Running GEOS-Chem

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Revision as of 19:14, 13 June 2019 by Bmy (Talk | contribs) (Pre-run checklist)

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


Overview

This page presents the basic information needed to run GEOS-Chem as well as how to verify a successful run and reuse a run directory.

Important things to know before you submit your run

  1. Please be aware of several options available for speeding up your GEOS-Chem simulations. See this wiki page for more information.
  2. The initial restart files do not reflect the actual atmospheric state and should only be used to "spin up" the model. In other words, they should be used as initial values in an initialization simulation to generate more accurate initial conditions for your production runs. See this wiki post for more information.
  3. Prior to running with GEOS-FP met fields, please be aware of several caveats regarding that data stream. See the GEOS-FP wiki page for more information.

Pre-run checklist

Prior to running GEOS-Chem, always run through the following checklist to ensure everything is set up properly.

  1. Your Unix run-time environment contains a netCDF library installation
  2. Your run directory contains the executable geos
  3. You have looked through and set all configurable settings in the following files:
    1. input.geos (specifies run-time settings)
    2. HEMCO_Config.rc (specifies emissions settings)
    3. HISTORY.rc (specifies diagnostic output settings)
  4. You have a run script (see below)
  5. You have enough memory and CPUs available

How to run GEOS-Chem

You can run GEOS-Chem locally from within your run directory (interactively) or by submitting your run to your cluster's job scheduler.

Running Interactively

To run GEOS-Chem interactively in your terminal window, navigate to your run directory and type:

./geos.mp

You may also send the GEOS-Chem output to a log file by using:

./geos.mp > GC.log

You may send the GEOS-Chem output to a log file and to your screen using:

./geos.mp 2>&1 | tee GC.log

Running as a Batch Job

You can then submit your GEOS-Chem simulation to your local cluster's queue using a simple script. For example:

#!/bin/bash

./geos.mp >> GC.log

exit 0

A sample run script benchmark.run can also be found in the GEOS-Chem Unit Tester. This run script is set up for the SLURM scheduler and can be submitted using the command sbatch benchmark.run. If your cluster utilizes a different job schedule, you may create your own run script or modify the sample run script as needed.

Verifying a Successful Run

There are several ways to verify that your run was successful.

  1. The following output can be found at the end of your GEOS-Chem log file:
    ************** E N D O F G E O S -- C H E M **************
  2. NetCDF files (GEOSChem.*.nc4) are present in the run directory directory.
  3. Your scheduler log (e.g. output from SLURM) does not contain any obvious errors.

If your run stopped with an error, please the following resources:


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