Quick Install and Run Mars PEM

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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 Install and Run of Mars Model and follow the "Prerequisites: Tools and Libraries" steps.

The PEM is dowlnload alongside with the LMDZ.COMMON repository. The Fortran code of the PEM is in the following directory : trunk/LMDZ.COMMON/libf/evolution/ The main program is in the file pem.F90

Compiling the test case

To compile the PEM at the sought resolution, run (in LMDZ.COMMON): 

./makelmdz_fcm -arch local -p mars -d 64x48x54 -j 8 pem

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 PEM will use the "mars" physics package
  • -d 64x48x54: the PEM grid will be 64x48 in longitude x latitude, with 54 vertical levels.

Upon successful compilation, the executable pem_64x48x29_phymars_seq.e should be generated in the bin subdirectory.

To run the PEM you'll also need a valid PCM, you can compile it using a similar command: 

./makelmdz_fcm -arch local -p mars -parallel mpi_omp -io XIOS -d 64x48x54 -j 8 gcm

To run the PEM you'll also need a tool (reshape_xios_output) that will we explained later, you can compile it using a similar command: 

./makelmdz_fcm -arch local -p mars -d 64x48x54 -j 8 reshape_xios_output

Inputs files

Then all the compilation stuff is done. You ll want to create a folder to run a simulation and copy all the executable there. In addition to these executables, you'll need a few other files:

Files for the PCM run:

  • A start.nc and startfi.nc, if you do a chained simulation you probably have to rename them start0.nc and startfi0.nc, the number correspond to the martian year. The dimensions should correspond to the dimension in which you compiled the executables, they can be found in the Q"uick Install and Run" of the Mars Model.
  • A datadir directory, this can be dowload by following the steps described in "Quick Install and Run" of the Mars Model.
  • A callphys.def : you can take one in LMDZ.MARS/deftank/
  • traceur.def : you can take one in LMDZ.MARS/deftank/
  • z2sig.def : you can take one in LMDZ.MARS/deftank/
  • diagfi.def: Optional; not necessary since we do the outputs using XIOS
  • A run.def, for chained simulation rename it run.def.ref, also available in LMDZ.MARS/deftank/ . If you do not want diagfi.nc output, you can change the variable ecritphy to 6699 for example.
  • xml files: iodef.xml, context_lmdz_physics.xml, field_def_physics_mars.xml, file_def_physics_mars.xml. For this last file you have to change to true the enable option of the FILE 3 (diurnal averages outputs for PEM) the other can be enable to false if you do not want other outputs.
  • run0 : the file used to run chained simulation, available in LMDZ.MARS/deftank/


Files for the PEM run:

  • ob_ex_lsp.asc
  • diagfi.def: Optional
  • run_pem1
  • run_PEM.def remember to include it in the run.def.ref or run.def_PEM
  • start_evol.nc
  • startfi_evol.nc
  • Optional : startfi_PEM.nc
  • Options : run.def_GCM, run.def_PEM

Ouputs files

run_pem1

xml files

reshape_xios_output

Input output

Choices of parameters (run_PEM.def) => advanced topic

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