Obtaining a GCHP Run Directory

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Revision as of 22:27, 29 June 2018 by Lizzie Lundgren (Talk | contribs) (→‎Step 1: Create Run Directory)

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  1. Downloading Source Code
  2. Obtaining a Run Directory
  3. Setting Up the GCHP Environment
  4. Compiling
  5. Basic Example Run
  6. Run Configuration Files
  7. Advanced Run Examples
  8. Output Data
  9. Developing GCHP


Overview

The procedure for acquiring 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

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:GCST/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/UTBE/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/UTBE)
    3. Change variable COPY_PATH to be the target directory where you want to store your run directories (e.g. /mypath/GCHP/rundirs)
    4. Comment out the line for the GEOS-FP standard simulation (MET=geosfp, GRID=4x5, SIMULATION=standard)
    5. Uncomment the line for the GCHP standard run directory (MET=gchp, SIMULATION=standard)
  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

v11-02c

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.

--Lizzie Lundgren (talk) 16:18, 25 September 2017 (UTC)

v11-02b

Prior to v11-02c, additional steps are required after downloading the GCHP run directory to set it up for compilation and runs. These include setting symbolic links to your restart file and data directories containing source code, input data, and tile files (mapping between lat/lon and cubed sphere grids), and are done using the initialSetup.sh bash script included in the run directory. If you are using Harvard's Odyssey compute cluster then most symbolic links will be set for you automatically. If you are on a system other than Odyssey then you will need to enter paths manually. Make sure that you have the full paths to all required directories before you start.

Prior to proceeding, you will need to download several directories and files for GCHP beyond what is used for GEOS-Chem classic v11-01 if they are not already present on your network. If someone at your school or institution has already set up GCHP on your network then these files likely already exist and you may skip this step. The necessary files and directories are as follows:

  • ExtData/GCHP/Tilefiles
  • ExtData/SPC_RESTARTS/initial_GEOSChem_rst.c24_standard.nc
  • gcdata/GEOS_NATIVE/MODIS_LAI_201204/For_Olson_2001/XLAI_for_GCHP/
  • gcdata/GEOS_NATIVE/Olson_Land_Map_201203/Olson_2001_Land_Map.025x025.generic.GCHP.nc

Steps to download these directories are the same as for GEOS-Chem classic as described on the Downloading Shared Data Directories wiki page.

Once you are certain you have all necessary inputs, run the initialSetup.sh bash script included in the run directory by typing: 

cd /mypath/GCHP/rundirs/gchp_c24_standard
./initialSetup.sh

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

Odyssey Users

  1. Enter the path to the source code you downloaded (specify full path without symbolic links).
  2. Enter y when asked if you are on Odyssey.

Non-Odyssey Users

  1. Enter the path to the source code you downloaded (specify full path without symbolic links).
  2. Enter n when asked if you are on Odyssey.
  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 (i.e. the path to ExtData). Within ExtData there should be subdirectories called HEMCO, CHEM_INPUTS, GCHP/TileFiles, and SPC_RESTARTS, as well as several met data subdirectories of format GEOS_{RESOLUTION}. If you are missing any of these subdirectories, exit out of initialSetup.sh (using Ctrl+C) and 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 at input grid resolution you wish to use. The default input meteorology in the run directory is 2x2.5 so enter /{LOCAL_PATH}/ExtData/GEOS_2x2.5/GEOS_FP for this tutorial. Instructions on how to update configuration files for other input resolutions are given later in the guide.
    2. For the path to HEMCO data directory, enter /{LOCAL_PATH}/ExtData/HEMCO.
    3. For the path to GEOS-Chem restart files, enter /{LOCAL_PATH}/ExtData/SPC_RESTARTS.
    4. For the path to CHEM_INPUTS directory, enter /{LOCAL_PATH}/ExtData/CHEM_INPUTS.
    5. For the path to tile files, enter /{LOCAL_PATH}/ExtData/GCHP/TileFiles.


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