This quickstart guide assumes your environment satisfies the requirements described in System Requirements. / This means you should load a compute environment so that programs like cmake and mpirun 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:
gcuser:~$ git clone 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
You can stay with this version or checkout an earlier version by its tag name:
gcuser:~/GCHP$ git checkout tags/13.3.4
You can see a list of all possible tables using the git tag command:
gcuser:~/GCHP$ git tag
When you have the version you wish to use you must initialize and update all the submodules:
gcuser:~/GCHP$ git submodule update --init --recursive
Repeat this last step every time you switch to a new version of GCHP.
2. Create a run directory¶
Navigate to the
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
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"
. 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
bin/gchp 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.
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
You should review this file as it explains most settings.
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
Run directories come with this file filled in based on date of the initial restart file in subdirectory
You can change the start date only if you have a restart file for the new date in
A symbolic link called
gchp_restart.nc4 points to the restart file for the date in
cap_restart and the grid resolution in
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¶
Running 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:
$ 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 from the command line.
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.
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 run directory called
gcchem_internal_checkpoint. This file is moved to subdirectory
Restarts and renamed to include the date and grid resolution. This is done by the run script and technically is optional. We recommend doing this since it is is good for archiving (restart files will contain date and grid res) and enables use of the
./setRestartLink.sh script to set the
gchp_restart.nc4 symbolic link.
Those are the basics of using GCHP! See the user guide, step-by-step guides, and reference pages for more detailed instructions.