Quick Install and Run Mars PCM - Revision history

Emillour at 16:14, 10 April 2026

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Jorge at 16:10, 25 February 2026

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Emillour at 13:26, 26 May 2023

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Emillour at 07:41, 24 May 2023

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Emillour at 08:10, 17 April 2023

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Mwolff: Created page with " == Dude, on est là. =="

2023-04-11T08:38:25Z

Created page with " == Dude, on est là. =="

New page

== Dude, on est là. ==

@@ Line 4: / Line 4: @@
 Note that there is a dedicated, install script, that attempts to do all these steps (up to and including running the simulation) that you can obtain here: https://web.lmd.jussieu.fr/~lmdz/planets/install_lmdz_mars.bash
 Automating the process is not trivial as there are many subtle variants of Linux flavors and user account setups, so the script may fail in your case, but hopefully the information given in this page should help you solve the encountered problems.
 == Prerequisites: Tools and Libraries ==

@@ Line 222: / Line 222: @@
 == Taking Things to the Next Level ==
 The short tutorial presented in this page is meant to be useful to get an overview of what is required to install and run the GCM, in addition to checking the results of a simulation. Moving on to a more intensive and problem-specific usage will require diving into additional topics and aspects such as:
 * Selecting the appropriate inputs and run parameters for a given study.

@@ Line 94: / Line 94: @@
 In order to run, the GCM needs some inputs, such as initial conditions (values of state variables), external inputs (e.g. optical properties of aerosols) and simulation setup (e.g. specifications on how long to run, which parametrizations should be activated, etc.)
-In the spirit of the illustrative example considered here (an "GCM6" simulation, i.e. simulation including CO2, dust and water cycles with a model top around 120 km), a set of necessary input data may be downloaded with:
+In the spirit of the illustrative example considered here (an "GCM6" simulation, i.e. simulation including CO2, dust and water cycles with a model top around 120 km), a set of necessary input data may be downloaded (note that a few reference cases are available on https://web.lmd.jussieu.fr/~lmdz/planets/mars/ ) with:
 <syntaxhighlight lang="bash">
 wget -nv --no-check-certificate http://www.lmd.jussieu.fr/~lmdz/planets/mars/reference_GCM6_64x48x54.tar.gz

@@ Line 94: / Line 94: @@
 In order to run, the GCM needs some inputs, such as initial conditions (values of state variables), external inputs (e.g. optical properties of aerosols) and simulation setup (e.g. specifications on how long to run, which parametrizations should be activated, etc.)
-In the spirit of the illustrative example considered here (an "GCM5" simulation, i.e. simulation including CO2, dust and water cycles with a model top around 100 km), a set of necessary input data may be downloaded with:
+In the spirit of the illustrative example considered here (an "GCM6" simulation, i.e. simulation including CO2, dust and water cycles with a model top around 120 km), a set of necessary input data may be downloaded with:
 <syntaxhighlight lang="bash">
-wget -nv --no-check-certificate http://www.lmd.jussieu.fr/~lmdz/planets/mars/bench_64x48x29.tar.gz
+wget -nv --no-check-certificate http://www.lmd.jussieu.fr/~lmdz/planets/mars/reference_GCM6_64x48x54.tar.gz
 </syntaxhighlight>
-Once unpacked ("tar xvzf bench_64x48x29.tar.gz") the resulting "bench_64x48x29" will contain all that is needed, namely:
+Once unpacked ("tar xvzf reference_GCM6_64x48x54.tar.gz") the resulting "reference_GCM6_64x48x54" will contain all that is needed, namely:
 <syntaxhighlight lang="bash">
-callphys.def  startfi.nc  traceur.def run.def    start.nc    z2sig.def
+callphys.def diagfi.def run.def startfi.nc start.nc stats.def traceur.def z2sig.def
 </syntaxhighlight>
-* Initial condition NetCDF files ''start.nc'' and ''startfi.nc''; the first containing initial condition values for the dynamics and the second initial condition values for the physics. These also define the model resolution and number of atmospheric layers (64x48x29 - the compiled GCM binary must match this!)
+* Initial condition NetCDF files ''start.nc'' and ''startfi.nc''; the first containing initial condition values for the dynamics and the second initial condition values for the physics. These also define the model resolution and number of atmospheric layers (64x48x54 - the compiled GCM binary must match this!)
-* Some ASCII *.def files containing run parameters, namely:
+* Some mandatory ASCII *.def files containing run parameters, namely:
 # [[The_run.def_Input_File | run.def]] : "master def file" containing main run parameters
 # [[The_callphys.def_Input_File | callphys.def]] : file containing flags and keys for the various physics parametrizations
 # [[The_z2sig.def_Input_File | z2sig.def]] : file describing the sought vertical discretization
 # [[The_traceur.def_Input_File | traceur.def]] : file specifying the tracer number and names
+* Some optional ASCII *def files containing names of variables to output:
 == Compiling the GCM ==
@@ Line 163: / Line 165: @@
 To compile the GCM at the sought resolution, run (in LMDZ.COMMON):
 <syntaxhighlight lang="bash">
-./makelmdz_fcm -arch local -p mars -d 64x48x29 -j 8 gcm
+./makelmdz_fcm -arch local -p mars -d 64x48x54 -j 8 gcm
 </syntaxhighlight>
 Here, we assume that you have generated the '''arch-local.*''' files as per what is suggested in the previous section.
 The options for ''makelmdz_fcm'' used here imply:
 * '''-p mars''': the GCM will use the "mars" physics package
-* '''-d 64x48x29''': the GCM grid will be 64x48 in longitude x latitude, with 29 vertical levels.
+* '''-d 64x48x54''': the GCM grid will be 64x48 in longitude x latitude, with 54 vertical levels.
 For a glimpse at all the possible ''makelmdz_fcm'' options and their meanings, run:
 <syntaxhighlight lang="bash">
@@ Line 175: / Line 177: @@
 and/or check the dedicated [[The_makelmdz_fcm_GCM_Compilation_Script|makelmdz_fcm page]].
-Upon successful compilation, the executable '''gcm_64x48x29_phymars_seq.e''' should be generated in the '''bin''' subdirectory.
+Upon successful compilation, the executable '''gcm_64x48x54_phymars_seq.e''' should be generated in the '''bin''' subdirectory.
 == Running the GCM ==
@@ Line 186: / Line 188: @@
 tar xvzf datadir.tar.gz
 </syntaxhighlight>
-Link the resulting '''datadir''' directory to where you will run (e.g. the '''bench_64x48x29''' directory), for instance if '''datadir''' is along side '''bench_64x48x29''', then in the later do:
+Link the resulting '''datadir''' directory to where you will run (e.g. the '''reference_GCM6_64x48x54''' directory), for instance if '''datadir''' is along side '''reference_GCM6_64x48x54''', then in the later do:
 <syntaxhighlight lang="bash">
 ln -s ../datadir .
 </syntaxhighlight>
-Secondly you need to copy (or move) the executable '''gcm_64x48x29_phymars_seq.e''' from '''LMDZ.COMMON/bin''' to the directory containing the initial conditions and parameter files, e.g. '''bench_64x48x29'''.
+Secondly you need to copy (or move) the executable '''gcm_64x48x54_phymars_seq.e''' from '''LMDZ.COMMON/bin''' to the directory containing the initial conditions and parameter files, e.g. '''reference_GCM6_64x48x54'''.
 You can now run the GCM.
@@ Line 199: / Line 201: @@
 The second step is to execute the model, e.g.,:
 <syntaxhighlight lang="bash">
-./gcm_64x48x29_phymars_seq.e > gcm.out 2>&1
+./gcm_64x48x54_phymars_seq.e > gcm.out 2>&1
 </syntaxhighlight>
-With this command line, the (text) outputs messages are redirected into a text file, '''gcm.out'''. It is convenient to keep this file for later inspection (e.g., to track a bug). If there is no redirection (only '''./gcm_64x48x29_phymars_seq.e'''), then the outputs will be directly on the screen.
+With this command line, the (text) outputs messages are redirected into a text file, '''gcm.out'''. It is convenient to keep this file for later inspection (e.g., to track a bug). If there is no redirection (only '''./gcm_64x48x54_phymars_seq.e'''), then the outputs will be directly on the screen.
 == Checking the Results of a Simulation ==

@@ Line 99: / Line 99: @@
 </syntaxhighlight>
-...TODO... DESCRIBE CONTENTS OF BENCH... +ADD OTHER BENCH CASES PCM5/PCM6) ??
+Once unpacked ("tar xvzf bench_64x48x29.tar.gz") the resulting "bench_64x48x29" will contain all that is needed, namely:
 == Compiling the GCM ==

← Older revision		Revision as of 13:26, 26 May 2023
Line 217:		Line 217:

	[[Category:Mars-Model]]		[[Category:Mars-Model]]
		+	[[Category:Mars-LMDZ]]

@@ Line 42: / Line 42: @@
 === the NetCDF library ===
-The GCM reads and writes input and output files in NetCDF format. Therefore a NetCDF library must be available. As this library is not quite standard you'll probably have to install it yourself on your system. You can use the following home-made "install_netcdf4_hdf5_seq.bash" script to do so. For this, ensure that you are in your home directory:
+The GCM reads and writes input and output files in NetCDF format. Therefore a NetCDF library must be available. As this library is not quite standard you'll probably have to install it yourself on your system (check out [[the netCDF library]] page for more). You can use the following home-made "install_netcdf4_hdf5_seq.bash" script to do so. For this, ensure that you are in your home directory:
 <syntaxhighlight lang="bash">
 mkdir netcdf