GEOS-Chem benchmarking

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Objectives

Benchmarking supports the maintenance of GEOS-Chem as a robust state-of-the-science facility with a nimble grass-roots approach and strong version control. Benchmarking has four main objectives:

  1. Document a consistent GEOS-Chem model configuration, and the expected characteristics of that configuration.
  2. Support version control through traceability, and by confirming the expected behavior of model developments submitted by the community.
  3. Track the evolution of the model over the years.
  4. Promote scientific transparency of GEOS-Chem.

Procedure

The GEOS-Chem benchmarking procedure is described below.

  1. Any update to the GEOS-Chem source code or run directories will change the GEOS-Chem version number (X.Y.Z).
  2. Z versions will be released at intervals determined by the GEOS-Chem Support Team (GCST) and may include bug fixes or updates that do not impact the full-chemistry simulation.
  3. Any change impacting the standard full-chemistry simulation will require a Y version change and a dedicated 1-month benchmark. The benchmark results will be posted on the wiki and an email will be sent to the developer(s) and the GEOS-Chem Steering Committee (GCSC).
  4. The developer(s) and GCSC will assess the benchmark results and review a benchmark assessment form on the wiki. If there are any concerns about the benchmark results, the GCST will be notified and further investigation and/or benchmarking may be required.
  5. If the update is for a specialty simulation (e.g. CO2, CH4, Hg), then a further benchmark may be conducted by the appropriate Working Group.
  6. Once the developer is satisfied with the changes in the 1-month benchmark, GEOS-Chem Model Scientist Daniel Jacob will review the results and approve the new internal version.
  7. 1-year full-chemistry and/or transport tracer benchmarks for Y versions will be conducted only if justifiably requested by the developer or by GEOS-Chem Steering Committee members.
  8. Each new major version release (i.e. X version) will be subject to a 1-year benchmark to be inspected by the GEOS-Chem Steering Committee before approval.

List of GEOS-Chem benchmarks

Links to past 1-month and 1-year benchmark simulations can be found on the GEOS-Chem versions wiki page. For information about 1-year benchmark simulations for GEOS-Chem v8-02-04 and earlier, see this website.

Benchmark output archive

Output files and evaluation plots for 1-month and 1-year benchmark simulations are archived at Harvard as summarized below. GEOS-Chem users may utilize these output for comparisons against their own simulations.

Directory Description
http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/ Contains the following data from the 1-month benchmarks used to evaluate GEOS-Chem:
  • Restart files
  • Model output
  • Log files
  • Input files
  • Evaluation plots
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/ Contains the following data from the 1-year benchmarks used to evaluate GEOS-Chem:
  • Restart files
  • Model output
  • Log files
  • Input files
  • Evaluation plots


1-month benchmark plotting routines

The 1-month benchmark plotting routines are included with GCPy, a Python took kit available for GEOS-Chem.

1-year benchmark plotting routines

The 1-year benchmark plotting routines are currently written in IDL and can be downloaded from Bitbucket via Git using:

 git clone https://bitbucket.org/gcst/gc_1yr_benchmark

The data files needed for the plots are included in the repository and are summarized in the table below.

Directory Data year Species Data source Provided by
BrO/ 2007-2008 BrO GOME-2 Justin Parrella
(Data used to reproduce Figure 5 of Parrella et al. (2012))
cmdl/ 2005, 2009
New data available
CO GMD (formerly CMDL) Jennifer Logan and Inna Megretskaia
co.prof.for.gmi/ 2001-2008
(varies by station)
CO MOZAIC Jennifer Logan and Inna Megretskaia
eval/aircraft/
NOTE: Other directories in eval/ aren't currently used
1995-2003
(varies by aircraft campaign)
C2H6, C3H8, CO, H2O2, HNO3, NO, O3, PAN

(Not currently used: ACET, ALK4, C2H2, CH2Br2, CH2BrCl, CH3Br, CH3OH, CH4, CHBr2Cl, CHBrCl2, CO2, ETHE, PRPE)

See README Jennifer Logan and Inna Megretskaia
netCDF/ N/A C2H6, C3H8, CH3I, CO, H2O2, HNO3, NO, O3, OH, PAN, Rn Various
(contains information about station locations)
Jennifer Logan and Inna Megretskaia
PAN/ Varies PAN ARCTAS-A, ARCTAS-B, ARCPAC, INTEX-B, ITCT-2K2 Emily Fischer
(Data used to reproduce Figure S1 of Fischer et al. (2014) Supplement)
pm25_data/ 2005 PM2.5 IMPROVE Colette Heald
sondes.for.gmi/ 1990-2008
(varies by station)
O3 Jennifer Logan and Inna Megretskaia
strat/ 2001-2010 NOy, O3 OSIRIS Dylan Jones
surface_ozone/ O3 CMDL Jennifer Logan and Inna Megretskaia

Update 2005/2009 CMDL CO data to 2013/2014 GMD CO data

This update was included in v11-02c and approved on 21 Sep 2017.

Jenny Fisher wrote:

Attached is a zip file containing routines to process the GMD (previously CMDL) CO data for use in the benchmarking scripts, as well as the 2013 and 2014 data. I added the 2014 data because there was no ships data for 2013 (or 2012), so this seemed like the best approximation.
To replace the existing benchmark data with these, you will want to do the following in the 1-year benchmark code:
  1. Put the 2013data/ and 2014data/ in the data/cmdl/ directory of the 1-year benchmark code
  2. Change newdata/ to 2013data/ in plot_cmdl_3_models_4_months.pro
  3. Change Feb09/ to 2013data/ in plot_surface_co_geos_3_models.pro
  4. Change newdata/ to 2014data/ in plot_ships_3_models_4_months.pro and plot_ships_3_models_co.pro
  5. Change the line file=pre+name_sta(kk)+'.mn' to file=pre+name_sta(kk)+’.mn.2013' in plot_cmdl_3_models_4_months.pro
  6. Change the line file=pre+name_sta(kk)+’.mn.2005' to file=pre+name_sta(kk)+’.mn.2013' in plot_surface_co_geos_3_models.pro
  7. Change the line file=pre+name_sta(kk)+'.mn' to file=pre+name_sta(kk)+’.mn.2014' in plot_ships_3_models_4_months.pro and plot_ships_3_models_co.pro
As I said before, I think this would be a useful improvement to our benchmarks, rather than using data >10 years old!