Difference between revisions of "Obtaining a GCHP Run Directory"

Revision as of 17:47, 8 August 2018

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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. Run Configuration Files
8. Advanced Run Examples
9. Output Data
10. Developing GCHP

Overview

The procedure for acquiring a GCHP run directory is the same as acquiring a GEOS-Chem Classic run directory.

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 starting in GEOS-Chem v11-02c. They are for the radon-lead-beryllium simulation, the standard full chemistry simulation, and the benchmarking simulation which now incorporates both simple and complex SOA. The default settings for all run directories are for a 72-level simulation using input 0.25x0.3125 meteorology, and internal c24 cubed sphere grid resolution (roughly equivalent to 4x5). Please note that internal resolution is now configurable within the run directory and the run directory name therefore does not include resolution (unlike GEOS-Chem "classic").

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 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. Change variable UNIT_TEST_ROOT to match the directory to which you cloned the unit tester (e.g. /mypath/UT)
   3. Change 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. 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 time files for mapping between lat-lon and cubed sphere grids are included in the run directory. Prior to compiling GCHP, however, you must 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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