GEOS-Chem Newsletter Fall 2011
Dear GEOS-Chem Users,
We apologize for not getting a newsletter out sooner. We have therefore combined several news items into a Fall 2011 newsletter. This issue is also the offical notification of the release of GEOS-Chem v9-01-02.
The GEOS-Chem Support Team
- 1 GEOS-Chem Steering Committee
- 2 GEOS-Chem Working Groups
- 3 GEOS-Chem Support Team
- 4 Release of GEOS-Chem v9-01-02
- 5 Submitting source code updates for GEOS-Chem
- 6 Unresolved issues in GEOS-Chem
- 7 GEOS-Chem v9-01-03
- 8 Grid-Independent GEOS-Chem update
- 9 Met field update
- 10 GEOS-Chem reference
GEOS-Chem Steering Committee
The GEOS-Chem Steering Committee met via telecon on November 9, 2011. We invite you to read the meeting minutes.
The next GEOS-Chem Steering Committee telecon will take place on February 15, 2012 at 10:00 AM ET. Please set your calendars. If you have any issues that you would like the Steering Committee to address, please contact your GEOS-Chem Working Group Co-Chairs.
GEOS-Chem Working Groups
We invite you (especially if you are a new GEOS-Chem user) to join the GEOS-Chem Working Group that is most relevant to your research. You can also sign up for the relevant Working Group email list(s) so that you will receive periodic updates from your group.
GEOS-Chem Support Team
Here is some news regarding the GEOS-Chem Support Team:
- Bob Yantosca recently began working on the code to process GEOS-5.7.2 data. He also oversees general GC development and the development of the grid-independent GEOS-Chem project.
- Michael Long is primarily working on the grid-independent GEOS-Chem project.
- Melissa Payer has completed merging Havala Pye's updates for SOA + nonvolatile POA into GEOS-Chem, which we will add to version v9-01-03. She has also been working on general GC development tasks (i.e. code merging, generating 1-month and 1-year benchmark simulations, user support, documentation, etc.).
- Matt Cooper (Dalhousie) has been working on regridding the MERRA met data to 2 x 2.5 degree resolution (see below). He has also begun replacing the existing regridding routines in GEOS-Chem with the MAP_A2A regridding package (which is what is currently use for regridding the GMAO met fields).
New Support Team position
GEOS-Chem Support Team/ Harvard University. A position is available for a support scientist, scientific programmer, or research assistant to join the GEOS-Chem Support Team in the Atmospheric Chemistry Modeling Group at Harvard (http://acmg.seas.harvard.edu and http://geos-chem.org). GEOS-Chem is a global 3-D model of atmospheric composition used by over 60 research groups worldwide for a very wide range of applications. Tasks will include model development and documentation, targeted research projects, and user support. The position may be filled at the Ph.D., M.S., or B.S. level. A degree in atmospheric science, applied mathematics, or engineering is required. Experience in scientific programming including knowledge of FORTRAN and UNIX is a must. Please email a CV, contact information for three references, and 1-paragraph statement of interest to (Prof. Daniel J. Jacob), School of Engineering and Applied Science, Harvard University. Harvard University is an equal opportunity / affirmative action employer.
Release of GEOS-Chem v9-01-02
We are happy to announce the official release of GEOS-Chem v9-01-02! This version is the first GEOS-Chem version to be rigorously tested with our new benchmarking protocol.
What's new in GEOS-Chem v9-01-02?
GEOS-Chem v9-01-02 contains some important new updates:
- GFED3 biomass burning emissions
- NOTE: at this time, only the monthly mean GFED3 product is available.
- RETRO anthropogenic VOC emissions inventory
- Now use 0.03 cm/s for aerosol drydep velocity when over ice and snow
- Implemented seasonality for NH3 emissions in Streets 2000 inventory
- Overhaul of aerosol optical depth diagnostics to remove inconsistencies
- Removal of legacy code constructs to facilitate grid-independent GEOS-Chem model development
- Several bug fixes
- Updated GEOS-Chem Online User's Guide
In addition, many new features in the offline Hg simulation have been standardized, including GEIA anthropogenic Hg emissions for 2005. For more information, please see the GEOS-Chem v9-01-02 wiki page.
We recommend that GEOS-Chem users upgrade to GEOS-Chem v9-01-02 as soon as convenient. For downloading instructions, please visit Chapter 2 of the GEOS-Chem Online User's Guide. We do not maintain older versions of GEOS-Chem and they will eventually become obsolete.
Also note that there are several new new data directories and files that need to be downloaded before using GEOS-Chem v9-01-02.
Validating GEOS-Chem v9-01-02
We tested GEOS-Chem v9-01-02 rigorously according to the new benchmarking protocol developed at the 5th International GEOS-Chem Meeting (aka IGC5).
1-month benchmark simulations
Every time a significant change was added to the source code, the GEOS-Chem Support Team performed a 1-month benchmark simulation. The person who initiated the source code change had to examine the 1-month benchmark output plots (which are posted on Harvard's FTP site) and fill out a Benchmark Assessment Form. Final approval for each 1-month benchmark was given by Model Scientist Daniel Jacob after the GEOS-Chem Steering Committee also had a chance to examine and comment on the benchmark output.
Please see our GEOS-Chem v9-01-02 benchmark history wiki page for a complete list of 1-month benchmarks that were done during the validation process.
1-year benchmark simulations
In accordance with the new benchmarking protocol, the GEOS-Chem Support Team also performed two 1-year NOx-Ox-HC-aerosol full-chemistry simulations. Each simulation used GEOS-5 met fields at 4° x 5° resolution for the year 2005 (with a 1-year spinup):
- v9-01-02-Run0 (with RETRO and GFED3 emissions turned off)
- v9-01-02-Run1 (with RETRO and GFED3 emissions turned on)
Comparing v9-01-02-Run1 to v9-01-02-Run0 is a clean comparison of the impact of the RETRO and GFED3 emissions inventories.
To view the output plots from each of these 1-year full chemistry simulations, point your browser to:
Rn-Pb-Be benchmark simulations
In addition to the 1-year full-chemistry benchmark simulations, the GEOS-Chem Support Team ran a 1-year Rn-Pb-Be benchmark simulation. Hongyu Liu computed the budget of Pb210 and the budget of Be7 from these simulations and compared them to prior versions.
Helen Amos ran several Rn-Pb-Be simulations in order to investigate differences in wet scavenging when using GEOS-5 vs. MERRA met fields. We invite you to view the comparison plots and comparison budgets that Helen created.
Submitting source code updates for GEOS-Chem
The GEOS-Chem Support Team would like to give GEOS-Chem users a couple of guidelines for submitting source code updates:
Send source-code updates in Git-compatible form
We enforce strict version control with the Git source code management software. With Git, all updates made to the GEOS-Chem source code can be easily logged and tracked. Because there are many changes being added to GEOS-Chem concurrently (both scientific changes and structural changes related to the grid-independent GEOS-Chem), the ability to keep track of several different lines of model development will be crucial.
Therefore, in order to eliminate confusion and potential sources of error, we prefer to receive any new source-code updates for GEOS-Chem in Git-compatible form. One way to do this is to create a Git patch file, which we can easily be easily ingested into the standard GEOS-Chem code repository. Or, if you prefer, you can provide us with a copy of your source code directory, from which we can pull your changes directly into the standard GEOS-Chem repository.
We would like to discourage GEOS-Chem users from sending us an email with a verbal description (i.e. modifications at specific line numbers) of the source-code changes to be made. Experience has shown that this method can lead to transcription errors. Also, please keep in mind that the version of the code that we have under development may differ drastically from your code, so line numbers will not match up.
Check your work
We would also like to remind all developers to please check your source-code updates for hidden errors before submitting them for inclusion into GEOS-Chem. Here are some suggestions:
- Compile with the BOUNDS=yes compiler option and run for 1 or 2 days. This will check to see if you have introduced any array out-of-bounds errors.
- Check to see if the changes you made do not conflict with any other grids (especially the nested-grid simulations)
- Check for documentation errors
- Check for numerical or floating-point math errors
- Try to adhere to standard Fortran syntax. Consult the GEOS-Chem Style Guide
- Avoid Fortran-77 coding constructs such as COMMON, DATA, EQUIVALENCE statemetnts, BLOCK DATA, etc. We are removing legacy code constructs such as these in order to facilitate construction of the grid-independent GEOS-Chem.
Unresolved issues in GEOS-Chem
For your convenience, we have created a wiki page that lists all currently unresolved issues in GEOS-Chem. These issues may be bugs or deficiencies in data and/or scientific algorithms. You should know about two issues in particular:
RETRO anthropogenic ethane emissions are too low
Bess Corbitt found that the anthropogenic ethane emissions in the RETRO inventory are much too low. Please see this wiki post for more details.
We will replace the RETRO ethane with the ethane emissions from Yaping Xiao's offline C2H6 simulation. This fix is slated for GEOS-Chem v9-01-03 or later.
Numerical noise in ISORROPIA II
Daven Henze noted that the ISORROPIA II aerosol thermodynamic equilibrium package does not produce the same results on single processor as on multi processor. Daven wrote:
- There is an unidentified OpenMP error which contributes to differences shown [in the v9-01-02a 1-month benchmark], as confirmed by independent tests of consecutive evaluations of a single executable compiled with and without parallelization. The impacts of this OpenMP error are typically less than a fraction of a percent, and negligible in terms of absolute value, with the exception of NIT and NH3. This is an issue to investigate further.
Bob Yantosca did extensive testing, which revealed that the numerical noise caused by ISORROPIA creeps into GC full-chemistry simulations of longer than about 2 weeks. See this PDF presentation for more details.
At present, this issue is still under investigation by Shannon Capps at Georgia Tech. If a new version of ISORROPIA is provided, then the GEOS-Chem Support Team will install that into GEOS-Chem.
Recommendation of the GEOS-Chem Support Team:
- Most GC users will not have to do anything. The numerical noise is small enough that it should not affect the results of long simulations.
- However, you should turn off ISORROPIA during your testing & debugging phase, if:
- If you are doing structural coding (i.e. rewriting source code but not changing any science), or
- If you expect to see identical results before and after your updates have been made
The next release of GEOS-Chem will be denoted GEOS-Chem v9-01-03. v9-01-03 will include many new scientific updates, most notably:
- Updated acetone chemistry
- OVOC dry deposition updates
- Improved sea salt aerosol emission & deposition
- Updated secondary organic aerosol chemistry
- PARANOX model for evolution of ship exhaust plumes
- Various emissions updates
- Updating photolysis to FAST-JX
- ... and more updates ...
For a complete list of updates that are slated to go into v9-01-03, please see this wiki post. We will keep you posted as to the progress of v9-01-03.
Grid-Independent GEOS-Chem update
As you may know, we have an ongoing project with NASA where we are attempting to interface GEOS-Chem into the NASA GEOS-5/GCM. This project (formerly known as the "Column Code") is now called the Grid-independent GEOS-Chem project. Our goal is to remove all hardwired specifications for the horizontal grid and to pass those down as arguments from a top-level calling routine. This step is necessary in order to let GEOS-Chem be driven by a GCM.
GEOS-Chem Support Team Member Mike Long is doing much of the coding for this project. Here is a status report:
Mike Long recently returned from a trip to NASA/GSFC. Mike consulted with Arlindo da Silva to begin the Grid-Independent GEOS-Chem code implementation within the GEOS-5 GCM. The Earth System Model Framework (ESMF) sandbox test code that Arlindo and Bob Yantosca had developed will provide the template for testing and ultimate completion of the Grid Independent GEOS-Chem at Harvard. The "ESMF sandbox" code simulates the computational environment at NASA/GSFC. This will allow the initial Grid-Independent model development work to be done locally at Harvard without having to have access to NASA machines.
The Grid-Independent code is being bootstrapped into the standard mainline GEOS-Chem source code through preprocessor switches. Unless these switches are intentionally activated, the typical GEOS-Chem user SHOULD never have to interact with the Grid-Independent code modifications. Furthermore, most or all of the Grid-Independent coding and ESMF interface will be at a high-level such that it will be invisible to GEOS-Chem users and developers. There will be no Grid-Independent functionality in the v9-01-02 release (although several modifications have been made in v9-01-02 in order to better implement Fortran-90 coding standards into GEOS-Chem).
The advantage of using preprocessor switches to block off Grid-Independent-specific code is that this approach will allow GEOS-Chem users to decide whether they want to invoke the ESMF and MPI functionality or not. During the transition to the Grid-Independent model, some GEOS-Chem users (especially those who utilize the simpler offline chemistry simulations) may wish to continue running GEOS-Chem in serial mode (i.e. with OpenMP) and without having to install ESMF or MPI libraries. Our approach will make this possible and will enable GEOS-Chem users to continue their research without interruption.
List of ongoing tasks
Here is a list of currently-ongoing tasks and their state of completion:
- Emissions: The Grid-Independent treatment of emissions routines is nearly complete. In the development code, all emissions will be stored in a single emissions tendency array with global scope. Emissions routines will no longer interact with the tracer (STT) or species (CSPEC) arrays directly, but will instead update the appropriate slot of the emissions tendency array. The emission tendency array will then be passed to the chemical solver setup routine (setemis.F) so that the emissions can be entered into the reaction rate matrix. Also, the units of all emissions will be standardized.
- Chemistry: The primary development effort in the chemistry routines is tied into reading and writing to/from generalized tracer & species arrays. This is progressing in tandem with Task (1). However, restructuring the spaghetti-esque legacy code routines has proven to be challenging. The work is ongoing.
- ESMF wrapping: Development of the ESMF interface wrappers is ongoing and the system is not yet capable of a full 'sandbox' test simulation. This is due in large part to the state of Tasks (1) and (2) listed above. The ESMF wrapper code is, as stated above, drawing heavily from column-model work and it already has matured somewhat.
There are a few major tasks that remain:
- File I/O libraries: These will be necessary for emissions files, history & diagnostic file writing, met fields, etc. for both the GEOS-5 coupled and the MPI-Parallel GEOS-Chem CTM. ESMF provides good library tools for this, while Bob & Philippe Le Sager had worked on some NetCDF routines that were not implemented; but are proving useful.
- Transport & Physics: It is becoming clear that we may be able to preserve the current structure of the physics and transport routines for use by GEOS-Chem as an MPI-parallel model. We won't make any predictions about scalability at this time.
General timeline to completion
Here is our estimate of the completion dates for the phases of Grid-Independent model development work:
- Standalone Grid-Independent model (Fortran-only): The Grid-Independent code may be in working form by the end of November or December. We do not expect to pass out any of the interim code to scientific developers until after completing a passing benchmark. Once the Grid-Independent code modifications have proven to be mature, it will be incorporated into the standard repository (possibly in time for the v9-01-03 release).
- ESMF-wrapped Grid-Independent model: We expect this to be completed by mid-2012.
- Stand-alone Grid-Independent model (parallel, with ESMF/MPI): This is not a priority at this time; therefore we cannot make a prediction as to when this will be completed. This task is contingent on the completion of the standalone GI (Task 1 above) and the ESMF wrapping (Task 2 above).
Met field update
GEOS-5.7.2 data product
GMAO recently updated to the GEOS-5.7.2 data product. This data will be 0.25° x 0.3125° lon horizontal resolution. This will supersede the older GEOS-5.2.0 product, which was 0.5° lat x 0.666° lon horizontal resolution.
The file naming convention, timestamps, and individual data fields used by GEOS-5.7.2 data are very similar to what is used in the MERRA data set. Therefore, the MERRA data processing software can be used as a starting point. However, it should be noted that the data file format for GEOS-5.7.2 is netCDF4, whereas previous GEOS data products used HDF4-EOS. This will require some rewriting of source code.
- 18 Jul 2011: GMAO released the file specification document for the GEOS-5.7.2 (v1.2) data. This document describes the file naming structure, time stamp structure, and which fields are contained in which files.
- 22 Aug 2011: GMAO sent sample GEOS-5.7.2 data to Harvard in order to test the filetransfer.
- Late August 2011: GMAO turned on the live GEOS-5.7.2 data stream.
- Late October 2011 (need to confirm date): GMAO turned off the GEOS-5.2.0 data stream.
Interfacing GEOS-5.7.2 data with GEOS-Chem
At present, Bob Yantosca has completed the following tasks:
- Created pages on the GC wiki with information about the GEOS-5.7.2 data.
- Contacted GSFC to establish a data subscription for the GEOS-5.7.2 data.
- Installed netCDF4 and HDF5 libraries locally. These are necessary for reading the GEOS-5.7.2 raw data files from disk. The netCDF4 library is an update from the previous (and more commonly used) netCDF-3 library. netCDF4 requires the HDF5 library to also be installed.
- Written scripts to transfer GEOS-5.7.2 data from NASA to Harvard and to automate the data download process.
- Created a new Git repository for GEOS-5.7.2 data processing code and scripts.
- Completed initial source code preparation and documentation. The source code is based on the existing data processing code for MERRA, with modifications for netCDF data I/O. Regridding will be done with the MAP_A2A algorithm (as was used for the regridding of previous GMAO data products).
GEOS-5.7.2 grids and time periods
We plan to store the GEOS-5.7.2 following data at Harvard (which will be downloadable by the community). Data will be processed for Aug 2011-onward. Priority will be given to these grids:
- Global 2° x 2.5°
- Global 4° x 5°
- SEA4CRS Nested grid 0.25° x 0.3125° : 20S-50N; 60E-150E
- 0.5° lon x 0.625° nested grid (exactly 2x the resolution of GEOS-5.7.2)
Consistent with our established nested grid protocol, we will distribute the GEOS-5.7.2 data processing code & scripts to any user groups who wish to pull the nested data themselves.
GEOS-5.2.0 data product
Production of GEOS-5 data product, aka GEOS-5.2.0, (at 0.5° x 0.666° resolution) ceased in Fall 2011. However, GEOS-5.2.0 data for Jan 2004 - Oct 2011 may still be accessed directly from NASA's GES-DISC.
Please note: Presently, the Harvard data server (ftp.as.harvard.edu) contains GEOS-5 met data thru July 31, 2010 regridded to the following GEOS-Chem resolutions:
- 4° x 5°
- 2° x 2.5°
- 0.5° x 0.666° nested China
- 0.5° x 0.666° nested North America
You may download data for August 1, 2010 and onwards from the Dalhousie data server (rain.ucis.dal.ca). In addition, the Dalhousie server contains met data for the 0.5° x 0.666° Europe nested grid.
MERRA data product
The MERRA data product is still being produced. We have currently processed the 30-year data archive (1979-2010) for GEOS-Chem to 4° x 5° resolution. Matthew Cooper (Dalhousie U.) is working on regridding MERRA to 2° x 2.5° resolution.
Several of you have asked us about how to obtain the "raw" 0.5° x 0.666° MERRA met field data for your own research projects. NASA's GES-DISC department has created a user interface from which you can request "subsetted" data files (i.e. data files that have been trimmed down to a specific geographic region and/or contain a reduced number of data fields). You can then download the subsetted files via FTP file transfer to your own disk space. For more information, please see the NASA GES-DISC user interface for requesting subsetted MERRA data.
Please take a moment to review your group's entry on the GEOS-Chem People and Projects web page. Kindly inform the GEOS-Chem Support Team if anyone has recently joined or left your research group.
We invite you to consult our Credits and References web page for guidance on how to give credit to GEOS-Chem developers in publications. Proper crediting and citation is critical for the good functioning of the GEOS-Chem community.
We encourage all GEOS-Chem code developers and users to check the wiki frequently, as this is the place where the latest information about GEOS-Chem will be posted. The wiki is designed to be a two-way street of communication. Users should feel free to add content to the wiki pages that are most closely related to their research.
In particular, the GEOS-Chem Support Team has started a new effort to make sure that all 3rd-party code and data that is submitted into GEOS-Chem has a corresponding wiki page. This will ensure that all information can be shared transparently.
Please see the Recent Changes wiki page to see which wiki pages have been updated.
Finally, if you have not already done so, consider signing up for automatic wiki notification. You will be updated whenever someone modifies the GEOS-Chem wiki...you'll never miss a discussion!
Subscribing to the GEOS-Chem email lists
We use several email lists to share information among the GEOS-Chem user community:
- We send information about new GEOS-Chem releases, bug fixes, and other notices of importance to the the GEOS-Chem "general" email list (firstname.lastname@example.org)
- Each GEOS-Chem Working Group uses its own email list to exchange information between group members.
We invite you to join the Working Group that is most appropriate to your research, and to subscribe to the relevant email list. Consider joining more than one Working Group (and email list) if your research spans several topics.
For complete instructions on how to subscribe to (or unsubscribe from) the GEOS-Chem email lists, please see our Subscribing to the GEOS-Chem email lists wiki page.
We have set up several GEOS-Chem search engines which will let you search for information in the GEOS-Chem website, wiki, and manual pages.
You can also search the GEOS-Chem wiki by means of the search box in the left column. It is often more efficient to search for a topic rather than to follow links down from the main page.
--Bob Y. 12:52, 9 December 2011 (EST)