Obtaining a GCHP Run Directory

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The GCHP documentation has moved to https://gchp.readthedocs.io/. The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!

Previous | Next | Getting Started with GCHP | GCHP Main Page

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

Create Run Directory

GCHP run directories are created from within the source code. A new run directory should be created for each different version of GEOS-Chem you use. Git version information is logged to file rundir.version within the run directory upon creation.

To create a run directory, navigate to the run/ subdirectory of the source code and execute shell script createRunDir.sh.

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

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

Enter ExtData directory path

The first time you create a GCHP run directory on your system you will be prompted for a path to GEOS-Chem shared data directories. The path should include the name of your ExtData directory and should not contain symbolic links. The path you enter 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. When creating additional run directories you will only be prompted again if the file is missing or if the path within it is not valid.

Enter path for ExtData:

Choose simulation type

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

Choose simulation type:
  1. Full chemistry
  2. TransportTracers

If creating a full chemistry run directory you will be given additional options. Enter the integer number that is next to the simulation option you want to run.

Choose additional simulation option:
 1. Standard
 2. Benchmark
 3. Complex SOA
 4. Marine POA
 5. Acid uptake on dust
 7. APM

Choose meteorology source

Enter the integer number that is next to the input meteorology source you would like to use.

Choose meteorology source:
 1. MERRA2 (Recommended)

Enter run directory path

Enter the target path where the run directory will be stored. You will be prompted to enter a new path if the one you enter does not exist.

Enter path where the run directory will be created:

Enter run directory name

Enter the run directory name, or accept the default. You will be prompted for a new name if a run directory of the same name already exists at the target path.

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

Put run directory under version control (optional)

Enter whether you would like your run directory tracked with git version control. With version control you can keep track of exactly what you changed relative to the original settings. This is useful for trouble-shooting as well as tracking run directory feature changes you wish to migrate back to the standard model.

Do you want to track run directory changes with git? (y/n)

Set Environment

Set the gchp.env symbolic link to the same GCHP environment file you used for building the executable. This generically named symbolic link exists for convenience for inclusion in reusable scripts to automate build and run. To set it, use shell script setEnvironment.

cd /home/gchp_fullchem
./setEnvironment /home/envs/gchp_ifort19_openmpi4.env


  • You can keep your environment file anywhere on your system for reuse across multiple run directories.
  • Always source gchp.env prior to building and running GCHP. It is included by default in all example run scripts.
  • Check CMake file CMakeCache.txt when in doubt about what environment was used to build the executable.

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