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, Philippe Le Sager, and Claire Carouge 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, Philippe, or Claire. 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.

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

Here is the contact information for Bob, Philippe, and Claire:

Name Title Group email Individual email Phone FAX
Bob Yantosca Software Engineer geos-chem-support@as.harvard.edu yantosca@seas.harvard.edu 617-496-9424 617-495-4551
Philippe Le Sager Research Associate geos-chem-support@as.harvard.edu plesager@seas.harvard.edu 617-496-9428 617-495-4551
Claire Carouge Research Associate geos-chem-support@as.harvard.edu ccarouge@seas.harvard.edu 617-495-2893 617-495-4551

Please send any and all GEOS-Chem related inquiries to the group email geos-chem-support@as.harvard.edu. This will send your email to Bob, Philippe, and Claire without you having to address your email to them individually.

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!)

We 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 GEOS-Chem Resources Page.

We invite you to read our document on User Resources, Code Development Guidelines, and Debugging Tips.

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, ...)

Subscribing to the GEOS-Chem email lists:

NOTE: If you are having problems subscribing to the GEOS-Chem email lists, please contact Bob, Philippe, and Claire at geos-chem-support@as.harvard.edu.

GEOS-Chem email list

To subscribe to the GEOS-Chem email list, please send an email to geos-chem-request@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@seas.harvard.edu

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

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@seas.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@seas.harvard.edu

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@seas.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@seas.harvard.edu

PLEASE 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.

GEOS-Chem website

The GEOS-Chem website is located at http://www.as.harvard.edu/ctm/geos/.

From this website you may:

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.

Also, please take a minute to read the GEOS-Chem management charter. This document outlines the responsibilities for all GEOS-Chem users.

PLEASE 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.

GEOS-Chem public wiki

The GEOS-Chem public wiki (i.e. this wiki) is located at: http://wiki.seas.harvard.edu/geos-chem/.

This wiki is meant to facilitate communication between GEOS-Chem users and developers. The following informaton is posted on the wiki:

  • General information about GEOS-Chem
  • Getting started with GEOS-Chem
  • Technical Information
  • Information about the specifics of:
    • Chemistry mechanism
    • Emissions
    • Aerosols
    • Diagnostics
    • Mercury
  • Machine and portability issues
  • Bugs and fixes
  • Information about met fields
  • Data Visualization and Analysis

We invite all GEOS-Chem users to register for the wiki by clicking the "create account" link at the top right corner of the screen. Only registered users may edit the wiki, but anyone without an account may read the wiki pages.

You can let the GEOS-Chem wiki inform you of recent updates to the site via RSS. Click here to find out how. You will never miss a discussion!

NOTE: Only registered users may edit the wiki. Please do not edit wiki pages unless you have new information to contribute!

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
login: anonymous
password: your email address
cd pub/geos-chem

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

HDF/
data/
evaluation/
internal_releases/
mean_OH/
patches/
standard_releases/

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

Directory Description
/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/ 2x2.5 emissions and other data files
/data/GEOS_2x2.5/GEOS_1/YYYY/MM GEOS-1 2x2.5 met data
/data/GEOS_2x2.5/GEOS_S/YYYY/MM GEOS-STRAT 2x2.5 met data
/data/GEOS_2x2.5/GEOS_3/YYYY/MM GEOS-3 2x2.5 met data
/data/GEOS_2x2.5/GEOS_4_v4/YYYY/MM GEOS-4 2x2.5 met data (late-look)
/data/GEOS_2x2.5/GEOS_4_flk/YYYY/MM GEOS-4 2x2.5 met data (1st-look)
/data/GEOS_2x2.5/GEOS_4_5/YYYY/MM GEOS-5 2x2.5 met data
   
/data/GEOS_4x5/ 4x5 emissions and other data files
/data/GEOS_4x5/GEOS_1/YYYY/MM GEOS-1 4x5 met data
/data/GEOS_4x5/GEOS_S/YYYY/MM GEOS-STRAT 4x5 met data
/data/GEOS_4x5/GEOS_3/YYYY/MM GEOS-3 4x5 met data
/data/GEOS_4x5/GEOS_4_v4/YYYY/MM GEOS-4 4x5 met data (late-look)
/data/GEOS_4x5/GEOS_4_flk/YYYY/MM GEOS-4 4x5 met data (1st-look)
/data/GEOS_4x5/GEOS_5/YYYY/MM GEOS-5 4x5 met data
   
/evaluation Plots from 1-yr benchmark simulations
/HDF Contains user code for reading HDF and HDF-EOS data files
/NRT-ARCTAS Contains output from the GEOS-Chem Near-Real-Time simulations for ARCTAS
/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.

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

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?
    • Turn off operations (e.g. transport, emissions, etc.) one at a time and run again
  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 for IFORT compiler) 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

Reporting GEOS-Chem bugs and problems

If you should encounter a bug or a problem running GEOS-Chem, then please send an email to geos-chem-support@as.harvard.edu with a description of the problem. Please include the following information:

GEOS-Chem Version Number (e.g. v8-01-01)
Met field type (e.g. GEOS-3, GEOS-4, GEOS-5, 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 to diagnose the problem without seeing the log file output.