Difference between revisions of "Quick Install and Run Mars PEM"

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(Created page with "== How to install the model == To download the model you'll need to follow exactly the same step as dowloading the martian model. You can have a look at the section Quick Ins...")
 
(Undo revision 2916 by Jbclement (talk))
 
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== How to install the model ==
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In this page, we give a hopefully exhaustive enough overview of the necessary prerequisites and steps to download, compile and run a simple simulation with the PEM, set up on a Linux computer.
  
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To download the model you'll need to follow exactly the same step as dowloading the martian model. You can have a look at the section Quick Install and Run of Mars Model and follow the "Prerequisites: Tools and Libraries" steps.
+
== Installation ==
  
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The PEM is dowlnload alongside with the LMDZ.COMMON repository.
+
The PEM is downloaded alongside the '''LMDZ.COMMON''' repository of your trunk, following the same step described in the related section of [[Quick Install and Run Mars PCM]]. The Fortran code is in the following directory: <code>trunk/LMDZ.COMMON/libf/evolution/</code>. The two PEM programs are '''pem.F90''' and '''reshape_XIOS_output.F90'''.
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The Fortran code of the PEM is in the following directory : trunk/LMDZ.COMMON/libf/evolution/
 
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The main program is in the file pem.F90
 
  
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=== Compiling the test case ===
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== Compilation ==
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To compile the PEM at the sought resolution, run (in LMDZ.COMMON):
+
 
 +
To compile the PEM, in LMDZ.COMMON, do:
 
<syntaxhighlight lang="bash">
 
<syntaxhighlight lang="bash">
−
./makelmdz_fcm -arch local -p mars -d 64x48x54 -j 8 pem
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./makelmdz_fcm -arch [local] -p [planet] -d [dimensions] -j 8 pem
 
</syntaxhighlight>
 
</syntaxhighlight>
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Here, we assume that you have generated the '''arch-local.*''' files as per what is suggested in the previous section.
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Options with example:
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The options for ''makelmdz_fcm'' used here imply:
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# [local]: ''root name of arch files'', assuming that they have been set up for your configuration;
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* '''-p mars''': the PEM will use the "mars" physics package
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# [planet]: ''mars'' to use the Mars planet physics package;
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* '''-d 64x48x54''': the PEM grid will be 64x48 in longitude x latitude, with 54 vertical levels.
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# [dimensions]: ''64x48x54'' to define the grid you want to use (longitude x latitude x atmospheric layers).
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For a glimpse at all the possible ''makelmdz_fcm'' options and their meanings, run:
+
To run the PEM, you need a dedicated reshaping tool with consistent options. To compile it, in LMDZ_COMMON, do:
 
<syntaxhighlight lang="bash">
 
<syntaxhighlight lang="bash">
−
./makelmdz_fcm -h
+
./makelmdz_fcm -arch [local] -p [planet] -d [dimensions] -j 8 reshape_XIOS_output
 
</syntaxhighlight>
 
</syntaxhighlight>
−
and/or check the dedicated [[The_makelmdz_fcm_GCM_Compilation_Script|makelmdz_fcm page]].
+
To run the PEM, you also need a PCM working with XIOS and consistent options. To compile it, in LMDZ.COMMON, do:
 +
<syntaxhighlight lang="bash">
 +
./makelmdz_fcm -arch [local] -p [planet] -parallel mpi_omp -io XIOS -d [dimensions] -j 8 gcm
 +
</syntaxhighlight>
 +
After compilation, the executable file can be found in the "bin" sub-directory.
  
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Upon successful compilation, the executable '''pem_64x48x29_phymars_seq.e''' should be generated in the '''bin''' subdirectory.
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== Usage ==
−
 
 
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To run the PEM you'll also need a valid PCM, you can compile it using a similar command:
 
  
 +
To run a PEM simulation, do:
 
<syntaxhighlight lang="bash">
 
<syntaxhighlight lang="bash">
−
./makelmdz_fcm -arch local -p mars -parallel mpi_omp -io XIOS -d 64x48x54 -j 8 gcm
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./launchPEM.sh [options]
 
</syntaxhighlight>
 
</syntaxhighlight>
 +
Options:
 +
# None: to start a simulation from scratch;
 +
# 're': to relaunch a simulation from a starting point (interactive prompt).
  
−
To run the PEM you'll also need a tool (reshape_xios_output) that will e explained later, you can compile it using a similar command:
+
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.
  
−
<syntaxhighlight lang="bash">
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== Requirements ==
−
./makelmdz_fcm -arch local -p mars -d 64x48x54 -j 8 reshape_xios_output
+
 
−
</syntaxhighlight>
+
To run the PEM, you can create a folder in which you need the following files:
 +
* your executable files for the PCM, the PEM and the reshaping tool 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 starting files you want to run the PCM: ''startfi.nc'', ''start.nc''/''start1D.txt''/profiles;
 +
* the necessary PEM files: ''launchPEM.sh'', ''lib_launchPEM.sh'', ''PCMrun.job'', ''PEMrun.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 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:
 +
#* '''n_mars_years''', '''n_earth_years''': the number of Mars/Earth years to be simulated in total (> 0);
 +
#* '''nPCM_ini''': the number of initial PCM runs (>= 2);
 +
#* '''nPCM''': the number of PCM runs between each PEM run (>= 2, usually 2);
 +
#* '''counting''': the counting method for the number of years to be simulated (0 = "only PEM runs count"; any other values = "PCM runs are taken into account"). The former option is the usual one;
 +
#* '''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.
 +
# In ''PCMrun.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 '''name of the PCM executable''' file should be adapted.
 +
#* The '''execution command''' should also be adapted according to the set-up.
 +
# In ''PEMrun.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 '''name of the PEM and Reshaping executable''' files 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).
 +
# 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 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''.
  
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run_pem1
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== Outputs ==
  
−
xml files
+
The PEM simulation generates the following files:
 +
* the usual outputs of the PCM: ''restartfi.nc'', ''restart.nc'', ''diagfi.nc'', etc;
 +
* the XIOS outputs of the PCM, then reshaped: ''Xdiurnalave.nc''/''data2reshape*.nc''/''data_PCM_Y*.nc'';
 +
* the outputs of the chained simulation: ''launchPEM.log'', ''info_PEM.txt'' and possibly ''kill_launchPEM.sh'';
 +
* the usual outputs of the PEM: ''"restartfi.nc'', ''restart.nc''/''restart1D.txt'' and ''diagpem.nc''.
  
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reshape_xios_output
+
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).
  
−
Input output
+
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.
  
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Choices of parameters (run_PEM.def) => advanced topic
+
[[Category:Planetary-Evolution-Model]]

Latest revision as of 11:09, 24 October 2025

In this page, we give a hopefully exhaustive enough overview of the necessary prerequisites and steps to download, compile and run a simple simulation with the PEM, set up on a Linux computer.

Installation

The PEM is downloaded alongside the LMDZ.COMMON repository of your trunk, following the same step described in the related section of Quick Install and Run Mars PCM. The Fortran code is in the following directory: trunk/LMDZ.COMMON/libf/evolution/. The two PEM programs are pem.F90 and reshape_XIOS_output.F90.

Compilation

To compile the PEM, in LMDZ.COMMON, do: 

./makelmdz_fcm -arch [local] -p [planet] -d [dimensions] -j 8 pem

Options with example:

  1. [local]: root name of arch files, assuming that they have been set up for your configuration;
  2. [planet]: mars to use the Mars planet physics package;
  3. [dimensions]: 64x48x54 to define the grid you want to use (longitude x latitude x atmospheric layers).

To run the PEM, you need a dedicated reshaping tool with consistent options. To compile it, in LMDZ_COMMON, do: 

./makelmdz_fcm -arch [local] -p [planet] -d [dimensions] -j 8 reshape_XIOS_output

To run the PEM, you also need a PCM working with XIOS and consistent options. To compile it, in LMDZ.COMMON, do: 

./makelmdz_fcm -arch [local] -p [planet] -parallel mpi_omp -io XIOS -d [dimensions] -j 8 gcm

After compilation, the executable file can be found in the "bin" sub-directory.

Usage

To run a PEM simulation, do: 

./launchPEM.sh [options]

Options:

  1. None: to start a simulation from scratch;
  2. 're': to relaunch 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.

Requirements

To run the PEM, you can create a folder in which you need the following files:

  • your executable files for the PCM, the PEM and the reshaping tool 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 starting files you want to run the PCM: startfi.nc, start.nc/start1D.txt/profiles;
  • the necessary PEM files: launchPEM.sh, lib_launchPEM.sh, PCMrun.job, PEMrun.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 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:

  1. In launchPEM.sh, the user has to specify:
    • n_mars_years, n_earth_years: the number of Mars/Earth years to be simulated in total (> 0);
    • nPCM_ini: the number of initial PCM runs (>= 2);
    • nPCM: the number of PCM runs between each PEM run (>= 2, usually 2);
    • counting: the counting method for the number of years to be simulated (0 = "only PEM runs count"; any other values = "PCM runs are taken into account"). The former option is the usual one;
    • 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.
  2. In PCMrun.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 name of the PCM executable file should be adapted.
    • The execution command should also be adapted according to the set-up.
  3. In PEMrun.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 name of the PEM and Reshaping executable files 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).
  4. The user has to specify the wanted options in the def files, especially for run_PEM.def, run_PCM.def, callphys.def.
  5. 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.

Outputs

The PEM simulation generates the following files:

  • the usual outputs of the PCM: restartfi.nc, restart.nc, diagfi.nc, etc;
  • the XIOS outputs of the PCM, then reshaped: Xdiurnalave.nc/data2reshape*.nc/data_PCM_Y*.nc;
  • the outputs of the chained simulation: launchPEM.log, info_PEM.txt and possibly kill_launchPEM.sh;
  • the usual outputs of the PEM: "restartfi.nc, restart.nc/restart1D.txt and diagpem.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.

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