Difference between revisions of "GEOS-Chem v11-02 benchmark history"

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|1-month benchmark finished on:
 
|1-month benchmark finished on:
−
|TBD
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|Sun Apr 16 01:37:36 EDT 2017
 
|-
 
|-
 
|Performance statistics:
 
|Performance statistics:
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|Comments on SURFACE differences:
 
|Comments on SURFACE differences:
 
|
 
|
 +
Below we summarize the notable changes caused by specific updates.
 +
 +
'''[[Updates_in_JPL_Publication_15-10|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.
 +
 +
'''[[Chemistry_Issues#Fixes_to_correct_ALK4_lumping_issue|Fixes to correct ALK4 lumping issue]]'''
 +
*This update caused a decrease in ALK4 and impacted other species, but it did not amount to >10% change.
 +
 +
'''[[PAN|PAN updates]]'''
 +
*Notable changes caused by this update:
 +
**PAN increases over oceans and decreases over land. The decrease over land is caused in part by updates to [[PAN#PAN_dry_deposition|PAN dry deposition]].
 +
**NO decreases over biomass burning regions due to [[PAN#Partitioning_of_NO_biomass_burning_emissions|partitioning of NO biomass burning emissions directly to PAN and HNO3]].
 +
**ALD2 increases global due to the addition of ALD2 emissions from decaying plants and an [[PAN#Acetaldehyde_ocean_source|ALD2 ocean source]].
 +
**MTPA changes are caused by (1) [[PAN#Introduction_of_new_NMVOCs|new monoterpene oxidation]] added to the chemical mechanism and (2) the addition of a [[PAN#GFED_emission_factors|biomass burning emissions source]].
 +
**BENZ, TOLU, and XYLE increase globally because of (1) the addition of a [[PAN#GFED_emission_factors|biomass burning emissions source]] and (2) [[PAN#Aromatic_emissions\scaling of biofuel and RETRO emissions over Asia]].
 +
 +
'''[[EPA/NEI11_North_American_emissions#Monthly_mean_emissions|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 [[Sulfate_aerosols#Fix_error_in_production_of_SO4s.2C_NITs_in_SEASALT_CHEM_routine|bug fix in <tt>SEASALT_CHEM</tt>]] caused a decrease in SO4s and NITs globally
 +
*The [[Sulfate_aerosols#Fix_bug_in_CHEM_NIT_routine|bug fix in <tt>CHEM_NIT</tt>]] did not cause any changes that amount to >10%.
 +
*The [[Sulfate_aerosols#Fix_for_sulfate_production_in_HET_DROP_CHEM|fix for sulfate production in <tt>HET_DROP_CHEM</tt>]] caused an increase in SO2, NH4, and NITs over the oceans and a decrease in SO4, SO4s, NH3, and NITs over the oceans
 +
*[[Sulfate_aerosols#Fix_bugs_in_sulfate_chemistry_routines|Fix bugs in sulfate chemistry routines]]
 +
 +
 +
 +
'''[[Dry_deposition#Bug_in_computation_of_aerodynamic_resistance_RA|Fix bug in dry deposition aerodynamic resistance]]'''
 
*
 
*
 +
 +
 +
'''[[Acetone#Fix_acetone_parameterization_in_hcox_seaflux_mod.F90|Fix acetone parameterization in <tt>hcox_seaflux_mod.F90</tt>]]'''
 +
*
 +
 +
'''[[GEOS-Chem_v11-01#Bug_in_cos.28SZA.29_for_start_of_timestep|Bug fix in cos(SZA) for start of timestep]]'''
 +
*
 +
 +
'''[[GEOS-Chem_v11-02#Include_TOA_pressure_when_calculating_dry_pressure_edges|Include TOA pressure when calculating dry pressure edges]]'''
 +
*
 +
 
|-
 
|-
 
|At 500 hPa, list all species that changed by 10% or more:
 
|At 500 hPa, list all species that changed by 10% or more:

Revision as of 17:56, 20 April 2017

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.

Fixes to correct ALK4 lumping issue

  • This update caused a decrease in ALK4 and impacted other species, but it did not amount to >10% change.

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:


Fix bug in dry deposition aerodynamic resistance


Fix acetone parameterization in hcox_seaflux_mod.F90

Bug fix in cos(SZA) for start of timestep

Include TOA pressure when calculating dry pressure edges

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:
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:
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.

Here are Mean OH and MCF lifetimes from both benchmarks: 

MEAN OH CONCENTRATION [1e5 molec/cm3/s]
---------------------------------------
v11-02a         : 12.3128108012973      # with ifort 11.1.069
v11-02a.GF      : 12.312863157030780    # with gfortran 6.2.0
% Difference    : 0.000425213497755144

MCF LIFETIME w/r/t TROP OH [years]
----------------------------------
v11-02a         : 5.1159                # with ifort 11.1.069
v11-02a.GF      : 5.1159                # with gfortran 6.2.0
% Difference    : 0

Here are the job statistics from both benchmarks: 

Machine information (identical for benchmarks w/ ifort and gfortran)
---------------------------------------------------------------------
Machine used    : holyjacob01.rc.fas.harvard.edu
CPU Type        : Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz

Timing results  : v11-02a benchmark      v11-02a benchmark
                : with ifort 11.1.069    with gfortran 6.2.0
-------------------------------------------------------------
Number of CPUs  :  24                     24
Memory used     :  5.2038 GB              4.5237 GB
Wall Time       :  04:22:54               05:07:26
CPU / Wall Time :  22.5986                17.3599
% of ideal      :  94.12 %                72.33 %
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

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