Quick Install and Run Mars PEM - Revision history

Jbclement: /* Outputs */

2026-03-30T09:00:40Z

‎Outputs

Jbclement: /* Requirements */

2026-03-05T09:19:21Z

‎Requirements

Jbclement at 09:18, 5 March 2026

2026-03-05T09:18:21Z

Jbclement at 09:48, 3 March 2026

2026-03-03T09:48:54Z

Jbclement at 09:08, 27 February 2026

2026-02-27T09:08:28Z

Jbclement: /* Requirements */

2026-02-12T11:22:03Z

‎Requirements

Jbclement: /* Requirements */

2026-02-12T11:10:05Z

‎Requirements

Jbclement: /* Requirements */

2025-11-28T16:58:27Z

‎Requirements

Jbclement: /* Outputs */

2025-11-27T14:01:19Z

‎Outputs

Jbclement: /* Requirements */

2025-11-26T09:42:27Z

‎Requirements

@@ Line 68: / Line 68: @@
 The PEM simulation generates the following files:
 * the usual outputs of the PCM: ''restartfi.nc'', ''restart.nc''/''restart1D.txt'', ''diagfi.nc'', etc;
-* the XIOS outputs of the PCM: ''Xoutdaily4pem*.nc''/''Xoutyearly4pem*.nc'';
+* the XIOS outputs of the PCM: ''xoutdaily4pem*.nc''/''xoutyearly4pem*.nc'';
 * the outputs of the chained simulation: ''pem_workflow.log'', ''pem_workflow.sts'' and possibly ''kill_pem_workflow.sh'';
 * the usual outputs of the PEM: ''restartevo.nc'', ''restartfi.nc'', ''restart.nc''/''restart1D.txt'' and ''diagevo.nc''.

@@ Line 61: / Line 61: @@
 #* '''pem_exe''', the name of the PEM executable file should be adapted.
 #* '''pem_arg''' which is an optional argument for the PEM executable. It should be specified according to the set-up ("--auto-exit" for SLURM and PBS/TORQUE | "" when the script is not run as a job).
-# The user has to specify the wanted options in the '''def files''', especially for ''run_pem.def'', ''run_pcm.def'' and ''callphys.def'' which must be consistent. In particular, ''run_pem.def'' needs to include some definitions in file ''run_pcm.def'' and "callphys.def" with <code>INCLUDEDEF=run_pcm.def</code>.
+# The user has to specify the wanted options in the '''def files''', especially for ''run_pem.def'', ''run_pcm.def'' and ''callphys.def'' which must be consistent. In particular, ''run_pem.def'' needs to include some definitions in file ''run_pcm.def'' and ''callphys.def'' with <code>INCLUDEDEF=run_pcm.def</code>.
 The user has to provide a ''startfi.nc'' whose orbital parameters are consistent with the initial date set in ''run_PEM.def''. The script '''ini_pem_orbit.sh''' can do it automatically reading ''obl_ecc_lsp.asc''.

@@ Line 61: / Line 61: @@
 #* '''pem_exe''', the name of the PEM executable file should be adapted.
 #* '''pem_arg''' which is an optional argument for the PEM executable. It should be specified according to the set-up ("--auto-exit" for SLURM and PBS/TORQUE | "" when the script is not run as a job).
-# The user has to specify the wanted options in the '''def files''', especially for ''run_pem.def'', ''run_pcm.def'' and ''callphys.def'' which must be consistent. In particular, ''run_pem.def'' needs to include some definitions for the physics in file ''run_pcm.def'' with <code>INCLUDEDEF=run_pcm.def</code>.
+# The user has to specify the wanted options in the '''def files''', especially for ''run_pem.def'', ''run_pcm.def'' and ''callphys.def'' which must be consistent. In particular, ''run_pem.def'' needs to include some definitions in file ''run_pcm.def'' and "callphys.def" with <code>INCLUDEDEF=run_pcm.def</code>.
 The user has to provide a ''startfi.nc'' whose orbital parameters are consistent with the initial date set in ''run_PEM.def''. The script '''ini_pem_orbit.sh''' can do it automatically reading ''obl_ecc_lsp.asc''.

@@ Line 41: / Line 41: @@
 * the starting files you want to run the PCM: ''startfi.nc'' and ''start.nc''/''start1D.txt'';
 * the necessary PEM files: ''pem_workflow.sh'', ''pem_workflow_lib.sh'', ''pcm_run.job'', ''pem_run.job'', ''run_pem.def'' and ''obl_ecc_lsp.asc'';
-* the optional PEM files ''diagevol.def'' to define the PEM variables to be ouputted and ''startevol.nc'' to set the initial state of the PEM.
+* the optional PEM files ''diagevo.def'' to define the PEM variables to be ouputted and ''startevo.nc'' to set the initial state of the PEM.
 The PEM files can be found in the deftank folder, where a ''README'' file recaps everything.
@@ Line 70: / Line 70: @@
 * the XIOS outputs of the PCM: ''Xoutdaily4pem*.nc''/''Xoutyearly4pem*.nc'';
 * the outputs of the chained simulation: ''pem_workflow.log'', ''pem_workflow.sts'' and possibly ''kill_pem_workflow.sh'';
-* the usual outputs of the PEM: ''restartevol.nc'', ''restartfi.nc'', ''restart.nc''/''restart1D.txt'' and ''diagevol.nc''.
+* the usual outputs of the PEM: ''restartevo.nc'', ''restartfi.nc'', ''restart.nc''/''restart1D.txt'' and ''diagevo.nc''.
 During the simulation, the PCM/PEM run files are renamed conveniently and stored in the sub-directories '''logs''' (log files), '''starts''' (starting files) and '''diags''' (diagnostic files).

@@ Line 13: / Line 13: @@
 Options with example:
 # [local]: ''root name of arch files'', assuming that they have been set up for your configuration;
-# [planet]: ''mars'' to use the Mars planet physics package;
+# [planet]: ''mars'' to use the PEM dedicated to the Mars planet;
 # [dimensions]: ''64x48x54'' to define the grid you want to use (longitude x latitude x atmospheric layers).
 To run the PEM, you need a PCM working with XIOS and consistent options. To compile it, in LMDZ.COMMON, do:
@@ Line 25: / Line 25: @@
 To run a PEM simulation, do:
 <syntaxhighlight lang="bash">
-./launchPEM.sh [options]
+./pem_workflow.sh [options]
 </syntaxhighlight>
 Options:
 # None: to start a simulation from scratch;
-# 're': to relaunch a simulation from a starting point (interactive prompt).
+# 're': to resume a simulation from a starting point (interactive prompt).
-The Bash file ''launchPEM.sh'' is the master script to launch the PEM chained simulation. It checks if necessary files and required options for your simulation are ok.
+The Bash file ''pem_workflow.sh'' is the master script to launch the PEM chained simulation. It checks if necessary files and required options for your simulation are ok.
 == Requirements ==
@@ Line 38: / Line 38: @@
 * your executable files for the PCM and the PEM with consistent options;
 * the xml files for XIOS which can be found in the PCM deftank folder: ''iodef.xml'', ''context_lmdz_physics.xml'', ''file_def_physics_mars.xml'' and ''field_def_physics_mars.xml'';
-* the def files you want to run the PCM: ''run.def'', ''callphys.def'', ''traceur.def'', etc. '''Be careful, do not forget to rename the PCM ''run.def'' into ''run_PCM.def''''';
+* the def files you want to run the PCM: ''run.def'', ''callphys.def'', ''traceur.def'', etc. '''Be careful, do not forget to rename the PCM ''run.def'' into ''run_pcm.def''''';
-* the starting files you want to run the PCM: ''startfi.nc'', ''start.nc''/''start1D.txt''/profiles;
+* the starting files you want to run the PCM: ''startfi.nc'' and ''start.nc''/''start1D.txt'';
-* the necessary PEM files: ''launchPEM.sh'', ''lib_launchPEM.sh'', ''PCMrun.job'', ''PEMrun.job'', ''run_PEM.def'' and ''obl_ecc_lsp.asc'';
+* the necessary PEM files: ''pem_workflow.sh'', ''pem_workflow_lib.sh'', ''pcm_run.job'', ''pem_run.job'', ''run_pem.def'' and ''obl_ecc_lsp.asc'';
-* the optional PEM files ''diagpem.def'' to define the PEM variables to be ouputted and ''startpem.nc'' to set the initial state of the PEM.
+* the optional PEM files ''diagevol.def'' to define the PEM variables to be ouputted and ''startevol.nc'' to set the initial state of the PEM.
 The PEM files can be found in the deftank folder, where a ''README'' file recaps everything.
 Before a simulation, you have to set up some parameters/options:
-# In ''launchPEM.sh'', the user has to specify:
+# In ''pem_workflow.sh'', the user has to specify:
-#* '''n_mars_years''', '''n_earth_years''': the number of Mars/Earth years to be simulated in total (> 0);
+#* '''n_planetary_years''' or '''n_earth_years''': the number of planetary/Earth years to be simulated in total (> 0);
-#* '''nPCM_ini''': the number of initial PCM years (>= 2);
+#* '''n_pcm_runs_ini''': the number of initial PCM years (>= 2);
-#* '''nPCM''': the number of PCM years between each PEM run (>= 2, usually 2);
+#* '''n_pcm_runs''': the number of PCM years between each PEM run (>= 2, usually 2);
-#* '''mode''': the launching mode (0 = "processing scripts"; any other values = "submitting jobs"). The former option is usually used to process the script on a local machine while the latter is used to submit jobs on a supercomputer with SLURM or PBS/TORQUE.
+#* '''exec_mode''': the execution mode (0 = "processing scripts"; any other values = "submitting jobs"). The former option is usually used to process the script on a local machine while the latter is used to submit jobs on a supercomputer with SLURM or PBS/TORQUE.
-# In ''PCMrun.job'', the user has to specify:
+# In ''pcm_run.job'', the user has to specify:
 #* the '''headers''' correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted.
-#* The '''path to source''' the arch file should be adapted to the machine.
+#* The '''path to source the arch file''' should be adapted to the machine.
-#* The '''name of the PCM executable''' file should be adapted.
+#* '''pcm_exe''', the name of the PCM executable file should be adapted.
-#* The '''execution command''' should also be adapted according to the set-up.
+#* '''exec_cmd''', the execution command should also be adapted according to the set-up.
-# In ''PEMrun.job'', the user has to specify:
+# In ''pem_run.job'', the user has to specify:
 #* The '''headers''' correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted.
-#* The '''path to source''' the arch file should be adapted to the machine.
+#* The '''path to source the arch file''' should be adapted to the machine.
-#* The '''name of the PEM executable''' file should be adapted.
+#* '''pem_exe''', the name of the PEM executable file should be adapted.
-#* The PEM executable can have an '''optional argument''' which should be specified according to the set-up ("--auto-exit" for SLURM and PBS/TORQUE | "" when the script is not run as a job).
+#* '''pem_arg''' which is an optional argument for the PEM executable. It should be specified according to the set-up ("--auto-exit" for SLURM and PBS/TORQUE | "" when the script is not run as a job).
-# The user has to specify the wanted options in the '''def files''', especially for ''run_PEM.def'', ''run_PCM.def'', ''callphys.def''.
+# The user has to specify the wanted options in the '''def files''', especially for ''run_pem.def'', ''run_pcm.def'' and ''callphys.def'' which must be consistent. In particular, ''run_pem.def'' needs to include some definitions for the physics in file ''run_pcm.def'' with <code>INCLUDEDEF=run_pcm.def</code>.
-# The user has to provide a ''startfi.nc'' whose orbital parameters are consistent with the initial date set in ''run_PEM.def''. The script '''inipem_orbit.sh''' can do it automatically with ''obl_ecc_lsp.asc''.
+The user has to provide a ''startfi.nc'' whose orbital parameters are consistent with the initial date set in ''run_PEM.def''. The script '''ini_pem_orbit.sh''' can do it automatically reading ''obl_ecc_lsp.asc''.
 == Outputs ==
 The PEM simulation generates the following files:
-* the usual outputs of the PCM: ''restartfi.nc'', ''restart.nc'', ''diagfi.nc'', etc;
+* the usual outputs of the PCM: ''restartfi.nc'', ''restart.nc''/''restart1D.txt'', ''diagfi.nc'', etc;
 * the XIOS outputs of the PCM: ''Xoutdaily4pem*.nc''/''Xoutyearly4pem*.nc'';
-* the outputs of the chained simulation: ''launchPEM.log'', ''launchPEM.info'' and possibly ''kill_launchPEM.sh'';
+* the outputs of the chained simulation: ''pem_workflow.log'', ''pem_workflow.sts'' and possibly ''kill_pem_workflow.sh'';
-* the usual outputs of the PEM: ''"restartfi.nc'', ''restart.nc''/''restart1D.txt'' and ''diagpem.nc''.
+* the usual outputs of the PEM: ''restartevol.nc'', ''restartfi.nc'', ''restart.nc''/''restart1D.txt'' and ''diagevol.nc''.
 During the simulation, the PCM/PEM run files are renamed conveniently and stored in the sub-directories '''logs''' (log files), '''starts''' (starting files) and '''diags''' (diagnostic files).
-If you run a simulation by submitting jobs, the script ''kill_launchPEM.sh'' is automatically generated. It can be used to kill in the queue of the job scheduler the jobs related to your chained simulation.
+If you run a simulation by submitting jobs, the script ''kill_pem_workflow.sh'' is automatically generated. It can be used to kill in the queue of the job scheduler the jobs related to your chained simulation.
 [[Category:Planetary-Evolution-Model]]