedata/_MY_LOGIN_/DESCRIBE_YOUR_RESEARCH_PROJECT/code/LMDZ.COMMON/FCM_V1.2/bin/:$PATH

then recompile the GCM compiling (which had failed previously by doing

cd /homedata/_MY_LOGIN_/DESCRIBE_YOUR_RESEARCH_PROJECT/
./compile_gcm.sh