GEOS-Chem Newsletter Winter 2013

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Dear GEOS-Chem users,

We are happy to bring you the Winter 2013 edition of the GEOS-Chem Newsletter! Please read below to find out the latest goings-on in the GEOS-Chem community.

Sincerely,

The GEOS-Chem Support Team
geos-chem-support@as.harvard.edu

Last call to register for the 6th International GEOS-Chem Meeting!

Daniel Jacob wrote:

Dear colleagues and GEOS-Chem users:
Please take note of the January 31 registration deadline for the 6th International GEOS-Chem Meeting (IGC6) at Harvard University on May 6-9, 2013. Go to the meeting website meeting.geos-chem.org to register. We expect the meeting to be oversubscribed. You will hear of acceptance in mid-February.
Daniel Jacob

GEOS-Chem Model Scientist

GEOS-Chem Steering Committee

GCSC Meetings

The GEOS-Chem Steering Committee (GCSC) last met on Tuesday January 8th, 2013. We invite you to read the meeting minutes.

The next GCSC telecon will take place in April 2013, date TBD.

GCSC Elections

Daniel Jacob wrote:

Dear GEOS-Chem user:
A number of GEOS-Chem Working Group Co-Chair positions on the GEOS-Chem Steering Committee (GCSC) will become available as terms end in May. New co-chairs will be elected at the 6th International GEOS-Chem Meeting. Please let me know if you are interested in serving. Click HERE to learn more about the functions and responsibilities of the GCSC and about the different WGs. We eagerly encourage qualified candidates to apply. We are particularly interested in maintaining the international character of the GCSC.
Daniel Jacob
GEOS-Chem Model Scientist
for the GCSC

GEOS-Chem Support Team

Here is a summary of GEOS-Chem Support Team activities:

  1. Bob Yantosca has been working on the code to process GEOS-5.7.2 data (see below). He also oversees general GC development and the development of the Grid-Independent model.
  2. Michael Long is primarily working on the Grid-Independent GEOS-Chem project (see below).
  3. Melissa Payer has been working on general GC development tasks (i.e. code merging, generating 1-month benchmark simulations, user support, documentation, etc.).
  4. 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).

GEOS-Chem v9-02 news

Development

As of this writing (09 Jan 2013), we have completed the following benchmarks for GEOS-Chem v9-02:

We have completed the following benchmarks:

  1. v9-02a: Correction for PBL heights
  2. v9-02b: New soil NOx emissions module + minor bug fixes
  3. v9-02c: Updates for the Hg simulaton: emissions + kinetics
  4. v9-02d: Structural updates for the Grid-Independnent GEOS-Chem
  5. v9-02e: Bug fix for regridding of anthro emissions (Streets, NEI2005)

We are still working on the following benchmarks:

  1. The Hg and POPs Working Group is working on a 1-yr Hg benchmark simulation, based on v9-02c.
  2. The Nested Model Working Group is performing a 1-yr simulation for the North American Nested Grid with GEOS-5 met (0.5&deg x 0.666°). They have completed 6 months of the benchmark.

The next set of updates to GEOS-Chem v9-02 shall be chemistry updates, including:

  1. Updating rate constants for consistency with observations
  2. Update to isoprene scheme
  3. Include HO2 uptake onto aerosol
  4. Putting inhibition to N2O5 uptake.

We shall run 1-month and 1-year benchmarks at intermediate points the development in order to better assess how these updates impact the simulation results.

Bugs and fixes

GEOS-Chem v9-02 shall contain fixes for the following bugs and/or technical issues:

  1. Correction for GEOS-5 PBL heights
  2. Bug fixes for tagged CO simulation
  3. Regridding error in NEI2005 emissions
  4. Bug fix for updated CAC emissions
  5. Fixed incorrect loop limits in Br2 emissions code
  6. Bugs in diurnal NOx scaling and biofuel double-counting

Grid-Independent GEOS-Chem

Much of the recent Grid-independent GEOS-Chem (aka GIGC) work has involved restructuring how data flows between routines in the standard GEOS-Chem code. In general, we now make use of derived-type objects to carry data fields instead of referencing arrays from other modules with USE statements. We have been making these types of structural updates concurrently with scientific development in GEOS-Chem in order to avoid the GIGC code from lagging behind the std GEOS-Chem code.

We’ve also streamlined the Earth System Model Framework (ESMF) interface that connects GEOS-Chem to the GEOS-5 GCM. GEOS-Chem now can obtain the following information from the GEOS-5 GCM, via ESMF:

  1. Size of data arrays on each CPU: (IIPAR, JJPAR, LLPAR)
  2. Size of the entire global grid: (IM_WORLD, JM_WORLD, LM_WORLD)
  3. Corner grid box indices on each CPU (I_LO, I_HI, J_LO, J_HI)
  4. Date and time from the GCM
  5. Level edge pressures from the GCM

We’ve also updated the ESMF interface to be consistent with the tracers and species introduced by the latest bromine chemistry updates. (Every time new tracers are added we have to also update the various input files etc. that are used by the ESMF interface.)

We've also updated the various GIGC wiki pages to reflect these recent updates. Please see these pages for details:

  1. Grid-Independent GEOS-Chem
  2. Grid-Independent GEOS-Chem: Chemistry Component
  3. Grid-Independent GEOS-Chem: Emissions Component
  4. Derived type objects used by the Grid-Independent GEOS-Chem
  5. Programming techniques used for the Grid-Independent GEOS-Chem

We recently performed a test simulation of GEOS-Chem in our ESMF “Sandbox” environment, which replicates the connection to the GEOS-5 GCM without having to run the full GCM. We demonstrated that GEOS-Chem could be successfully run within the ESMF environment with MPI parallelization.

Christoph Keller is working on the GIGC Emissions Component, which will run independently of the chemistry. The Emissions Component will combine emissions from several inventories, apply the relevant scale factors, regrid the emissions, and pass them to the GIGC Chemistry Component via the ESMF interface. Christoph has been making use of a new data structure to store emissions. He is also handling disk I/O operations separately from the data structure, which is necessary in order to be run in the ESMF environment. Please see this presentation for further details.

Still to do:

  1. Modify the GIGC code to read data from ASCII input files (i.e. input.geos, globchem.dat, ratj.d) on the root CPU, and to broadcast the data to other CPUs. This is necessary in order to prevent all CPUs on the system from performing disk I/O operations simultaneously.
  2. Bring dry depositions into the ESMF interface. Mike Long has been working on this.
  3. Port the updated GEOS-Chem source code back to NASA/GSFC to allow testing of the GEOS-5/GEOS-Chem combined model on NASA machines.

We anticipate to be able to run a GEOS-5 GCM/GEOS-Chem simulation before the IGC6 meeting in May].

GEOS-5.7.2 met field update

This past summer, NASA/GMAO updated the operational GEOS system from GEOS-5.2.0 to GEOS-5.7.2. Here is a quick summary of the new GEOS-5.7.2 data product:

  1. Horizontal resolution: 0.25° lat x 0.3125° lon (i.e. 1/4° x 5/16°)
  2. Vertical resolution: 72 hybrid layers (identical to the vertical grids used by the GEOS-5.2.0 and MERRA met data products)
  3. Time resolution: Hourly and 3-hourly data (timestamps very similar to MERRA)
  4. Input data format: netCDF-4 (as opposed to HDF4-EOS, used for past GMAO data products)

Bob Yantosca has been preparing GEOS-Chem to run with the new GEOS-5.7.2 met data. He has completed the following tasks:

  1. Added documentation to the GC wiki with information about the GEOS-5.7.2 data.
  2. Activated a “data subscription” for the GEOS-5.7.2 data.
  3. Written scripts to transfer GEOS-5.7.2 data from NASA to Harvard and to automate the data download process.
  4. Finalized the GEOS-5.7.2 data processing/regridding software.
  5. Created a new Git repository for GEOS-5.7.2 data processing code and scripts.
  6. Completed initial modifications in GEOS-Chem to read the GEOS-5.7.2 data.

For more information about the implementation of GEOS-5.7.2 into GEOS-Chem (including a detailed list of all modifications made to individual GEOS-Chem routines), please see the following wiki pages:

  1. GEOS-5.7.2
  2. List of GEOS-5.7.2 met fields
  3. GEOS-5.7.2 implementation details

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:

  1. Global 2° x 2.5°
  2. Global 4° x 5°
  3. SEA4CRS Nested grid 0.25° x 0.3125°: 20S-50N; 60E-150E

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.

One important new feature is that the GEOS-Chem Support Team shall be archiving the processed GEOS-5.7.2 data in netCDF format instead of the traditional binary format (see below for more information).

At present, GEOS-Chem can read the GEOS-5.7.2 met data from within the timestepping loop in the main program for 2° x 2.5°, 4° x 5° global grids and the 0.25° x 0.3125° SEA4CRS nested China grid. Further testing is required to make sure that the individual operations (i.e. convection, deposition, chemistry) will work properly with the GEOS-5.7.2 data.

Bob Yantosca and the SEA4CRS team (Jenny Fisher, Patrick Kim, Lin Zhang, Yuxuan Wang) are coordinating several of the remaining tasks (e.g. regridding emissions data files, debugging, etc.) among themselves.

MERRA met field update

Matt Cooper has been regridding the GMAO MERRA data to 2° x 2.5° resolution at Dalhousie. He will continue the data processing until the full record is completed. He writes:

As for MERRA 2x2.5, I have finished processing the whole data record, and we have 1979-2010 available on our server here at Dal. I've already updated the wiki to indicate that, and have been contacted by a few people already. Feel free to spread the word that we have these met fields available.

Transition to netCDF file format

Several GEOS-Chem users have identified a clear need to migrate GEOS-Chem from the traditional sequential binary file format (aka “binary punch” or “bpch”) to netCDF format. NetCDF is a self-describing file format that allows one to save the data along with any descriptions of the data (field names, units, descriptions. Several software packages for data visualization and analysis support netCDF format.

The GEOS-Chem Support Team recommends migration to netCDF format in order to facilitate the Grid-Independent GEOS-Chem (GIGC) project. As described above, the GIGC seeks to incorporate GEOS-Chem within larger Earth System Models, Climate Models, GCMs, and data assimilation systems. These larger models employ Message Passing Interface (MPI) parallelization in order distribute or “decompose” data among several hundreds or thousands of CPUs.

The current “binary punch” format used by GEOS-Chem is incompatible with MPI parallelization in the sense that small chunks of a binary punch file cannot be read simultaneously across CPUs in a distributed memory environment. Rather, the entire file must be read on each CPU that is executing, thus adding much more file I/O overhead to the system, which in turn negatively impacts model performance and scalability. On the other hand, it is possible to read small chunks from a netCDF file independently on several CPUs simultaneously, thus preserving scalability.

The transition to netCDF file format will involve several steps. We realize that the full transition cannot be achieved overnight. The first step shall be to modify GEOS-Chem to be able to read netCDF data files from disk, starting with the new GEOS-5.7.2 met data product. To this end, Bob Yantosca has installed his NcdfUtilities package into a development version of GEOS-Chem v9-01-03. Bob has also written a Fortran module (“geos57_read_mod.F90”) which calls NcdfUtilities routines to read the GEOS-5.7.2 met data from disk. The netCDF functionality can be activated simply by compiling GEOS-Chem code with an additional switch (NETCDF=yes).

At a later time, in conjunction with the GIGC project, we shall also begin to convert GEOS-Chem’s diagnostic outputs to netCDF format. Fortran code for writing netCDF files is necessarily much more “wordy“ than code for reading from netCDF files because one must supply information (aka “metadata”) about the variables that will constitute each netCDF file. To simplify the coding process for the GEOS-Chem community, Bob Yantosca has included into GEOS-Chem some Perl scripts which will automatically generate the proper Fortran for both writing to and reading from netCDF files.

The Earth System Model Framework environment contains many file I/O and regridding utilities. Once the GIGC code becomes fully compatible with ESMF, we will take advantage of ESMF’s regridding capabilities. During construction of the GIGC, we will need to continue to provide a Fortran-only package for netCDF I/O (cf. Bob Yantosca’s NcdfUtilities, or similar programs).

The migration to netCDF will require that GEOS-Chem end users install the netCDF libraries on their system. We shall provide instructions for installing these libraries on the GEOS-Chem wiki.

The next release of the GAMAP visualization software (v2-16) will feature improved support for reading and plotting data in netCDF files. The GAMAP routines BPCH2COARDS and MAKE_MULTI_NC may be used to convert existing binary punch files to netCDF format.

De-supporting of GEOS-3 meteorology

The GMAO GEOS-3 met data product is now several versions behind the current GMAO operational product (GEOS-5.7.2). The GEOS-3 data period only covered the years 2000-2002 (with some data in 1998).

Bob Yantosca queried the GEOS-Chem user community to see if there were any users who still relied on the GEOS-3 met data for their research. He found that none of the GEOS-Chem users still rely on GEOS-3 meteorology.

Therefore, the GEOS-Chem Support Team recommends that we remove support for GEOS-3 met data from within GEOS-Chem. This will help to clean up the GEOS-Chem source code and remove unnecessary routines and coding constructs which may impede development of the Grid-independent GEOS-Chem.

Other development tasks

Matt Cooper has been working on replacing the traditional GEOS-Chem regridding routines (which sometimes involve two separate regrdidding processes) with the MAP_A2A regridding package. He writes:

I'm making progress on getting MAP_A2A into GEOS-Chem. I have made the switch in some places and now am just working my way through the code finding all the places where it needs to be switched. Hopefully it doesn't take me too much longer.

Downtime at Harvard: Feb 19-23, 2012

The Harvard Atmospheric Chemistry Modeling Group will be moving its computational resources from its existing location into a more modern server room. The transition will take place starting on Sunday Feb 19, 2012 and will take at 3-4 days to complete.

Our sysadmin Jack Yatteau writes:

Downtime:
        1) Sunday, February 19, 16:00. Most services will go down.
        Running jobs on the computational cluster will be rescheduled.
        Minimal services will remain up overnight and go down early Monday
        morning.  Some services might be available Tuesday.  Interactive
        and batch systems should be available by EOB Wednesday 2/22.

        2) Thursday, February 23.  Backup power for our equipment
        will be unavailable for a few hours due to UPS maintenance.
        No downtime is anticipated, but we will not be protected against
        power failure while the work is being performed.

The following services will be unavailable during the transition:

  1. ftp.as.harvard.edu: main FTP site for data downloads
  2. git.as.harvard.edu: Git server for GEOS-Chem source code & run directory downloads
  3. GEOS-Chem web site
  4. GAMAP web site
  5. Jacob Group web site

The GEOS-Chem wiki is hosted on a different server and should not be affected. However, some links to documents on the GEOS-Chem web server will not function during the downtime.

Please plan accordingly. Met data may also be obtained from the Dalhousie server (rain.ucis.dal.ca)

--Bob Y. 11:21, 14 February 2012 (EST)