Example: Create a full-chemistry simulation run directory
Let us walk through the process of creating a run directory for a global GEOS-Chem full-chemistry simulation.
Navigate to the GCClassic superproject folder and get a directory listing:
$ cd /path/to/your/GCClassic $ ls -CF 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 thesrc/GEOS-Chem/run/GCClassic
folder. This folder contains several scripts and template files for run directory creation.
Navigate to the run folder and get a directory listing:
$ cd run $ ls -CF archiveRun.sh* gitignore init_rd.sh* createRunDir.sh* HEMCO_Config.rc.templates/ README.md geoschem_config.yml.templates/ HEMCO_Diagn.rc.templates/ runScriptSamples/ getRunInfo* HISTORY.rc.templates/ setupForRestarts.sh*
You can see several folders (highlighted in the directory display with
/
) and a few executable scripts (highlighted with*
). The script we are interested in iscreateRunDir.sh
.
Run the
createRunDir.sh
script. Type:$ ./createRunDir.sh
You will then be prompted to supply information about the run directory that you wish to create:
=========================================================== GEOS-CHEM RUN DIRECTORY CREATION =========================================================== ----------------------------------------------------------- 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 create a run directory for the full-chemistry simulation, type 1 followed by the ENTER key.
Tip
To exit, the run directory creation process, type
Ctrl-C
at any prompt.You will then be asked to specify any additional options for the full-chemistry simulation (such as adding the RRTMG radiative transfer model, APM or TOMAS microphysics, etc.)
----------------------------------------------------------- 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 >>>
For the standard full-chemistry simulation, type 1 followed by ENTER.
To add an option to the full-chemistry simulation, type a number between 2 and 8 and press ENTER.
You will then be asked to specify the meteorology type for the simulation (GEOS-FP, MERRA-2), or GCAP 2.0).
Attention
We are still evaluating GEOS-Chem with the new NASA GEOS-IT meterorology product. Please select one of the other meteorology options for the time being.
----------------------------------------------------------- Choose meteorology source: ----------------------------------------------------------- 1. MERRA-2 (Recommended) 2. GEOS-FP 3. GEOS-IT (Beta release) 4. GISS ModelE2.1 (GCAP 2.0) >>>
You should use the recommended option (MERRA-2) if possible. Type 1 followed by ENTER.
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 >>>
Select your preferred horizontal domain, followed by ENTER.
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.
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 (e.g.
$HOME/myusername/my-run-dirs
followed by ENTER).You may also enter a relative path (e.g
~/my-run-dirs
followed by ENTER). In this case you will see that the./createRunDir.sh
script will expand the path to an absolute path.
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 to select the default. You will then see output similar to this:
-- Using default directory name gc_4x5_merra2_fullchem
or if you are creating a nested grid simulation:
-- Using default directory name gc_05x0625_merra2_fullchem
and then:
-- See rundir_vars.txt for summary of default run directory settings -- This run directory has been set up to start on 20190701 -- A restart file for this date has been copied to the Restarts subdirectory -- You may add more restart files using format GEOSChem.Restart.YYYYMMDD_HHmmz.nc4 -- Change simulation start and end dates in configuration file geoschem_config.yml -- Default frequency and duration of diagnostics are set to monthly -- Modify diagnostic settings in HISTORY.rc and HEMCO_Config.rc
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.
You will then see this output:
Initialized empty Git repository in /path/to/gc_4x5_merra2_fullchem/.git/ Created /path/to/gc_4x5_merra2_fullchem
You may now navigate to this directory and start editing the GEOS-Chem configuration files.