Downloading data with the GEOS-Chem dry-run option

From Geos-chem
Revision as of 23:29, 3 January 2020 by Bmy (Talk | contribs) (What can I do with the output of a GEOS-Chem dry-run?)

Jump to: navigation, search

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements
  2. Configuring your computational environment
  3. Downloading source code
  4. Downloading data directories
  5. Creating run directories
  6. Configuring runs
  7. Compiling
  8. Running
  9. Output files
  10. Visualizing and processing output
  11. Coding and debugging
  12. Further reading


The GEOS-Chem dry-run option will be available in GEOS-Chem 12.7.0 and later versions. This version should be released by mid-to-late January 2020 (pending successful benchmarking).

What is a GEOS-Chem dry-run?

A "dry-run" is a is a GEOS-Chem "Classic" simulation that steps through time, but does not perform computations or read data files from disk. Instead, a dry-run simulation prints a list of all data files that a regular GEOS-Chem simulation would have read. The dry-run output also denotes whether each data file was found on disk, or if it is missing.

Why should I perform a GEOS-Chem dry-run?

A GEOS-Chem dry-run is a good way for you to check if you have properly configured your computational environment. This is especially important if you are porting GEOS-Chem to run on a new computer system, or on the AWS cloud.

For example:

Problem encountered in dry-run What this can indicate
GEOS-Chem "Classic" does not compile
  • Your system does not have a supported compiler
  • Your system is missing one or more required software libraries
  • You have invalid settings in your Unix startup scripts (e.g. .bashrc, etc.)
GEOS-Chem "Classic" compiles but does not run
  • Your GEOS-Chem configuration files (input.geos, HEMCO_Config.rc, etc.) contain errors
  • You have invalid settings in your Unix startup scripts (e.g. .bashrc, etc.)

Once you have can successfully finished a GEOS-Chem dry-run, you can have confidence that GEOS-Chem can run on your system.

More importantly, output from the GEOS-Chem dry-run simulation can be used to download required met field and emissions data for a GEOS-Chem simulation (see next section).

What can I do with the output of a GEOS-Chem dry-run?

When you run GEOS-Chem in dry-run mode, you must pipe the output to a log file (as you would do for any other GEOS-Chem simulation). The log file containing dry-run output looks similar to a regular GEOS-Chem log file, but will also contain text such as:

HEMCO: Opening /path/to/ExtData/HEMCO/EDGARv43/v2016-11/

NOTE: /path/to/ExtData denotes the full pathname of the ExtData folder. This is the root of the directory tree containing all GEOS-Chem met fields and emissions data. This will of course be different on each system.

This text lets you know if GEOS-Chem was able to find each input file on disk or not. This information can be parsed by a Python script (, which is included in each run directory) to produce:

  1. A unique list of required data files (with all duplicates removed). This can be useful for documentation purposes.
  2. A bash script that will download all MISSING data files from one of the GEOS-Chem data repositories:
    • Compute Canada repository
    • Amazon Web Services s3://gcgrid repository

In the following sections, we will describe the commands that are needed to execute a complete GEOS-chem dry-run workflow.

Which GEOS-Chem simulations can execute in dry-run mode?

Any of the supported GEOS-Chem "Classic" simulations (e.g. standard, benchmark, complexSOA, CH4, TransportTracers, etc.) can be executed in dry-run mode.

As of this writing (Jan 2020), GCHP cannot execute in dry-run mode. Dry-run functionality may be added in the future, but this will require modifications to the NASA MAPL software library. Because GCHP uses the same data files as GEOS-Chem "Classic", you can use a GEOS-Chem "Classic" dry-run to facilitate downloading met fields and emissions data for a GCHP simulation.

Executing GEOS-Chem in dry-run mode

Downloading data from dry-run output

Further reading

  1. A
  2. B

Previous | Next | Getting Started with GEOS-Chem