Difference between revisions of "GEOS-Chem 13.0.0"

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(Benchmark assessment form)
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This page includes information about all benchmark simulations for [[GEOS-Chem 13#13.0.0|GEOS-Chem 13.0.0]].
 
This page includes information about all benchmark simulations for [[GEOS-Chem 13#13.0.0|GEOS-Chem 13.0.0]].
  
== GEOS-Chem Classic 1-month benchmark ==
+
=== Version overview ===
  
=== Benchmark plots ===
+
The following items have been added to GEOS-Chem 13.0.0 since the last benchmark for GEOS-Chem 12.9.0.
  
Enable PDF bookmarks<sup>1</sup> in the files linked below to navigate between species. See the [[Species in GEOS-Chem]] wiki page for species definitions and details.
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="500px"|Feature
 +
!width="200px"|Submitted by
 +
!width="100px"|Type
 +
 
 +
|-valign="top"
 +
!colspan="3" bgcolor="#CCFFFF"|Updates that will affect full-chemistry simulations
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/447 CEDS_GBD-MAPS emission inventory (1970 - 2017)]
 +
|Erin McDuffie (Dalhousie)
 +
|Science
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/309 Retire carbon-based units for VOCs]
 +
|Melissa Sulprizio (GCST)
 +
|Science
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/311 Removal of HEMCO code from within the non-local PBL mixing modules]
 +
|Bob Yantosca (GCST)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/396 Heterogeneous chem fixes, performance improvements, and clarification]
 +
|Chris Holmes (FSU)
 +
|Bug fix
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/344 Fix handling of NOx coefficients in ucx_mod.F90]
 +
|Sebastian Eastham (MIT)
 +
|Bug fix
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/402 Prevent divide-by-zero errors in UCX routine UCX_NOX]
 +
|Bob Yantosca (GCST)
 +
|Bug fix
 +
 
 +
|-valign="top"
 +
!colspan="4" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/388 Use GEOS-FP 5.22 data for Jan - May 2020 and store GEOS-FP 5.25 for April - May 2020 as option]
 +
|Jun Meng (GCST)<br>Melissa Sulprizio (GCST)
 +
|Data
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/424 Update QFED emissions through July 2020]
 +
|Christoph Keller (NASA GMAO)
 +
|Science
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem-unittest/pull/19 ODIAC fossil fuel emissions for CO2 simulations]
 +
|Jenny Fisher (UOW)<br>Yi Cao (UOW)
 +
|Science
 +
 
 +
|-valign="top
 +
|[https://github.com/geoschem/geos-chem-unittest/pull/24 Global Hg emissions from Streets et al. (2019)] (as option)
 +
|Colin Thackray (Harvard)
 +
|Science
 +
 
 +
|-valign="top
 +
|[https://github.com/geoschem/geos-chem-unittest/pull/25 Global Hg emissions from EDGARv4.tox2] (as option)
 +
|Amanda Giang (UBC)
 +
|Science
 +
 
 +
|-valign="top"
 +
|[https://essd.copernicus.org/articles/12/563/2020/essd-12-563-2020.pdf Global Inventory of Methane Emissions from Fuel Exploitation]
 +
|Tia Scarpelli (Harvard)
 +
|Science
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/332 Retire tropchem mechanism; implement new tropchem simulation using Standard mechanism below the tropopause and archived P/L rates above]
 +
|Melissa Sulprizio (GCST)
 +
|Science
 +
 
 +
|-valign="top"
 +
|RRTMG fixes and updates
 +
*[https://github.com/geoschem/geos-chem/pull/347 Fix bug with stratospheric aerosol]
 +
*[https://github.com/geoschem/geos-chem/issues/350 Shift RRTMG call time sequence to begin first timestep]
 +
*[https://github.com/geoschem/geos-chem/issues/350 Fix bugs in GEOS-Chem 12 implementation of netCDF diagnostics]
 +
*[https://github.com/geoschem/geos-chem/issues/350 Complete remaining implementation of netCDF diagnostics to match binary]
 +
*[https://github.com/geoschem/geos-chem/issues/438 Fix seg fault when building RRTMG with Intel compilers]
 +
*[https://github.com/geoschem/geos-chem/pull/429 Allow turning RRTMG off when using RRTMG-enabled executable]
 +
|Sebastian Eastham (MIT)<br>Lizzie Lundgren (GCST)
 +
|Bug fix
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/242 Add global mean OH and CH4 lifetime diagnostics]
 +
|Bob Yantosca (GCST)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[http://wiki.seas.harvard.edu/geos-chem/index.php/Compiling_with_CMake Retire the GNU Make build system in both GEOS-Chem Classic and GCHP and replace with CMake]
 +
|Liam Bindle (WashU)<br>GCST
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/283 Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem source code repository]
 +
|Melissa Sulprizio (GCST)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/334 Updates to GEOS-Chem and HEMCO interface for compatibility with CESM]
 +
|Haipeng Lin (Harvard)<br>Thibaud Fritz (MIT)<br>Lizzie Lundgren (GCST)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/270 Dynamically allocate diagnostic arrays based on HISTORY.rc content to minimize memory footprint]
 +
|Bob Yantosca (GCST)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|Fixes for typos:
 +
*[https://github.com/geoschem/geos-chem/issues/442 Incorrect density value used to calculate cloud ice volume]
 +
*[https://github.com/geoschem/geos-chem/issues/410 Fix stratospheric loss in CH4 simulation using 12.9.0]
 +
*[https://github.com/geoschem/geos-chem/issues/444 Update format statements in fast_jx_mod.F90 for 3 integers]
 +
*[https://github.com/geoschem/geos-chem/issues/430 Fix typo in mercury_mod.F for saving EmisHg0land]
 +
*[https://github.com/geoschem/geos-chem/issues/415 Fix for reading archived OH and Cl in CH4 simulations]
 +
*[https://github.com/geoschem/geos-chem/issues/416 Fix species name typo in Init_HetInfo subroutine]
 +
|GCST
 +
|Bug fix
 +
 +
|-
 +
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/gchp/issues/63 Retire the existing GCHP repository and replace with a new wrapper repository that uses ESMF as an external library and integrates GEOS-Chem and NASA/GMAO GEOS-ESM git repositories as git submodules]
 +
|Lizzie Lundgren (GCST)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/246 Separate HEMCO from GEOS-Chem to use as an ESMF gridded component in GCHP]
 +
|Lizzie Lundgren (GCST)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[https://gchp.readthedocs.io/en/latest/stretched-grid.html Enable a stretched grid capability in GCHP to run global simulations at regional high resolution]
 +
|Liam Bindle (WashU)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/GCHPctm/commit/004ca996312028037774820c8398502561489697 Update MAPL (v2.2.7) and GMAO library dependencies]
 +
|Lizzie Lundgren (GCST)
 +
|Structural
 +
 
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/348 Enable GCHP to be compiled with RRTMG]
 +
|Sebastian Eastham (MIT)<br>Lizzie Lundgren (GCST)
 +
|Science
 +
 
 +
|}
 +
 
 +
==== New data directories ====
 +
 
 +
The following data directories have been added or updated in this version.  You will have to [[Downloading_GEOS-Chem_data_directories|download the directories]] relevant to your simulation.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="100px"|Inventory
 +
!width="200px"|Type
 +
!width="400px"|What was added?
 +
!width="300px"|Directory
 +
 
 +
|-valign="top"
 +
|CEDS
 +
|DEFAULT<br>(full-chemistry simulations)
 +
|[https://github.com/geoschem/geos-chem/issues/447 CEDS_GBD-MAPS emission inventory (1970 - 2017)]
 +
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CEDS/v2020-08/README <tt>HEMCO/CEDS/v2020-08/</tt>]
 +
 
 +
|-valign="top"
 +
|QFED
 +
|OPTIONAL
 +
||[https://github.com/geoschem/geos-chem/issues/424 Update QFED emissions through July 2020]
 +
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/QFED/v2018-07/README <tt>HEMCO/QFED/v2018-07/</tt>]
 +
 
 +
|-valign="top"
 +
|ODIAC CO2
 +
|DEFAULT<br>(CO2 simulations)
 +
|[https://github.com/geoschem/geos-chem-unittest/pull/19 ODIAC fossil fuel emissions for CO2 simulations]
 +
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CO2/v2019-12/FOSSIL/README <tt>HEMCO/CO2/v2019-12/</tt>]
 +
 
 +
|-valign="top"
 +
|MERCURY
 +
|OPTIONAL<br>(Hg simulations)
 +
|[https://github.com/geoschem/geos-chem-unittest/pull/24 Updated Streets Hg emissions]<br>
 +
[https://github.com/geoschem/geos-chem-unittest/pull/25 Updated EDGAR 4.3 Hg emissions]
 +
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MERCURY/v2020-07/ <tt>HEMCO/MERCURY/v2020-07/</tt>]
 +
 
 +
|-valign="top"
 +
|CH4
 +
|DEFAULT<br>(CH4 simulations)
 +
|[https://essd.copernicus.org/articles/12/563/2020/essd-12-563-2020.pdf Global Inventory of Methane Emissions from Fuel Exploitation]
 +
[http://acmg.seas.harvard.edu/publications/2020/zhang_yuzhong2020ACP.pdf Updated wetland and seep CH4 emissions]
 +
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CH4/v2020-02/README <tt>HEMCO/CH4/v2020-02/</tt>]
 +
[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CH4/v2020-04/README <tt>HEMCO/CH4/v2020-04/</tt>]
 +
 
 +
|}
 +
 
 +
== 1-month benchmarks ==
 +
 
 +
=== Model setup ===
 +
 
 +
The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-month benchmark simulations.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
 
 +
|-valign="top"
 +
|width="250px"|Meteorology fields:
 +
|width="350px"|[[MERRA-2]]
 +
 
 +
|-valign="top"
 +
|Benchmark month:
 +
|July 2019
 +
 
 +
|-valign="top"
 +
|Git tag(s):
 +
|[https://github.com/geoschem/geos-chem/releases/tag/13.0.0-rc.0 13.0.0-rc.0]
 +
 
 +
|-valign="top"
 +
|Compared to previous benchmark:
 +
|[[GEOS-Chem_12#12.9.0|12.9.0]]
 +
 
 +
|-valign="top"
 +
|This version will impact:<br>(select all that apply with '''boldface''')
 +
|
 +
*Advection
 +
*BL Mixing
 +
*Convection
 +
*'''Meteorology Fields'''
 +
*Dry Deposition*
 +
*Wet Deposition
 +
*'''Emissions'''
 +
*Photolysis
 +
*'''Chemistry'''
 +
*Other (please specify):
 +
 
 +
|}
 +
 
 +
=== Benchmark Plots and Tables ===
 +
 
 +
NOTES:
 +
*Enable PDF bookmarks in the files linked above to navigate between species. See the [[Species in GEOS-Chem]] wiki page for species definitions and details. If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
 +
* [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.0.0-beta.0/GCClassic/BenchmarkResults/benchmark_categories.yml Species categories] and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.0.0-beta.0/GCClassic/BenchmarkResults/lumped_species.yml lumped species] definitions are simple to adjust. Updating them requires only editing the YAML files.
 +
 
 +
==== GCClassic version comparison ====
 +
 
 +
Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 12.9.0 (Ref) and GEOS-Chem Classic 13.0.0 (Dev).  
  
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
  
 
|-
 
|-
!colspan="1" bgcolor="#CCFFFF" width="325px"|Species Category<sup>2</sup>
+
!colspan="1" bgcolor="#CCFFFF" width="325px"|Species Category
 
!colspan="5" bgcolor="#CCFFFF"|Plots
 
!colspan="5" bgcolor="#CCFFFF"|Plots
 
!colspan="1" bgcolor="#CCFFFF"|Additional Information
 
!colspan="1" bgcolor="#CCFFFF"|Additional Information
Line 183: Line 431:
 
|}
 
|}
  
<sup>1</sup>All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
+
==== GCHP version comparison ====
  
<sup>2</sup>[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.0.0-beta.0/GCClassic/BenchmarkResults/benchmark_categories.yml Species category] and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.0.0-beta.0/GCClassic/BenchmarkResults/lumped_species.yml lumped species] definitions are simple to adjust. Updating them requires only editing the YAML files.
+
Below are links to plots and tables comparing 1-month simulations for GCHP 12.9.0 (Ref) and GCHP 13.0.0 (Dev).  
 
+
=== Benchmark assessment form ===
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-bgcolor="#CCCCCC"
+
!width="325px"|Description
+
!
+
|-valign="top"
+
|New features added into GEOS-Chem
+
|
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-bgcolor="#CCCCCC"
+
!width="500px"|Feature
+
!width="200px"|Submitted by
+
 
+
|-
+
!colspan="2" bgcolor="#CCFFFF"|Updates that WILL AFFECT the full-chemistry simulation
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/447 CEDS_GBD-MAPS emission inventory (1970 - 2017)]
+
|Erin McDuffie (Dalhousie)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/309 Retire carbon-based units for VOCs]
+
|Melissa Sulprizio (GCST)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/311 Removal of HEMCO code from within the non-local PBL mixing modules]
+
|Bob Yantosca (GCST)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/pull/396 Heterogeneous chem fixes, performance improvements, and clarification]
+
|Chris Holmes (FSU)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/pull/344 Fix handling of NOx coefficients in ucx_mod.F90]
+
|Sebastian Eastham (MIT)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/402 Prevent divide-by-zero errors in UCX routine UCX_NOX]
+
|Bob Yantosca (GCST)
+
 
+
|-valign="top"
+
!colspan="2" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/388 Use GEOS-FP 5.22 data for Jan - May 2020 and store GEOS-FP 5.25 for April - May 2020 as option]
+
|Jun Meng (GCST)<br>Melissa Sulprizio (GCST)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/424 Update QFED emissions through July 2020]
+
|Christoph Keller (NASA GMAO)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem-unittest/pull/19 ODIAC fossil fuel emissions for CO2 simulations]
+
|Jenny Fisher (UOW)<br>Yi Cao (UOW)
+
 
+
|-valign="top
+
|[https://github.com/geoschem/geos-chem-unittest/pull/24 Global Hg emissions from Streets et al. (2019)] (as option)
+
|Colin Thackray (Harvard)
+
 
+
|-valign="top
+
|[https://github.com/geoschem/geos-chem-unittest/pull/25 Global Hg emissions from EDGARv4.tox2] (as option)
+
|Amanda Giang (UBC)
+
 
+
|-valign="top"
+
|[https://essd.copernicus.org/articles/12/563/2020/essd-12-563-2020.pdf Global Inventory of Methane Emissions from Fuel Exploitation]
+
|Tia Scarpelli (Harvard)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/332 Retire tropchem mechanism; implement new tropchem simulation using Standard mechanism below the tropopause and archived P/L rates above]
+
|Melissa Sulprizio (GCST)
+
 
+
|-valign="top"
+
|RRTMG fixes and updates
+
*[https://github.com/geoschem/geos-chem/pull/347 Fix bug with stratospheric aerosol]
+
*[https://github.com/geoschem/geos-chem/issues/350 Shift RRTMG call time sequence to begin first timestep]
+
*[https://github.com/geoschem/geos-chem/issues/350 Fix bugs in GEOS-Chem 12 implementation of netCDF diagnostics]
+
*[https://github.com/geoschem/geos-chem/issues/350 Complete remaining implementation of netCDF diagnostics to match binary]
+
*[https://github.com/geoschem/geos-chem/issues/438 Fix seg fault when building RRTMG with Intel compilers]
+
*[https://github.com/geoschem/geos-chem/pull/429 Allow turning RRTMG off when using RRTMG-enabled executable]
+
|Sebastian Eastham (MIT)<br>Lizzie Lundgren (GCST)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/242 Add global mean OH and CH4 lifetime diagnostics]
+
|Bob Yantosca (GCST)
+
 
+
|-valign="top"
+
|[http://wiki.seas.harvard.edu/geos-chem/index.php/Compiling_with_CMake Retire the GNU Make build system in both GEOS-Chem Classic and GCHP and replace with CMake]
+
|Liam Bindle (WashU)<br>GCST
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/283 Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem source code repository]
+
|Melissa Sulprizio (GCST)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/pull/334 Updates to GEOS-Chem and HEMCO interface for compatibility with CESM]
+
|Haipeng Lin (Harvard)<br>Thibaud Fritz (MIT)<br>Lizzie Lundgren (GCST)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/issues/270 Dynamically allocate diagnostic arrays based on HISTORY.rc content to minimize memory footprint]
+
|Bob Yantosca (GCST)
+
 
+
|-valign="top"
+
|Fixes for typos:
+
*[https://github.com/geoschem/geos-chem/issues/442 Incorrect density value used to calculate cloud ice volume]
+
*[https://github.com/geoschem/geos-chem/issues/410 Fix stratospheric loss in CH4 simulation using 12.9.0]
+
*[https://github.com/geoschem/geos-chem/issues/444 Update format statements in fast_jx_mod.F90 for 3 integers]
+
*[https://github.com/geoschem/geos-chem/issues/430 Fix typo in mercury_mod.F for saving EmisHg0land]
+
*[https://github.com/geoschem/geos-chem/issues/415 Fix for reading archived OH and Cl in CH4 simulations]
+
*[https://github.com/geoschem/geos-chem/issues/416 Fix species name typo in Init_HetInfo subroutine]
+
|GCST
+
+
|-
+
!colspan="2" bgcolor="#CCFFFF"|Features only affecting GCHP:
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/gchp/issues/63 Retire the existing GCHP repository and replace with a new wrapper repository that uses ESMF as an external library and integrates GEOS-Chem and NASA/GMAO GEOS-ESM git repositories as git submodules]
+
|Lizzie Lundgren (GCST)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/pull/246 Separate HEMCO from GEOS-Chem to use as an ESMF gridded component in GCHP]
+
|Lizzie Lundgren (GCST)
+
 
+
|-valign="top"
+
|[https://gchp.readthedocs.io/en/latest/stretched-grid.html Enable a stretched grid capability in GCHP to run global simulations at regional high resolution]
+
|Liam Bindle (WashU)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/GCHPctm/commit/004ca996312028037774820c8398502561489697 Update MAPL (v2.2.7) and GMAO library dependencies]
+
|Lizzie Lundgren (GCST)
+
 
+
|-valign="top"
+
|[https://github.com/geoschem/geos-chem/pull/348 Enable GCHP to be compiled with RRTMG]
+
|Sebastian Eastham (MIT)<br>Lizzie Lundgren (GCST)
+
 
+
|}
+
 
+
|-valign="top"
+
|Version, resolution, met fields used:
+
|MERRA-2 (72L), 4x5, July 2019
+
 
+
|-valign="top"
+
|1-month benchmark finished on:
+
|Mon Nov 2 03:24:27 EST 2020
+
 
+
|-valign="top"
+
|Performance statistics:
+
|
+
*Compiled with ifort 18.0.5
+
*Ran on 24 CPUs of holy7c20304.rc.fas.harvard.edu (Intel(R) Xeon(R) Platinum 8268 CPU @ 2.90GHz)
+
*Wall time: 06:54:01
+
*[[Scalability|CPU time / wall time]]: 19.4750
+
*% of ideal performance: 81.15%
+
*Memory:  13.6795 GB
+
 
+
|-valign="top"
+
|Git tag
+
|[https://github.com/geoschem/geos-chem/releases/tag/13.0.0-rc.0 13.0.0-rc.0]
+
 
+
|-valign="top"
+
|Compared to previous benchmark:
+
|[[GEOS-Chem_12#12.9.0|12.9.0]]
+
 
+
|-valign="top"
+
|This update will impact:<br>(select all that apply with '''boldface''')
+
|Advection, BL Mixing, Convection, '''Met Fields''', Dry Dep, Wet Dep, Stratosphere, '''Emissions''', Photolysis, '''Chemistry''', Other (please specify):
+
 
+
|-valign="top" bgcolor="#cccccc"
+
!Metrics
+
!
+
 
+
|-valign="top"
+
|Global mean OH from log file (% change):
+
|11.22769648880 x 10<sup>5</sup> molec/cm<sup>3</sup> (-8.60)
+
 
+
|-valign="top"
+
|Methyl chloroform lifetime (% change):
+
|5.5460 years (+8.20%)
+
 
+
|-valign="top"
+
|Methane lifetime (% change):
+
|9.3297 years (+8.09%)
+
 
+
|-valign="top" bgcolor="#cccccc"
+
!Overview
+
!
+
 
+
|-valign="top"
+
|Comments on observed differences:
+
|'''''Below we summarize the notable changes caused by specific updates.'''''
+
 
+
 
+
 
+
|-valign="top" bgcolor="#cccccc"
+
!Details
+
!
+
 
+
|-valign="top"
+
|List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
+
|
+
 
+
|-valign="top"
+
|List all 500 hPa species and J-Values that changed by 10% or more :
+
|
+
 
+
 
+
|-valign="top"
+
|List all ZONAL MEAN species and J-Values that changed by 10% or more:
+
|
+
 
+
 
+
|-valign="top"
+
|List all EMISSIONS that changed by 10% or more:
+
|
+
 
+
|-bgcolor="#cccccc"
+
!Approval
+
!
+
 
+
|-valign="top"
+
|Requires further investigation:
+
|
+
 
+
|-valign="top"
+
|Approved by:
+
|
+
 
+
|-valign="top"
+
|Date of approval:
+
|
+
|}
+
 
+
== GCHP 1-month benchmark ==
+
 
+
The following sections contain validation plots for GCHP 13.0.0.
+
 
+
=== Comparison of GCHP versions ===
+
 
+
This table contains plots comparing GCHP 13.0.0 (Ref) and GCHP 12.9.0 (Dev) for a 1-month simulation.
+
  
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
Line 597: Line 604:
 
|}
 
|}
  
=== Comparison of GCHP and GEOS-Chem Classic ===
+
==== GCHP and GEOS-Chem Classic comparison ====
  
This table contains plots comparing GEOS-Chem Classic 13.0.0 (Ref) against GCHP 13.0.0 (Dev) for a 1-month simulation.  
+
Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.0.0 (Ref) and GCHP 13.0.0 (Dev).  
  
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
Line 770: Line 777:
 
|}
 
|}
  
=== GCHP and GEOS-Chem Classic difference of differences ===
+
==== GCHP and GEOS-Chem Classic difference of differences ====
  
 
This table contains plots comparing the difference [GCHP 13.0.0 - GCHP 12.9.0] against the difference [GC Classic 13.0.0 - GC Classic 12.9.0], taken from 1-month benchmark simulations.
 
This table contains plots comparing the difference [GCHP 13.0.0 - GCHP 12.9.0] against the difference [GC Classic 13.0.0 - GC Classic 12.9.0], taken from 1-month benchmark simulations.
Line 865: Line 872:
  
 
NOTE: At present, we have only created the diff-of-diffs plots for species concentration.  This can be extended to other categories in the future.
 
NOTE: At present, we have only created the diff-of-diffs plots for species concentration.  This can be extended to other categories in the future.
 +
 +
=== Benchmark assessment form ===
 +
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="325px"|Description
 +
!
 +
 +
 +
|-valign="top"
 +
|1-month benchmark finished on:
 +
|Mon Nov 2 03:24:27 EST 2020
 +
 +
|-valign="top"
 +
|Performance statistics:
 +
|
 +
*Compiled with ifort 18.0.5
 +
*Ran on 24 CPUs of holy7c20304.rc.fas.harvard.edu (Intel(R) Xeon(R) Platinum 8268 CPU @ 2.90GHz)
 +
*Wall time: 06:54:01
 +
*[[Scalability|CPU time / wall time]]: 19.4750
 +
*% of ideal performance: 81.15%
 +
*Memory:  13.6795 GB
 +
 +
|-valign="top" bgcolor="#cccccc"
 +
!Metrics
 +
!
 +
 +
|-valign="top"
 +
|Global mean OH from log file (% change):
 +
|11.22769648880 x 10<sup>5</sup> molec/cm<sup>3</sup> (-8.60)
 +
 +
|-valign="top"
 +
|Methyl chloroform lifetime (% change):
 +
|5.5460 years (+8.20%)
 +
 +
|-valign="top"
 +
|Methane lifetime (% change):
 +
|9.3297 years (+8.09%)
 +
 +
|-valign="top" bgcolor="#cccccc"
 +
!Overview
 +
!
 +
 +
|-valign="top"
 +
|Comments on observed differences:
 +
|'''''Below we summarize the notable changes caused by specific updates.'''''
 +
 +
 +
 +
|-valign="top" bgcolor="#cccccc"
 +
!Details
 +
!
 +
 +
|-valign="top"
 +
|List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
 +
|
 +
 +
|-valign="top"
 +
|List all 500 hPa species and J-Values that changed by 10% or more :
 +
|
 +
 +
 +
|-valign="top"
 +
|List all ZONAL MEAN species and J-Values that changed by 10% or more:
 +
|
 +
 +
 +
|-valign="top"
 +
|List all EMISSIONS that changed by 10% or more:
 +
|
 +
 +
|-bgcolor="#cccccc"
 +
!Approval
 +
!
 +
 +
|-valign="top"
 +
|Requires further investigation:
 +
|
 +
 +
|-valign="top"
 +
|Approved by:
 +
|
 +
 +
|-valign="top"
 +
|Date of approval:
 +
|
 +
|}

Revision as of 03:40, 6 November 2020


This page includes information about all benchmark simulations for GEOS-Chem 13.0.0.

Version overview

The following items have been added to GEOS-Chem 13.0.0 since the last benchmark for GEOS-Chem 12.9.0.

Feature Submitted by Type
Updates that will affect full-chemistry simulations
CEDS_GBD-MAPS emission inventory (1970 - 2017) Erin McDuffie (Dalhousie) Science
Retire carbon-based units for VOCs Melissa Sulprizio (GCST) Science
Removal of HEMCO code from within the non-local PBL mixing modules Bob Yantosca (GCST) Structural
Heterogeneous chem fixes, performance improvements, and clarification Chris Holmes (FSU) Bug fix
Fix handling of NOx coefficients in ucx_mod.F90 Sebastian Eastham (MIT) Bug fix
Prevent divide-by-zero errors in UCX routine UCX_NOX Bob Yantosca (GCST) Bug fix
Updates that will NOT affect full-chemistry simulations
Use GEOS-FP 5.22 data for Jan - May 2020 and store GEOS-FP 5.25 for April - May 2020 as option Jun Meng (GCST)
Melissa Sulprizio (GCST)
Data
Update QFED emissions through July 2020 Christoph Keller (NASA GMAO) Science
ODIAC fossil fuel emissions for CO2 simulations Jenny Fisher (UOW)
Yi Cao (UOW)
Science
Global Hg emissions from Streets et al. (2019) (as option) Colin Thackray (Harvard) Science
Global Hg emissions from EDGARv4.tox2 (as option) Amanda Giang (UBC) Science
Global Inventory of Methane Emissions from Fuel Exploitation Tia Scarpelli (Harvard) Science
Retire tropchem mechanism; implement new tropchem simulation using Standard mechanism below the tropopause and archived P/L rates above Melissa Sulprizio (GCST) Science
RRTMG fixes and updates Sebastian Eastham (MIT)
Lizzie Lundgren (GCST)
Bug fix
Add global mean OH and CH4 lifetime diagnostics Bob Yantosca (GCST) Structural
Retire the GNU Make build system in both GEOS-Chem Classic and GCHP and replace with CMake Liam Bindle (WashU)
GCST
Structural
Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem source code repository Melissa Sulprizio (GCST) Structural
Updates to GEOS-Chem and HEMCO interface for compatibility with CESM Haipeng Lin (Harvard)
Thibaud Fritz (MIT)
Lizzie Lundgren (GCST)
Structural
Dynamically allocate diagnostic arrays based on HISTORY.rc content to minimize memory footprint Bob Yantosca (GCST) Structural
Fixes for typos: GCST Bug fix
Features only affecting GCHP:
Retire the existing GCHP repository and replace with a new wrapper repository that uses ESMF as an external library and integrates GEOS-Chem and NASA/GMAO GEOS-ESM git repositories as git submodules Lizzie Lundgren (GCST) Structural
Separate HEMCO from GEOS-Chem to use as an ESMF gridded component in GCHP Lizzie Lundgren (GCST) Structural
Enable a stretched grid capability in GCHP to run global simulations at regional high resolution Liam Bindle (WashU) Structural
Update MAPL (v2.2.7) and GMAO library dependencies Lizzie Lundgren (GCST) Structural
Enable GCHP to be compiled with RRTMG Sebastian Eastham (MIT)
Lizzie Lundgren (GCST)
Science

New data directories

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory Type What was added? Directory
CEDS DEFAULT
(full-chemistry simulations)
CEDS_GBD-MAPS emission inventory (1970 - 2017) HEMCO/CEDS/v2020-08/
QFED OPTIONAL Update QFED emissions through July 2020 HEMCO/QFED/v2018-07/
ODIAC CO2 DEFAULT
(CO2 simulations)
ODIAC fossil fuel emissions for CO2 simulations HEMCO/CO2/v2019-12/
MERCURY OPTIONAL
(Hg simulations)
Updated Streets Hg emissions

Updated EDGAR 4.3 Hg emissions

HEMCO/MERCURY/v2020-07/
CH4 DEFAULT
(CH4 simulations)
Global Inventory of Methane Emissions from Fuel Exploitation

Updated wetland and seep CH4 emissions

HEMCO/CH4/v2020-02/

HEMCO/CH4/v2020-04/

1-month benchmarks

Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-month benchmark simulations.

Meteorology fields: MERRA-2
Benchmark month: July 2019
Git tag(s): 13.0.0-rc.0
Compared to previous benchmark: 12.9.0
This version will impact:
(select all that apply with boldface)
  • Advection
  • BL Mixing
  • Convection
  • Meteorology Fields
  • Dry Deposition*
  • Wet Deposition
  • Emissions
  • Photolysis
  • Chemistry
  • Other (please specify):

Benchmark Plots and Tables

NOTES:

  • Enable PDF bookmarks in the files linked above to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details. If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
  • Species categories and lumped species definitions are simple to adjust. Updating them requires only editing the YAML files.

GCClassic version comparison

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 12.9.0 (Ref) and GEOS-Chem Classic 13.0.0 (Dev).

Species Category Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere sfc
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA

sfc 500hPa full column stratosphere sfc AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere sfc
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO

sfc 500hPa full column stratosphere sfc
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3

sfc 500hPa full column stratosphere sfc
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere sfc
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere sfc
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

sfc 500hPa full column stratosphere sfc
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere sfc
ROy

H2O2, H, H2, H2O, HO2, O1D, OH, RO2

sfc 500hPa full column stratosphere --
J-values sfc 500hPa full column stratosphere -- --
 
Emissions by HEMCO category Total

Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes

Emission totals Tables by species

Tables by inventory

Global mass Entire atmosphere

Troposphere only

Metrics OH concentration, MCF lifetime, CH4 lifetime
Budgets Budgets after operations


GCHP version comparison

Below are links to plots and tables comparing 1-month simulations for GCHP 12.9.0 (Ref) and GCHP 13.0.0 (Dev).

Species Category2 Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere sfc
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA

sfc 500hPa full column stratosphere sfc AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere sfc
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO

sfc 500hPa full column stratosphere sfc
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3

sfc 500hPa full column stratosphere sfc
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere sfc
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere sfc
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

sfc 500hPa full column stratosphere sfc
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere sfc
ROy

H2O2, H, H2, H2O, HO2, O1D, OH, RO2

sfc 500hPa full column stratosphere --
J-values sfc 500hPa full column stratosphere -- --
 
Emissions by HEMCO category Total

Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes

Emission totals Tables by species

Tables by inventory

Global mass Entire atmosphere

Troposphere only

Budgets Budgets after operations

GCHP and GEOS-Chem Classic comparison

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.0.0 (Ref) and GCHP 13.0.0 (Dev).

Species Category2 Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere sfc
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA

sfc 500hPa full column stratosphere sfc AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere sfc
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO

sfc 500hPa full column stratosphere sfc
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3

sfc 500hPa full column stratosphere sfc
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere sfc
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere sfc
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

sfc 500hPa full column stratosphere sfc
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere sfc
ROy

H2O2, H, H2, H2O, HO2, O1D, OH, RO2

sfc 500hPa full column stratosphere --
J-values sfc 500hPa full column stratosphere -- --
 
Emissions by HEMCO category Total

Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes

Emission totals Tables by species

Tables by inventory

Global mass Entire atmosphere

Troposphere only

Budgets Budgets after operations

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 13.0.0 - GCHP 12.9.0] against the difference [GC Classic 13.0.0 - GC Classic 12.9.0], taken from 1-month benchmark simulations.

Category Plots
Level Map Zonal Mean
Oxidants sfc 500hPa full column stratosphere
Aerosols sfc 500hPa full column stratosphere
Bromine sfc 500hPa full column stratosphere
Chlorine sfc 500hPa full column stratosphere
Iodine sfc 500hPa full column stratosphere
Nitrogen sfc 500hPa full column stratosphere
Primary Organics sfc 500hPa full column stratosphere
Secondary Organics sfc 500hPa full column stratosphere
Secondary Organic Aerosols sfc 500hPa full column stratosphere
Sulfur sfc 500hPa full column stratosphere
ROy sfc 500hPa full column stratosphere

NOTE: At present, we have only created the diff-of-diffs plots for species concentration. This can be extended to other categories in the future.

Benchmark assessment form

Description


1-month benchmark finished on: Mon Nov 2 03:24:27 EST 2020
Performance statistics:
  • Compiled with ifort 18.0.5
  • Ran on 24 CPUs of holy7c20304.rc.fas.harvard.edu (Intel(R) Xeon(R) Platinum 8268 CPU @ 2.90GHz)
  • Wall time: 06:54:01
  • CPU time / wall time: 19.4750
  • % of ideal performance: 81.15%
  • Memory: 13.6795 GB
Metrics
Global mean OH from log file (% change): 11.22769648880 x 105 molec/cm3 (-8.60)
Methyl chloroform lifetime (% change): 5.5460 years (+8.20%)
Methane lifetime (% change): 9.3297 years (+8.09%)
Overview
Comments on observed differences: Below we summarize the notable changes caused by specific updates.


Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
List all 500 hPa species and J-Values that changed by 10% or more :


List all ZONAL MEAN species and J-Values that changed by 10% or more:


List all EMISSIONS that changed by 10% or more:
Approval
Requires further investigation:
Approved by:
Date of approval: