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Welcome to the Mars Climate Modeling Center (MCMC) Legacy Mars Global Climate Model (GCM) installation tutorial. By the end of this tutorial, you will know how to configure, compile, and run the GCM, and how to check the initial model results for accuracy. The analysis pipeline tutorial will build on what you learn here by expanding on model analysis capabilities.
The GCM presented here is extensively documented in Haberle et al. 2019 (Documentation of the NASA/Ames Legacy Mars Global Climate Model: Simulations of the present seasonal water cycle).
This tutorial has been tested on Mac, Linux, and Windows 10. The commands below are assumed to be utilized in the terminal on Mac and Linux machines, and in either the native terminal or Cygwin on Windows machines (depending on the version of the Windows). If you need Cygwin for a Windows machine, you can find instructions for download and installation here.
A FORTRAN compiler is required to compile the GCM. We recommend the Intel or GNU compiler. While the Intel (ifort) FORTRAN compiler requires purchasing a license, the GNU (gfortran) FORTRAN compiler is freely available. Information on the Intel compiler can be found here: https://www.intel.com. The GNU compiler can be installed with a package manager such as Homebrew, MacPorts or Cygwin, or directly from the source code. Once you have installed the compiler, make sure you have the path to it included in your bash or csh profile.
The first steps are to install and compile the GCM on your machine.
% git clone https://github.com/nasa/legacy-mars-global-climate-model.gitThis will produce a directory called legacy-mars-global-climate-model. Navigate into that directory and list its contents:
% cd legacy-mars-global-climate-model
% ls -lThe following directories will be visible:
./documentation # contains GCM documentation
./code # contains the GCM source code
./run # is where you will run the model
./run/data # contains the required input files for the GCM
./analysis # contains a simple analysis routine for checking a simulation
./analysis/validation # contains sample plots from the default settings
./tutorial # contains files used in this tutorialA Note on Directory Configuration
While not necessary, it may be useful to place the different directories described above in different locations on your computer. The source code and data files are relatively small and can be placed anywhere. The GCM history files can take up large amounts of disk space (a typical 2 year run uses ~20 gigabytes) so you may want to place the
run/ directory in a scratch directory or somewhere similar. Note that any changes you make to the default directory structure need to be taken into account in the instructions below, so if you are unsure about how to do this, it is probably best to start with the default structure.
From the main model directory (legacy-mars-global-climate-model/), navigate to the source code (code/) directory:
% cd codeThe Makefile is set up to use the GNU Fortran (gfortran) compiler by default. Settings for the Intel (ifort) compiler are also available. You will need to modify the Makefile to use ifort. To do this, open the Makefile and comment the gfortran options and uncomment the ifort options. The original lines are:
#F90_COMP = ifort
#F_OPTS = -c -O2
F90_COMP = gfortran
F_OPTS = -c -O3 -finit-local-zero -frecord-marker=4and the lines modified for ifort will instead be:
F90_COMP = ifort
F_OPTS = -c -O2
#F90_COMP = gfortran
#F_OPTS = -c -O3 -finit-local-zero -frecord-marker=4Once the Makefile is ready, you can proceed with compiling the model. First, remove all object files (*.o), and module files (*.mod) to ensure a clean build by typing:
% make cleanNext, compile the code by typing:
% makewhich creates an executable file called gcm2.3. Note that warnings that are not fatal may appear during the compile. If the executable is written, the compilation was successful. If fatal errors are produced during the compile and the compile fails, no executable will be created. In this case, check that the compiler can be found on the command line (i.e., set the $PATH correctly) and that the Makefile is set up properly for your compiler.
Before running the model, you will need to move (or copy) the executable file (gcm2.3) to the run/ directory as well as the tutorial namelist file (tutorial/mars_tutorial). Navigate into that directory, and list its contents (note that this command assumes you're using the default directory structure):
% cp gcm2.3 ../run/
% cd ../run/
% lsYou will see the following in this directory, which are all the necessary components for running the model:
gcm2.3 # the executable
mars_tutorial # the input file that includes runtime optionsThe mars_tutorial file has the default set-up for your initial test simulation. The parameters and options in the mars_tutorial file are described in more detail below, but for now, no editing of this file is needed.
To run the model, type:
% ./gcm2.3 <mars_tutorial> m.out &In this command, m.out is the name of the output log file that will be produced, and the & will make the model run in the background.
If the model is running correctly, you will see fort.11, fort.51, and fort.91 files being created in the current directory (run/). The initial default simulation will simulate 20 sols (Martian days) and take approximately an hour to complete.
To check that the simulation ran properly, we will run a simple analysis routine called htest.f90. Navigate to the tutorial/ directory:
% cd ../tutorial/To compile htest.f90 using gfortran, type:
% gfortran -c historymod.f90
% gfortran -o htest htest.f90 historymod.oTo compile using ifort, type:
% ifort -c historymod.f90
% ifort -o htest htest.f90 historymod.oNext, copy the htest executable and htest.in input file to the run/ directory and navigate to it:
% cp htest htest.in ../run/
% cd ../run/htest is a routine that prints out information from one location (in latitude, longitude, and vertical coordinate) at one time step of the simulation. To print out information from latitude index number 18 (the equator), longitude index 1 (-180 East), and vertical coordinate index 24 (first atmospheric layer above the ground) at the first output from the 20th martian day of simulation, type:
% ./htest < htest.inThe output from htest will be:
You should reproduce the information above quite closely. There may be variations in the fourth or fifth decimal place due to hardware and compiler differences but they should be small. If you reproduce these htest results, you have successfully installed and run the GCM.
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