Create a Run Directory

Run directories are created with the script in the run/ subdirectory of the source code. Run directories are version-specific, so you need to create new run directories for every GEOS-Chem version. The gist of creating a run directory is simple: navigate to the run/ subdirectory, run ./, and answer the prompts:

gcuser:~$ cd GCHP/run
gcuser:~/GCHP/run$ ./
... <answer the prompts> ...


Use absolute paths when responding to prompts.

If you are unsure what a prompt is asking, see their explanations below, or ask a question on GitHub. After following all prompts a run directory should be created for you with a confirmation message, and, you can move on to the next section.

Explanations of Prompts

Below are detailed explanations of the prompts in ./

Enter ExtData path

The first time you create a GCHP run directory on your system you will be prompted to register as a GEOS-Chem user. Please provide this information so that we can track GEOS-Chem user groups around the world and get to know what GEOS-Chem is used for.

Following registration you will be prompted for a path to GEOS-Chem shared data directories. The path should include the name of your ExtData/ directory and should not contain symbolic links. The path you enter will be stored in file .geoschem/config in your home directory as environment variable GC_DATA_ROOT. If that file does not already exist it will be created for you. When creating additional run directories you will only be prompted again if the file is missing or if the path within it is not valid.

Enter path for ExtData:

Choose a simulation type

Enter the integer number that is next to the simulation type you want to use.

Choose simulation type:
  1. Full chemistry
  2. TransportTracers
  3. CO2 w/ CMS-Flux emissions
  4. Tagged O3
  5. Carbon

If creating a full chemistry run directory you will be given additional options. Enter the integer number that is next to the simulation option you want to run.

Choose additional simulation option:
  1. Standard
  2. Benchmark
  3. Complex SOA
  4. Marine POA
  5. Acid uptake on dust
  6. TOMAS
  7. APM
  8. RRTMG

Choose meteorology source

Enter the integer number that is next to the input meteorology source you would like to use. Note that choosing GEOS-FP or GEOS-IT will result in additional questions to refine the meteorology inputs you would like to use from the dataset.

Choose meteorology source:
  1. MERRA-2 (Recommended)
  2. GEOS-FP
  3. GEOS-IT (Beta release)

Enter run directory path

Enter the target path where the run directory will be stored. You will be prompted to enter a new path if the one you enter does not exist.

Enter path where the run directory will be created:

Enter run directory name

Enter the run directory name, or accept the default. You will be prompted for a new name if a run directory of the same name already exists at the target path.

Enter run directory name, or press return to use default:

NOTE: This will be a subfolder of the path you entered above.

Enable version control (optional)

Enter whether you would like your run directory tracked with git version control. With version control you can keep track of exactly what you changed relative to the original settings. This is useful for trouble-shooting as well as tracking run directory feature changes you wish to migrate back to the standard model.

Do you want to track run directory changes with git? (y/n)

You will then see a message printed to screen about the run directory created and brief instructions for us. For example: