GEOS-Chem v11-02 benchmark history

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On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for GEOS-Chem v11-02.

1-year full-chemistry benchmarks

TBD

1-month benchmarks

v11-02a

Here is the assessment form for 1-month benchmark simulation v11-02a.

Description
Features affecting the full-chemistry simulation in this benchmark:
Feature Submitted by
Update chemistry rate constants based on JPL Publication 15-10 Barron Henderson (US EPA),
Mat Evans (U. York), &
Oxidants and Chemistry WG
Fixes to correct ALK4 lumping issue Barron Henderson (US EPA)
PAN updates Emily Fischer (CSU)
Monthly mean NEI2011 emissions GCST &
Katie Travis (Harvard)
Bug fixes in the GEOS-Chem sulfate module:
Prasad Kasibhatla (Duke)
Prasad Kasibhatla (Duke)
Qianjie Chen (UW)
Viral Shah (UW)
Fix bug in dry deposition aerodynamic resistance Brian Boys (Dalhousie)
Fix acetone parameterization in hcox_seaflux_mod.F90 GCST
Bug fix in cos(SZA) for start of timestep Lizzie Lundgren (GCST)
Bug fixes for diagnostics:
Aaron van Donkelaar (Dalhousie)
Jenny Fisher (U. Wollongong)
GCST
GCST
Jenny Fisher (U. Wollongong)
Chris Holmes (Florida State)
Include TOA pressure when calculating dry pressure edges Seb Eastham (Harvard)
Features not affecting the full-chemistry simulation in this benchmark:
Feature Submitted by
Implement ISORROPIA v2.0 as a Fortran module Seb Eastham (Harvard)
GCST
Updates to the HEMCO emissions component:
Christoph Keller (NASA GMAO)
Seb Eastham (Harvard)
Jessica Morena (Dalhousie)
Brian Boys (Dalhousie) & GCST
Updates to gain computational speedup:
Mike Long (Harvard)
Bob Yantosca (GCST)
Fixed typo in routineINIT_WINDOW Bob Yantosca (GCST)
netCDF file I/O updates:
Chris Holmes (Florida State)
Andy Jacobson (NOAA)
GCST
Makefile and build sequence updates:
Jiawei Zhang (Harvard)
GCST
Bug fixes for running UCX in ESMF environment Christoph Keller (NASA GMAO)
Removal of obsolete variables: GCST
Version, resolution, met fields used: v11-02, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Sun Apr 16 01:37:36 EDT 2017
Performance statistics:
  • Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 04:22:54
  • CPU time / wall time: 22.5896
  • % of ideal performance: 94.12%
  • Memory: 5.2038 GB
Compared to previous benchmark: v11-01 public release
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-02/v11-02a/v11-02a.results.html
Plots may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-02/v11-02a/
Metrics
Global mean OH (from log file): 12.3128108012973 x 105 molec/cm3
Methyl chloroform lifetime: 5.1159 years
Did either of these change by more than 5%? No. Mean OH changed by -2.57% and MCF lifetime changed by 2.94%.
At the SURFACE, list all species that changed by 10% or more: NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, CHBr3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG2, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASO3G3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on SURFACE differences:

Below we summarize the notable changes caused by specific updates.

Update chemistry rate constants based on JPL Publication 15-10

  • Notable changes caused by this update:
    • >10% increase in MVK, PRPE, N2O5, Cl2O2
    • >10> decrease in MACR, PMN, CHBr3
  • Matt Evans wrote
    The only major changes [from JPL 15-10] are to do with the MVK / MACR + OH changes we expected, changes in the PRPE +OH and changes in the N2O5 / HO2NO2 formation / loss rates. Unless I’ve missed something I think we are happy with all of this.

PAN updates

Monthly mean NEI2011 emissions

  • This update caused numerical noise differences over the US in NO, ALK4, RCHO, N2O5, DMS, SO2, NH3, NIT, BCPO, OCPO, NO2, NO3, HNO2, BENZ, TOLU, XYLE

Bug fixes in the GEOS-Chem sulfate module:

  • The bug fix in SEASALT_CHEM caused a decrease in SO4s and NITs globally
  • The bug fix in CHEM_NIT did not cause any changes that amount to >10%.
  • The fix for sulfate production in HET_DROP_CHEM caused an increase in SO2, NH4, and NITs over the oceans and a decrease in SO4, SO4s, NH3, and NITs over the oceans
  • The bug fixes in sulfate chemistry routines caused changes in SO2, SO4, SO4s, NH3, NH4, NIT, and NITs.
    • Viral Shah wrote:
      The effects of my proposed fixes are a bit more pronounced during the NH winter. The plots show significant increases in sulfate concentrations over large areas of the NH. The SO4 increases are accompanied by decreases in NIT in some areas. The increase in SO4 in the cold areas of NH is mostly because of the correction to HNO3 effective Henry's law coefficient that leads to higher cloud water pH (between 4 and 5) and higher production by in-cloud oxidation by O3. The lower SO4 concentrations in the SH are probably due to the fix to ∆H/R parameter. I expect the effects [of the LWC units fix] to be relatively small.

Fix bug in dry deposition aerodynamic resistance

  • This update caused slight decreases in many species at the surface. Species changed by >10% from this update include HNO3, H2O2, N2O5, and NIT.

The following updates impacted species concentrations slightly, but the changes did not amount to >10%.

At 500 hPa, list all species that changed by 10% or more: NO, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, CHBr3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClO, HOCl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG2, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASO3G3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on 500 hPa differences: See comments on surface differences.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, PAN, ALK4, ISOP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, PRPE, C3H8, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, Br2, Br, BrO, HOBr, HBr, BrNO2, CHBr3, MPN, ISOPND, ISOPNB, MOBA, HAC, GLYC, MVKN, MACRN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClO, HOCl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on ZONAL MEAN differences: See comments on surface differences.
In the EMISSION RATIO maps, list all species that changed by 10% or more:
  • Anthropogenic: ALD2, ALK4, BC, C2H6, C3H8, CH2O, CO, MEK, NH3, NO, OC, PRPE, SO2, SO4
  • Biomass: ACET, ALD2, ALK4, BC, C2H6, C3H8, CH2O, CO, MEK, NH3, NO, OC, PRPE, SO2
  • Biogenic: ALD2, ISOP, PRPE
  • CO from MONOT
  • NO fertilizer and soil
Comments on EMISSION RATIO differences:
Additional or summary comments: Results from our v11-02a benchmark using the GNU Fortran Compiler

We also performed an identical v11-02a benchmark, having compiled GEOS-Chem with gfortran 6.2.0. We obtained essentially identical results to the benchmark reported in this table, which used ifort 11.1.069 to compile GEOS-Chem. For more details, see this post on our GNU Fortran compiler wiki page.

Approval
Requires further investigation: TBD
Approved by: TBD
Date of approval: TBD

--Melissa Sulprizio (talk) 18:46, 14 April 2017 (UTC)
--Bob Yantosca (talk) 16:05, 20 April 2017 (UTC)

1-year Rn-Pb-Be benchmarks

TBD