Example: Create a carbon gases simulation run directory
The process of creating run directories for the GEOS-Chem specialty simulations is similar to that of the previous example. But the number of menus that you need to select from will likely be fewer than for the full-chemistry simulation. We’ll use the carbon gases simulation as an example.
Navigate to the
GCClassic
superproject folder and get a directory listing:$ cd /path/to/your/GCClassic $ ls -CF AUTHORS.txt CMakeLists.txt CONTRIBUTING.md LICENSE.txt run@ src/ test@ CHANGELOG.md CMakeScripts/ docs/ README.md spack@ SUPPORT.md
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. Carbon 4. Hg 5. POPs 6. Tagged O3 7. Trace metals 8. TransportTracers 9. CH4 10. CO2 11. Tagged CO >>>
To select the GEOS-Chem carbon gases specialty simulation, type 3 followed by ENTER.
Tip
To exit, the run directory creation process, type
Ctrl-C
at any prompt.You will be asked if you wish to set up a carbon simulation with all species (CH4, CO, CO2, OCS), or with just one of these species:
----------------------------------------------------------- Do you wish to use a single advected species? ----------------------------------------------------------- 1. Use all species 2. Use CH4 only 3. Use CO2 only 4. Use CO only 5. Use OCS only >>>
Let’s pick the carbon simulation with all species. Type 1 followed by 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) >>>
To accept the recommended meteorology (MERRA-2), type 1 followed by ENTER.
Important
The convection scheme used for GEOS-FP met generation changed from RAS to Grell-Freitas with impact on GEOS-FP meteorology files starting June 1, 2020. For this reason we recommend using MERRA-2 instead of GEOS-FP if running a simulation across June 1, 2020 to avoid unexpected discontinuities. Additional information about the impact of the convection change is at geoschem/geos-chem#1409.
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.
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-directories
) followed by ENTER.You may also enter a relative path (e.g.
~/my-run-directories
) 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. The script will display the following output:
-- Using default directory name gc_4x5_merra2_carbon
or if you are creating a nested grid simulation:
-- Using default directory name gc_05x0625_merra2_carbon
and then
-- See rundir_vars.txt for summary of default run directory settings -- This run directory has been set up to start on 20190101 -- 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 output similar to this:
Initialized empty Git repository in /path/to/gc_4x5_merra2_carbon/.git/ Created /path/to/gc_4x5_merra2_carbon >>>> REMINDER: You must compile with options: -DMECH=carbon <<<<
You can navigate to this directory and then start editing the GEOS-Chem configuration files.
Because the carbon simulation requires special compilation instructions, a reminder will be displayed with the proper command to use during the configuration step.
The procedure to set up run directories for other GEOS-Chem Classic simulations is similar to that shown above.