Frequently asked questions about GEOS-Chem

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On this page we shall answer some commonly asked questions about GEOS-Chem.

Basic information about GEOS-Chem

For new users

--Bob Yantosca (talk) 17:45, 2 January 2019 (UTC)

Science questions

Where can I find information about ...

--Bob Yantosca (talk) 17:45, 2 January 2019 (UTC)

Technical issues

--Bob Yantosca (talk) 17:45, 2 January 2019 (UTC)

Parallelization issues

--Bob Yantosca (talk) 17:45, 2 January 2019 (UTC)

High-Performance GEOS-Chem (GCHP)

Please see the GCHP main wiki page for information about GCHP.

Where can I get restart files for GEOS-Chem?

For instructions on how to obtain a set of sample restart files that you can use to spin up your own simulations, please see the Restart Files section of our GEOS-Chem basics wiki page.

--Bob Yantosca (talk) 16:24, 6 January 2017 (UTC)

Running GEOS-Chem

Please see our Running GEOS-Chem wiki page.

How long does GEOS-Chem take to run?

It depends on your particular computing environment. We have posted several timing results from GEOS-Chem 7-day time test simulations.

GEOS-Chem seems to be running too slowly. What can I do?

You should be aware of several compile-time options that will slow down GEOS-Chem. Use these options only for debugging, but not in your production runs.

If you are archiving many diagnostic quantities are a high temporal resolution (e.g. every hour), then this will increase the run time of your simulation. You can try saving out less diagnostic quantities, or archiving at a lower temporal resolution (e.g. every day).

GEOS-Chem errors

Please also see our Guide to GEOS-Chem error messages.

GEOS-Chem died with an error. What can I do?

Please see Understanding the different categories of errors section of our Guide to GEOS-Chem error messages.

--Bob Yantosca (talk) 14:40, 17 June 2019 (UTC)

Where does GEOS-Chem error output get printed?

GEOS-Chem, like all Unix programs, sends its output to two streams:

  1. stdout
  2. stderr

The stdout stream

Most GEOS-Chem output will go to the stdout stream, which takes I/O from the Fortran WRITE and PRINT commands. If you run GEOS-Chem by just typing the executable name at the Unix prompt: 

geos

then the stdout stream will be printed to the terminal window. You can also redirect the stdout stream to a log file with the Unix redirect command: 

geos > log

We recommend that you create GEOS-Chem log files so that you can reexamine the output from your run at a later time.

Most GEOS-Chem errors will be printed to stdout (and hence, to the log file). Most errors flagged by GEOS-Chem use a standard error message format, such as: 

==============================================================
GEOS-CHEM ERROR: No output scheduled on last day of run!
STOP at IS_LAST_DAY_GOOD ("input_mod.f")
==============================================================

The stderr stream

The stderr stream takes I/O from various Unix system commands, including exit. If your GEOS-Chem run died as a result of a system problem (i.e. you ran up against a system time or memory limit, you are over disk quota, etc.), then the error message will more than likely go to stderr instead of stdout. As a result, these error messages will not be printed to the GEOS-Chem log file output.

If you use a queue system then the stderr output may be printed to a file. For example, if you submit a GEOS-Chem job to the SGE queue system, and your job script is named run.geos, SGE will send the stderr output to a file named run.geos.oXXXXX (where XXXXX is the job ID #).

--Bob Y. 15:44, 8 November 2010 (EST)

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