Difference between revisions of "Downloading GCHP"

Revision as of 21:24, 14 August 2019

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

Overview

GCHP is built to wrap around a standard GEOS-Chem Classic installation. The first step to obtaining GCHP is therefore to clone the standard GEOS-Chem source code repository. Enabling GCHP functionality simply involves the added step of cloning the GCHP source code repository to store as a subdirectory within GEOS-Chem.

Acquiring the GCHP subdirectory does not change anything in the standard GEOS-Chem code; you can use the same source code to run regular non-GCHP GEOS-Chem simulations. However, we recommend that you keep separate GEOS-Chem source code directories for use with GCHP and GEOS-Chem Classic, e.g. Code.gchp and Code.gcc. This avoids confusion and extra work since each requires separate compilation. Using git, you can exchange GEOS-Chem code between the two GEOS-Chem repository clones even when the GCHP clone is in one and not the other.

Please note that certain files in GEOS-Chem Classic source code will be present but ignored when running GCHP. Most notably this includes GeosCore/main.F, all advection code, and everything in the History folder.

Step 1: Download GEOS-Chem

Clone or fork (recommended) the GEOS-Chem repository located at https://github.com/geoschem/geos-chem.git. Forking is a simple tool to acquire a copy of the repository in your own GitHub account. You can then clone that copy from your own account rather than from the GEOS-Chem GitHub. The advantage of this is that you have push permissions to send updates to GitHub for back-up storage, you can access and share your code publicly, and you can do pull requests to transfer your updates to the GEOS-Chem Support Team for inclusion in the standard model. Create a fork by simply clicking fork in the upper right corner of the GEOS-Chem GitHub page while logged into your account.

If you are cloning from the GEOS-Chem GitHub directly:

git clone https://github.com/geoschem/geos-chem.git Code.gchp

If you are cloning a fork from your own GitHub account:

git clone https://github.com/{username}/geos-chem.git Code.gchp

Take note of the path where the code was downloaded. You can name your cloned repository anything you would like.

Step 2: Download GCHP within GEOS-Chem

Navigate to your GEOS-Chem code directory that you just downloaded and clone the GCHP repository from Github:

cd /mypath/GCHP/Code.GCHP
git clone https://github.com/geoschem/gchp.git GCHP

Step 3: Choose version

When you clone GEOS-Chem and GCHP you will always get the master branch. This is always the current stable version of GEOS-Chem. You can determine the version label by typing git log --decorate within each repository and looking at the git tag string printed for the top-most commit. Always be sure that the versions you have in the two repositories are compatible.

Example output of git log. Notice tag name at top indicating what version this is.

If you would like an earlier version you can checkout the version tag for that specific version in both the GEOS-Chem and GCHP repositories. To see a list of available tags for a repository type git tag. To checkout a tagged version type git checkout tags/tagname.

When you checkout a tag beware that you will be in what is called a detached HEAD status. This means you are not officially on a git branch. Committing in this state risks losing your changes since they are not associated with an actual git branch. If you plan on developing code in the version you checkout you should therefore create a branch to work in: git checkout -b mybranch. However, we request that new updates always be built off of the master branch that is current at the time you begin work. We further recommend that you pull in future version updates as they are released.

If you are in doubt about how to use git with GEOS-Chem please contact the GEOS-Chem Support Team for help.

Step 4: Download Shared Data Directories

Steps for downloading data directories used in GCHP are the same as for GEOS-Chem Classic. Please see Downloading GEOS-Chem data directories for instructions and resources. See also the GEOS-Chem version information on the wiki for a list of new data directories required per version. For example, new data directories added for GEOS-Chem 12.2.0 are located here.

Beyond downloading the data directories you would typically use for GEOS-Chem Classic, GCHP requires that you also download directory ExtData/GCHP/TileFiles. This contains files for mapping between lat-lon and cubed sphere grids and is available from the Harvard ftp server (ftp.as.harvard.edu) at gcgrid/geos-chem/data/ExtData/GCHP/TileFiles. Please note that the need for tile files will be retired in an upcoming version when we update the version of MAPL, likely GEOS-Chem 12.5.0. At that time all regridding weights will be generated by ESMF at run-time.

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