View source for Installing Mars mesoscale model on spirit

== Set up environment ==
=== Option 1 ===
Add this in your ~/.bashrc then source the file

<syntaxhighlight lang="Bash">
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
</syntaxhighlight>

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

<syntaxhighlight lang="Bash">
declare -x PATH=./:$PATH
</syntaxhighlight>

It is necessary to unlimit the stacksize to avoit unwanted segmentation faults by adding this to your ~/.bashrc
<syntaxhighlight lang="Bash">
ulimit -s unlimited
</syntaxhighlight>

In the end, source the .bashrc file!

=== Option 2 ===
If you prefer to not modify your .bashrc file, you should instead put all the lines in a "mesoscale.env" file and add a
<syntaxhighlight lang="bash">
source mesoscale.env
</syntaxhighlight>
at the beginning of the meso_install.sh script.

Note that you will still need to have "." in your PATH and unlimited stacksize. So you will definitely need to have:
<syntaxhighlight lang="Bash">
declare -x PATH=./:$PATH
ulimit -s unlimited
</syntaxhighlight>
in your .bashrc file

=== Extra technical details===
* WRF needs a NETCDF environment variable where everything is in the same dir (Fortran and C stuff). If this is not available one needs to create a uniquer dire with links to all the C and Fortran stuff. NCDFLIB and NCDFINC are for the physics.
* WHERE_MPI env variable is used by some scripts to make sure we use the right one


== 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
<syntaxhighlight lang="Bash">
svn co https://svn.lmd.jussieu.fr/Planeto/trunk/MESOSCALE/LMD_MM_MARS/SIMU
</syntaxhighlight>

Make sure the installer can be executed
<syntaxhighlight lang="Bash">
chmod 755 SIMU/meso_install.sh
</syntaxhighlight>

Make a link (e.g. where you are, in the parent directory of /data) to the main script in this SIMU directory
<syntaxhighlight lang="Bash">
ln -sf SIMU/meso_install.sh .
</syntaxhighlight>

Run the installer with a simple display of possible options
<syntaxhighlight lang="Bash">
./meso_install.sh -h
</syntaxhighlight>

== Install the code ==

Update to the latest version of installer
<syntaxhighlight lang="Bash">
cd SIMU
svn update
chmod 755 meso_install.sh
cd ..
</syntaxhighlight>

Run the installer by providing a name for your specific directory
<syntaxhighlight lang="Bash">
./meso_install.sh -n DESCRIBE_YOUR_RESEARCH_PROJECT
</syntaxhighlight>
''Important'': This will only work if you have access (i.e. an account) to the IN2P3 Gitlab project "La communauté des modèles atmosphériques planétaires" AND if you have added your personal ssh key there. Otherwise proceed as indicated below.

''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
<syntaxhighlight lang="Bash">
./meso_install.sh -n DESCRIBE_YOUR_RESEARCH_PROJECT -a git-trunk-mesoscale-compile-run-spirit
</syntaxhighlight>


=== Troubleshooting (in case this happens to you) ===
''Weird!'' fcm is not working interactively (this seems to happen if "." is in your PATH before "FCM_V1.2/bin") It only works if being declared in the environment file by adding
<syntaxhighlight lang="Bash">
declare -x PATH=/homedata/_MY_LOGIN_/DESCRIBE_YOUR_RESEARCH_PROJECT/code/LMDZ.COMMON/FCM_V1.2/bin/:$PATH
</syntaxhighlight>
then recompile the GCM compiling (which had failed previously) by doing
<syntaxhighlight lang="Bash">
cd /homedata/_MY_LOGIN_/DESCRIBE_YOUR_RESEARCH_PROJECT/
./compile_gcm.sh
</syntaxhighlight>
and recreate start files from a sample start_archive.nc by doing (in subdirectory gcm/newstart)
<syntaxhighlight lang="Bash">
./mini_startbase.sh
</syntaxhighlight>


=== Extra technical stuff ===

* in meso_install.sh is hard coded the git tag of the version that will be installed e.g. version="tags/mesoscale-compile-run_MESOIPSL_exploration". the tags point to specific versions which have been tested and are thus reference. e.g. mesoscale_compile-run_MESOIPSL on the git-trunk

* To recompile WRF (see "readme" file)
<syntaxhighlight lang="Bash">
cd code/MESOSCALE/LMD_MM_MARS
makemeso -p mars_lmd_new
</syntaxhighlight>
To recompile WRF in debug mode:
<syntaxhighlight lang="Bash">
cd code/MESOSCALE/LMD_MM_MARS
makemeso -p mars_lmd_new -g
</syntaxhighlight>
The compilation script (and options) is in MESOSCALE/LMD_MM_MARS/SRC/WRFV2/mars_lmd_new/makegcm_mpifort for physics
And in MESOSCALE/LMD_MM_MARS/makemeso for WRF

== Run the full workflow GCM + initialization + mesoscale model ==

Have a look in the script named launch just for info or to change the number of processors or the step at which you start. Send the launch job to the cluster by typing (note that you can change the number of core to run with in the header of the script, e.g. ''#SBATCH --ntasks=24'' to use 24 cores, but this doesn't work for now...)
<syntaxhighlight lang="Bash">
sbatch launch
</syntaxhighlight>
IMPORTANT: if you have used "Option 2" in the setup/environment, i.e. creating a dedicated "mesoscale.env" file, then you should source it in the "launch" script with something of the likes of:
<syntaxhighlight lang="Bash">
source ../mesoscale.env
</syntaxhighlight>


You can check the status of the run by typing
<syntaxhighlight lang="Bash">
squeue -u $USER
</syntaxhighlight>

=== Extra technical stuff ===
* The namelist.input file contains inputs for WRF. One can change output rate by specifying "history_interval_s" in seconds (instead of "history_interval"), e.g. set to the timestep for an output at every step to debug.
<syntaxhighlight lang="Bash">
history_interval_s=20
</syntaxhighlight>
* to run in hydrostatic mode: it is a parameter for "&dynamics" namelist
<syntaxhighlight lang="Bash">
non_hydrostatic=F
</syntaxhighlight>
* Note that the full list of options for namelist.in can be found in "SIMU/namelist.input_full"

== A more detailed run ==

The best is probably to use a more complete startbase than the minimal one that was created. For instance, to get a more complete startbase, link 'data_gcm' to point towards '/data/spiga/2021_STARTBASES_rev2460/MY35'

To use the tyler cap setting in namelist.wps, download the tylerall archive here 'https://web.lmd.jussieu.fr/~aslmd/mesoscale_model/data_static/' and extract the content in the folder named data_static

[[Category:Mars-Mesoscale]]