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.
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 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
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/ createRunDir.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 select the GEOS-Chem methane specialty simulation, type
3
followed byENTER
.Tip
To exit, the run directory creation process, type
Ctrl-C
at any prompt.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 byENTER
.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
or2
followed byENTER
.If you wish to set up a nested-grid simulation, type
3
and hitENTER
. 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 byENTER
.For some memory-intensive simulations (such as nested-grid simulations), you can use 47 levels. Type
2
followed byENTER
.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
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.
The last menu will prompt you with:
----------------------------------------------------------- Do you want to track run directory changes with git? (y/n) ----------------------------------------------------------- >>>
Type
y
and thenENTER
. 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.- The script will display the full path to the run directory. You can navigate there and then start editing the
GEOS-Chem configuration files <cfg>
.
The procedure to set up run directories for other GEOS-Chem Classic simulations is similar to that shown above.