Difference between revisions of "Frequently asked questions about GEOS-Chem"

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Revision as of 18:44, 10 November 2010

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

Basic information about GEOS-Chem

For new users

Science questions

Where can I find information about ...

Technical questions

Specific questions

How long does GEOS-Chem take to run?

It depends on your particular computing environment. We have posted several timing results from GEOS-Chem 4° x 5° (1-month benchmark) and 2° x 2.5° (1-year benchmark) 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.

Also, the following run-time options may also slow down GEOS-Chem:

"Normal" diagnostics (e.g. saved out to the ctm.bpch file)
The more diagnostic quantities you choose to archive, the more memory and disk I/O operations this will require.
"Timeseries" diagnostics (ND48, ND49, ND50, ND51, ND51b)
If you choose to archive many diagnostic quantities at hourly or bi-hourly intervals, then the increased memory and disk I/O usage can slow down GEOS-Chem.

To speed up GEOS-Chem, you can try to reduce the number of diagnostics that you are saving to disk.

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

First, you should try to understand the type of error that has occurred. There are several different classes of errors, such as:

  1. File I/O errors
  2. Abnormal exits
  3. Technical errors

Once you have understood the type of GEOS-Chem error that has occurred, you can take steps to fix it. In some cases, the fixes will be simple (i.e. selecting the proper option and starting over, or replacing missing or corrupted data files, etc.). In other cases, the error may be more difficult to diagnose (such as a convergence error in the chemical solver). In that case you may have to "dig in" to the code so that you can modify its behavior (e.g. modify convergence criteria, add error checks, etc.).

Try to isolate the error to a particular GEOS-Chem routine. You can use a debugger such as idb or Totalview, or you can turn on the ND70 debug printout option. (ND70 will print debug messages to the log file after key operations have been completed.) Once you know where the error is occurring, try to print out values for a given grid box and tracer, either in the debugger or by adding PRINT statements to the code. You will gain great insight into what is happening by using this technique.

Try to determine if the error is persistent (i.e. if it always occurs at the same model time/date) or if it occurs at different times and dates in the simulation). A persistent error could indicate a missing or corrupted data file, or a flaw in the scientific algorithm being used. Non-persistent errors (i.e. those that don't happen at the same model date & time) may indicate memory errors, such as array-out-of-bounds, segmentation faults, or that the code is using more memory than is available.

Please see our Common GEOS-Chem errors wiki page, which contains strategies for recognizing and fixing several commonly-encountered error conditions. If you still cannot determine the source of your error, please contact the GEOS-Chem Support Team and provide a detailed description of your error.

Can I run two GEOS-Chem jobs simultaneously?

Timmy Francis wrote:

I would like to know if I can run more than one executables (.geos) by renaming them as .geos1, .geos2 etc. For example using the same restart file, I want to run two simulations, one 'with chemistry' and the other 'without chemistry' after make and rename the executables to geos1 and geos2 and run these in two terminals. Will they interfere with each other and affect the result?

Bob Yantosca replied:

I recommend creating separate run directories for each executable. You can place the identical restart file and input files into each run directory. Then in one run directory you can turn on chemistry in input.geos, and then in the other run directory, you turn off chemistry in input.geos. If you run the GEOS-Chem executables in two separate directories, you will ensure that one executable will not overwrite the files that the other executable creates.
In theory, you should be able to run two simultaneous GEOS-Chem executables in two separate run directories. However, I don't know much about your particular machine. You might find that there is not enough memory to run two simulations at the same time. That is not a problem with GEOS-Chem, but with your system (and is something that the GEOS-Chem Support Team wouldn't be able to help you with).
I would recommend talking with your local IT department to find out how much memory etc. is available to you, and if you would be able to run two simulations at the same time. I think a 4x5 full chemistry simulation takes 2-3 GB of memory, and a 2x2.5 simulation can take up to 8GB of memory.

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

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