Example: Create a CH4 simulation run directory

The process of creating run directories for the GEOS-Chem specialty simulations is similar to that as listed in Example 1 above. However, the number of menus that you need to select from will likely be fewer than for the full-chemistry simulation. We’ll use the methane simulation as an example.

  1. Navigate to the GCClassic superproject folder and get a directory listing:

    $ cd /path/to/your/GCClassic
    $ ls -CF

    You should see this output:

    AUTHORS.txt     CMakeScripts/    LICENSE.txt  SUPPORT.md  run@  test@
    CMakeLists.txt  CONTRIBUTING.md  README.md    docs/       src/

    As mentioned previously, run@ is a symbolic link. It actually points to the to the src/GEOS-Chem/run/GCClassic folder. This folder contains several scripts and template files for run directory creation.

  2. Navigate to the run folder and get a directory listing:

    $ cd run
    $ ls -CF

    and you should see this output:

    HEMCO_Config.rc.templates/  geoschem_config.yml.templates/
    HEMCO_Diagn.rc.templates/   getRunInfo*
    HISTORY.rc.templates/       gitignore
    README                      init_rd.sh*
    archiveRun.sh*              runScriptSamples/

    You can see several folders (highlighted in the directory display with /) and a few executable scripts (highlighted with *). The script we are interested in is createRunDir.sh.

  3. Run the createRunDir.sh script.. Type:

    $ ./createRunDir.sh

  4. You will then be prompted to supply information about the run directory that you wish to create:

    Choose simulation type:
       1. Full chemistry
       2. Aerosols only
       3. CH4
       4. CO2
       5. Hg
       6. POPs
       7. Tagged CH4
       8. Tagged CO
       9. Tagged O3
      10. TransportTracers
      11. Trace metals
      12. Carbon

    To select the GEOS-Chem methane specialty simulation, type 3 followed by ENTER.


    To exit, the run directory creation process, type Ctrl-C at any prompt.

  5. You will then be asked to specify the meteorology type for the simulation (GEOS-FP, MERRA-2), or GCAP 2.0):

    Choose meteorology source:
      1. MERRA-2 (Recommended)
      2. GEOS-FP
      3. GISS ModelE2.1 (GCAP 2.0)

    To accept the recommended meteorology (MERRA-2), type 1 followed by ENTER.

  6. The next menu will prompt you for the horizontal resolution that you wish to use:

    Choose horizontal resolution:
      1. 4.0  x 5.0
      2. 2.0  x 2.5
      3. 0.5  x 0.625

    If you wish to set up a global simulation, type either 1 or 2 followed by ENTER.

    If you wish to set up a nested-grid simulation, type 3 and hit ENTER. Then you will be followed by a nested-grid menu:

    Choose horizontal grid domain:
      1. Global
      2. Asia
      3. Europe
      4. North America
      5. Custom

    Type the number of your preferred option and then hit ENTER.

  7. You will then be prompted for the vertical dimension of the grid.

    Choose number of levels:
      1. 72 (native)
      2. 47 (reduced)

    For most simulations, you will want to use 72 levels. Type 1 followed by ENTER.

    For some memory-intensive simulations (such as nested-grid simulations), you can use 47 levels. Type 2 followed by ENTER.

  8. You will then be prompted for the folder in which you wish to create the run directory.

    Enter path where the run directory will be created:

    You may enter an absolute path (such as $HOME/myusername/ followed by ENTER).

    You may also enter a relative path (such as ~/rundirs followed by ENTER). In this case you will see that the ./createRunDir.sh script will expand the path to:

    Expanding to: /n/home09/myusername/rundirs

  9. The next menu will prompt you for the run directory name.

    Enter run directory name, or press return to use default:
    NOTE: This will be a subfolder of the path you entered above.

    You should use the default run directory name whenever possible. Type ENTER. The script will display the following output:

    -- Using default directory name gc_4x5_merra2_CH4

    or if you are creating a nested grid simulation:

    -- Using default directory name gc_05x0625_merra2_CH4

    and then

    -- This run directory has been set up for 20190701 - 20190801.
       You may modify these settings in geoschem_config.yml.
    -- The default frequency and duration of diagnostics is set to monthly.
       You may modify these settings in HISTORY.rc and HEMCO_Config.rc.

  10. The last menu will prompt you with:

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

    Type y and then ENTER. Then you will be able to track changes that you make to GEOS-Chem configuration files with Git. This can be a lifesaver when debugging – you can revert to an earlier state and then start fresh.

  11. The script will display the full path to the run directory. You can navigate there and then start editing the GEOS-Chem configuration files.

The procedure to set up run directories for other GEOS-Chem Classic simulations is similar to that shown above.