Quick Install and Run - Revision history

Martin.turbet at 09:19, 13 April 2026

2026-04-13T09:19:00Z

Emillour at 16:12, 10 April 2026

2026-04-10T16:12:01Z

Emillour at 12:52, 8 April 2026

2026-04-08T12:52:23Z

Emillour at 13:33, 4 February 2026

2026-02-04T13:33:41Z

Emillour at 15:06, 2 October 2025

2025-10-02T15:06:48Z

Martin.turbet: /* Compiling the GCM */

2025-10-02T10:26:34Z

‎Compiling the GCM

Martin.turbet: /* GCM Input Datafiles and Datasets */

2025-10-02T10:21:41Z

‎GCM Input Datafiles and Datasets

Martin.turbet: /* FCM */

2025-10-02T10:19:00Z

‎FCM

Martin.turbet: /* Subversion */

2025-10-02T10:13:42Z

‎Subversion

Martin.turbet: /* Subversion */

2025-10-02T10:12:20Z

‎Subversion

@@ Line 90: / Line 90: @@
 In the spirit of the illustrative example considered here (an "Early Mars" simulation), a set of necessary input data may be downloaded with:
 <syntaxhighlight lang="bash">
-wget -nv --no-check-certificate https://web.lmd.jussieu.fr/~lmdz/planets/generic/reference_setups/reference_earlymars_64x48x26_b32x36.tar.gz
+wget -nv --no-check-certificate https://web.lmd.jussieu.fr/~lmdz/planets/generic/reference_setups/reference_earlymars_64x48x26_b40x38.tar.gz
 </syntaxhighlight>
-Once unpacked (to do that, you can execute the command "tar xvzf reference_earlymars_64x48x26_b32x36.tar.gz") the resulting "reference_earlymars_64x48x26_b32x36" will contain all that is needed, namely:
+Once unpacked (to do that, you can execute the command "tar xvzf reference_earlymars_64x48x26_b40x38.tar.gz") the resulting "reference_earlymars_64x48x26_b40x38" will contain all that is needed, namely:
 <syntaxhighlight lang="bash">
 callphys.def  gases.def  startfi.nc  traceur.def
@@ Line 170: / Line 170: @@
 To compile the GCM at the sought resolution for the Early Mars test case run (in LMDZ.COMMON):
 <syntaxhighlight lang="bash">
-./makelmdz_fcm -arch local -p generic -d 64x48x26 -b 32x36 gcm
+./makelmdz_fcm -arch local -p generic -d 64x48x26 -b 40x38 gcm
 </syntaxhighlight>
 <!-- -s option is no more needed ; * '''-s 2''': the physics parametrizations will handle 2 radiatively active tracers (water ice and dust for the Early Mars setup) -->
@@ Line 177: / Line 177: @@
 * '''-p generic''': the GCM will use the "generic" physics package
 * '''-d 64x48x26''': the GCM grid will be 64x48 in longitude x latitude, with 26 vertical levels.
-* '''-b 32x36''': the physics radiative transfer will be done using 32 bands in the IR and 36 in the visible.
+* '''-b 40x38''': the physics radiative transfer will be done using 40 bands in the IR and 38 in the visible.
 For a glimpse at all the possible ''makelmdz_fcm'' options and their meanings, run:
 <syntaxhighlight lang="bash">
@@ Line 184: / Line 184: @@
 and/or check the dedicated [[The_makelmdz_fcm_GCM_Compilation_Script|makelmdz_fcm page]].
-Upon successful compilation, the executable '''gcm_64x48x26_phygeneric_b32x36_seq.e''' should be generated in the '''bin''' subdirectory.
+Upon successful compilation, the executable '''gcm_64x48x26_phygeneric_b40x38_seq.e''' should be generated in the '''bin''' subdirectory.
 === Known issues ===
@@ Line 208: / Line 208: @@
 == Running the GCM ==
-To run your first simulation, you need to first copy (or move) the executable '''gcm_64x48x26_phygeneric_b32x36_seq.e''' to the directory containing the initial conditions and parameter files, e.g. '''reference_earlymars_64x48x26_b32x36''' and run it.
+To run your first simulation, you need to first copy (or move) the executable '''gcm_64x48x26_phygeneric_b40x38_seq.e''' to the directory containing the initial conditions and parameter files, e.g. '''reference_earlymars_64x48x26_b40x38''' and run it.
 This is usually a two-step process: the (optional) first step is to source the environment architecture file (the very same that was used to compile the model), e.g.,:
 <syntaxhighlight lang="bash">
@@ Line 215: / Line 215: @@
 The second step is to execute the model, e.g.,:
 <syntaxhighlight lang="bash">
-./gcm_64x48x26_phygeneric_b32x36_seq.e > gcm.out 2>&1
+./gcm_64x48x26_phygeneric_b40x38_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_64x48x26_phygeneric_b32x36_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_64x48x26_phygeneric_b40x38_seq.e'''), then the outputs will be directly on the screen.
 == Checking the Results of a Simulation ==

@@ Line 3: / Line 3: @@
 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/generic/install_scripts/install_lmdz_generic_earlymars.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 88: / Line 88: @@
 In the spirit of the illustrative example considered here (an "Early Mars" simulation), a set of necessary input data may be downloaded with:
 <syntaxhighlight lang="bash">
-wget -nv --no-check-certificate https://web.lmd.jussieu.fr/~lmdz/planets/generic/reference_setups/reference_earlymars_32x32x15_b32x36.tar.gz
+wget -nv --no-check-certificate https://web.lmd.jussieu.fr/~lmdz/planets/generic/reference_setups/reference_earlymars_64x48x26_b32x36.tar.gz
 </syntaxhighlight>
-Once unpacked (to do that, you can execute the command "tar xvzf reference_earlymars_32x32x15_b32x36.tar.gz") the resulting "reference_earlymars_32x32x15_b32x36" will contain all that is needed, namely:
+Once unpacked (to do that, you can execute the command "tar xvzf reference_earlymars_64x48x26_b32x36.tar.gz") the resulting "reference_earlymars_64x48x26_b32x36" will contain all that is needed, namely:
 <syntaxhighlight lang="bash">
 callphys.def  gases.def  startfi.nc  traceur.def
@@ Line 168: / Line 168: @@
 To compile the GCM at the sought resolution for the Early Mars test case run (in LMDZ.COMMON):
 <syntaxhighlight lang="bash">
-./makelmdz_fcm -arch local -p generic -d 32x32x15 -b 32x36 gcm
+./makelmdz_fcm -arch local -p generic -d 64x48x26 -b 32x36 gcm
 </syntaxhighlight>
 <!-- -s option is no more needed ; * '''-s 2''': the physics parametrizations will handle 2 radiatively active tracers (water ice and dust for the Early Mars setup) -->
@@ Line 174: / Line 174: @@
 The options for ''makelmdz_fcm'' used here imply:
 * '''-p generic''': the GCM will use the "generic" physics package
-* '''-d 32x32x15''': the GCM grid will be 32x32 in longitude x latitude, with 15 vertical levels.
+* '''-d 64x48x26''': the GCM grid will be 64x48 in longitude x latitude, with 26 vertical levels.
 * '''-b 32x36''': the physics radiative transfer will be done using 32 bands in the IR and 36 in the visible.
 For a glimpse at all the possible ''makelmdz_fcm'' options and their meanings, run:
@@ Line 182: / Line 182: @@
 and/or check the dedicated [[The_makelmdz_fcm_GCM_Compilation_Script|makelmdz_fcm page]].
-Upon successful compilation, the executable '''gcm_32x32x15_phygeneric_b32x36_seq.e''' should be generated in the '''bin''' subdirectory.
+Upon successful compilation, the executable '''gcm_64x48x26_phygeneric_b32x36_seq.e''' should be generated in the '''bin''' subdirectory.
 === Known issues ===
@@ Line 206: / Line 206: @@
 == Running the GCM ==
-To run your first simulation, you need to first copy (or move) the executable '''gcm_32x32x15_phygeneric_b32x36_seq.e''' to the directory containing the initial conditions and parameter files, e.g. '''reference_earlymars_32x32x15_b32x36''' and run it.
+To run your first simulation, you need to first copy (or move) the executable '''gcm_64x48x26_phygeneric_b32x36_seq.e''' to the directory containing the initial conditions and parameter files, e.g. '''reference_earlymars_64x48x26_b32x36''' and run it.
 This is usually a two-step process: the (optional) first step is to source the environment architecture file (the very same that was used to compile the model), e.g.,:
 <syntaxhighlight lang="bash">
@@ Line 213: / Line 213: @@
 The second step is to execute the model, e.g.,:
 <syntaxhighlight lang="bash">
-./gcm_32x32x15_phygeneric_b32x36_seq.e > gcm.out 2>&1
+./gcm_64x48x26_phygeneric_b32x36_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_32x32x15_phygeneric_b32x36_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_64x48x26_phygeneric_b32x36_seq.e'''), then the outputs will be directly on the screen.
 == Checking the Results of a Simulation ==
@@ Line 235: / Line 235: @@
-To check that you have successfully run the simulation, we provide some graphs to evaluate the results of your simulations, for the simulation described in this tutorial (early Mars reference, 32x32x15 resolution).
+To check that you have successfully run the simulation, we provide some graphs to evaluate the results of your simulations, for a simulation similar to the one described in this tutorial (early Mars, 32x32x15 resolution). TODO : update plots to current example
 In the plots shown here, we present maps of the surface temperatures ('tsurf' variable) and the water ice cloud column ('h2o_ice_col' variable), both plotted using Panoply.

@@ Line 168: / Line 168: @@
 To compile the GCM at the sought resolution for the Early Mars test case run (in LMDZ.COMMON):
 <syntaxhighlight lang="bash">
-./makelmdz_fcm -arch local -p std -d 32x32x15 -b 32x36 gcm
+./makelmdz_fcm -arch local -p generic -d 32x32x15 -b 32x36 gcm
 </syntaxhighlight>
 <!-- -s option is no more needed ; * '''-s 2''': the physics parametrizations will handle 2 radiatively active tracers (water ice and dust for the Early Mars setup) -->
 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 std''': the GCM will use the "std" physics package (i.e. the generic physics)
+* '''-p generic''': the GCM will use the "generic" physics package
 * '''-d 32x32x15''': the GCM grid will be 32x32 in longitude x latitude, with 15 vertical levels.
 * '''-b 32x36''': the physics radiative transfer will be done using 32 bands in the IR and 36 in the visible.
@@ Line 182: / Line 182: @@
 and/or check the dedicated [[The_makelmdz_fcm_GCM_Compilation_Script|makelmdz_fcm page]].
-Upon successful compilation, the executable '''gcm_32x32x15_phystd_b32x36_seq.e''' should be generated in the '''bin''' subdirectory.
+Upon successful compilation, the executable '''gcm_32x32x15_phygeneric_b32x36_seq.e''' should be generated in the '''bin''' subdirectory.
 === Known issues ===
@@ Line 206: / Line 206: @@
 == Running the GCM ==
-To run your first simulation, you need to first copy (or move) the executable '''gcm_32x32x15_phystd_b32x36_seq.e''' to the directory containing the initial conditions and parameter files, e.g. '''reference_earlymars_32x32x15_b32x36''' and run it.
+To run your first simulation, you need to first copy (or move) the executable '''gcm_32x32x15_phygeneric_b32x36_seq.e''' to the directory containing the initial conditions and parameter files, e.g. '''reference_earlymars_32x32x15_b32x36''' and run it.
 This is usually a two-step process: the (optional) first step is to source the environment architecture file (the very same that was used to compile the model), e.g.,:
 <syntaxhighlight lang="bash">
@@ Line 213: / Line 213: @@
 The second step is to execute the model, e.g.,:
 <syntaxhighlight lang="bash">
-./gcm_32x32x15_phystd_b32x36_seq.e > gcm.out 2>&1
+./gcm_32x32x15_phygeneric_b32x36_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_32x32x15_phystd_b32x36_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_32x32x15_phygeneric_b32x36_seq.e'''), then the outputs will be directly on the screen.
 == Checking the Results of a Simulation ==

@@ Line 88: / Line 88: @@
 In the spirit of the illustrative example considered here (an "Early Mars" simulation), a set of necessary input data may be downloaded with:
 <syntaxhighlight lang="bash">
-wget -nv --no-check-certificate https://web.lmd.jussieu.fr/~lmdz/planets/generic/reference_setups/bench_earlymars_32x32x15_b32x36.tar.gz
+wget -nv --no-check-certificate https://web.lmd.jussieu.fr/~lmdz/planets/generic/reference_setups/reference_earlymars_32x32x15_b32x36.tar.gz
 </syntaxhighlight>
-Once unpacked (to do that, you can execute the command "tar xvzf bench_earlymars_32x32x15_b32x36.tar.gz") the resulting "bench_earlymars_32x32x15_b32x36" will contain all that is needed, namely:
+Once unpacked (to do that, you can execute the command "tar xvzf reference_earlymars_32x32x15_b32x36.tar.gz") the resulting "reference_earlymars_32x32x15_b32x36" will contain all that is needed, namely:
 <syntaxhighlight lang="bash">
 callphys.def  gases.def  startfi.nc  traceur.def
@@ Line 206: / Line 206: @@
 == Running the GCM ==
-To run your first simulation, you need to first copy (or move) the executable '''gcm_32x32x15_phystd_b32x36_seq.e''' to the directory containing the initial conditions and parameter files, e.g. '''bench_earlymars_32x32x15_b32x36''' and run it.
+To run your first simulation, you need to first copy (or move) the executable '''gcm_32x32x15_phystd_b32x36_seq.e''' to the directory containing the initial conditions and parameter files, e.g. '''reference_earlymars_32x32x15_b32x36''' and run it.
 This is usually a two-step process: the (optional) first step is to source the environment architecture file (the very same that was used to compile the model), e.g.,:
 <syntaxhighlight lang="bash">
@@ Line 220: / Line 220: @@
 == Checking the Results of a Simulation ==
 Once the simulation is finished, you'll know that all went well ("everything is cool") if the last few lines of the standard text output reads:
-[[File:tsurf_benchmark_early_Mars.png|300px|thumb|Final surface temperature map of the benchmark simulation (plotted using Panoply).]]
+[[File:tsurf_benchmark_early_Mars.png|300px|thumb|Final surface temperature map of the reference simulation (plotted using Panoply).]]
-[[File:water_ice_cloud_column_benchmark_early_Mars.png|300px|thumb|Final water ice cloud column map of the benchmark simulation (plotted using Panoply).]]
+[[File:water_ice_cloud_column_benchmark_early_Mars.png|300px|thumb|Final water ice cloud column map of the reference simulation (plotted using Panoply).]]
 <pre>
   in abort_gcm
@@ Line 235: / Line 235: @@
-To check that you have successfully run the simulation, we provide some graphs to evaluate the results of your simulations, for the simulation described in this tutorial (early Mars benchmark, 32x32x15 resolution).
+To check that you have successfully run the simulation, we provide some graphs to evaluate the results of your simulations, for the simulation described in this tutorial (early Mars reference, 32x32x15 resolution).
 In the plots shown here, we present maps of the surface temperatures ('tsurf' variable) and the water ice cloud column ('h2o_ice_col' variable), both plotted using Panoply.

← Older revision		Revision as of 10:26, 2 October 2025
Line 162:		Line 162:

	Note that if you are using a recent version of gfortran (10 or more), you have to add an extra option in the %BASE_FFLAGS, that is '''-fallow-argument-mismatch'''		Note that if you are using a recent version of gfortran (10 or more), you have to add an extra option in the %BASE_FFLAGS, that is '''-fallow-argument-mismatch'''
		+
		+	Also note that you can find in the '''LMDZ.COMMON/arch/''' many examples of arch files that you can re-use as is if you compile the model on our usual computing clusters (e.g. Spirit, Adastra, etc.). Just check the content of the directory to see if your favorite computing cluster already has arch files.

	=== Compiling a test case (early Mars) ===		=== Compiling a test case (early Mars) ===

@@ Line 40: / Line 40: @@
 svn checkout https://forge.ipsl.jussieu.fr/fcm/svn/PATCHED/FCM_V1.2
 </syntaxhighlight>
-You'll then need to add the resulting FCM_V1.2/bin to your PATH environment variable so that the command "fcm" may be used from anywhere on your machine. e.g. by adding the following line in your .bashrc:
+You'll then need to add the resulting FCM_V1.2/bin to your PATH environment variable so that the command "fcm" may be used from anywhere on your machine. e.g. by adding the following line in your .bashrc (the .bashrc file is a hidden configuration script in your home directory (~/.bashrc) that runs whenever you start a new Bash shell):
 <syntaxhighlight lang="bash">
 export PATH=$PATH:$HOME/FCM_V1.2/bin

@@ Line 29: / Line 29: @@
 As a side note: the source code that will be fetched by svn can also be browsed online here: https://trac.lmd.jussieu.fr/Planeto
-%Note: if the command line above doesn't work, you may also try to replace 'http' by 'https'.
+<!--Note: if the command line above doesn't work, you may also try to replace 'http' by 'https'.-->
 === Git ===