Obtaining a GCHP Run Directory

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Revision as of 21:34, 8 August 2018 by Lizzie Lundgren (Talk | contribs) (Step 1: Create Run Directory)

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


The procedure for acquiring a GCHP run directory is the same as acquiring a GEOS-Chem Classic run directory. Once you have your run directory you must set your source code directory path prior to moving onto the next steps of setting up your environment, compiling, and running.

Step 1: Create Run Directory

You can create a GCHP run directory using the GEOS-Chem Unit Tester. From your primary GCHP directory (e.g. /mypath/GCHP), download a clean copy the development version of the GEOS-Chem Unit Tester on Github:

git clone git@github.com:geoschem/geos-chem-unittest.git UT

There are three run directories available for GCHP: the radon-lead-beryllium simulation, the standard full chemistry simulation, and the benchmarking simulation which incorporates both simple and complex SOA for validation. The default settings for all run directories are a 72-level simulation using 0.25x0.3125 GEOS-FP meteorology and internal c24 cubed sphere grid resolution (roughly equivalent to 4x5). Please note that unlike GEOS-Chem Classic there are not separate run directories for different grid resolutions.

Example steps for creating a standard full-chemistry run directory called gchp_standard:

  1. Change directories into /mypath/GCHP/UT/perl
  2. Open CopyRunDirs.input in a text editor and make the following changes:
    1. Update GCGRID_ROOT and DATA_ROOT to point to the GEOS-Chem shared data directories on your system. The default settings are compatible with the Harvard Odyssey compute cluster.
    2. Update variable UNIT_TEST_ROOT to match the directory to which you cloned the unit tester (e.g. /mypath/UT)
    3. Update variable COPY_PATH to be the target directory where you want to store your run directories (e.g. /mypath/GCHP/rundirs)
    4. Uncomment the lines for the GCHP run directories you would like to download (search for gchp_standard)
    5. Set the start and end dates for the simulations you are creating.
    6. Make sure all other run directory options are commented out
  3. Run the following perl script to create the run directory /mypath/GCHP/rundirs/gchp_standard:
    ./gcCopyRunDirs CopyRunDirs.input

See the Creating GEOS-Chem run directories wiki page for more information.

Step 2: Set Up the Run Directory

Symbolic links to restart files, input data, and tile files for mapping between lat-lon and cubed sphere grids are automatically included in the run directory and do not require additional setup. However, you should check that the links were properly set by ensuring none are broken symbolic links.

Then manually set a symbolic link to your source code directory. A utility bash script included in the run directory called setCodeDir will do this for you. Execute it as follows:

./setCodeDir /path/to/code

Note that there should not be any symbolic links within the path that you pass to setCodeDir as this will cause a compile error within ESMF.

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