Difference between revisions of "DYNAMICO with LMDZ physics"

Latest revision as of 14:28, 19 December 2024

This page describes the compilation procedure for the coupling between the DYNAMICO dynamical core and the PCM LMDZ.* physics packages. It describes the directory structure of the ICOSA_LMDZ directory which contains the interface. Please read the DYNAMICO installation process first.

The ICOSA_LMDZ directory

Once downloaded from the svn server, the ICOSA_LMDZ directory contents should be:

arch  bld.cfg  build  clean  compile_adastra-gnu  compile_irene-amd  make_icosa_lmdz  src  xml

Where the noteworthy elements are:

• The make_icosa_lmdz script, which is the master script to use to compile all components (DYNAMICO, physics package, the interface between the two and the IOIPSL and XIOS libraries).

To list available options, run "make_icosa_lmdz -h", which should return something like:

Usage :
make_icosa_lmdz [options] -arch arch_name -p phys
[-h]                       : help
[-prod / -dev / -debug]    : compilation mode: production (default) / developpement / debug .
[-full]                    : recompile all code from scratch
[-nodeps]                  : do not build dependencies (XIOS and IOIPSL libraries)
 -arch arch_name           : target architecture
[-arch_path path]          : relative PATH to directory containing multi-model
                             path and environment arch files
 -p phys                   : physics package (e.g. std , venus , mars, ...)
[-p_opt "options"]         : additional options for physics package
[-parallel type]           : parallelism (none|mpi|omp|mpi_omp)
[-with_xios]               : compile and link with XIOS (default)
[-job num]                 : speed up compilation by using num simulateneous 
                             compilation steps (when possible)

Upon successful completion of the compilation step the bin subdirectory will contain the executable icosa_lmdz.exe

• Example scripts compile_adastra-gnu and compile_irene-amd which are wrappers to the make_icosa_lmdz script with a set of given options. The general idea here is that a user would likewise write his/her own wrapper script.
• The arch directory which contains architecture files used by the make_icosa_lmdz script
• The src directory which contains the source code for the interface
• The xml directory which contains an example of the iodef.xml file to use, along with related instructions to combining it with other xml file gathered from DYNAMICO and physics packages

The src subdirectory

This directory contains the source code for the interface, along with subdirectories related to each of the physics packages (currently Generic, Mars and Venus). More general code, i.e. which apply to all the physics packages, such as plugins for the vertical discretization or dissipation factors are located at this level. In practice that directory currently contains:

distrib_icosa_lmdz.f90  phymars   phyvenus
disvert_icosa_lmdz.f90  phypluto  vert_prof_dissip_icosa_lmdz.f90
icosa_lmdz.f90          phystd    wrapper.f90

where

• icosa_lmdz.f90 is the main program which is in fact quite minimal as it only needs to set-up pointers for plugin routines and call DYNAMICO's icosa_init routine
• distrib_icosa_lmdz.f90 and wrapper.f90 are quite technical routines handling the parallelism and correspondances between physics and dynamics grids
• disvert_icosa_lmdz.f90 is the plugin (inherited from LMDZ.COMMON and follows the vertical coordinate and associated discretization choices made there)
• vert_prof_dissip_icosa_lmdz.f90 is the plugin (inherited from LMDZ.COMMON) to set the multiplicative coefficient along the vertical for lateral dissipation

The src/phy* subdirectories

These contain the interface to call the main physics driver from the Mars (phymars), Pluto (phypluto), Generic (phystd) or Venus (phyvenus) physics packages

Compiling DYNAMICO with a PCM LMDZ.* physics package

Once you have downloaded DYNAMICO into the ICOSAGCM/ folder, go to the ICOSA_LMDZ folder and compile there using one of the compile example files:

• compile_adastra-gnu
• compile_irene-amd

It might be wise to make a copy, i.e.:

cp compile_adastra-gnu compile

You can then edit the file to match your architecture (the arch parameter). The file should look like this:

arch=ifort_MESOIPSL # change according to your arch file

# Gas Giants/generic:
make_icosa_lmdz -p std -p_opt "-b 17x23" -parallel mpi -arch ${arch} -arch_path ../ARCH -job 8  -full -nodeps

# Venus:
#make_icosa_lmdz -p venus -parallel mpi -arch ${arch} -arch_path ../ARCH -job 8 -full -nodeps

# Mars:
# make_icosa_lmdz -p mars -parallel mpi -arch ${arch} -arch_path ../ARCH -job 8 -full -nodeps

# Pluto:
# make_icosa_lmdz -p pluto -p_opt "-b 17x23" -parallel mpi -arch ${arch} -arch_path ../ARCH -job 8 -full -nodeps

You can change the options such as the parallel version you will use (-parallel mpi or mpi_omp) and the parameters for the physics package (with the -p_opt options (for example -b 17x23 to specify a spectral resolution), these are the option of The makelmdz fcm GCM Compilation Script).

Using the -full option, the script make_icosa_lmdz will recompile from scratch:

• IOIPSL
• XIOS
• LMDZ.COMMON (your physics)
• ICOSAGCM (DYNAMICO)

and then link everything in the ICOSA_LMDZ/bin folder, under the name of the executable icosa_lmdz.exe.

If you use the -nodeps option, XIOS and IOIPSL will *not* be compiled (you should therefore follow the corresponding pages for their installation).

The script should stop at each step of the compilation if it fails (for example the compilation of the physics package).

You can also compile each step on its own and remove the -full option (you can keep the -nodeps option) (please click on each package name for explanations on how to install it).

Known issues

If you obtain an error of the type:

XIOS/src/io/netcdf.hpp:20:12: fatal error: netcdf_par.h: Aucun fichier ou dossier de ce nom
   20 | #  include <netcdf_par.h>
      |            ^~~~~~~~~~~~~~
compilation terminated.

This is due to the parallel version of netcdf not being recognized by the compilation module, typically for XIOS. In that case, please open the arch.path file used by the module and change the path pointing to netcdf_par.h. The default path should look like this:

NETCDF_INCDIR="$(nc-config --cflags) $(nf-config --fflags) -I/usr/lib/x86_64-linux-gnu/netcdf/mpi/include"

You can find the path where netcdf_par.h is located via:

locate netcdf_par.h

And you can set the new_path found (without netcdf_par.h) like this:

NETCDF_INCDIR="-Inew_path"

You should probably do this for the lib too:

NETCDF_LIBDIR="-L/path/to/libnetcdf_mpi.so"

Running DYNAMICO with a physics package

You will now need to find the .xml files specific to your physics package, hopefully found in the deftank/ folder of each package (for example LMDZ.PLUTO/deftank/dynamico).

To transform an initial state (start.nc and startfi.nc) from LMDZ.* physics (lat x lon grid) to a dynamico initial state (icosahedral grid), please follow the tutorial here: LMDZ to DYNAMICO start files.

Please refer to

• Venus - DYNAMICO
• Mars - DYNAMICO
• Pluto - DYNAMICO

for the specific details over each physics package.