Benchmark/GEOS-Chem 12.9.0: Difference between revisions

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'''[https://github.com/geoschem/geos-chem/issues/362 Bug fix: Remove inefficient code that was slowing down computation of heterogenous chemistry rates]'''
'''[https://github.com/geoschem/geos-chem/issues/362 Bug fix: Remove inefficient code that was slowing down computation of heterogenous chemistry rates]'''
:This update introduces small changes due to slight differences in molecular weight and Henry's law constants used in the heterogeneous chemistry module. Previously, many of these values were hardcoded, but they are now obtained from the species database for consistency with the rest of the source code. This update also vastly improves the wall clock time spent in the heterogeneous chemistry functions as shown below by the results from internal 1-month benchmark simulations (all completed on all 24 CPUs of holyjacob01.rc.fas.harvard.edu; Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz).
:This update introduces small changes due to slight differences in molecular weight and Henry's law constants used in the heterogeneous chemistry module. Previously, many of these values were hardcoded, but they are now obtained from the species database for consistency with the rest of the source code. In addition, we have eliminated needless computations that were being done for every grid box but only needed to be done in the troposphere.  These updates also vastly improves the wall clock time spent in the heterogeneous chemistry functions as shown below by the results from internal 1-month benchmark simulations (all completed on all 24 CPUs of holyjacob01.rc.fas.harvard.edu; Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz).


   Total seconds spent in heterogeneous chemistry code:
   Total seconds spent in heterogeneous chemistry code:

Revision as of 13:57, 1 July 2020


This page includes information about all benchmark simulations for GEOS-Chem 12.9.0.

GEOS-Chem Classic 1-month benchmark

Benchmark plots

Enable PDF bookmarks1 in the files linked below to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details.

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

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


1All 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.

2Species category and lumped species definitions are simple to adjust. Updating them requires only editing the YAML files.

Benchmark assessment form

Description
New features added into GEOS-Chem
Feature Submitted by
Updates that WILL AFFECT the full-chemistry simulation


Updated halogen chemistry Xuan Wang (Harvard)
Improved cloudwater pH Viral Shah (Harvard)
Jonathan Moch (Harvard)
Update offline lightning data through Dec 2019 Lee Murray (Rochester)
Convert GEOS-Chem species database to YAML format, includes: Melissa Sulprizio (GCST)
Bob Yantosca (GCST)
Update GEOS-Chem core to apply masking and scaling to HEMCO inputs Lizzie Lundgren (GCST)
Bug fix: Restore missing photolysis reactions from 12.8.0 and add an extra error check Melissa Sulprizio (GCST)
Bug fix: Remove inefficient code that was slowing down computation of heterogenous chemistry rates Bob Yantosca (GCST)
Updates that WILL NOT AFFECT the full-chemistry simulation
Corrected issue in GEOS-Chem dry-run where some files were not being properly marked for download Bob Yantosca (GCST)
Bug fixes for the ObsPack diagnostic: Bob Yantosca (GCST)
Skip reading FLASH_DENS and CONV_DEPTH fields when lightning NOx extension is turned off Melissa Sulprizio (GCST)
Updates that affect GCHP only
Fix bug where non-advected species not updated in restart file Sebastian Eastham (MIT)
Version, resolution, met fields used: GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on: Tue Jun 30 04:27:21 EDT 2020
Performance statistics:
  • Compiled with ifort 17.0.4
  • Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
  • Wall time: 08:27:00
  • CPU time / wall time: 20.8684
  • % of ideal performance: 86.95%
  • Memory: 13.5412 GB
Git tag 12.9.0-rc.0
Compared to previous benchmark: 12.8.0
This update will impact:
(select all that apply with boldface) 		Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Emissions, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.9.0/GCC/Plots/GC_12.9.0_Jun26.results.html
Metrics
Global mean OH from log file (% change): 12.2836928383580 x 105 molec/cm3 (+3.55%)
Methyl chloroform lifetime (% change): 5.1257 years (-1.91%)
Methane lifetime (% change): 8.6311 years (-1.69%)
Overview
Comments on observed differences: Below we summarize the notable changes caused by specific updates.

Updated halogen chemistry

Four new species are introduced in this update: sea salt alkalinity (SALAAL, SALCAL) and sea salt chloride (SALACL, SALCCL). This update also includes updated Henry's law constants for several halogen species, update chemical reactions, and updated heterogeneous chemistry as described in Wang et al. (2019). It also includes improved cloudwater pH from Shah et al. (2020). This update causes large differences most notably in the halogen species and is responsible for a 3% increase in the global OH concentration.


Update offline lightning data through Dec 2019

This change causes differences in lightning NOx emissions due to updating the climatology:
###############################################################################
### Emissions totals for inventory LIGHTNOX                                 ###
### Ref = GC_12.8.0; Dev = GC_12.9.0                                        ###
###############################################################################
                                       Ref                 Dev      Dev - Ref
LIGHTNOX NO           :           1.700865            1.828790       0.127925 Tg


Convert GEOS-Chem species database to YAML format

This update introduces minor differences because all species properties are now defined in the species database, not just advected species. This means, chemical species are now defined with molecular weights and this introduces numerical differences when performing unit conversions to the species concentrations throughout the model. Overall differences attributed to these updates are small. This update changed the global mean OH concentration by -0.05%.


Update GEOS-Chem core to apply masking and scaling to HEMCO inputs

This updated introduced small numerical changes. The global mean OH concentration changed by 0.01%.


Bug fix: Restore missing photolysis reactions from 12.8.0 and add an extra error check

This update introduces photolysis reactions that should have been included in 12.7.0 with updated isoprene chemistry from Bates et al. (2019), but were not because of a hardcoded maximum value in the number of photolysis reactions. The largest changes are to the species involved in those photolysis reactions (RIPA, RIPB, RIPC, RIPD, HPALDS1-4, IHN1-4, INPB, INPD, ICPDH, IDHDP, IDHPE, IDCHP, ITHN, ITCN).


Bug fix: Remove inefficient code that was slowing down computation of heterogenous chemistry rates

This update introduces small changes due to slight differences in molecular weight and Henry's law constants used in the heterogeneous chemistry module. Previously, many of these values were hardcoded, but they are now obtained from the species database for consistency with the rest of the source code. In addition, we have eliminated needless computations that were being done for every grid box but only needed to be done in the troposphere. These updates also vastly improves the wall clock time spent in the heterogeneous chemistry functions as shown below by the results from internal 1-month benchmark simulations (all completed on all 24 CPUs of holyjacob01.rc.fas.harvard.edu; Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz).
  Total seconds spent in heterogeneous chemistry code:

  Before halogen chemistry updates      4863
  After  halogen chemistry updates     26348
  After  this fix                        448


Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
  • Aerosols: NH4 NIT SO4 Complex_SOA AERI BrSALA BrSALC ISALA ISALC NITs SO4s
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH2I2 HI HOI OIO
  • Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3
  • Oxidants: O3 OH NOx
  • Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO TOLU XYLE
  • ROy: H2O2 H HO2 O1D OH RO2
  • Secondary_Organic_Aerosols: ASOA3 ASOAN ASOG3 INDIOL LVOCOA SOAIE SOAGX
  • Secondary_Organics: ACTA CH2O HPALDs MACR IEPOX MVK ISOPN GLYX MAP RCHO MP
  • Sulfur: SOx DMS SO2 SO4
  • J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b HCFC22 N2O O2
  • Column AOD: BCPI OCPI SALA SALC SO4 SOA_from_Aqueous_ISOP
List all 500 hPa species and J-Values that changed by 10% or more :
  • Aerosols: NH4 NIT BrSALA BrSALC ISALA ISALC NITs SO4s
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH2I2 HI HOI OIO
  • Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN NHx NH3 NH4 MENO3
  • Oxidants: O3 OH NOx
  • Primary_Organics: EOH ISOP MTPA MTPO LIMO ALK4 C2H6 C3H8 TOLU
  • ROy: H2O2 H HO2 O1D OH RO2
  • Secondary_Organic_Aerosols: ASOA1 ASOA3 ASOG1 ASOG3 SOAGX
  • Secondary_Organics: CH2O HPALDs MACR IEPOX MVK ISOPN GLYX
  • Sulfur: DMS SO2
List all ZONAL MEAN species and J-Values that changed by 10% or more:
  • Aerosols: NH4 NIT SO4 BrSALA BrSALC ISALA ISALC NITs SO4s
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH2I2 CH2ICl CH2IBr HI HOI OIO
  • Nitrogen: NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3
  • Oxidants: O3 OH NOx
  • Primary_Organics: ISOP MTPA MTPO LIMO ALK4 C2H6 C3H8 PRPE TOLU XYLE
  • ROy: H2O2 H HO2 O1D OH RO2
  • Secondary_Organic_Aerosols: ASOA1 ASOA3 ASOG1 ASOG3 SOAGX
  • Secondary_Organics: ACTA ALD2 CH2O MACR IEPOX MEK MVK ISOPN GLYX HCOOH MAP RCHO MP
  • Sulfur: SOx DMS SO2 SO4
List all EMISSIONS that changed by 10% or more:
  • Lightning: NO
  • Ship: NO2 NO O3
  • Total: NO
Approval
Requires further investigation:
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.9.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.8.0 (Ref) and GCHP 12.9.0 (Dev) for a 1-month simulation.

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

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.9.0 (Ref) against GCHP 12.9.0 (Dev) for a 1-month simulation.

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


GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.9.0 - GCHP 12.8.0] against the difference [GC Classic 12.9.0 - GC Classic 12.8.0], 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.

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