GEOS-Chem welcome letter for new users

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Welcome to the GEOS-Chem user community! Here is a quick guide to getting started:

GEOS-Chem programming staff

Bob Yantosca (Software Engineer) and Philippe Le Sager (Research Associate) are responsible for developing and maintaining the GEOS-Chem source code for the user community. They are available during regular business hours (M-F, 9AM-5PM ET).

The general rule of thumb is that if you have a question about the GEOS-Chem code itself, or if your question deals with a programming or coding matter, then you should ask Bob and Philippe. On the other hand, if you have a question about a scientific matter, a data source, etc., then you should direct your question to the person(s) who have worked on that particular topic.

For a list of GEOS-Chem users and their primary areas of research, please visit the GEOS-Chem People & Projects page:

    http://www.as.harvard.edu/ctm/geos/

Of course, if you do not know whom is the best person to ask, then feel free to contact Bob and Philippe, and they will be happy to forward your query to the proper person.

Contact information for Bob & Philippe is listed below:


                          Email                  Phone           FAX

Bob Yantosca yantosca@seas.harvard.edu 617-496-9424 617-495-4551 Philippe Le Sager plesager@seas.harvard.edu 617-496-7446 617-495-4551


(1a) Expectations and responsibilities


We expect that each GEOS-Chem user will possess at least some familiarity with the following:

  • The Fortran programming language (F77 OK, F90 preferred)
  • IDL (preferred), or other graphics software (e.g. Splus, Matlab)
  • The Unix environment (i.e. commands, file paths, etc.)
  • Unix scripts (not strictly required but is very helpful to know!)

Bob & Philippe cannot provide you with general instruction in programming languages or answer general programming questions. We would like to invite you to view to view the list of tutorials and other relevant resources that are listed on the GEOS-Chem web page at:

    http://www.as.harvard.edu/ctm/geos/geos_resources.html

Also please note:

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %%%   GEOS-Chem cannot be used in a Windows (XP/Vista) environment!   %%%
  %%%          You will need a Unix-like operating system !!!           %%%   
  %%%        (e.g. IRIX, Sun/Solaris, Linux, Ubuntu, Fedora, ...)       %%%
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

(2) Subscribing to the GEOS-Chem email lists:

===================================================================

(2a) GEOS-Chem email list


To subscribe to the GEOS-Chem email list, please send an email to:

    geos-chem-requests@geos.as.harvard.edu

with the word "subscribe" in the subject line. You should receive an automatic reply with more instructions.

All GEOS-Chem users should subscribe to the GEOS-Chem email list because information about new model versions, bug fixes, and other relevant information will be announced to the GEOS-Chem user community via email.

To send an email to all of the GEOS-Chem list members, use the address:

    geos-chem@geos.as.harvard.edu

There are also two "specialty" mailing lists that will be of interest to some (but probably not all) GEOS-Chem users:


(2b) GEOS-Chem Aerosols email list


People who are using GEOS-Chem to perform aerosol simulations should also subscribe to the GEOS-Chem aerosol email list. To subscribe, please send an email to:

    geos-chem-aerosol-requests@geos.as.harvard.edu

with the word "subscribe" in the subject line. You should receive an automatic reply with more instructions.

To send an email to all of the GEOS-Chem-Aerosol list members, use the address:

    geos-chem-aerosol@geos.as.harvard.edu


(2c) GEOS-Chem Adjoint & Data Assimilation email list


Likewise, those users who are working on the Adjoint of GEOS-Chem and/or on using GEOS-Chem for data assimilation should subscribe to the GEOS-Chem Adjoint email list. To subscribe, please send an email to:

    geos-chem-adjoint-request@geos.as.harvard.edu

with the word "subscribe" in the subject line. You should receive an automatic reply with more instructions.

To send an email to all of the GEOS-Chem-Adjoint members, use the address:

geos-chem-adjoint@geos.as.harvard.edu

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%% NOTE: If you wish to send an email message to the rest of the     %%%
 %%% people on one of the above GEOS-Chem mailing lists, then please   %%%
 %%% be sure to send your email from the same address with which you   %%%
 %%% subscribed to the list.  Otherwise your email may bounce back to  %%%
 %%% you.                                                              %%%
 %%%                                                                   %%%
 %%% The GEOS-Chem mailing lists are set up to reject emails from      %%%
 %%% non-list members.  This is done in order to prevent spam.         %%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


(3) GEOS-Chem website:

===================================================================

The GEOS-Chem website is located at:

    http://www.as.harvard.edu/ctm/geos/

From this website you may:

    - Download the GEOS-Chem source code and run directories
    - Read the online GEOS-Chem User's Guide
    - See which years of meteorological data are available
    - Access GEOS-Chem-related publications
    - View online presentations from GEOS-Chem user meetings
    - Link to the GEOS-Chem Near-Real-Time simulation website
    - See a list of who is using GEOS-Chem at other institutions
    - Obtain information about the GAMAP visualization package

We also ask that you provide your contact information, a list of people who will be using GEOS-Chem, and a short description of your research for the "GEOS-Chem People and Projects" page. See:

    http://www.as.harvard.edu/ctm/geos/geos_people.html

for examples.

You will be asked for a password when downloading the source code, run directories, and some output plots from the GEOS-Chem website. The password is "geos".

Also, please take a minute to read the GEOS-Chem management charter

    http://www.as.harvard.edu/ctm/geos/geos_charter.html

which outlines the responsibilities for all GEOS-Chem users.

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%% NOTE: At this time, the GEOS-Chem User's Guide is only viewable   %%% 
 %%% in HTML.  This has not been saved into PDF format at this time.   %%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


(4) GEOS-Chem data directory access:

===================================================================

The GEOS-Chem source code, data and meteorological field directories may be accessed by anonymous FTP from

    ftp ftp.as.harvard.edu
    cd pub/geos-chem

The geos-chem directory is further divided into the following subdirectories:

    1yr_benchmarks
    HDF/
    data/
    internal_releases/
    mean_OH/
    patches/
    standard_releases/

Here is a quick look at the contents of these subdirectories:

/data  : Root data directory

/data/GEOS_1x1  : 1x1 global grid emissions etc. files

/data/GEOS_1x1_CH  : 1x1 China-nested grid emissions etc files /data/GEOS_1x1_CH/GEOS_3  : 1x1 China-nested grid GEOS-3 met fields

/data/GEOS_1x1_NA/  : 1x1 NA-nested grid emissions etc files /data/GEOS_1x1_NA/GEOS_3  : 1x1 NA-nested grid GEOS-3 met fields

/data/GEOS_2x2.5/  : 2x25 emissions and other data files /data/GEOS_2x2.5/GEOS_1/YYYY/MM  : GEOS-1 2 x 2.5 met data /data/GEOS_2x2.5/GEOS_S/YYYY/MM  : GEOS-STRAT 2 x 2.5 met data /data/GEOS_2x2.5/GEOS_3/YYYY/MM  : GEOS-3 2 x 2.5 met data /data/GEOS_2x2.5/GEOS_4_v4/YYYY/MM  : GEOS-4 2 x 2.5 met data (late-look) /data/GEOS_2x2.5/GEOS_4_flk/YYYY/MM : GEOS-4 2 x 2.5 met data (1st-look)

/data/GEOS_4x5/  : 4x5 emissions and other data files /data/GEOS_4x5/GEOS_1/YYYY/MM  : GEOS-1 4 x 5 met data /data/GEOS_4x5/GEOS_S/YYYY/MM  : GEOS-STRAT 4 x 5 met data /data/GEOS_4x5/GEOS_3/YYYY/MM  : GEOS-3 4 x 5 met data /data/GEOS_4x5/GEOS_4_v4/YYYY/MM  : GEOS-4 4 x 5 met data (late-look) /data/GEOS_4x5/GEOS_4_flk/YYYY/MM  : GEOS-4 4 x 5 met data (1st-look)

/1yr_benchmarks  : Output, data files, and plots from

                                     various 1-year benchmark simulations
                                     (see the README file for more info)

/HDF  : Contains user code for reading HDF

                                     and HDF-EOS data files

/public_releases  : Directory containing TAR file source

                                     code and run directories for standard
                                     GEOS-Chem public releases

/internal_releases  : Directory containing TAR file source

                                     code and run directories for "internal"
                                     GEOS-Chem releases

patches/  : Directory containing bug-fix software

                                     patches (if necessary)

mean_OH/  : Directory containing 3-D mean OH fields

                                     archived from previous GEOS-Chem
                                     simulations.


(5) GEOS-Chem Code development cycle

===================================================================

How GEOS-Chem code development works:

1. First download a recent standard code version (public or internal) 2. Add your modifications into the code 3. Test your code thoroughly and make sure that it works 4. Contact Bob & Philippe and request that your changes be included

  in the standard code

5. Bob & Philippe will add your changes to the standard code and benchmark it 6. Daniel approves the benchmark results and declares the version APPROVED 7. GOTO 1


(6) GEOS-Chem debugging tips

===================================================================

When your run dies with an error, the most important thing is to try to isolate the place where the error occurs (i.e. does it die in chemistry, in transport, in dry deposition, etc.)

Here are a list of things that you can try if your run dies w/ an error:

1. Look at the log file? Can you tell where the run stopped?

2. If not, re-run with the ND70 diagnostic turned on (debug output)

   - This will print debug output and should let you pinpoint the 
     location of the error

3. Did you run out of time in the queue?

4. Did you modify the standard code?

   - If so, then focus on your most recent changes
   - You should keep a *clean* (unmodified) version for comparison

5. Can you isolate the error to a particular operation?

6. Does the error happen consistently?

   - If the error happens at the same model date & time, 
     it could indicate bad input data
   - If it happened only once, it could be caused by a 
     network problem or other such transient condition

7. Also check for math errors

   - Is there a division by zero, logarithm of negative number, etc?

8. Recompile with -C (or -CB on Altix) option to check for

   array-out-of-bounds errors
   - Out-of-bounds errors can produce segmentation faults

9. When in doubt, print it out!

   - Print out the values of variables in the area where you suspect 
     the error lies
   - Also use "call flush(6)" to flush the output buffer after writing
   - Maybe you will see something wrong in the output

10. When all else fails, USE THE BRUTE FORCE METHOD!

   - Comment out code until you find where the failure occurs


(7) Reporting GEOS-Chem bugs and problems:

===================================================================

If you should encounter a bug or a problem running GEOS-Chem, then please contact both

    Bob Yantosca      (yantosca@seas.harvard.edu)  AND
    Philippe Le Sager (plesager@seas.harvard.edu)

with a description of the problem. Please include the following information:

    GEOS-Chem Version #    (e.g. v7-03-06, v7-04-01            )
    Met field type         (e.g. GEOS-3, GEOS-4, GCAP          )
    Horizontal Resolution  (e.g. 4x5, 2x25, 1x1                )
    Type of Simulation     (e.g. full-chemistry, Hg, Tagged CO )
    Platform               (e.g. Altix, SGI-Origin, Linux box  )
    Compiler               (e.g. IFORT, Sun, SGI Mips, PGI ... )
    Number of Processors
    Diagnostics Requested  (e.g. ND28, ND43, ND45, etc.        )
    Description of problem
    Error Message
   

also, please attach a copy of the log file from the simulation. It is very difficult for us Bob & Philippe to diagnose the problem without seeing the log file output.


Regards,

Bob Yantosca yantosca@seas.harvard.edu

Philippe Le Sager plesager@seas.harvard.edu