LMDZ to DYNAMICO start files - Revision history

Emillour at 12:43, 14 April 2025

2025-04-14T12:43:34Z

Aurelien.falco: /* startarchive2icosa */

2024-12-19T14:26:22Z

‎startarchive2icosa

Aurelien.falco at 14:23, 19 December 2024

2024-12-19T14:23:16Z

Aurelien.falco at 12:44, 4 December 2024

2024-12-04T12:44:20Z

Aurelien.falco at 12:23, 4 December 2024

2024-12-04T12:23:25Z

Aurelien.falco at 12:23, 4 December 2024

2024-12-04T12:23:02Z

Aurelien.falco at 16:54, 2 December 2024

2024-12-02T16:54:37Z

Aurelien.falco at 16:55, 28 November 2024

2024-11-28T16:55:43Z

Aurelien.falco: add categories

2024-11-28T13:21:33Z

add categories

Aurelien.falco at 15:19, 27 November 2024

2024-11-27T15:19:24Z

@@ Line 1: / Line 1: @@
 This page explains how to convert a start.nc startfi.nc to a [[The DYNAMICO dynamical core|Dynamico]]
 There is a wiki page specific for Dynamico just in case: https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core ).
 == Compilation ==
@@ Line 108: / Line 114: @@
 </pre>
 [[Category:DYNAMICO]]
 [[Category:Pluto-DYNAMICO]]

@@ Line 71: / Line 71: @@
 <pre>
 ln -s path/to/LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa/
-cp -r startarchive2icosa/*.e startarchive2icosa/*.def startarchive2icosa/*.xml startarchive2icosa/job* startarchive2icosa/*sh .
+cp -r startarchive2icosa/*.e startarchive2icosa/run* startarchive2icosa/*.xml startarchive2icosa/job* startarchive2icosa/*sh .
 </pre>
@@ Line 88: / Line 89: @@
 The script creates a folder '''icosa_starts/''' with the dynamico '''startfi.nc and start.nc'''.
 . NOT NEEDED? update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc.
 == Run Dynamico simulation ==

@@ Line 2: / Line 2: @@
 There is a wiki page specific for Dynamico just in case: https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core ).
-The first step is to compile DYNAMICO using the LMDZ physics. Please refer to [[DYNAMICO with LMDZ physics]] for this step.
+== Compilation ==
-. Get start.nc and startfi.nc from your simulation via newstart or the PCM.
+* The first step is to compile DYNAMICO using the LMDZ physics. Please refer to [[DYNAMICO with LMDZ physics]] for this step. This implies the compilation of [[IOIPSL]], [[XIOS]], [[DYNAMICO]] and [[Quick Install and Run|LMDZ package]] (Generic, Mars, Pluto, ...). It will create the executable '''icosa_lmdz.exe''' in your '''[[ICOSA_LMDZ]]/bin''' directory.
-.  Get an archive file using '''start2archive'''
+* Compile '''start_archive.e''' using the following command. Replace architecture, dimensions and <your_physics> by your package (mars/pluto/...)
 <pre>
 makelmdz_fcm -arch <architecture> -d <dimensions (lonxlatxalt)>  -p <your_physics> start2archive
 </pre>
-* b) run it:
 <pre>
 start2archive.e
 </pre>
-* c) Copy start archive to your new dynamico simulation folder
 <pre>
-  cp start_archive.nc dynamico_runs
-</pre>
+# short run
-*d) Convert the start archive to netCDF4
+run_length=1500
-<pre>
+# isothermal could a bad initial state, you can try  etat0=temperature_profile, which reads a 'profile.in' file.
- nccopy -k 4 start_archive.nc start_archive_nc4.nc
+etat=isothermal
 </pre>
-. Create an initial conditions files for dynamico by running a  dynamico simulation without an initial physics file (startphy_file=false).
+*b) run '''icosa_lmdz.exe''' (fingers crossed it run smoothly) and copy its output files.
 <pre>
 cp restartfi.nc startphy_icosa_ref.nc
 cp restart.nc start_icosa_ref.nc
 </pre>
-. Convert the LMDZ start files to the DYNAMCIO grid.
+) Create a '''surface_nc4.nc''' based on your topography (could be a symbolic link).
-* a) Create a '''surface_nc4.nc''' based on your topography (could be a symbolic link). It may fail if the format is netCDF 3. You can convert the file with '''nc3tonc4''' or '''nccopy -k 4'''.
-* b) Compile the files in LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa (where YOUR_PHYSICS is MARS/PLUTO/...) with the '''compile''' script, which will create start_archive2icosa and rearrange_startphy.
+It may fail if the format is netCDF 3. You can convert the file with '''nc3tonc4''' or '''nccopy -k 4'''.
-* c) Then, copy all the files in your simulation folder, but WARNING: there are some xml files that could overwrite your own files (like iodef.xml).
 <pre>
-cp path/to/LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa/* .
+ln -s path/to/LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa/
 </pre>
-*  d) run '''start_archive2icosa''' as a job (requires a lot of memory). Make sure that '''iodef.xml''' is the one from the '''startarchive2icosa''' folder.
 <pre>
 sbatch job_start_archive_2icosa
 </pre>
-*  e) the script creates '''start_icosa_prefinalize.nc''' and  '''startfi_prefinalize.nc'''. You will need to run a final script:
+The script creates '''start_icosa_prefinalize.nc''' and  '''startfi_prefinalize.nc'''.
 <pre>
 ./icosa_finalize.bash
 </pre>
 There could be an issue with the location of the LMDZ root folder. Please change the icosa_finalize.bash file accordingly.
-The script outputs startfi.nc and start_icosa.nc.
+There could be an issue with the location of the LMDZ root folder. Please change the icosa_finalize.bash file accordingly or set the '''LMDZ''' variable in your environment.
 . NOT NEEDED? update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc.
-. Run Dynamico simulation
+== Run Dynamico simulation ==
-*  a) change the iodef.xml to the one in '''deftank/dynamico'''
-*  b) in run.def, change the following variables:
+Create another folder, with the xml and def files from '''deftank/dynamico'''.
 <pre>
 etat0=start_file
@@ Line 65: / Line 100: @@
 </pre>
 Make sure the run.def also lists '''llm''' equal to your start.nc '''lev''' count. If you encounter an error about '''n_glo''' not being equal to your model '''n_glo''', change '''llm''' to match '''lev'''.
 [[Category:DYNAMICO]]
 [[Category:Pluto-DYNAMICO]]

@@ Line 64: / Line 64: @@
 etat0_start_file_colocated=true
 </pre>
 [[Category:DYNAMICO]]
 [[Category:Pluto-DYNAMICO]]

@@ Line 58: / Line 58: @@
 . Run Dynamico simulation
-  a) change the iodef.xml to the one in '''deftank/dynamico'''
+*  a) change the iodef.xml to the one in '''deftank/dynamico'''
-  b) in run.def, change the following variables:
+*  b) in run.def, change the following variables:
 <pre>
 etat0=start_file

@@ Line 7: / Line 7: @@
 .  Get an archive file using '''start2archive'''
-* a) Compile '''start_archive.e''' using the following command. Replace dimensions and <your_physics> by your package (mars/pluto/...)
+* a) Compile '''start_archive.e''' using the following command. Replace architecture, dimensions and <your_physics> by your package (mars/pluto/...)
 <pre>
-makelmdz_fcm -arch <archive> -d <dimensions (lonxlatxalt)>  -p <your_physics> start2archive
+makelmdz_fcm -arch <architecture> -d <dimensions (lonxlatxalt)>  -p <your_physics> start2archive
 </pre>
 * b) run it:
@@ Line 39: / Line 39: @@
 . Convert the LMDZ start files to the DYNAMCIO grid.
 * a) Create a '''surface_nc4.nc''' based on your topography (could be a symbolic link)
-* b) Compile the files in LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa (where YOUR_PHYSICS is MARS/PLUTO/...) with the '''compile''' script, which will create '''start_archive2icosa''' and '''rearrange_startphy'''. Copy all the files in your simulation folder, but WARNING: there are some xml files that could overwrite your own files (like iodef.xml).
+* b) Compile the files in LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa (where YOUR_PHYSICS is MARS/PLUTO/...) with the '''compile''' script, which will create start_archive2icosa and rearrange_startphy.
-*  c) run '''start_archive2icosa''' as a job (requires a lot of memory) and make sure that iodef.xml is the one from the '''startarchive2icosa''' folder.
+* c) Then, copy all the files in your simulation folder, but WARNING: there are some xml files that could overwrite your own files (like iodef.xml).
-*  d) the script creates '''start_icosa_prefinalize.nc''' and  '''startfi_prefinalize.nc'''
+<pre>
-*  e) run '''icosa_finalize.bash'''
+cp path/to/LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa/* .
 *  f) TODO change the XIOS and the for startfi0.nc  paths in icosa_finalize.bash and run it. It adds and changes variables in the startfiles.
 *  g) The scripts outputs startfi.nc and start_icosa.nc
@@ Line 53: / Line 62: @@
 [[Category:DYNAMICO]]
 [[Category:Pluto-DYNAMICO]]

← Older revision		Revision as of 13:21, 28 November 2024
Line 53:		Line 53:

	[[Category:DYNAMICO]]		[[Category:DYNAMICO]]
		+	[[Category:Generic-DYNAMICO]]
	[[Category:Pluto-DYNAMICO]]		[[Category:Pluto-DYNAMICO]]
		+	[[Category:Mars-DYNAMICO]]