GEOS-Chem v9-01-02 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 v9-01-02.

NOTE: to save disk space, we have created TARBALL (*.tar.gz) files for the 1-month benchmark plots. You can download each TARBALL file and extract (with tar xvzf) it to view the plots.

1-year benchmarks

For each benchmark run, plots comparing modeled aerosols to observations are now available. The plotting program and observations were provided by Colette Heald.

Run0

Three GEOS-Chem model versions were compared to each other:

Color Quantity Plotted Met Type Anthro
emissions
Biofuel
emissions
Biomass
emissions
Lightning
Emissions
Linoz Annual Mean OH
[105 molec/cm3]
Red v9-01-01-Run0 GEOS-5, 4x5 Same as v8-02-04-Run0
+ ICOADS ship emissions
+ Bug fixes for ship emissions
Same as v8-02-04-Run0
+ Bug fix for biofuels in EPA/NEI05
Same as v8-02-04-Run0
(GFED2 monthly inventory)
Same as v8-02-04-Run0 ON 11.865
Green v9-01-01-Run1 GEOS-5, 4x5 " " " " " " + Updated LNOx algorithm from Lee Murray ON 12.242
Blue v9-01-02-Run0 GEOS-5, 4x5 + Fix for GEIA emissions scaling factor
+ Imposed seasonality on Streets 2000 NH3 emissions
+ Bug fix in ship NOx emissions
+ Bug fix for Streets biofuel emissions
" " " " ON 12.233
Black Observations              

The output plots for Run0 (both PostScript and PDF format) may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v9-01-02/geos5/2005/Run0/output/ps
mget *
cd gcgrid/geos-chem/1yr_benchmarks/v9-01-02/geos5/2005/Run0/output/pdf
mget *

You may also view the PDF files online by pointing your browser to

ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-01-02/geos5/2005/Run0/output/pdf/

--Bob Y. 15:11, 15 November 2011 (EST)

Run1

Three GEOS-Chem model versions were compared to each other:

Color Quantity Plotted Met Type Anthro
emissions
Biofuel
emissions
Biomass
emissions
Lightning
emissions
Linoz Annual Mean OH
[105 molec/cm3]
Red v9-01-01-Run1 GEOS-5, 4x5 Same as v9-01-01-Run0 Same as v9-01-01-Run0 Same as v9-01-01-Run0
(GFED2 monthly inventory)
Same as v9-01-01-Run0
+ Updated LNOx algorithm from Lee Murray
ON 12.242
Green v9-01-02-Run0 GEOS-5, 4x5 + Fix for GEIA emissions scaling factor
+ Imposed seasonality on Streets 2000 NH3 emissions
+ Bug fix in ship NOx emissions
+ Bug fix for Streets biofuel emissions
" " " " ON 12.233
Blue v9-01-02-Run1 GEOS-5, 4x5 + RETRO anthropogenic VOC emissions " " + GFED3 monthly inventory " " ON 12.332
Black Observations              

The output plots for Run1 (both PostScript and PDF format) may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v9-01-02/geos5/2005/Run1/output/ps
mget *
cd gcgrid/geos-chem/1yr_benchmarks/v9-01-02/geos5/2005/Run1/output/pdf
mget *

You may also view the PDF files online by pointing your browser to

ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-01-02/geos5/2005/Run1/output/pdf/

--Bob Y. 16:06, 15 November 2011 (EST)

Rn-Pb-Be simulation

We also conducted a 1-year Rn-Pb-Be_simulation with GEOS-Chem v9-01-02. Please follow the links below to see the budget of Pb210 and Be7 from 1-year Rn-Pb-Be simulations for v9-01-02 and previous versions:

  1. Budget of Pb210 from 1-year benchmark simulations
  2. Budget of Be7 from 1-year benchmark simulations

Helen Amos has run several 1-year Rn-Pb-Be simulations to test the impact of the GEOS-5 and MERRA met fields on the wet scavenging algorithms used by GEOS-Chem. We invite you to view the comparison plots and budgets that she created.

--Bob Y. 14:03, 29 November 2011 (EST)

Comments about the 1-year benchmarks

Dylan Jones wrote:

I only looked at the tracers relevant to our work and they seem fine. Ethane was the only one that we noticed was problem; we do care about ethane here. Kim Strong's group is retrieving ethane from their ground-based FTIR measurements and attached is a comparison from Cyndi Whaley of v9-01-02 with those measurement for 2006. Previously, v8-02-01 was high relative to the TAO (Toronto Atmospheric Observatory) measurements, but now the model is way too low, with a very weak seasonal cycle. Replacing the emissions would be helpful.

Dylan Millet wrote:

The benchmark plots look reasonable to me. Along with C2H6, the C3H8 emissions are now a lot lower with RETRO (as we knew already). Looking at the aircraft profile plots in the benchmark, while the agreement for ethane is fairly consistently degraded with the lower emissions, the same is not the case for propane where on balance there seems an improvement.

Jennifer Logan wrote:

The benchmark results look OK to me too. The changes in ozone in the tropics seem to be related to the changes in NOx, and I expect they result from lower GFED3 emissions in early 2005 from SE Asia and Indonesia. I noticed the propane results also. I focused mostly on the comparisons with observations and the difference plots for O3, NOx, CO.

Jeffrey Pierce wrote:

There are certainly differences in all aerosols that are either secondary (e.g. SO4), partitioning (e.g. NH4 and NIT) or aging (e.g. OCPI, OCPO). The inert aerosols (dust and sea-salt) are unchanged. I'm guessing that oxidation fields changed somewhat which changed the formation rate of SO4. This will feedback on NH4 and NIT. The OC and BC might be changing due to the biomass fields changing.
Nothing seems alarming to me. There are some large changes in NH4 and NIT at 500 hpa, but I expect this to just be due to the non-linearities of partitioning.
I'm ok to approve 9.1.2.

v9-01-02s

Here is the assessment form for 1-month benchmark simulation v9-01-02s.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • RETRO fix: Chris Holmes (UC Irvine) and Dylan Millet (U. Minnesota)
  • Streets biofuel fix: Chris Millet (Harvard)
  • EDGAR ship fix: GEOS-Chem Support Team and Chris Holmes (UC Irvine)
  • Ship NOx fix: Chris Holmes (UC Irvine)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Tue Oct 25 16:42:13 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 1:38
  • CPU time / wall time: 7.6247
  • % of ideal performance: 95.31
Compared to previous benchmark: v9-01-02r
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02s.tar.gz
Metrics
Global mean OH (from log file): 13.2015757058258 x 105 molec cm-3
Methyl chloroform lifetime: 4.7383 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: NOx, ALK4, HNO3, MEK, ALD2, PPN, PRPE, C3H8, C2H6, N2O5, HNO4, NIT, NITs
Comments on SURFACE differences: Minor increase in NOx and its oxidation products mainly over N. midlatitude oceans. HNO3 increases by up to ~30-40% in some locations. This HNO3 increase is expected from the bug fix to ship NOx emissions (37% increase). N2O5 increases by 50% or more over part of the N. Pacific. Decreases for several VOCs mainly over Europe, Africa, S. America, where RETRO is not overwritten by regional inventories.
At 500 hPa, list all species that changed by 10% or more: ALK4, MEK, ALD2, PRPE, C3H8,
Comments on 500 hPa differences: Surface changes propagate to free troposphere in a few cases.
In the ZONAL MEAN differences, list all species that changed by 10% or more: HNO3, N2O5, NIT, NITs, MEK, PRPE
Comments on ZONAL MEAN differences: HNO3, N2O5, NIT, NITs appears to have increased by 10% or a bit more between 40-50N. Zonal mean decreases for MEK, PRPE exceed 10% due to decreases over Europe, S. America, Africa.
In the EMISSION RATIO maps, list all species that changed by 10% or more: ACET, ALD2, ALK4, C2H6, C3H8, CH2O, MEK, PRPE
Comments on EMISSION RATIO differences: Only biofuel emissions changed, as expected due to the biofuel bug fix.
Additional or summary comments:
Approval
Requires further investigation:
Approved: Chris Holmes
Date of approval: 5 Nov 2011

--Melissa Payer 17:12, 25 October 2011 (EDT)

v9-01-02r

Here is the assessment form for 1-month benchmark simulation v9-01-02r.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Daven Henze (Colorado U)
  • Prasad Kasibhatla (Duke)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Thu Oct 20 12:37:34 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.925 GHz x 8 CPU)
  • Wall time: 0:56
  • CPU time / wall time: 7.5528
  • % of ideal performance: 94.41%
Compared to previous benchmark: v9-01-02q
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02r.tar.gz
Metrics
Global mean OH (from log file): 13.1888783819852 x 105 molec cm-3
Methyl chloroform lifetime: 4.7442 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: None.
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more: MVK, MACR, PMN, PRPE, NH3, NIT
Comments on 500 hPa differences: The only large fractional changes occur for very small absolute values.
In the ZONAL MEAN differences, list all species that changed by 10% or more: Almost all change by more than 10% somewhere near/above the tropopause. Only the species identified above at the 500 hPa level are changing much below the tropopause. NH3 and NIT seem to have the largest / most random changes, likely owing to previously identified issue with inorganic aerosol partitioning.
Comments on ZONAL MEAN differences: None of the changes are large with respect to absolute values. The only species that even registers in terms of an absolute difference is HNO4, which changes by a few ppt in the stratosphere.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None.
Comments on EMISSION RATIO differences:
Additional or summary comments: This is a minor correction to the update made in v9-01-02a.
Approval
Requires further investigation: No
Approved: Yes, Daven Henze
Date of approval: 10/20/2011

--Melissa Payer 12:40, 20 October 2011 (EDT)

v9-01-02q

Here is the assessment form for 1-month benchmark simulation v9-01-02q.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Fri Oct 14 15:09:19 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-06-c.as.harvard.edu (2.792 GHz x 16 CPU)
  • Wall time: 1:32
  • CPU time / wall time: 7.6359
  • % of ideal performance: 95.45%
Compared to previous benchmark: v9-01-02p
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02q.tar.gz
Metrics
Global mean OH (from log file): 13.1979262548812 x 105 molec cm-3
Methyl chloroform lifetime: 4.7416 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: NH3, NIT
Comments on SURFACE differences: Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.
At 500 hPa, list all species that changed by 10% or more: NH3, NIT
Comments on 500 hPa differences: Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NH3, NIT
Comments on ZONAL MEAN differences: Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
Additional or summary comments: ISORROPIA still introduces numerical noise in GEOS-Chem simulations. To eliminate the effect from ISORROPIA, we re-ran 1-month benchmarks for v9-01-02p and v9-01-02q with ISORROPIA turned off. We have created this frequency distribution histogram plot. When ISORROPIA is turned off, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram).


This update should affect the 2° x 2.5° resolution simulation. To examine the changes caused by the centralized chemistry time step, we also ran 1-month benchmarks for v9-01-02p and v9-01-02q at 2° x 2.5° resolution. The benchmark plots may be viewed at ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02q_2x2.5.tar.gz.

Approval
Requires further investigation: No
Approved: Yes --Jmao 17:09, 17 October 2011 (EDT)
Date of approval: 10/17/2011

--Melissa Payer 14:47, 17 October 2011 (EDT)

v9-01-02p

Here is the assessment form for 1-month benchmark simulation v9-01-02p.

Description
New features added into GEOS-Chem: Various bug fixes that will have no impact on the standard 1-month full-chemistry benchmark simulation:
Developer name(s) and institution(s):
  • OH fix: Chris Holmes (UC Irvine)
  • Hg fixes: Chris Holmes (UC Irvine)
  • Nested-grid fixes: Luke Schiferl (Colo. State U.) and Aaron van Donkelaar (Dalhousie)
  • APM fixes: Gan Luo (SUNY Albany)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Sep 28 18:15:24 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 1:39
  • CPU time / wall time: 7.6389
  • % of ideal performance: 95.49%
Compared to previous benchmark: v9-01-02o
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, Diagnostics, Other (please specify): We expect to see no changes from v9-01-02o
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02p.tar.gz
Metrics
Global mean OH (from log file): 13.1979474791340 x 105 molec cm-3
Methyl chloroform lifetime: 4.7416 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: NH3, NIT
Comments on SURFACE differences: Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.
At 500 hPa, list all species that changed by 10% or more: NH3, NIT
Comments on 500 hPa differences: Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.
In the ZONAL MEAN differences, list all species that changed by 10% or more: ISOP, NH3, NIT
Comments on ZONAL MEAN differences: Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
Additional or summary comments: ISORROPIA still introduces numerical noise in GEOS-Chem simulations. To eliminate the effect from ISORROPIA, we re-ran 1-month benchmarks for v9-01-02o and v9-01-02p with ISORROPIA turned off. We have created this frequency distribution histogram plot. When ISORROPIA is turned off, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram).
Approval
Requires further investigation: No
Approved: Yes
Date of approval: 29 Sep 2011

--Melissa Payer 16:53, 28 September 2011 (EDT)

v9-01-02o

Here is the assessment form for 1-month benchmark simulation v9-01-02o.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Dylan Millet (U. Minnesota)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Fri Sep 23 16:58:05 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 01:39
  • CPU time / wall time: 7.6378
  • % of ideal performance: 95.47%
Compared to previous benchmark: v9-01-02n
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02o.tar.gz
Metrics
Global mean OH (from log file): 13.1978858937111 x 105 molec cm-3
Methyl chloroform lifetime: 4.7416 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: Decreases in ALK4, MEK, ALD2, PRPE, C3H8, mainly over N. Africa and Europe. Smaller decreases for species PPN, PAN, R4N2, RCHO, C3H8, C2H6, N2O5, NOx (a couple grid boxes) over the same area. ACET increases ~30% over Europe because of a fix to RETRO ketone partitioning between MEK and acetone. CO decreases ~10ppb (but <10%) in surface air over Europe.
Comments on SURFACE differences: Magnitude and pattern of changes as expected for getting rid of residential biofuel double counting.
At 500 hPa, list all species that changed by 10% or more: ALK4, MEK, PRPE.
Comments on 500 hPa differences: The change propagates to the free troposphere for just a couple species.
In the ZONAL MEAN differences, list all species that changed by 10% or more: MEK decreases ~10% around 35S and 20N. ALK4 decreases ~6% in the zonal mean around 20N. PRPE decreases ~10% around 40N.
Comments on ZONAL MEAN differences: Patterns consistent with surface changes noted above.
In the EMISSION RATIO maps, list all species that changed by 10% or more: ALK4, MEK
Comments on EMISSION RATIO differences: Patterns consistent with surface changes noted above.
Additional or summary comments:
Approval
Requires further investigation: No
Approved: Yes. --Dbm 11:03, 27 September 2011 (EDT) (Dylan Millet)
Date of approval: 9/27/2011

--Melissa Payer 12:32, 23 September 2011 (EDT)

v9-01-02n

Here is the assessment form for 1-month benchmark simulation v9-01-02n.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • GFED3: Prasad Kasibhatla (Duke U.)
  • APM fixes: Gan Luo (SUNY Albany)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Thu Sep 8 16:57:34 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-03-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 1:39
  • CPU time / wall time: 7.5995
  • % of ideal performance: 94.99%
Compared to previous benchmark: v9-01-02m
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, Diagnostics, Other (please specify): APM Microphysics (will not affect the standard simulation)
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02n.tar.gz
Metrics
Global mean OH (from log file): 13.1946336476655 x 105 molec cm-3
Methyl chloroform lifetime: 4.7422 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: Most species changed in specific regions by more than 10%
Comments on SURFACE differences: Changes reflect changes from GFED2 to GFED3 inventory, as well as due to the resulting change in OH
At 500 hPa, list all species that changed by 10% or more: A few species changed is specific region
Comments on 500 hPa differences: Smaller effect of change from GFED2 to GFED3 at 500 hPa relative to surface
In the ZONAL MEAN differences, list all species that changed by 10% or more: Most species changed, especially at high northern latitudes
Comments on ZONAL MEAN differences: Changes reflect changes from GFED2 to GFED3 inventory, as well as due to the resulting change in OH in lower troposphere
In the EMISSION RATIO maps, list all species that changed by 10% or more: Most species changed in specific regional locations
Comments on EMISSION RATIO differences: Reflects changes from GFED2 to GFED3
Additional or summary comments: Zonal-mean OH diff plots seems to show large change in stratosphere - I assume this is some sort of artifact of how plot was done?

NOTE: For the zonal-mean OH difference plots, you should look at the plot with the dynamic range, i.e. v9-01-02n.zonal_differences.dyn_range.pdf. In the OH plots, the gray areas are where the stratosphere occurs and OH isn't plotted there.

Approval
Requires further investigation: No
Approved: Yes (Prasad Kasibhatla)
Date of approval: 9/22/11

--Melissa Payer 13:42, 9 September 2011 (EDT)

v9-01-02m

Here is the assessment form for 1-month benchmark simulation v9-01-02m.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Aug 31 11:22:03 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 01:39
  • CPU time / wall time: 7.6143
  • % of ideal performance: 95.18%
Compared to previous benchmark: v9-01-02l
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02m.tar.gz
Metrics
Global mean OH (from log file): 13.1547959532210 x 105 molec cm-3
Methyl chloroform lifetime: 4.7594 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: None
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more: NH3, NIT
Comments on 500 hPa differences: Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NH3, NIT
Comments on ZONAL MEAN differences: Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
Additional or summary comments: Further testing by Bob Yantosca has shown that the current implementation of ISORROPIA still introduces numerical noise in GEOS-Chem simulations after a few days of run time. The -fp-model source is not sufficient to eliminate this numerical noise.

To eliminate the effect from ISORROPIA, we re-ran the benchmarks for v9-01-02l and v9-01-02m with ISORROPIA turned off. We have created this frequency distribution histogram plot. As you can see, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram).

We have received a fix from Shannon Capps that should eliminate the ISORROPIA numerical noise issue. We will evaluate this fix in the next benchmark.

Approval
Requires further investigation: No
Approved: Yes
Date of approval: 07 Sep 2011

--Bob Y. 15:42, 7 September 2011 (EDT)

v9-01-02l

Here is the assessment form for 1-month benchmark simulation v9-01-02l.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • APM: Fangqun Yu and Gan Luo (SUNY Albany)
  • ISORROPIA fix: Shannon Capps (Georgia Tech)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Mon Aug 22 17:05:14 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.926 GHz x 8 CPU)
  • Wall time: 00:58
  • CPU time / wall time: 7.2856
  • % of ideal performance: 91.07%
Compared to previous benchmark: v9-01-02k
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, Diagnostics, Other (please specify): APM code should not affect 1-month standard simulation
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02l.tar.gz
Metrics
Global mean OH (from log file): 13.1547627780606 x 105 molec cm-3
Methyl chloroform lifetime: 4.7594 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: None
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more: NH3, NIT
Comments on 500 hPa differences: The concentrations of NH3, NIT in the areas where differences occur are very small. This is the numerical noise caused by ISORROPIA in version v9-01-02k.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NH3, NIT
Comments on ZONAL MEAN differences: Small numerical differences cause large percent differences. Also attributable to the ISORROPIA numerical noise issue in v9-01-02k.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
Additional or summary comments: In v9-01-02l, we have added the fix to prevent numerical noise in ISORROPIA from entering into the output. This fix was not present in the previous benchmark v9-01-02k. Therefore, in the benchmark output plots we see some minor numerical differences in NH3 and NIT, which are species directly affected by ISORROPIA II.

To remove the effect of the numerical noise in ISORROPIA II, we ran two 1-week simulations of v9-01-02k and v9-01-02l with the numerical fix applied. The binary punch files from both simulations were 100% binary identical. Also, both simulations had an identical Mean OH concentration (12.9882039409349 x 1e5 molec/cm3). We created this frequency distribution plot from both 1-week simulations. As you can see, the output of both simulations are identical.

Therefore, we can say that the source code updates made to implement APM microphysics do not affect the 1-month benchmark simulation. (We recommend that the developers of APM do further testing to make sure that the microphysics package is working properly.)

Approval
Requires further investigation: No
Approved: Yes
Date of approval: 23 Aug 2011

--Bob Y. 14:37, 26 August 2011 (EDT)

v9-01-02k

Here is the assessment form for 1-month benchmark simulation v9-01-02k.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Wes Reinhart (U. Minnesota)
  • Dylan Millet (U. Minnesota)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Aug 17 12:52:36 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.926 GHz x 8 CPU)
  • Wall time: 00:57
  • CPU time / wall time: 7.3259
  • % of ideal performance: 91.57%
Compared to previous benchmark: v9-01-02j
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02k.tar.gz
Metrics
Global mean OH (from log file): 13.1547845430825 x 105 molec cm-3
Methyl chloroform lifetime: 4.7594 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: Large relative changes for ALK4, PRPE, C3H8. Smaller relative changes for PAN, ACET, MEK, ALD2, RCHO, PPN, R4N2, C2H6, N2O5 and HNO4, DMS (the last three barely 10% in 1 spot)
Comments on SURFACE differences: Emission changes relative to GEIA and to the regional inventories are described here. Absolute differences are as expected based on the emission changes. ALK4 emissions do not change very much globally but there are large regional changes. RETRO includes non-zero hydrocarbon emissions over the oceans due to ship traffic; this leads to quite large relative but small absolute changes for some hydrocarbons over the oceans (e.g., PRPE, ALK4, C3H8). Acetone changes are due to changes in precursor emissions as anthropogenic acetone emissions are not in RETRO.
At 500 hPa, list all species that changed by 10% or more: ALK4, MEK, ALD2, RCHO, R4N2, PRPE, C3H8. NH3 and NIT exhibit random changes as noted previously.
Comments on 500 hPa differences: The larger surface changes propagate to 500 hPa to a certain extent.
In the ZONAL MEAN differences, list all species that changed by 10% or more: ALK4 and C3H8 change by >10% over much of NH. Absolute differences generally < 0.5ppbC. Zonal means for MEK, RCHO, PPN, R4N2 also change by >10% in certain latitudes in line with precursor emission changes. Large relative changes for PRPE, but absolute changes only exceed 0.01 ppbC in the tropics due to emission changes over Africa and S. America.
Comments on ZONAL MEAN differences: See above.
In the EMISSION RATIO maps, list all species that changed by 10% or more: ALK4, C2H6, C3H8, MEK, PRPE.
Comments on EMISSION RATIO differences: Emission changes as expected. They are described in more detail here, including the chemical impacts. One point to note is that global emissions of C3H8 and C2H6 decrease by >2x with RETRO. Applications looking specifically at these tracers will need to keep this in mind. Other compounds such as ALK4 and PRPE have large regional emission changes but don't change as much globally.
Additional or summary comments:
Approval
Requires further investigation: No
Approved: Yes (dbm), Yes (wfr).
Date of approval: 08/17/2011

--Bob Y. 12:59, 17 August 2011 (EDT)

v9-01-02j

Here is the assessment form for 1-month benchmark simulation v9-01-02j.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Jenny Fisher (Harvard)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Tue Aug 16 12:44:35 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 01:31
  • CPU time / wall time: 7.6058
  • % of ideal performance: 95.07%
Compared to previous benchmark: v9-01-02i
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection (MERRA only), Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics (MERRA only), Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02j.tar.gz
Metrics
Global mean OH (from log file): 13.1516003618353 x 105 molec cm-3
Methyl chloroform lifetime: 4.7610 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: HNO3, NH3, NH4, NIT
Comments on SURFACE differences: New simulation introduces seasonal variation in NH3 emissions in Asia (previously used annual mean values). This 1-month benchmark is for July, when agricultural emissions in India and China are high, so as expected surface NH3 is higher in this simulation. NH3 is lower over Indonesia, which is consistent with the monthly scalars for July for that region. Other species (NH4, HNO3, NIT) are affected via thermodynamic partitioning with NH3.
At 500 hPa, list all species that changed by 10% or more: HNO3, NH3, NH4, NIT
Comments on 500 hPa differences: As expected from changes at surface
In the ZONAL MEAN differences, list all species that changed by 10% or more: HNO3, NH3, NH4, NIT
Comments on ZONAL MEAN differences: As expected from NH3 emission changes, differences are greatest at ~30N at surface, but extend latitudinally and vertically.
In the EMISSION RATIO maps, list all species that changed by 10% or more: NH3 anthro
Comments on EMISSION RATIO differences: This update directly changes NH3 anthro emissions
Additional or summary comments: NOTE: The minor fixes in routine DO_MERRA_CONVECTION do not impact the results of this benchmark simulation.
Approval
Requires further investigation: No
Approved: Yes
Date of approval: 16 Aug 2011

--Bob Y. 16:32, 16 August 2011 (EDT)

v9-01-02i

Here is the assessment form for 1-month benchmark simulation v9-01-02i.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Jenny Fisher (Harvard)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Mon Aug 15 13:00:01 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU)
  • Wall time: 01:32
  • CPU time / wall time: 7.5741
  • % of ideal performance: 94.68%
Compared to previous benchmark: v9-01-02h
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/1mo_benchmarks/v9-01-02/v9-01-02i.tar.gz/
Metrics
Global mean OH (from log file): 13.1718619904482 x 105 molec cm-3
Methyl chloroform lifetime: 4.7556 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: HNO3, SO4, MSA, NH3, NH4, NIT, BCPI, OCPI, BCPO, OCPO
Comments on SURFACE differences: Dry deposition velocity generally decreased, so aerosol concentrations at the polar surface increased (60-90S, 70-90N). Related impacts on a few gas-phase species (NH3, HNO3) with concentrations governed by thermodynamic equilibrium of aerosol species.
At 500 hPa, list all species that changed by 10% or more: NH3, NIT
Comments on 500 hPa differences: Quasi-random differences due to change in aerosol species that drive thermodynamic partitioning.
In the ZONAL MEAN differences, list all species that changed by 10% or more: HNO3, SO4, MSA, NH3, NH4, NIT, BCPI, OCPI, BCPO, OCPO
Comments on ZONAL MEAN differences: Dry deposition velocity generally decreased, so aerosol concentrations at the polar surface increased (60-90S, 70-90N). Related impacts on a few gas-phase species (NH3, HNO3) with concentrations governed by thermodynamic equilibrium of aerosol species.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences: N/A
Additional or summary comments: NOTE: The ND67 diagnostic modification for MERRA does not impact the results of this benchmark simulation.
Approval
Requires further investigation: No
Approved: Yes
Date of approval: 15 Aug 2011

--Bob Y. 09:56, 16 August 2011 (EDT)

v9-01-02h

Here is the assessment form for 1-month benchmark simulation v9-01-02h.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Dylan Millet (U. Minnesota)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Thu Aug 11 11:30:21 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-05-c.as.harvard.edu (2.793 GHz x 16 CPU)
  • Wall time: 00:58
  • CPU time / wall time: 7.6116
  • % of ideal performance: 95.15%
Compared to previous benchmark: v9-01-02g
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02h.tar.gz
Metrics
Global mean OH (from log file): 13.1718562359138 x 105 molec cm-3
Methyl chloroform lifetime: 4.7556 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: Large changes (> 50%) for: ALK4, PAN, ACET, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6, N2O5, MP. Smaller changes (~10-25%) for NOx, ISOP, HNO3, H2O2, MVK, MACR, PMN, CH2O, HNO4, DMS, SO4, NH3, NH4, NIT
Comments on SURFACE differences: Changes are all over and immediately downwind of southern Africa, as expected. Large changes to the anthropogenic hydrocarbons because their emissions were strongly decreased over Botswana to correct scaling bug. Large changes to some of their immediate oxidation products (ACET, RCHO, PPN, ALD2, PAN, etc.). Some smaller changes to other species due to secondary chemical effects (OH has increased somewhat in the outflow from southern Africa because we no longer have the artificially elevated VOC concentrations).
At 500 hPa, list all species that changed by 10% or more: ALK4, ISOP, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6. NH3 and NIT exhibit random noisy changes at 500 hPa.
Comments on 500 hPa differences: The changes over and downwind of southern Africa propagate to the free troposphere for some of the species. Changes are weaker than at the surface and exhibit the expected patterns. For NH3 and NIT the 500 hPa absolute changes are near zero; this issue has been reported previously.
In the ZONAL MEAN differences, list all species that changed by 10% or more: PAN, ALK4, ACET, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6, N2O5, NH3, NIT. OH changes by ~5% in the zonal mean around 25 degrees South.
Comments on ZONAL MEAN differences: Zonal mean differences of >10% are restricted to the emitted anthropogenic hydrocarbons and some of their immediate oxidation products, as expected. Same issue as above for NH3 and NIT; the absolute changes are negligible. Changes in N2O5 just exceed 10% due to corresponding changes in NOx of <10%.
In the EMISSION RATIO maps, list all species that changed by 10% or more: ACET, ALK4, C2H6, C3H8, MEK, PRPE
Comments on EMISSION RATIO differences: Emission changes for the anthropogenic hydrocarbons over southern Africa as expected.
Additional or summary comments:
Approval
Requires further investigation: No
Approved: Yes
Date of approval: 12 Aug 2011

--Bob Y. 11:31, 15 August 2011 (EDT)

v9-01-02g

Here is the assessment form for 1-month benchmark simulation v9-01-02g.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Sungshik Patrick Kim (Harvard)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Aug 3 15:00:30 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 01:32
  • CPU time / wall time: 7.6115
  • % of ideal performance: 95.14%
Compared to previous benchmark: v9-01-02f
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02g.tar.gz
Metrics
Global mean OH (from log file): 13.1512226781986 x 105 molec cm-3
Methyl chloroform lifetime: 4.7648 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: None
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more: NH3, NIT
Comments on 500 hPa differences: These are are likely due to small number differences, probably caused by ISORROPIA.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NIT
Comments on ZONAL MEAN differences: Caused by small number differences near the limit of single precision.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
Additional or summary comments: Aerosol optical depths (AOD) are recomputed after chemistry but before diagnostics are archived. This will make sure that any removal of aerosol by chemistry or deposition will be reflected in the archived AOD diagnostics.

There is a known issue in ISORROPIA that can cause random differences, especially in species like HNO3, NH3, and NIT. This issue has not been resolved in v9-01-02g.

In order to remove the effects of the ISORROPIA II issue, we have created this frequency distribution histogram. The histogram reflects results from GEOS-Chem 1-week simulations of v9-01-02g vs v9-01-02f with ISORROPIA turned off. As you can see, 100% of all of the transported tracers fall into the central bin in the histogram. This lets us say with certainty that the small differences that we see in the output plots for v9-01-02g are not caused by the AOD diagnostic updates, but are caused by the bug in ISORROPIA II.

  • Update 8/17/11: We now understand the source of this ISORROPIA error. Please see this wiki post for more information.
Approval
Requires further investigation: No
Approved: Yes
Date of approval: 10 Aug 2011

--Bob Y. 13:38, 18 August 2011 (EDT)

v9-01-02f

Here is the assessment form for 1-month benchmark simulation v9-01-02f. This is a re-submission of v9-01-02b.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Helen Amos (Harvard)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Mon Aug 1 13:36:33 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-03-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 01:28
  • CPU time / wall time: 7.6258
  • % of ideal performance: 95.32%
Compared to previous benchmark: v9-01-02e
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, Diagnostics, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02f.tar.gz
Metrics
Global mean OH (from log file): 13.1512320861717 x 105 molec cm-3
Methyl chloroform lifetime: 4.7648 years
Did either of these change by more than 5%? No.
At the SURFACE, list all species that changed by 10% or more: ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT
Comments on SURFACE differences: Largest changes: H2O2, NIT, NH3
At 500 hPa, list all species that changed by 10% or more: ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, MP, DMS, SO2, SO4, NH3, NH4, NIT
Comments on 500 hPa differences: Largest changes: H2O2, ISOP, NIT, NH3
In the ZONAL MEAN differences, list all species that changed by 10% or more: ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT,
Comments on ZONAL MEAN differences: Species change by 10% north of 30N and south of 30S.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None.
Comments on EMISSION RATIO differences: None.
Additional or summary comments:
Approval
Requires further investigation: No
Approved: YES
Date of approval: 01 Aug 2011

--Bob Y. 12:32, 1 August 2011 (EDT)

v9-01-02e

Here is the assessment form for 1-month benchmark simulation v9-01-02e.

Description
New features added into GEOS-Chem: Various source-code updates and fixes that will have no impact on the standard 1-month full-chemistry benchmark simulation:
  1. Various bug fixes for the offline Hg simulation
  2. Bug fixes for leap years when using GCAP met fields
  3. Minor bug fixes for emissions routines affecting offline simulations
  4. Fixes for minor issues affecting nested-grid simulations
  5. Fixes for better compatibility with the PGI compiler
  6. Add MERRA SEAICExx fields to the planeflight diagnostic
Developer name(s) and institution(s):
  1. Jenny Fisher (Harvard); Helen Amos (Harvard); Chris Holmes (UC Irvine)
  2. GEOS-Chem Support Team
  3. GEOS-Chem Support Team
  4. Luke Schiferl (Colo. State); Lin Zhang (Harvard)
  5. Gan Luo (SUNY Albany)
  6. Jenny Fisher (Harvard)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Fri Jul 29 16:00:03 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 01:30
  • CPU time / wall time: 7.6186
  • % of ideal performance: 95.23%
Compared to previous benchmark: v9-01-02d
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, Diagnostics, Other (please specify): We expect to see no changes from v9-01-02d
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02e.tar.gz
Metrics
Global mean OH (from log file): 13.1838752732688 x 105 molec cm-3
Methyl chloroform lifetime: 4.7493 years
Did either of these change by more than 5%? No. Both are identical to the previous run v9-01-02d.
At the SURFACE, list all species that changed by 10% or more: None
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more: None
Comments on 500 hPa differences:
In the ZONAL MEAN differences, list all species that changed by 10% or more: None
Comments on ZONAL MEAN differences:
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
Additional or summary comments: All of the changes were to fix mostly minor issues in (1) the Hg simulation, (2) the GCAP simulation, (3) nested-grid simulations, (4) offline simulations, and (5) the planeflight diagnostics. We did not add any scientific updates to the code; therefore, the standard chemistry simulation was not affected. The output file from this benchmark (ctm.bpch.v9-01-02e) is 100% binary identical to the output file from the previous benchmark (ctm.bpch.v9-01-02d).
Approval
Requires further investigation: No
Approved: YES
Date of approval: 01 Aug 2011

--Bob Y. 10:37, 1 August 2011 (EDT)

v9-01-02d

Here is the assessment form for 1-month benchmark simulation v9-01-02d.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Tue Jul 26 12:35:13 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-01-c.as.harvard.edu (2.926 GHz x 16 CPU)
  • Wall time: 01:07
  • Scalability: 7.4958
Compared to previous benchmark: v9-01-02c
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, Diagnostics, Other (please specify): We expect to see no changes from v9-01-02c
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02d.tar.gz
Metrics
Global mean OH (from log file): 13.1838752732688 x 105 molec cm-3
Methyl chloroform lifetime: 4.7493 years
Did either of these change by more than 5%? No.
At the SURFACE, list all species that changed by 10% or more: none
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more: none
Comments on 500 hPa differences:
In the ZONAL MEAN differences, list all species that changed by 10% or more: none
Comments on ZONAL MEAN differences:
In the EMISSION RATIO maps, list all species that changed by 10% or more: none
Comments on EMISSION RATIO differences:
Additional or summary comments: This benchmark was to test the initial importation of source code for ESMF. We did this in such a way so that the standard chemistry simulation is not affected. The output file from this benchmark (ctm.bpch.v9-01-02d) is 100% binary identical to the output file from the previous benchmark (ctm.bpch.v9-01-02c).
Approval
Requires further investigation: No
Approved: YES
Date of approval: 26 Jul 2011

--Bob Y. 14:52, 26 July 2011 (EDT)

v9-01-02c

Here is the assessment form for 1-month benchmark simulation v9-01-02c.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Jul 20 16:47:00 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-06-c.as.harvard.edu (2.792 GHz x 16 CPU)
  • Wall time: 00:57
  • Scalability: 7.5008
Compared to previous benchmark: v9-01-02a
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, Diagnostics, Other (please specify): Chemical species restart file
Plots may be viewed at: ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02c.tar.gz
Metrics
Global mean OH (from log file): 13.1838752732688 x 105 molec cm-3
Methyl chloroform lifetime: 4.7493 years
Did either of these change by more than 5%? No. The Mean OH is identical to v9-01-02a and the MCL lifetime has a small difference in the very last digit (see Summary Comments).
At the SURFACE, list all species that changed by 10% or more: none
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more:
Comments on 500 hPa differences:
In the ZONAL MEAN differences, list all species that changed by 10% or more: none
Comments on ZONAL MEAN differences:
In the EMISSION RATIO maps, list all species that changed by 10% or more: none
Comments on EMISSION RATIO differences:
Additional or summary comments: NOTE: This update corrects an erroneous situation in the chemical species restart file (aka "CSPEC restart file". This fix ONLY gets invoked for long GEOS-Chem simulations that have to be broken into several stages for the purpose of submitting to computational queues with fixed time limits. When each run stage ends, GEOS-Chem will write the chemical species concentrations into a restart file. When the next run stage begins, GEOS-Chem will read the chemical species information back into the CSPEC array (which gets passed to the SMVGEAR and KPP solvers).

For short simulations that can finish within the time limits of the computatational queues (such as this 1-month benchmark simulation), we do not use the CSPEC restart file. Therefore, when comparing v9-01-01c to v9-01-01a, we should expect to see identical results to v9-01-02a (which we do see as evidenced by the plots and Mean OH concentration).

In v9-01-02c, we use the grid box surface areas saved out directly from GEOS-Chem (via the ND69 diagnostic) to compute the MCL lifetime. In v9-01-02a, we computed the grid box surface areas using IDL code. The surface areas from both methods should be similar, but perhaps not strictly numerically equal to all double-precision digits. This causes the very slight difference in the last digit of the MCL lifetime for v9-01-02c.

Approval
Requires further investigation: No
Approved: YES
Date of approval: 21 Jul 2011

--Bob Y. 10:51, 21 July 2011 (EDT)

v9-01-02b

GEOS-Chem 1-month benchmark simulation v9-01-02b was withdrawn and re-submitted as v9-01-02f.

--Bob Y. 12:30, 1 August 2011 (EDT)

v9-01-02a

Here is the assessment form for 1-month benchmark simulation v9-01-02a.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Dynamic tropopause fix: Daven Henze (Colorado University) and Jamin Koo (MIT)
  • Out-of-bounds error: GEOS-Chem Support Team
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Mon Jun 13 18:02:07 EDT 2011
Performance statistics:
  • Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 01:29
  • Scalability: 7.6141
Compared to previous benchmark: v9-01-01
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): Tropopause
Plots may be viewed at: ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02/v9-01-02a.tar.gz
Metrics
Global mean OH (from log file): 13.1838752732688 x 105 molec/cm3
Methyl chloroform lifetime: 4.7490 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: None
Comments on SURFACE differences: None
At 500 hPa, list all species that changed by 10% or more: NIT, NH3
Comments on 500 hPa differences: Follow up calculations indicate that these changes are owing to an unresolved OpenMP issue, not the v9-01-02a code updates. NIT seems particularly sensitive to this issue, and this probably drives changes in NH3.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NOx, N2O5, NIT, NH3
Comments on ZONAL MEAN differences:
  • Small changes in tropospheric OH on order of +/-0.05%.
  • NOx changes follow from the variable tropopause fix and are small in absolute value.
  • There are also small percent changes for most gas-phase species near the tropopause.
  • The changes to NIT and NH3 have a random structure with large (>1000%) differences in spots throughout the troposphere, likely owing to the issue mentioned above. However, absolute changes are still small.
  • There are small (a few percent or less) changes visible for all chemically active gas and aerosol species. These changes are likely owing to both the code updates and the random OpenMP error, with the former having structure around the tropopause and the latter contributing to random scatter throughout the troposphere.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences: No changes in emissions.
Additional or summary comments:
  • There is an unidentified OpenMP error which contributes to differences shown here, as confirmed by independent tests of consecutive evaluations of a single executable compiled with and without parallelization. The impacts of this OpenMP error are typically less than a fraction of a percent, and negligible in terms of absolute value, with the exception of NIT and NH3. This is an issue to investigate further.
    • Update 8/17/11: We now have attributed this error to ISORROPIA. Please see this wiki post for more information.
  • I think this code update obfuscates the need to copy CSPEC to CSPEC_FULL and back when variable tropopause is turned on, as this fix now recalls the proper mapping from the previous time step when performing partitioning. Perhaps a future update could clean this up.
Approval
Requires further investigation: See above
Approved: Daven Henze
Date of approval: 06/28/2011

--Bob Y. 13:37, 18 August 2011 (EDT)