Difference between revisions of "Mars Dynamico Installation manual"
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| − | This page follows a manual for installing Mars Dynamico | + | This page follows a manual for installing Mars [[The DYNAMICO dynamical core|Dynamico]] (use the following link to access the wiki page of Dynamico https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core ). |
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| + | The first step is to compile DYNAMICO using the LMDZ-MARS physics. Please refer to [[DYNAMICO with LMDZ physics]] for this step. | ||
1. Install the LMDZ Mars GCM and newstart | 1. Install the LMDZ Mars GCM and newstart | ||
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b) run strart2archice_SSO | b) run strart2archice_SSO | ||
c) cp start_archive.nc to the dynamico_runs folder | c) cp start_archive.nc to the dynamico_runs folder | ||
| − | 3 | + | |
| − | + | 3. Create an initial condiations files for dynamico by running a dynamico simulation without the physics. | |
| − | + | a) Copy from '''ICOSA_LMDZ/bin/icosa_lmdz.exe''' to a dynamico_runs folder (you should have followed [[DYNAMICO with LMDZ physics]] first, to compile '''icosa_lmdz.exe'''). | |
| − | + | b) Copy the xml files and the start files and the def files in the dynamico_runs directory and have access to the datadir. | |
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input file start_archive.nc need be converted to NetCDF4 format | input file start_archive.nc need be converted to NetCDF4 format | ||
nccopy -k 4 start_archive.nc start_archive_nc4.nc | nccopy -k 4 start_archive.nc start_archive_nc4.nc | ||
| − | + | 4. run dynamic. | |
a) In run_icosa.def change to run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false(not start_file) | a) In run_icosa.def change to run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false(not start_file) | ||
b) copy datadir to the running directory | b) copy datadir to the running directory | ||
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1. cp restartfi.nc startphy_icosa_ref.nc | 1. cp restartfi.nc startphy_icosa_ref.nc | ||
2. cp restart_icosa.nc start_icosa_ref.nc | 2. cp restart_icosa.nc start_icosa_ref.nc | ||
| − | + | 5. move to LMDZ.mars/util/startarchive2icosa then change compile script to adapt for the right location of XIOS and run compile u should get start_archive2icosa and rearrange_startphy | |
a) copy start_archive2icosa and rearrange_startphy to the dynamico_runs folder. | a) copy start_archive2icosa and rearrange_startphy to the dynamico_runs folder. | ||
b) Create surface_nc4.nc and copy it dynamico_runs folder | b) Create surface_nc4.nc and copy it dynamico_runs folder | ||
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h) The scripts outputs startfi.nc and start_icosa.nc | h) The scripts outputs startfi.nc and start_icosa.nc | ||
| − | + | 6. update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc | |
| − | + | 7. Run Dynamico simulation | |
a) change the iodef.xml | a) change the iodef.xml | ||
b) change in run_icosa.def etat0=start_file and add etat0_start_file_colocated=true | b) change in run_icosa.def etat0=start_file and add etat0_start_file_colocated=true | ||
| + | [[Category:DYNAMICO]] | ||
[[Category:Mars-DYNAMICO]] | [[Category:Mars-DYNAMICO]] | ||
Revision as of 15:01, 18 October 2024
This page follows a manual for installing Mars Dynamico (use the following link to access the wiki page of Dynamico https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core ).
The first step is to compile DYNAMICO using the LMDZ-MARS physics. Please refer to DYNAMICO with LMDZ physics for this step.
1. Install the LMDZ Mars GCM and newstart
a) make sure u have the datafir and all of the *.def files. b) create start.nc and startfi.nc
2. Compile start2archive_SSO
a) run : makelmdz_fcm -arch <archive> -d <dimensions (lonxlatxalt)> -p mars start2archive_SSO to create start_archive b) run strart2archice_SSO c) cp start_archive.nc to the dynamico_runs folder
3. Create an initial condiations files for dynamico by running a dynamico simulation without the physics.
a) Copy from ICOSA_LMDZ/bin/icosa_lmdz.exe to a dynamico_runs folder (you should have followed DYNAMICO with LMDZ physics first, to compile icosa_lmdz.exe). b) Copy the xml files and the start files and the def files in the dynamico_runs directory and have access to the datadir. input file start_archive.nc need be converted to NetCDF4 format nccopy -k 4 start_archive.nc start_archive_nc4.nc
4. run dynamic.
a) In run_icosa.def change to run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false(not start_file)
b) copy datadir to the running directory
c) run icosa_lmdz.exe
d) copy the files outputed by icosa_lmdz.exe
1. cp restartfi.nc startphy_icosa_ref.nc
2. cp restart_icosa.nc start_icosa_ref.nc
5. move to LMDZ.mars/util/startarchive2icosa then change compile script to adapt for the right location of XIOS and run compile u should get start_archive2icosa and rearrange_startphy
a) copy start_archive2icosa and rearrange_startphy to the dynamico_runs folder. b) Create surface_nc4.nc and copy it dynamico_runs folder c) source arch.env d) run ./start_archive2icosa as a job (requires a lot of memory) and make sure that Iodef.xml is the one for compile. e) the script create start_icosa_prefinalize.nc and startfi_prefinalize.nc f) copy icosa_finalize script form /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash to dynamico_runs folder g) change the XIOS and the for startfi0.nc paths in icosa_finalize.bash and run it. It adds and changes variables in the startfiles. h) The scripts outputs startfi.nc and start_icosa.nc
6. update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc
7. Run Dynamico simulation
a) change the iodef.xml b) change in run_icosa.def etat0=start_file and add etat0_start_file_colocated=true
