Quick Install and Run Mars PCM

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 Mars PCM, set up on a Linux computer.

Note that there is a dedicated, install script, that attempts to do all these steps (up to and including running the simulation) that you can obtain here: https://web.lmd.jussieu.fr/~lmdz/planets/install_lmdz_mars.bash Automating the process is not trivial as there are many subtle variants of Linux flavors and user account setups, so the script may fail in your case, but hopefully the information given in this page should help you solve the encountered problems.

Prerequisites: Tools and Libraries

In order to use (i.e. compile and run) the GCM, one needs to have some tools and installed libraries at hand. We list below a (minimal) set that you should check that is available and/or that you'll need to first install on your machine. Note that we assume in this tutorial that you are on a Linux native-OS/cluster.

Fortran compiler

The GCM source code is in Fortran. One thus needs a Fortran compiler to build (compile) the executable. The most easily available one (on Linux) is gfortran and examples discussed here will assume it is the one used. You can check that you indeed have a gfortran compiler at hand with the following Bash command:

which gfortran

which should return something like

/usr/bin/gfortran

Subversion

The source code is managed using subversion (svn), which you'll need to download or update. Leaving aside the subtleties of svn and code organization for now, downloading the code amounts to doing the following:

svn checkout https://svn.lmd.jussieu.fr/Planeto/trunk --depth empty
cd trunk
svn update LMDZ.COMMON LMDZ.MARS

As a side note: the source code that will be fetched by svn can also be browsed online here: https://trac.lmd.jussieu.fr/Planeto

FCM

The FCM (Flexible Configuration Management) tool is a suite of perl scripts to help building and managing codes. We use a slightly modified version which can be obtained using subversion (svn). Ideally you'll want to download it somewhere on your computer once in for all. To do this:

svn checkout https://forge.ipsl.jussieu.fr/fcm/svn/PATCHED/FCM_V1.2

You'll then need to add the resulting FCM_V1.2/bin to your PATH environment variable so that the command "fcm" may be used from anywhere on your machine. e.g. by adding the following line in your .bashrc:

export PATH=$PATH:$HOME/FCM_V1.2/bin

The assumption here is that the downloaded FCM_V1.2 directory is in your home ($HOME) directory. Adapt accordingly if not.

the NetCDF library

The GCM reads and writes input and output files in NetCDF format. Therefore a NetCDF library must be available. As this library is not quite standard you'll probably have to install it yourself on your system (check out the netCDF library page for more). You can use the following home-made "install_netcdf4_hdf5_seq.bash" script to do so. For this, ensure that you are in your home directory:

mkdir netcdf
cd netcdf
wget -nv --no-check-certificate http://www.lmd.jussieu.fr/~lmdz/pub/script_install/install_netcdf4_hdf5_seq.bash
chmod u=rwx install_netcdf4_hdf5_seq.bash
./install_netcdf4_hdf5_seq.bash > netcdf.log 2>&1

Compiling the library and dependencies can take a while (>>15 minutes; be patient). Once this is done, check file netcdf.log to verify that all went well. You may want to also add its "bin" directory to your PATH environment variable by adding in your .bashrc a line of:

export PATH=$PATH:$HOME/netcdf/bin

The assumption here is that you have run the "install_netcdf4_hdf5_seq.bash" script in a "netcdf" subdirectory of your home directory. Adapt accordingly if not.

As a side note: The NetCDF library provides a very simple command line tool (ncdump) to inspect the contents of NetCDF files, but you'll need more advanced visualization tools (e.g., Panoply, Python scripts, etc. - see further down this page in the "Checking the Results" section) for more advanced post-processing of the outputs.

the IOIPSL library

The IOIPSL (Input/Output IPSL) library is a library designed to handle both the reading of some input files used by the GCM (the *.def files which are described further below) and the writing of some NetCDF output files.

Prior to a first compilation: ksh to bash conversion

Some of the IOIPSL install scripts are written in ksh (Korn shell). Given that most systems currently use Bash (Bourne Again Shell) as their command-line interpreter and not ksh (Korn Shell), you might need to install ksh on your system (assuming you have super-user privileges), for e.g., on Linux-Ubuntu:

sudo apt install ksh

Or, if that is not an option, change the occurrences in the package's scripts (ins_m_prec) from:

#!/bin/ksh

to

#!/bin/bash

Automated IOIPSL install script

Scripts to download and install the IOIPSL library can be found in the "ioipsl" subdirectory of the "LMDZ.COMMON" library. Since here we assume we're working with gfortran, the relevant one is "install_ioipsl_gfortran.bash". If your PATH environment variable is already such that it includes the path to your NetCDF library distribution's bin directory (see previous section) then all you need to do is execute the script:

./install_ioipsl_gfortran.bash

If all went well the script should end with:

OK: ioipsl library is in ...

(for further details about the IOIPSL library and installing it, follow the link and/or use the Search Box at the top of this page)

GCM Input Datafiles and Datasets

In order to run, the GCM needs some inputs, such as initial conditions (values of state variables), external inputs (e.g. optical properties of aerosols) and simulation setup (e.g. specifications on how long to run, which parametrizations should be activated, etc.)

In the spirit of the illustrative example considered here (an "GCM6" simulation, i.e. simulation including CO2, dust and water cycles with a model top around 120 km), a set of necessary input data may be downloaded (note that a few reference cases are available on https://web.lmd.jussieu.fr/~lmdz/planets/mars/ ) with:

wget -nv --no-check-certificate http://www.lmd.jussieu.fr/~lmdz/planets/mars/reference_GCM6_64x48x54.tar.gz

Once unpacked ("tar xvzf reference_GCM6_64x48x54.tar.gz") the resulting "reference_GCM6_64x48x54" will contain all that is needed, namely:

callphys.def diagfi.def run.def startfi.nc start.nc stats.def traceur.def z2sig.def

• Initial condition NetCDF files start.nc and startfi.nc; the first containing initial condition values for the dynamics and the second initial condition values for the physics. These also define the model resolution and number of atmospheric layers (64x48x54 - the compiled GCM binary must match this!)
• Some mandatory ASCII *.def files containing run parameters, namely:

1. run.def : "master def file" containing main run parameters
2. callphys.def : file containing flags and keys for the various physics parametrizations
3. z2sig.def : file describing the sought vertical discretization
4. traceur.def : file specifying the tracer number and names

• Some optional ASCII *def files containing names of variables to output:

1. diagfi.def : list of variables that will be included in output file diagfi.nc (if there is no diagfi.def file then ALL variables will be included; you probably don't want that as the resulting file will rapidly grow to be HUGE)
2. stats.def : list of variables that will be included in output file stats.nc (if there is no stats.def file then ALL variables will be included and the resulting file will be large)

Compiling the GCM

Now that all the prerequisites are fulfilled, it is (almost!) time to compile the GCM

Prior to a first compilation: setting up the target architecture files

Compiling the model is done using a dedicated Bash script makelmdz_fcm located in the LMDZ.COMMON directory. This script however relies on architecture files. These files contain information on which compiler to use, what compilation options to use, where relevant libraries are located etc. In practice, one must thus create these ASCII text files in the arch/ subdirectory of LMDZ.COMMON. The naming convention is rather straightforward, when the script makelmdz_fcm is run with the option -arch somename, it will look for files arch/arch-somename.env, arch/arch-somename.path and arch/arch-somename.fcm. Leaving aside a detailed description for later (see this page), here we mention that:

• the arch*.env is an optional file containing environment information, such as setting up environment variables or loading modules on some machines, e.g.

export NETCDF_HOME=/path/to/the/netcdf/distribution

• the arch*.path is a mandatory file containing information relative to external libraries such as NetCDF and IOIPSL, e.g.

ROOT=$PWD

NETCDF_LIBDIR="-L${NETCDF_HOME}/lib"
NETCDF_LIB="-lnetcdf -lnetcdff"
NETCDF_INCDIR="-I${NETCDF_HOME}/include"

IOIPSL_INCDIR="-I$ROOT/../IOIPSL/inc"
IOIPSL_LIBDIR="-L$ROOT/../IOIPSL/lib"
IOIPSL_LIB="-lioipsl"

Each library is referenced by a fixed identifier (NETCDF, IOIPSL, XIOS, ...) and 3 trailing strings: _LIBDIR, for the path to the library, _LIB, for the library name(s), and _INCDIR for the path to the library's include directory.

• the arch*.fcm is a mandatory file containing information relative to the compiler and compilation options, e.g.

%COMPILER            gfortran
%LINK                gfortran
%AR                  ar
%MAKE                make
%FPP_FLAGS           -P -traditional
%FPP_DEF             NC_DOUBLE
%BASE_FFLAGS         -c -fdefault-real-8 -fdefault-double-8 -ffree-line-length-none -fno-align-commons
%PROD_FFLAGS         -O3
%DEV_FFLAGS          -O
%DEBUG_FFLAGS        -ffpe-trap=invalid,zero,overflow -fbounds-check -g3 -O0 -fstack-protector-all -finit-real=snan -fbacktrace
%MPI_FFLAGS
%OMP_FFLAGS         
%BASE_LD     
%MPI_LD
%OMP_LD

Again, not going into a detailed description (follow this link for that), just note here that each line corresponds to a keyword (starting with "%") followed by the relevant options. Here, we mention a few of the main ones:

•  %COMPILER: The compiler to use (here, gfortran)
•  %BASE_FFLAGS: compiler options (always included)
•  %PROD_FFLAGS: compilation flags to include if makelmdz_fcm is run with the "-prod" option
•  %DEBUG_FFLAGS: compilation flags to include if makelmdz_fcm is run with the "-debug" option
•  %BASE_LD: flags to add at the linking step of the compilation

Compiling the test case

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

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

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

For a glimpse at all the possible makelmdz_fcm options and their meanings, run:

./makelmdz_fcm -h

and/or check the dedicated makelmdz_fcm page.

Upon successful compilation, the executable gcm_64x48x54_phymars_seq.e should be generated in the bin subdirectory.

Running the GCM

To run your first simulation, you first need to have a datadir at hand, which is a directory containing some input datafiles (e.g. driving dust scenarios, aerosol properties, etc.) that the GCM will need at run time.

wget -nv --no-check-certificate http://www.lmd.jussieu.fr/~lmdz/planets/mars/datadir.tar.gz

And simply, after having un-tarred it

tar xvzf datadir.tar.gz

Link the resulting datadir directory to where you will run (e.g. the reference_GCM6_64x48x54 directory), for instance if datadir is along side reference_GCM6_64x48x54, then in the later do:

ln -s ../datadir .

Secondly you need to copy (or move) the executable gcm_64x48x54_phymars_seq.e from LMDZ.COMMON/bin to the directory containing the initial conditions and parameter files, e.g. reference_GCM6_64x48x54.

You can now run the GCM. This is usually a two-step process: the (optional) first step is to source the environment architecture file (the very same that was used to compile the model), e.g.,:

source ../LMDZ.COMMON/arch.env

The second step is to execute the model, e.g.,:

./gcm_64x48x54_phymars_seq.e > gcm.out 2>&1

With this command line, the (text) outputs messages are redirected into a text file, gcm.out. It is convenient to keep this file for later inspection (e.g., to track a bug). If there is no redirection (only ./gcm_64x48x54_phymars_seq.e), then the outputs will be directly on the screen.

Checking the Results of a Simulation

Once the simulation is finished, you'll know that all went well ("everything is cool") if the last few lines of the standard text output are:

 in abort_gcm
 Stopping in leapfrog
 Reason = Simulation finished 
 Everything is cool

If not, start looking for an error message and a way to fix the problem...

Apart from the standard text output messages from the GCM, which are mostly for monitoring and checking the simulation progress, the user will more likely be interested in checking the contents of the diagfi.nc file produced by the GCM, as it contains instantaneous values of the main model variables (atmospheric temperature, winds, etc.).

...TODO...ADD HERE SOME ILLUSTRATIVE PLOTS OF THE EXPECTED BENCH OUTPUTS...

Taking Things to the Next Level

The short tutorial presented in this page is meant to be useful to get an overview of what is required to install and run the GCM, in addition to checking the results of a simulation. Moving on to a more intensive and problem-specific usage will require diving into additional topics and aspects such as:

• Selecting the appropriate inputs and run parameters for a given study.
• Compiling and running in parallel (MPI and/or OpenMP) to obtain results in a reasonable time frame.
• post-processing and analysis of model outputs.

All these points and much more are detailed in the many pages of this site (do check out the menu on the left and dare use intensively the site's search engine)!