Quickstart Guide

This quickstart guide assumes your environment satisfies the requirements described in System Requirements. This means you should load a compute environment so that software like cmake and a fortran compiler are available before continuing. If you do not have some of GCHP’s software dependencies, you can find instructions for installing GCHP’s external dependencies in our Spack instructions. More detailed instructions on downloading, compiling, and running GCHP can be found in the User Guide.

1. Clone GCHP

Download the source code. The --recurse-submodules option will automatically initialize and update all the submodules:

gcuser:~$ git clone --recurse-submodules https://github.com/geoschem/GCHP.git ~/GCHP
gcuser:~$ cd ~/GCHP

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.

gcuser:~/GCHP$ git log -n 1


To use an older GCHP version (e.g. 14.0.0), follow these additional steps:

gcuser:~/GCHP$ git checkout tags/14.0.0                  # Points HEAD to the tag "14.0.0"
gcuser:~/GCHP$ git branch version_14.0.0                 # Creates a new branch at tag "14.0.0"
gcuser:~/GCHP$ git checkout version_14.0.0               # Checks out the version_14.0.0 branch
gcuser:~/GCHP$ 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:

gcuser:~/GCHP$ 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 ./createRunDir.sh and answer the prompts:

gcuser:~/GCHP$ cd run/
gcuser:~/GCHP$ ./createRunDir.sh

3. Configure your build

Building GCHP will require 1.4G of storage space. You may build GCHP from within the run directory or from anywhere else on your system. Building from within the run directory is convenient because it keeps all build files in close proximity to where you will run GCHP. For this purpose the GCHP run directory includes a build directory called build/. However, you can create a build directory elsewhere, such as within the GCHP source code. In this guide we will do both, starting with building from the source code.

gcuser:~/GCHP$ mkdir ~/GCHP/build
gcuser:~/GCHP$ cd ~/GCHP/build

Initialize your build directory by running cmake, passing it the path to your source code. Make sure you have loaded all libraries required for GCHP prior to this step.

gcuser:~/GCHP/build$ cmake ~/GCHP

Now you can configure build options. These are persistent settings that are saved to your build directory. A useful build option is -DRUNDIR. This option lets you specify one or more run directories that GCHP is “installed” to, meaning where the executable is copied, when you do make install. Configure your build so it installs GCHP to the run directory you created in Step 2.

gcuser:~/GCHP/build$ cmake . -DRUNDIR="/path/to/your/run/directory"


The . in the cmake command above is important. It tells CMake that your current working directory (i.e., .) is your build directory.

If you decide instead to build GCHP in your run directory you can do all of the above in one step. This makes use of the CodeDir symbolic link in the run directory:

gcuser:/path/to/your/run/directory/$ cd build
gcuser:/path/to/your/run/directory/build$ cmake ../CodeDir -DRUNDIR=..

GEOS-Chem has a number of optional compiler flags you can add here. For example, to compile with RRTMG:

gcuser:/path/to/your/run/directory/build$ cmake ../CodeDir -DRUNDIR=.. -DRRTMG=y

A useful compiler option is to build in debug mode. Doing this is a good idea if you encountered a segmentation fault in a previous run and need more information about where the error happened and why.

gcuser:/path/to/your/run/directory/build$ cmake ../CodeDir -DRUNDIR=.. -DCMAKE_BUILD_TYPE=Debug

See the GEOS-Chem documentation for more information on compiler flags.

4. Compile and install

Compiling GCHP takes about 20 minutes, but it can vary depending on your system, your compiler, and your compiler flags. To maximize build speed you should compile GCHP in parallel using as many cores as are available. Do this with the -j flag:

gcuser:~/GCHP/build$ make -j

Upon successful compilation, install the compiled executable to your run directory (or directories):

gcuser:~/GCHP/build$ make install

This copies bin/gchp and supplemental files to your run directory.


You can update build settings at any time:

  1. Navigate to your build directory.

  2. Update your build settings with cmake (only if they differ since your last execution of cmake)

  3. Recompile with make -j. Note that the build system automatically figures out what (if any) files need to be recompiled.

  4. 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.

5. Configure your run directory

Now, navigate to your run directory:

$ cd path/to/your/run/directory

Commonly changed simulation settings, such as grid resolution, run duration, and number of cores, are set in setCommonRunSettings.sh. You should review this file as it explains most settings. Note that setCommonRunSettings.sh is actually a helper script that updates other configuration files. You therefore need to run it to actually apply the settings:

$ vim setCommonRunSettings.sh           # edit simulation settings here
$ ./setCommonRunSettings.sh             # applies the updated settings

Simulation start date is set in cap_restart. Run directories come with this file filled in based on date of the initial restart file in subdirectory Restarts. You can change the start date only if you have a restart file for the new date in Restarts. A symbolic link called gchp_restart.nc4 points to the restart file for the date in cap_restart and the grid resolution in setCommonRunSettings.sh. You need to set this symbolic link before running:

$ ./setRestartLink.sh                   # sets symbolic link to target file in Restarts

If you used an environment file to load libraries prior to building GCHP then you should load that file prior to running. A simple way to make sure you always use the correct combination of libraries is to set the GCHP environment symbolic link gchp.env in the run directory:

$ ./setEnvironment.sh /path/to/env/file # sets symbolic link gchp.env
$ source gchp.env                       # applies the environment settings

6. Run GCHP

GCHP requires a minimum of 6 processors to run. How to run GCHP is slightly different depending on your MPI library (e.g., OpenMPI, Intel MPI, MVAPICH2, etc.) and scheduler (e.g., SLURM, LSF, etc.). If you aren’t familiar with running MPI programs on your system, see Running GCHP in the user guide, or ask your system administrator.

Your MPI library and scheduler will have a command for launching MPI programs—it’s usually something like mpirun, mpiexec, or srun. This is the command that you will use to launch the gchp executable. You’ll have to refer to your system’s documentation for specific instructions on running MPI programs, but generally it looks something like this to run GCHP with the minimum number of processors allowed:

$ mpirun -np 6 ./gchp   # example of running GCHP with 6 slots with OpenMPI

It’s recommended you run GCHP as a batch job. This means that you write a script (usually bash) that configures and runs your GCHP simulation, and then you submit that script to your local job scheduler (SLURM, LSF, etc.). Example job scripts are provided in subdirectory ./runScriptSamples in the run directory. That folder also includes an example script for running GCHP interactively, meaning without a job scheduler.

Several steps beyond running GCHP are included in the example run scripts. These include loading the environment, updating commonly changed run settings, and setting the restart file based on start time and grid resolution. In addition, the output restart file is moved to the Restarts subdirectory and renamed to include start date and grid resolution upon successful completion of the run.


File cap_restart is over-written to contain the run end date upon successful completion of a GCHP run. This is done within GCHP and not by the run script. You can then easily submit a new GCHP run starting off where your last run left off. In addition, GCHP outputs a restart file to your Restarts directory called gcchem_internal_checkpoint. This file is renamed by the run script (not GCHP) to include the date and grid resolution. Since this is done by the run script it is technically is optional. However, we recommend doing this since it avoids overwriting your restart file upon consecutive runs, is useful for archiving, and enables use of the ./setRestartLink.sh script to set the gchp_restart.nc4 symbolic link, something that is done by the run script prior to executing GCHP.

Those are the basics of using GCHP! See the user guide, step-by-step guides, and reference pages for more detailed instructions.