Difference between revisions of "Creating run directories for GEOS-Chem 13.0.0 and later"

Revision as of 15:03, 8 December 2020

Previous | Next | Getting Started with GEOS-Chem

1. Minimum system requirements
2. Installing required software
3. Configuring your computational environment
4. Downloading source code
5. Downloading data directories
6. Creating GEOS-Chem run directories
   • ... for GEOS-Chem 13.0.0 and later versions
   • ... for GEOS-Chem 12.9.3 and earlier versions
7. Configuring runs
8. Compiling
9. Running
10. Output files
11. Visualizing and processing output
12. Coding and debugging
13. Further reading

Overview

We have greatly simplified run directory creation in GEOS-Chem 13.0.0 and later versions. You no longer need to download the separate GEOS-Chem Unit Tester repository any longer, but can create run directories from a script in the GEOS-Chem source code itself.

Example 1: Creating a run directory for a full-chemistry simulation

Let us walk through the process of creating a run directory for a global GEOS-Chem full-chemistry simulation.

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

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

You should see this output:

 CMakeLists.txt  LICENSE  run@  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:

     archiveRun.sh*    gitignore                   HISTORY.rc.templates/  runScriptSamples/
     createRunDir.sh*  HEMCO_Config.rc.templates/  input.geos.templates/
     getRunInfo*       HEMCO_Diagn.rc.templates/   README

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:

     ===========================================================
     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

To create a run directory for the full-chemistry simulation, type 1 followed by the ENTER key.

5. You will then be prompted to specify whether you want to perform chemistry in the stratosphere or not:

     -----------------------------------------------------------
     Choose chemistry domain:
     -----------------------------------------------------------
       1. Troposphere + stratosphere (Recommended)
       2. Troposphere only

Select the recommended option: Type 1 and then ENTER.

6. 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

6a: For the standard full-chemistry simulation, type 1 followed by ENTER.

6b: To add an option to the full-chemistry simulation, type a number between 2 to 8 and press ENTER.

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

     -----------------------------------------------------------
     Choose meteorology source:
     -----------------------------------------------------------
       1. MERRA-2 (Recommended)
       2. GEOS-FP 

You should use the recommended option (MERRA-2) if possible. Type 1 followed by ENTER.

8. 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

8a. If you wish to set up a global simulation, type either 1 or 2 followed by ENTER.

8b. 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.

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

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

9a. For most simulations, you will want to use 72 levels. Type 1 followed by ENTER.

9b. For some memory-intensive simulations (such as nested-grid simulations), you can use 47 levels. Type 2 followed by ENTER.

10. 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:
     -----------------------------------------------------------

10a. You can enter an absolute path (such as /n/home09/ryantosca/ followed by ENTER).

10b. Or you can 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/ryantosca/rundirs

11. 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.

The script will display the following output:

     -- Using default directory name gc_4x5_fullchem        

or if you are creating a nested grid simulation:

     -- Using default directory name gc_05x0625_fullchem

and then:

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

12. 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.

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

Example 2: Creating a run directory for the methane simulation

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:

     CMakeLists.txt  LICENSE  run@  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:

     archiveRun.sh*    gitignore                   HISTORY.rc.templates/  runScriptSamples/
     createRunDir.sh*  HEMCO_Config.rc.templates/  input.geos.templates/
     getRunInfo*       HEMCO_Diagn.rc.templates/   README

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. Type:

 ./createRunDir.sh

4. 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

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

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

 -----------------------------------------------------------
 Choose meteorology source:
 -----------------------------------------------------------
   1. MERRA-2 (Recommended)
   2. GEOS-FP 

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

6a. If you wish to set up global simulation, type either 1 or 2 followed by ENTER.

6b. 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)

7a. For most simulations, you will want to use 72 levels. Type 1 followed by ENTER

7b. 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:
 -----------------------------------------------------------

8a. You enter this an absolute path (such as /n/home09/ryantosca/ followed by ENTER).

8b. Or you can 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/ryantosca/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.
 -----------------------------------------------------------

In most cases, you should use the default run directory name. So type ENTER. The script will display the following output:

 -- Using default directory name gc_4x5_CH4       
 

or if you are creating a nested grid simulation:

 -- Using default directory name gc_05x0625_CH4

and then:

 -- This run directory has been set up for 20190701 - 20190801.
    You may modify these settings in input.geos.
 
 -- 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.

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

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