== Running in parallel ==

For large simulation (long runs, high resolution etc...), the computational cost can be huge and hence the run time quite long.
To somewhat overcome this issue, the model can be run in parallel. This however requires a few extra steps (compared to compiling and running the serial version of the code, as described in the [[Quick Install and Run Mars PCM]] page).

=== Various comments and disambiguations around parallelism and related tools ===
For users not used to compilers and/or compiling and running codes in parallel, there is often some confusion which hopefully the following paragraph might help clarify:
* the compiler (typically gfortran, ifort, pgfortran, etc.) is the required tool to compile the Fortran source code and generate an executable. It is strongly recommended that libraries used by a program are also compiled using the same compiler. Thus if you plan to use different compilers to compile the model, note that you should also have at hand versions of the libraries it uses also compiled with these compilers.
* A first level of parallelism is obtained using MPI. The MPI (Message Passing Interface) library is a library used to solve problems using multiple processes by enabling message-passing between the otherwise independent processes. There are a number of available MPI libraries out there, e.g. OpenMPI, MPICH or IntelMPI to name a few (you can check out the [[Building an MPI library]] page for some information about installing an MPI library). The important point here is that on a given machine the MPI library is related to a given compiler and that it provides related wrappers to compile and run with. Typically (but not always) the compiler wrapper is '''mpif90''' and the execution wrapper is '''mpirun'''. If you want to know which compiler is wrapped in the '''mpif90''' compiler wrapper, check out the output of:
<pre>
mpif90 --version
</pre>
* In addition a second type of parallelism, shared memory parallelism known as OpenMP, is also implemented in the code. In contradistinction to MPI, OpenMP does not require an external library but is instead implemented as a compiler feature. At run time one must then specify some dedicated environment variables (such as OMP_NUM_THREADS and OMP_STACKSIZE) to specify the number of threads to use per process.

=== Compiling the Mars PCM ===
* In practice one should favor compiling and running with both MPI and OPenMP enabled, and therefore compile with the
<pre>
-parallel mpi_omp
</pre>
option of the [[The makelmdz fcm GCM Compilation Script|makelmdz_fcm]] compilation script
* It is also advised (but not mandatory) to use the XIOS library for outputs when in parallel, in which case one should also compile with the
<pre>
-io xios
</pre>
option of the [[The makelmdz fcm GCM Compilation Script|makelmdz_fcm]] compilation script

=== Running the Mars PCM in Parallel ===
Check out pages like [[Parallelism]] for an overview of how it's done.

== Other Mars PCM configurations worth knowing about ==

=== Running the 1D version of the Mars PCM ===
One can run the PCM in a single column configuration, i.e. as a 1D model. It is the same physics package that is used in 1D than in 3D. Compilation is also done using the [[The makelmdz fcm GCM Compilation Script|makelmdz_fcm]] script except that only a number of vertical layers needs be specified and that the main program is called "testphys1d". For example, to compile a version of 32 vertical layers of "testphys1d", one would run the following command:
<pre>
./makelmdz_fcm -arch somearch -p mars -d 32 -j 8 testphys1d
</pre>
See the dedicated page: [[Mars 1D testphys1d program]] for more.

=== Running with the DYNAMICO dynamical core ===
TODO: Some intro and link to relevent pages here.

=== Running with the WRF dynamical core ===
TODO: Some intro and link to relevent pages here.

[[Category:Mars-Model]]

2025-01-14T08:22:09Z

Jbclement:

This mediawiki site hosts a collection of pages dedicated to various aspects of the PEM, such as its installation and its use.

For a first glimpse or even an initial use of the model, the links in the menu of the left panel on this page, under "Mars PEM", should be good starting points.

Beyond that, you have the following possibilities:
# Check out the [[Category:Planetary-Evolution-Model| dedicated category page]] referencing of individual pages which are tagged with "Planetary-Evolution-Model";
# Check out the [[Special:AllPages| dedicated page]] referencing all the pages in this mediawiki site;
# Use the '''Search Box''' at the top right-hand corner of the page with keywords.

[[Category:FAQ]]
[[Category:Planetary-Evolution-Model]]

Tool Box Mars PEM

2025-01-14T08:19:45Z

Jbclement:

There are few tools provided along the PEM which can be found in the directory <code>LMDZ.COMMON/libf/evolution/deftank/</code>. A <code>README</code> text file gives information about the different files that this directory contains.

The current tools available for the PEM in this directory are:
* <code>clean.sh </code>
* <code>concat_diagpem.sh </code>
* <code>inipem_orbit.sh </code>
* <code>modify_startfi_orbit.sh </code>
* <code>modify_startfi_var.sh </code>
* <code>multiple_exec.sh </code>
* <code>visu_evol_layering.py </code>
* <code>visu_layering.py </code>

The purpose of these tools is described in the sections below. Their usage is quite straightforward and all the parameters to be modified by the user are always gathered at the beginning of the file, in the header, with short explanations.

== Cleaning of files (post-processing) ==

The bash script file <code>clean.sh</code> cleans the folder after a PEM simulation.

== Merging the PEM outputs (post-processing) ==

The bash script <code>concat_diagpem.sh</code> allows to concatenate along the variable 'Time' all the "diagpem" files (PEM outputs) into one NetCDF file. 'Time' is re-indexed with the numbering of Martian years simulated by the PEM run. It is useful if one wants to visualize and analyse the evolution of variables during all the PEM runs of the chained simulation.

== Initialization of orbital parameters (pre-processing) ==

The bash script file <code>inipem_orbit.sh</code> modifies the orbital parameters of a file "startfi.nc" according to the date set in the file "run_PEM.def".

== Setting the orbital parameters (pre-processing) ==

The bash script <code>modify_startfi_orbit.sh</code> allows to modify the orbital parameters in a "startfi.nc" file, that is obliquity, eccentricity, Ls perihelion and the initial Ls. It is useful when one wants a chained simulation to start at a specific date. In this case, the orbital parameters should be consistent with Laskar's data in "obl_ecc_lsp.asc" which can be found in the PEM deftank.

== Setting a variable in a NetCDF file (pre-processing) ==

The bash script file <code>modify_startfi_var.sh </code> modifies the value of a variable in a file "startfi.nc".

== Lauching multiple simulations (pre-processing) ==

The bash script <code>modify_startfi_var.sh</code> executes multiple scripts in subdirectories. It is useful to launch multiple simulations at once.

== Layering visualization overged time (post-processing) ==

The Python script file <code>visu_evol_layering.py</code> outputs the stratification data over time from the "startpem.nc" files.

== Layering visualization (post-processing) ==

The Python script file <code>visu_layering.py</code> outputs the stratification data from the "startpem.nc" files.

[[Category:Planetary-Evolution-Model]]