GEOS-Chem benchmarking

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.

Types of benchmark simulations

The GEOS-Chem Support Team (GCST) runs several types of benchmark simulations in order to assess the performance of GEOS-Chem. These are described in the following sections.

1-hour benchmarks

1-hour benchmarks primarily serve as sanity checks. They are useful in determining if two successive updates to GEOS-Chem result in identical model output. These are triggered when:

1. A commit is pushed to any development branch² in the geoschem/GCClassic "superproject" repository
2. A commit is pushed to any development branch² in the geoschem/GCHP "superproject" repository.

Evaluation tables are posted to gc-dashboard.org upon successful completion of each 1-hour benchmark simulation. The evaluation tables include information on OH metrics, emissions totals, global mass, and a summary table.

Automatic 1-hour benchmarks are only performed for the full-chemistry simulation.

1-month benchmarks

1-month benchmarks (aka alpha benchmarks) are primarily used to quantify the changes in model output that occur when adding a new science feature into GEOS-Chem. These are triggered when:

1. An alpha tag³ is pushed to any development branch¹ in the geoschem/GCClassic superproject repository
2. An alpha tag³ is pushed to any development branch¹ in the geoschem/GCHP "superproject" repository.

Evaluation plots and tables are posted to gc-dashboard.org upon successful completion of each 1-hour benchmark simulation. These include comparison plots of species concentrations, emissions, aerosol optical depth, J-Values, as well as the same tables produced for the 1-hour benchmarks.

Automatic 1-month benchmarks are only performed for the full-chemistry simulation.

1-year benchmarks

1-year benchmarks are performed before every feature version (X.Y.0) release. They are used to compare the version currently in preparation against the the previous feature version. Due to the size of the output and length of the simulation, the GCST runs 1-year benchmark simulations on the Harvard Cannon cluster.

1-year benchmarks may be run for either the [[Simulations using KPP-built mechanisms|full-chemistry simulation] or for the TransportTracers simulation. Ad-hoc 1-year benchmarks for the Carbon simulation may also be performed in order to assess scientific updates made to that particular simulation.

Full-chemistry 1-year benchmarks are performed before each feature version (X.Y.0) release. On the other hand, 1-year TransportTracers benchmarks are only performed for feature versions containing changes to transport and/or wet deposition. 1-year TransportTracers benchmarks are spun up for 10 years before the evaluation year in order to make sure the model atmosphere is in steady-state.

Benchmark output consists of similar plots and tables as in the 1=month simulation but for January, April, July, and October 2019, plus annual means.

10-year benchmarks

10-year benchmarks are performed before every major version (X.0.0) release. These benchmarks are intended to evaluate how well GEOS-Chem full-chemistry simulation is performing in the stratosphere. Oxidant fields and prod/loss rates from the 10-year benchmarks are also used as input to some GEOS-Chem specialty simulations (such as the Carbon simulation and Tagged O3 simulation).

Notes

1. GEOS-Chem uses semantic versioning (i.e. X.Y.Z version labels).
2. Development branches are dev/X.Y.0 and dev/no-diff-to-benchmark.
3. An alpha tag is a Git tag using the format X.Y.Z-alpha.N, where X.Y.Z is the version number and N is a sequential index starting at 0.
   • Alpha tags indicate the locations in the Git revision history where 1-month full-chemistry benchmarks were run.
   • Alpha tags are used to link changes in `-month full chemistry benchmark simulation results to a specific update (or group of updates).

Procedure

The GEOS-Chem benchmarking procedure is described below. GEOS-Chem uses semantic versioning (i.e. X.Y.Z version labels).

1. Any update to GEOS-Chem source code, input data, or run directories must be evaluated with a benchmark simulation.
   
   
2. Updates to GEOS-Chem source code, input data, or run directories impacting the full-chemistry simulation are considered to be science updates.
   • Science updates are pushed to the dev/X.Y.0 branch of the geoschem/geos-chem repository.
   • Corresponding submodule hash updates are added to the dev/X.Y.0 branches of the geoschem/GCClassic and geoschem/GCHP repositories.
     • This triggers automatic 1-hour benchmarks for GEOS-Chem Classic and GCHP.
   • The 1-hour GEOS-Chem Classic and GCHP benchmarks are examined to ensure they executed properly.
     
     
3. Updates not impacting the full-chemistry simulation (including updates to specialty simulations) are considered to be no-diff updates.
   • No-diff updates are pushed to the dev/no-diff-to-benchmark branch of the geoschem/geos-chem repository.
   • Corresponding submodule hash updates are added to the dev/X.Y.0 branches of the geoschem/GCClassic and geoschem/GCHP repositories.
   • This triggers automatic 1-hour benchmarks for GEOS-Chem Classic and GCHP.
   • The 1-hour GEOS-Chem Classic and GCHP benchmarks are examined to ensure they executed properly.
   • No-diff updates are considered to be mergeable at any time.
     • These could go into a standalone bugfix version (X.Y.Z) or into the next feature version (X.Y.0), as circumstances dictate.

.

1. Once the GEOS-Chem Classic and GCHP 1-hour benchmarks corresponding to a particular science update have been evaluated, the update can be assigned an alpha tag³, which can be pushed to the dev/X.Y.0 branches of the GCClassic and GCHP repositories.
   • This will trigger 1-month benchmarks, as described ab
   • Links to the 1-month benchmark plots will be added to the GEOS-Chem X.Y.0 wiki page for examination by the GEOS-Chem Steering Committee.

1. 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.
2. 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).
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.

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
https://gc-dashboard.org/search?searchString=&1Hr=1Hr&GCHP=GCHP&GCC=GCC	Contains the following data from the 1-hour benchmarks used to evaluate GEOS-Chem: Evaluation plots & tables Run log Run directory (tarball) Diagnostic files (tarball) Restart Files (tarball)
https://gc-dashboard.org/search?searchString=&1Mon=1Mon&GCHP=GCHP&GCC=GCC	Contains the following data from the 1-month benchmarks used to evaluate GEOS-Chem: Evaluation plots & tables Run log Run directory (tarball) Diagnostic files (tarball) Restart Files (tarball)
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/	Contains the following data from the 1-year benchmarks used to evaluate GEOS-Chem: Evaluation plots Restart files (tarball) Model output (tarball) Log files (tarball) Input files (tarball)
http://ftp.as.harvard.edu/gcgrid/geos-chem/10yr_benchmarks/	Contains the following data from the 10-year benchmarks used to evaluate GEOS-Chem: Evaluation plots & tables Restart files (tarball) Model output (tarball) Log files (tarball) Input files (tarball)

NOTE: "tarball" refers to a *.tar.gz file. This is an archive of files & folders created with tar cvzf and can be extracted with tar xzvf.

Benchmark plotting routines

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