Difference between revisions of "Running GEOS-Chem"

Revision as of 15:53, 13 June 2019

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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

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.

Pre-run checklist

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

1. You have the proper libraries loaded
2. Your run directory contains the executable geos.
3. You have looked through and set all configurable settings in input.geos, HEMCO_Config.rc, and HISTORY.rc
4. You have a run script (see below for information about run scripts)
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:

• Common GEOS-Chem error messages
• Tips on how to debug GEOS-Chem effectively
• Submitting GEOS-Chem support requests

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