Obtaining a GCHP Run Directory

From Geos-chem
Revision as of 17:42, 20 April 2017 by Lizzie Lundgren (Talk | contribs) (Created page with "Go to GCHP Main Page The procedure to acquire a GCHP run directory is the same as acquiring a GCC run directory. However, you will need to take the added ste...")

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Go to GCHP Main Page

The procedure to acquire a GCHP run directory is the same as acquiring a GCC run directory. However, you will need to take the added step of setting up your run directory by running a bash script included in the directory files.

Step 1: Create Run Directory

There is currently only one GCHP run directory available. It is the standard 72-level simulation with internal c24 cubed sphere resolution (roughly equivalent to 4x5) and both c24 and regridded 4x5 output.

As for GCC, you can create a GCHP run directory using the GEOS-Chem unit tester. First, download the preliminary GEOS-Chem v11-01 unit tester to /mypath/UT by cloning the GCHP_master branch of the GEOS-Chem Unit Test development repository ut_bleeding_edge from BitBucket. Note that starting in GEOS-Chem v11-01b, the GCHP run directory will be available from the </tt> UT_Bleeding_Edge</tt> master branch instead.

git clone -b GCHP_master https://bitbucket.org/gcst/ut_bleeding_edge.git UT

Next, complete the following steps to create a GCHP c24 standard run directory:

  1. Change directories into /mypath/UT/perl
  2. Open the configuration text file CopyRunDirs.input
  3. Make the following edits:
    1. Update DATA_ROOT as needed to point to your system's shared data directory
    2. Change variable UNIT_TEST_ROOT as needed to match the directory to which you cloned the unit tester (/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 GCHP c24 standard run directory ("gchp" will be in the MET column)
  4. Run the following perl program to create the run directory /mypath/GCHP/rundirs/gchp_c24_standard:
./gcCopyRunDirs CopyRunDirs.GCHP

See the GEOS-Chem wiki page on creating GEOS-Chem run directories wiki page for more information about creating general GEOS-Chem run directories.

Step 2: Set Up the Run Directory

Additional steps are required after downloading the GCHP run directory to set it up for GCHP compilation and runs. These include setting symbolic links to your restart file and data directories containing source code, input data, and tile files. Tile files are used in GCHP to map between the cubed sphere and lat/lon grids. Run the initialSetup.sh bash script included in the run directory to set these up.


If you are an Odyssey user at Harvard then most of the symbolic links will be set for you automatically. If you are outside of Odyssey then you will need to enter paths manually. Make sure that you have the full paths to all required directories before you start. Note that you must write out the full path to the source code directory without any symbolic links.

For all users, you will need to specify input meteorology resolution. Recall that the c24 degree resolution in the run directory name indicates the GCHP internal cubed sphere resolution only. Unlike GCC, the lat/lon input meteorology resolution can be a different resolution than the regridded GCHP lat/lon output. We recommend using 2x25 input meteorology when using a GCHP run directory for the first time.

Based on what system you are using, Odyssey or elsewhere, you may expect to go through the following steps for set up:

Odyssey Users

  1. Enter y when asked if you are on Odyssey.
  2. Enter the path to the source code you downloaded.
  3. Enter 2 for the input meteorology field resolution. This will result in setting up symbolic link MetDir which points to the default Odyssey GEOS-FP 2⨉2.5 meteorological data directory.

Non-Odyssey Users

  1. Enter n when asked if you are on Odyssey.
  2. Enter the path to the source code you downloaded.
  3. You will go through a series of prompts asking you to set up the paths to your data directories. You should have the primary path for your group's shared data directories handy for this step. Within that directory should be subdirectories called HEMCO, CHEM_INPUTS, TileFiles, and SPC_RESTARTS, as well as several GEOS met data subdirectories of format GEOS.{res}.d. If you are missing any of these subdirectories, exit out of initialSetup.sh to find out where they are located prior to continuing.
    1. For path containing met data, specify the location of the folder containing GEOS-FP formatted meteorological data for the input data resolution you want to use. For example, enter /{shared_data_path}/GEOS_2x2.5.d/GEOS_FP if you want to input 2x2.5 met data.
    2. For the HEMCO data directory, enter {shared_data_path}/HEMCO.
    3. For the GEOS-Chem restart files, enter {shared_data_path>/SPC_RESTARTS.
    4. For the CHEM_INPUTS directory, enter {shared_data_path}/CHEM_INPUTS.
    5. For the TileFiles directory, enter {shared_data_path}/TileFiles.

Note that meteorology data paths in input.geos are ignored by GCHP and are superceded by paths in ExtData.rc. See the GEOS-5 wiki for detailed information about ExtData component. If you run into a problem with met fields when you later run GCHP, first check ExtData.rc to ensure you have the correct data paths.

Go to GCHP Main Page