Difference between revisions of "GEOS-Chem v9-01-02 benchmark history"

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|The output file from this benchmark (<tt>ctm.bpch.v9-01-02d</tt>) is 100% binary identical to the output file from the previous benchmark (<tt>ctm.bpch.v9-01-02c</tt>).   
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|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 (<tt>ctm.bpch.v9-01-02d</tt>) is 100% binary identical to the output file from the previous benchmark (<tt>ctm.bpch.v9-01-02c</tt>).   
 
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!Approval
 
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Revision as of 00:19, 27 July 2011

On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for GEOS-Chem v9-01-02.

v9-01-02d

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

Description
New features added into GEOS-Chem:
  • Initial source code modifications for compatibility with Earth System Model Framework
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
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):
Plots may be viewed at: ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02d/
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
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/v9-01-02c/
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

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

NOTE: This benchmark requires further investigation, so we are moving ahead with other updates. (Bob Y, 21 Jul 2011)

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Washout fix: Helen Amos (Harvard)
  • Hardwire fix: Chris Holmes (UC Irvine)
Version, resolution, met fields used: v9-01-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Jul 6 15:14:37 EDT 2011
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):
Plots may be viewed at: ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02b/
Metrics
Global mean OH (from log file): 13.0621353054878 x 105 molec cm-3
Methyl chloroform lifetime: 4.7987 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: NOx, PAN, ALK4, ISOP, HNO3, H2O2, RCHO, MVK, MACR, PMN, PPN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs
Comments on SURFACE differences: The color scale saturates (implying large differences) for HNO3, H2O2, CH2O, MP, SO2, NH3, NIT
At 500 hPa, list all species that changed by 10% or more: NOx, ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs
Comments on 500 hPa differences: The color scale saturates (implying large differences) for ISOP, H2O2, MVK, MACR, PMN, PRPE, CH2O, MP, NH3, NIT
In the ZONAL MEAN differences, list all species that changed by 10% or more: NOx, ALK4, ISOP, HNO3, H2O2, MEK, ALD2, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, OH
Comments on ZONAL MEAN differences: Changes are typically are mid and high latitudes.
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: Pending discussion with Daniel Jacob. (Helen Amos, 07 Jul 2011)
Approved:
Date of approval:

--Bob Y. 10:30, 21 July 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
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/v9-01-02a/
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.
  • 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. 10:30, 21 July 2011 (EDT)