This quickstart guide is for quick reference on how to download, build, and run GEOS-Chem Classic, which is the single-node instance of GEOS-Chem.
Please also see our GCHP Quickstart Guide if you would like to run GEOS-Chem across using more than one computational node.
This guide assumes that your environment satisfies GEOS-Chem Classic hardware and software requirements. This means you should load a compute environment such that programs like cmake are available before continuing. If you do not have some of the required software dependencies, you can find instructions for installing external dependencies in our Spack instructions.
For simplicity we will also refer to GEOS-Chem Classic as simply GEOS-Chem on this page. More detailed instructions on downloading, compiling, and running GEOS-Chem can be found in the User Guide elsewhere on this site.
1. Clone GEOS-Chem Classic¶
Download the source code:
$ git clone --recurse-submodules https://github.com/geoschem/GCClassic.git GCClassic $ cd GCClassic
If you wish, you may choose a different name for the source code folder, e.g.
$ git clone --recurse-submodules https://github.com/geoschem/GCClassic.git my_code_dir $ cd my_code_dir
Upon download you will have the most recently released version. You can check what this is by printing the last commit in the git log and scanning the output for tag.
$ git log -n 1
To use an older GEOS-Chem Classic version (e.g. 14.0.0), follow these additional steps:
$ git checkout tags/14.0.0 # Points HEAD to the tag "14.0.0" $ git branch version_14.0.0 # Creates a new branch at tag "14.0.0" $ git checkout version_14.0.0 # Checks out the version_14.0.0 branch $ git submodule update --init --recursive # Reverts submodules to the "14.0.0" tag
You can do this for any tag in the version history. For a list of all tags, type:
$ git tag
If you have any unsaved changes, make sure you commit those to a branch prior to updating versions.
2. Create a run directory¶
Navigate to the
run/ subdirectory. To create a run
directory, run the script
$ cd run/ $ ./createRunDir.sh
Creating a run directory is interactive, meaning you will
be asked multiple questions to set up the simulation. For example,
createRunDir.sh will prompt questions about
configurable settings such as simulation type, grid resolution,
meteorology source, and number of vertical levels. It will also ask
you where you want to store your run directory and what you wish to
name it, including whether you want to use the default name,
gc_4x5_merra2_fullchem. We recommend storing run
directories in a place that has a large storage capacity. It does
not need to be in the same location as your source code. When
creating a run directory you can quit and start from scratch at any
For demonstration purposes, we will use a full chemistry simulation
run directory with the default name (
The steps to setup and run other types of GEOS-Chem simulations follow
the same pattern as the examples shown below.
3. Load your Environment¶
Prior to building GEOS-Chem always make sure all libraries and environment variables are loaded. An easy way to do this is to write an environment file and load that file every time you work with GEOS-Chem. To make this extra easy you can create a symbolic link to your environment file within your run directory or for reference. For example, do the following in your new run directory to have a handy link to the environment you plan on using.
$ cd /path/to/gc_4x5_merra2_fullchem # Skip if you are already here $ ln -s ~/envs/gcc.gfortran10.env gcc.env
Then every time you start up a session to work with GEOS-Chem in your run directory you can easily load your environment.
$ source gcc.env
4. Configure your build¶
You may build GEOS-Chem from within the run directory or from anywhere
else on your system. But we recommend that you always build GEOS-Chem
from within the run directory. This is convenient because it keeps
all build files in close proximity to where you will run the model.
For this purpose the GEOS-Chem run directory includes a build
First, navigate to the
build/ folder of your run directory:
$ cd /path/to/gc_4x5_merra2_fullchem # Skip if you are already here $ cd build
The next step is to configure your build. These
are persistent settings that are saved to your build directory. A
useful configuration option is
-DRUNDIR. This option lets you
specify one or more run directories that GEOS-Chem is “installed” to;
that is, where where the executable is copied, when you do
Configure your build so it installs GEOS-Chem to the run directory you
created in Step 2. The run directory is one directory level higher
build directory. Also located one level higher than
the build directory is the
CodeDir symbolic link to the
top-level GEOS-Chem source code directory. Use the following command to
configure your build:
$ cmake ../CodeDir -DRUNDIR=..
GEOS-Chem has a number of additional configuration options you can add here. For example, to compile with RRTMG after running the above command:
. in the cmake command above is
important. It tells CMake that your current working directory
.) is your build directory.
$ cmake . -DRRTMG=y
A useful configuration option is to build in debug mode. Doing this is a good idea if you encountered an error (such as a segmentation fault) in a previous run and need more information about where the error happened and why.
$ cmake . -DCMAKE_BUILD_TYPE=Debug
See the GEOS-Chem documentation for more information on configuration options.
5. Compile and install¶
Compiling GEOS-Chem Classic should take about a
minute, but it can vary depending on your system, your compiler, and
your configuration options. To maximize build speed you should compile
GEOS-Chem in parallel using as many cores as are available. Do this
-j flag from the
# cd /path/to/gc_4x5_merra2_fullchem/build # Skip if you are already here $ make -j
Upon successful compilation, install the compiled executable to your run directory:
$ make install
This copies executable
build/bin/gcclassic and supplemental
files to your run directory.
You can update build settings at any time:
Navigate to your build directory.
Update your build settings with cmake (only if they differ since your last execution of cmake)
Recompile with make -j. Note that the build system automatically figures out what (if any) files need to be recompiled.
Install the rebuilt executable with make install.
If you do not install the executable to your run directory you can always get the executable from the directory build/bin.
6. Configure your run directory¶
Now, navigate to your run directory:
$ cd /path/to/gcc_4x5_merra2_fullchem
You should review these files before starting a simulation:
Controls several frequently-updated simulation settings (e.g. start and end time, which operations to turn on/off, etc.)
Controls GEOS-Chem diagnostic settings.
Please see our Customize simulations with research options Supplemental Guide to learn how you can customize your simulation by activating alternate science options in your simulations.
Once you are satisfied that your simulation settings are correct, you may proceed to run GEOS-Chem.
7. Run GEOS-Chem Classic¶
If you wish to send output to a log file, use:
$ ./gcclassic > GC.log 2>&1
We recommend running GEOS-Chem Classic as a batch job, although you can also do short runs interactively. Running GEOS-Chem as a batch job means that you write a script (usually bash) and then you submit that script to your local job scheduler (SLURM, LSF, etc.). If you write a batch script you can include sourcing your environment file within the script to ensure you always use the intended environment. Submitting GEOS-Chem as a batch job is slightly different depending on your scheduler. If you aren’t familiar with scheduling jobs on your system, ask your system administrator for guidance.
Those are the basics of using GEOS-Chem Classic! See this user guide, step-by-step guides, and reference pages for more detailed instructions.