Obtaining a GCHP Run Directory

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Revision as of 18:09, 20 October 2020 by Lizzie Lundgren (Talk | contribs) (Step 2: Set Environment File Symbolic Link)

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  1. Hardware and Software Requirements
  2. Downloading Source Code and Data Directories
  3. Obtaining a Run Directory
  4. Setting Up the GCHP Environment
  5. Compiling
  6. Running GCHP: Basics
  7. Running GCHP: Configuration
  8. Output Data
  9. Developing GCHP
  10. Run Configuration Files

Step 1: Create Run Directory

Navigate to the run/ subdirectory of the source code. To create a run directory, use createRunDir.sh and follow the prompts.

$ cd ~/GCHPctm/run
$ ./createRunDir.sh

During the course of script execution you will be asked a series of questions:

Data directory path

The very first time you create a run directory you will be prompted for your ExtData path where you store GEOS-Chem shared data directories. The path will be stored in file .geoschem/config in your home directory as environment variable GC_DATA_ROOT. If that file does not already exist it will be created for you.

Follow the prompts to enter the paths. The ExtData path should include the name of your ExtData directory. It is a good idea to have this ready prior to creating your first run directory. Make sure you do not include any symbolic links in the path.

NOTE: Subsequent runs of createRunDir.sh will always source the .geoschem/config file to get your location for shared data directories. You will not be prompted to enter it again. If the path changes in the future you must provide the new paths in .geoschem/config. The run directory creation script will prompt you to do so only if the file is missing or if the paths within it are not valid.

Simulation type

You will next be prompted for what simulation you wish to create a run directory for.

Choose simulation type:
 1. TransportTracers
 2. Standard
 3. Benchmark

Enter the integer number next to the simulation type you want to use that is displayed on the screen.

Meteorology source

Next, choose which meteorology source you would like to use.

Choose meteorology source:
 1. MERRA2 (recommended)

Currently GCHP supports GEOS-FP and MERRA2 data only. Input data resolution is 0.25x0.325 for GEOS-FP and 0.5x0.625 for MERRA2 by default. Unlike GEOS-Chem Classic, GCHP input meteorology data does not need to be the same grid type or grid resolution as the grid and resolution you run at.

Storage location

Next, enter the target path where you want your run directory to be stored.

Enter path where the run directory will be created:

Do not include symbolic links in the path. Choose your path wisely to keep your runs organized.

Run directory name

You will then be prompted to enter a run directory name if you did not pass one as an optional argument when calling the script. You are given the option to simply press return and use the default run directory name of format gchp_{simulation_type}. Here is an example of what you will see if using the default name for the standard full chemistry simulation:

Enter run directory name, or press return to use default:

Using default directory name gchp_standard

Run directory version control

Finally, you will be asked if you want to track run directory changes with git version control. This feature is useful if you plan on making feature updates to GEOS-Chem that involve changes to the run directory, such as adding emissions or turning components on or off. With version control you can keep track of exactly what you changed relative to the original settings.

This is what you will see if you use to put your run directory under version control with git:

Do you want to track run directory changes with git? (y/n)
Initialized empty Git repository in /n/home/user003/gchp_standard/.git/

We strongly recommend using this feature if you plan on submitting an update for inclusion in the standard model since you can copy changes directly from your version history to GCHP/Run, and then commit those changes with your source code updates. If you forked the repository you can then push to your fork and do a pull request to send us your updates.

Step 2: Set Environment

Once you have created a run directory you need to set the gchp.env symbolic link to your GCHP environment file. This file will be sourced automatically every time you compile using the Makefile and every time you run using one of the provided run scripts (more on this later in the manual). If you write your own run script, be sure to include source gchp.env at the top to use the same environment that you compiled with.

To set the gchp.env symbolic link, navigate to your newly created run directory and execute shell script setEnvironment and pass the path to your environment file. You can keep your environment file anywhere on your system; it does not need to be stored in the run directory.

cd /n/home/user003/gchp_standard
./setEnvironment /n/home/user003/envs/gchp_ifort17_openmpi.env

Several examples of GCHP environment files are provided in subdirectory environmentFileSamples within the created run directory. For more information on developing a working environment file for GCHP see the next chapter in this online manual.

Additional information

Please note that run directories should be created for each different version of GEOS-Chem you use. If you are uncertain which version your run directory corresponds to you can check file rundir.version for version information about the source code used to generate it.

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