Difference between revisions of "Obtaining a GCHP Run Directory v12"

From Geos-chem
Jump to: navigation, search
Line 12: Line 12:
#[[GCHP_Run_Configuration_Files_v12|Run Configuration Files]]
#[[GCHP_Run_Configuration_Files_v12|Run Configuration Files]]
Please note that documentation on this page primarily reflects the latest GCHP public release which is currently the GCHP 12 series. The documentation will be updated for the GCHP 13.0.0 release over the coming months.
== Overview ==
== Overview ==

Latest revision as of 17:35, 20 October 2020

Previous | Next | Getting Started with GCHP v12 | GCHP Main Page

  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


Starting in version 12.1.0, GCHP no longer uses the Unit Tester to create run directories. For versions 12.1 through 12.6, create run directories directly from the GCHP source code repository, in directory Run. For 12.7 and beyond, create run directories from the GEOS-Chem source code repository, in directory run/GCHPctm. If you are uncertain about what version you have, please contact the GEOS-Chem Support Team. Please note that we always recommend upgrading to the latest version.

Step 1: Create Run Directory

If using version 12.7 or later, navigate to GEOS-Chem subdirectory run/GCHPctm and run shell script createRunDir.sh. If you using an earlier version, navigate to GCHP subdirectory Run/ instead.


You can pass a run directory name as an optional argument if you wish, or you can set it interactively later on.

./createRunDir.sh gchp_standard_12.7.0

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

External library paths

The very first time you create a run directory you will be prompted for (1) your ExtData path where you store GEOS-Chem shared data directories, and (2) your Goddard Fortran Template Library (gFTL) path where your gFTL repository is located. Both paths 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.

Follow the prompts to enter the paths. The ExtData path should include the name of your ExtData directory. It is a good idea to have this ready prior to creating your first run directory. Make sure you do not include any symbolic links in the path. The gFTL path should also include the name of the gFTL directory as well as the install directory. This means that if you built gFTL in an install folder as described previously, then your gFTL path should look something like /n/home/user003/gFTL/install rather than /n/home/user003/gFTL. The interactive script will print out a list of instructions on downloading gFTL in case you have not already downloaded it.

NOTE: Subsequent runs of createRunDir.sh will always source the .geoschem/config file to get your location for shared data directories and gFTL. You will not be prompted to enter them again. If the paths changes in the future you must provide the new paths in .geoschem/config. The run directory creation script will prompt you to do so only if the file is missing or if the paths within it are not valid.

Simulation type

You will next be prompted for what simulation you wish to create a run directory for.

Choose simulation type:
 1. TransportTracers
 2. Standard
 3. Benchmark

Enter the integer number next to the simulation type you want to use that is displayed on the screen. There are currently three options for GCHP simulations. If you would like to run additional simulation types with GCHP please contact the GCHP Working Group with why you think adding the additional simulation type should be a priority.

Meteorology source

Next, choose which meteorology source you would like to use.

Choose meteorology source:
 2. MERRA2

Currently GCHP supports GEOS-FP and MERRA2 data only. Input data resolution is 0.25x0.325 for GEOS-FP and 0.5x0.625 for MERRA2 by default. Unlike GEOS-Chem Classic, GCHP input meteorology data does not need to be the same grid type or grid resolution as the grid and resolution you run at.

Storage location

Next, enter the target path where you want your run directory to be stored.

Enter path where the run directory will be created:

Do not include symbolic links in the path. Choose your path wisely to keep your runs organized.

Run directory name

You will then be prompted to enter a run directory name if you did not pass one as an optional argument when calling the script. You are given the option to simply press return and use the default run directory name of format gchp_{simulation_type}. Here is an example of what you will see if using the default name for the standard full chemistry simulation:

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

Using default directory name gchp_standard

If you are not storing your run directory at a path that indicates GEOS-Chem version, we recommend storing the version number directly in the run directory name to avoid later confusion. However, please note that you can always look up the run directory version within the run directory itself in file rundir.version if you have doubts about what GCHP version your run directory is compatible with.

Run directory version control

Finally, you will be asked if you want to track run directory changes with git version control. This feature is useful if you plan on making feature updates to GEOS-Chem that involve changes to the run directory, such as adding emissions or turning components on or off. With version control you can keep track of exactly what you changed relative to the original settings.

This is what you will see if you use to put your run directory under version control with git:

Do you want to track run directory changes with git? (y/n)
Initialized empty Git repository in /n/home/user003/gchp_standard/.git/

We strongly recommend using this feature if you plan on submitting an update for inclusion in the standard model since you can copy changes directly from your version history to GCHP/Run, and then commit those changes with your source code updates. If you forked the repository you can then push to your fork and do a pull request to send us your updates.

Step 2: Set Environment File Symbolic Link

Once you have created a run directory you need to set the gchp.env symbolic link to your GCHP environment file. This file will be sourced automatically every time you compile using the Makefile and every time you run using one of the provided run scripts (more on this later in the manual). If you write your own run script, be sure to include source gchp.env at the top to use the same environment that you compiled with.

To set the gchp.env symbolic link, navigate to your newly created run directory and execute shell script setEnvironment and pass the path to your environment file. You can keep your environment file anywhere on your system; it does not need to be stored in the run directory.

cd /n/home/user003/gchp_standard
./setEnvironment /n/home/user003/envs/gchp_ifort17_openmpi.env

Several examples of GCHP environment files are provided in subdirectory environmentFileSamples within the created run directory. For more information on developing a working environment file for GCHP see the next chapter in this online manual.

Previous | Next | Getting Started with GCHP v12 | GCHP Main Page