Creating run directories for GEOS-Chem 12.9.3 and prior

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Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements
  2. Installing required software
  3. Configuring your computational environment
  4. Downloading source code
  5. Downloading data directories
  6. Creating GEOS-Chem run directories
  7. Configuring runs
  8. Compiling
  9. Running
  10. Output files
  11. Python tools for use with GEOS-Chem
  12. Coding and debugging
  13. Further reading


On this page we show you how to use the GEOS-Chem Unit Tester to generate and use fresh copies of run directories for your GEOS-Chem simulations.

Downloading the GEOS-Chem Unit Tester

First, make sure that your system has these software packages installed. (Most of these come standard with your Unix-based operating system.)

Next, clone the GEOS-Chem Unit Tester package with these commands:

git clone UT
cd UT
git checkout master

This will download a fresh copy of the GEOS-Chem-UnitTest repository into a directory named UT, and place you in the master branch. The master branch always corresponds to the last benchmarked GEOS-Chem version.

If you would like to check out the Unit Tester that corresponds to a specific numbered GEOS-Chem version you can type one of the following commands:

git checkout 12.0.0
git checkout v11-02-rc
git checkout v11-02e


NOTE: The Git clone process may take a few minutes to complete depending on your connection speed.

--Bob Yantosca (talk) 21:10, 21 June 2018 (UTC)

Available run directories

Benchmark run directory

The GEOS-Chem Unit Tester includes a run directory called 4x5_standard (GEOS-Chem v11-01 and later) or 4x5_benchmark (GEOS-Chem v10-01). The standard GEOS-Chem benchmark simulation utilizes the GEOS-FP met fields (4° x 5 °, 72 levels) with the UCX tropospheric-stratospheric chemistry mechanism and secondary organic aerosols included.

To reproduce our latest 1-month benchmark simulation, you can edit the CopyRunDirs.input file so that the following line is uncommented under RUNS:

 geosfp   4x5         -      benchmark     2016070100   2016080100   -

Make sure to check the start and end date so that your simulation will run for July 2016. You can then create the GEOS-Chem benchmark run directory by typing ./gcCopyRunDirs. Navigate to your the newly created geosfp_4x5_benchmark run directory. To compile the GEOS-Chem source code, type:

make -j4 build

That will create a executable file that you can use to submit your GEOS-Chem benchmark simulation to a queue system.

For older versions of GEOS-Chem, the compile command was formerly

make -j4 mpbuild

Other run directories

Run directories are provided for a combination of met field, grid, and simulation type and are named accordingly. For more details on the simulation types, please see our GEOS-Chem chemistry mechanism wiki page.

Editing the CopyRunDirs.input file

Once you have downloaded the GEOS-Chem Unit Tester to your disk space, switch to the perl/ directory:

cd UT/perl

In this directory there is a Perl script named gcCopyRunDirs that you will use to generate fresh copies of GEOS-Chem run directories. This script uses an input file named CopyRunDirs.input, which is also located in the perl directory.

IMPORTANT: The CopyRunDirs.input file that comes with the Unit Tester provides only a small sample of the possible run directories that you can create. You can add as many entries to the RUNS section as you wish. See the UnitTest.input file for a complete list of all possible run directories that you can add to CopyRunDirs.input.

Your CopyRunDirs.input file will look something like this:

#                  GEOS-Chem Global Chemical Transport Model                  !
# !DESCRIPTION: Input file that specifies configuration for creating and
#  copying a run directory from the UnitTester. 
#  For a complete description of how to customize the settings in the
#  INPUTS and RUNS sections, see the following wiki posts:
#  18 Mar 2015 - R. Yantosca - Initial version
#  19 Mar 2015 - E. Lundgren - Simplify content for only copying run dirs
#  19 May 2015 - R. Yantosca - Now can specify VERBOSE and WARNINGS options
# %%% ID tags %%%
   VERSION        : v11-01
   DESCRIPTION    : Create run directory from UnitTest
# %%% Data path and HEMCO settings %%%
   DATA_ROOT      : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData
   VERBOSE        : 0
   WARNINGS       : 1
# %%% Unit tester path names %%%
   RUN_ROOT       : {UTROOT}/runs
   RUN_DIR        : {RUNROOT}/{RUNDIR}
   PERL_DIR       : {UTROOT}/perl
# %%% Target directory and copy command %%%
   COPY_PATH      : {HOME}/GC/rundirs
   COPY_CMD       : cp -rfL
# !RUNS:
#  Specify the runs directories that you want to copy below.
#  Here we provide a few examples, but you may copy additional entries from
#  UnitTest.input and modify the dates as needed. You can deactivate copying
#  run certain directories by commenting them out with "#".
  geosfp   4x5         -      standard     2013070100   2013080100   -
# geosfp   4x5         -      gc_timing    2013070100   2013070800   -
# geosfp   4x5         -      tropchem     2013070100   2013070101   -
# geosfp   4x5         -      soa          2013070100   2013070101   -
# geosfp   4x5         -      soa_svpoa    2013070100   2013070101   -
# geosfp   4x5         -      aciduptake   2013070100   2013070101   -
# geosfp   4x5         -      UCX          2013070100   2013070101   -
# geosfp   4x5         -      RRTMG        2013070100   2013070101   -
# geosfp   4x5         -      RnPbBe       2013070100   2013070101   -
# geosfp   4x5         -      Hg           2013010100   2013010101   -
# geosfp   4x5         -      POPs         2013070100   2013070101   -
# geosfp   4x5         -      TOMAS40      2013070100   2013070101   -
# geosfp   4x5         -      CH4          2013070100   2013070101   -
# geosfp   4x5         -      tagO3        2013070100   2013070101   -
# geosfp   4x5         -      tagCO        2013070100   2013070101   -
# geosfp   2x25        -      CO2          2013070100   201307010030 -
# geosfp   4x5         -      aerosol      2013070100   2013070101   - 
# geosfp   025x03125   ch     tropchem     2013070100   201307010010 -
# geosfp   025x03125   na     tropchem     2013070100   201307010010 -
# gchp     4x5         -      tropchem     2013070100   2013070101   -

NOTE: Lines starting with a # character will be treated as comments.

The CopyRunDirs.input file has a layout that is very similar to the GEOS-Chem Unit Tester input files (UnitTest.input located within this directory). Like the GEOS-Chem Unit Tester input files, CopyRunDirs.input is composed of an INPUTS section and a RUNS section, which are described below.

Section 1: INPUTS

Under the INPUTS section, you can customize the directory paths and other options for your system. Each configurable input is described in the table below.

Option Description
VERSION An ID tag that will be added to all log files and output files.
DESCRIPTION A short (1-sentence) description of the purpose of this specific file (optional). This may be used to differentiate different input files, such as if you pre-configure several for future re-use.
DATA_ROOT Specifies the path for your root-level data directory.
HEMCO_ROOT Specifies the top-level path for the HEMCO data directory tree.
  • The {DATAROOT} token in HEMCO_ROOT will be replaced with the value you specify for RUN_ROOT option.

Leave this as-is.

VERBOSE Specifies the level of debug output that will be sent to the HEMCO log file. (0=no debug output; 3=max debug output)
  • Recommended setting: 0
WARNINGS Specifies the level of warning messages that will be sent to the HEMCO log file. (0=no warnings; 3=max warnings)
  • Recommended setting: 1
UNIT_TEST_ROOT Specifies the path to the GEOS-Chem Unit Tester.
RUN_ROOT Specifies the top-level unit test run directories.

Leave this as-is.

RUN_DIR Specifies the run directory subdirectory.

Leave this as-is.

PERL_DIR Specifies the directory where the unit test Perl scripts are found.

Leave this as-is.

COPY_PATH Specifies the directory on your disk server where copies of the GEOS-Chem run directories will be created.
COPY_CMD Specifies the command used to copy run directories from the GEOS-Chem Unit Tester to COPY_PATH.
  • The default setting is cp -rfL. This will create a new copy of the directory, even if the prior copy exists.
  • The -L option to the cp will create "hard" copies of files that are symbolic links. This command may differ slightly depending on the flavor of your Unix-based Operating system.

Section 2: RUNS

The layout of the RUNS section is identical to the RUNS section in the GEOS-Chem Unit Tester input file. This enables copying and pasting simulation settings text from UnitTest.input into CopyRunDirs.input.

For example, the following line:

# !RUNS:
#  Specify the debugging runs that you want to perform below.
#  You can deactivate runs by commenting them out with "#".
  geosfp   4x5         -      standard     2013070100   2013080100   -

will tell the gcCopyRunDirs script to create a run directory for a GEOS-Chem simulation with the following settings:

The date range will be used to initialize the input.geos file that is read during a GEOS-Chem simulation. Once the run directory is created, you may edit these dates within the input.geos file. Note, however, that time ranges must remain within the time range covered by the MET field you are using. You can check the MET field temporal coverage on the GMAO met data products wiki page. Also note that we recommend using the restart files to spin up GEOS-Chem for at least one year prior to your simulation start date. You may use the resulting output restart files as initial values for your simulation.

You can add as many entries to the RUNS section as you wish. See the UnitTest.input file for a complete list of all possible run directories entries that you can add to CopyRunDirs.input.

Generating a GEOS-Chem Run Directory

Once you have edited the CopyRunDirs.input script to your liking, you can use that to generate fresh copies of GEOS-Chem run directories. Make sure you are in the perl directory, and then type:


If you do not pass a file name to gcCopyRunDirs, then the gcCopyRunDirs script will use the CopyRunDirs.input file that you just modified.

If you wish, you can create many customized copies of CopyRunDirs.input. For example, suppose you edit CopyRunDirs.input to generate a full-chemistry run directory. You can then save it as a separate file and use it explicitly with gcCopyRunDirs.

cp CopyRunDirs.input CopyRunDirs.fullchem   # Input file set up to only copy the full-chemistry run directories
./gcCopyRunDirs CopyRunDirs.fullchem            

Executing gcCopyRunDirs will create a new GEOS-Chem run directory corresponding to each entry that you specified in the input file RUNS section. Each run directory will be created as a subdirectory of COPY_PATH that you specified in the input file INPUTS section.

Let's examine the contents of a sample geosfp_4x5_standard run directory. Navigate to your newly created run directory and tssue the following commands:

make fileclean                       # Remove any files left over from previous unit test runs

ls -1                                # Get directory listing

And you will see this directory listing:

NOTE: Run directories for other simulations may contain other files not pictured here.

The input.geos and HEMCO_Config.rc files have been customized for this particular simulation. They were created from the corresponding template files input.geos.template and HEMCO_Config.template in the Unit Tester. The Perl script getRunInfo is used by the Makefile to extract information about the simulation from input.geos. HEMCO and tracer restart files are also included in every run directory but care must be taken when using them. See the section below for more information about restart files.

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