Difference between revisions of "Bugs and fixes"

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On this page we list the GEOS-Chem bugs that users have recently encountered, and how to fix them.   Please also see the following wiki pages:
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On this page we list the GEOS-Chem specific bugs and issues that users have recently encountered, and how to fix them.
  
;[[Outstanding issues yet to be resolved]]: This page contains a list of known issues (e.g. shortcomings in scientific algorithms, diagnostics, technical problems, etc.) which are slated to be fixed in an upcoming version.  
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Please also be sure to visit our [[Common GEOS-Chem error messages]] wiki page for more general information about some frequently encountered errors. Also visit our [[Currently unresolved issues in GEOS-Chem]] and [[Known issues caused by compiler bugs]] wiki pages for more information about unresolved issues.
  
== Issues resolved in GEOS-Chem v8-02-04 ==
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== Bugs and fixes lists have now been migrated to Github ==
  
* [[GEOS-Chem v8-02-04#Memory issue with KPP|Memory issue with KPP]]
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We have been migrating bug reports to our GEOS-Chem issue tracker, which is located on our Github repository: https://github.com/geoschem/geos-chem/issues/. We recommend that you also look through both the open and closed issues on this page, as your issue might be listed there.
* [[GEOS-Chem v8-02-04#Updated reactions in sulfate_mod.f|Updated reactions in sulfate_mod.f]]
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* [[GEOS-Chem v8-02-04#Bug fix for EMEP ship emissions|Bug fix for EMEP ship emissions]]
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* [[GEOS-Chem v8-02-04#Minor fix for molecular weights in drydep_mod.f|Minor fix for molecular weights in drydep_mod.f]]
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* [[GEOS-Chem v8-02-04#Bug fix in biomass_mod.f|Bug fix in biomass_mod.f]]
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* [[GEOS-Chem v8-02-04#Minor bug fix in gamap_mod.f|Minor bug fix in gamap_mod.f]]
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* [[GEOS-Chem v8-02-04#Fixes and updates in seasalt_mod.f|Fixes and updates in seasalt_mod.f]]
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* [[GEOS-Chem v8-02-04#Bug fix in emfossil.f for 0.5 x 0.666 nested grid tagged-CO option|Bug fix in emfossil.f for 0.5 x 0.666 nested grid tagged-CO option]]
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* [[GEOS-Chem v8-02-04#Bug fix in DIAG20 (diag_pl_mod.f)|Bug fix in DIAG20 (diag_pl_mod.f)]]
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* [[GEOS-Chem v8-02-04#Div-by-zero error encountered in arsl1k.f|Div-by-zero error encountered in arsl1k.f]]
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* [[GEOS-Chem v8-02-04#Fix for diagnostic arrays in TPCORE|Fix for diagnostic arrays in TPCORE]]
+
  
--[[User:Bmy|Bob Y.]] 10:11, 12 January 2010 (EST)
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{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!Version
 +
!Released
 +
!colspan="2"|List of bugs and issues (now posted on the listed Github repository)
  
== Issues resolved in GEOS-Chem v8-02-03 ==
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|-valign="top"
 +
|13.0.0
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|
 +
*[https://github.com/geoschem/geos-chem/milestone/8 '''Milestone 13.0.0''' (open issues)]
 +
*[https://github.com/geoschem/geos-chem/milestone/8?closed=1 '''Milestone 13.0.0''' (closed issues)]
  
* [[GEOS-Chem_v8-02-03#Corrected_Bond_et_al_BC.2FOC_emissions|Corrected_Bond_et_al_BC/OC_emissions]]
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|-valign="top"
* [[GEOS-Chem_v8-02-03#Several_bug_fixes_in_sulfate_mod.f|Several bug fixes in sulfate_mod.f]]
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|[[GEOS-Chem 12#12.9.0|12.9.0]]
* [[GEOS-Chem_v8-02-03#Missing_NOx_data_in_S.E.-Asia|Missing NOx data in S.E.-Asia]]  
+
|TBD
* [[GEOS-Chem_v8-02-03#Mis-calculation_of_Courant_numbers_in_tpcore_fvdas_mod.f90|Mis-calculation of Courant numbers in tpcore_fvdas_mod.f90]]  
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
* [[GEOS-Chem_v8-02-03#Format_problem_in_planeflight_mod.f|Format problem in planeflight_mod.f]]
+
|
 +
*[https://github.com/geoschem/geos-chem/milestone/10 '''Milestone 12.9.0''' (open issues)]
 +
*[https://github.com/geoschem/geos-chem/milestone/10?closed=1 '''Milestone 12.9.0''' (closed issues)]
  
--[[User:Bmy|Bob Y.]] 16:38, 11 January 2010 (EST)
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|-valign="top"
 +
|[[GEOS-Chem 12#12.8.1|12.8.1]]
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|
 +
*[https://github.com/geoschem/geos-chem/milestone/12 '''Milestone 12.8.1''' (open issues)]
 +
*[https://github.com/geoschem/geos-chem/milestone/12?closed=1 '''Milestone 12.8.1''' (closed issues)]
  
== Issues resolved in GEOS-Chem v8-02-02 ==  
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|-valign="top"
 +
|[[GEOS-Chem 12#12.8.0|12.8.0]]
 +
|pending
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/7?closed=1 '''Milestone 12.8.0''']
  
* [[GEOS-Chem_v8-02-02#EPA.2FNEI_inventory:_reset_other_species_to_zero|EPA/NEI inventory: reset other species to zero]]
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|-valign="top"
* [[GEOS-Chem_v8-02-02#Scale_factor_for_oceanic_acetone_for_GEOS5_2x2.5|Scale factor for oceanic acetone for GEOS5 2x2.5]] was fixed in GEOS-Chem v8-02-02.
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|[[GEOS-Chem 12#12.7.2|12.7.2]]
* [[GEOS-Chem_v8-02-02#Bug_with_PRIVATE_declaration_in_sulfate_mod.f|Bug with PRIVATE declaration in sulfate_mod.f]]
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|09 Mar 2020
* [[GEOS-Chem_v8-02-02#Bug_with_online_2ndary_aerosol|Bug with online 2ndary aerosol]]
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
* [[GEOS-Chem v8-02-02#Typo in HO2 uptake|Typo in HO2 uptake]]
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|[https://github.com/geoschem/geos-chem/milestone/11?closed=1 '''Milestone 12.7.2''']
  
--[[User:Bmy|Bob Y.]] 16:40, 11 January 2010 (EST)
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|-valign="top"
 +
|[[GEOS-Chem 12#12.7.1|12.7.1]]
 +
|19 Feb 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/9?closed=1 '''Milestone 12.7.1''']
  
== Issues resolved in GEOS-Chem v8-02-01 ==
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|-valign="top"
 +
|[[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|03 Feb 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/4?closed=1 '''Milestone 12.7.0''']
  
* [[GEOS-Chem_v8-02-01#Output selected tracers only for dry and wet deposition, convection and rain diagnotics|Output selected tracers only for dry and wet deposition, convection and rain diagnotics]]
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|-valign="top"
* [[GEOS-Chem_v8-02-01#On-the-fly regridding for 0.5x0.667 nested grids|On-the-fly regridding for 0.5x0.667 nested grids]]
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|[[GEOS-Chem 12#12.6.3|12.6.3]]
* [[GEOS-Chem_v8-02-01#Bug with EMEP ship emissions for nested grids|Bug with EMEP ship emissions for nested grids]]
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|25 Nov 2019
* [[GEOS-Chem_v8-02-01#Bug in sulfate_mod.f to turn off biomass emissions|Bug in sulfate_mod.f to turn off biomass emissions]]
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|[https://github.com/geoschem/gchp geoschem/gchp]
* [[GEOS-Chem_v8-02-01#Minor error in gamap_mod.f|Minor error in gamap_mod.f]]
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|[https://github.com/geoschem/gchp/milestone/2?closed=1 '''Milestone 12.6.3''']
* [[GEOS-Chem_v8-02-01#Bug fix for Streets emissions on 0.5x0.666 nested grid|Bug fix for Streets emissions on 0.5x0.666 nested grid]]
+
  
--[[User:Bmy|Bob Y.]] 09:55, 12 January 2010 (EST)
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|-valign="top"
 +
|[[GEOS-Chem 12#12.6.2|12.6.2]]
 +
|15 Nov 2019
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/6?closed=1 '''Milestone 12.6.2''']
  
== Issues resolved in GEOS-Chem v8-01-04 ==
+
|-valign="top"
 +
|[[GEOS-Chem 12#12.6.1|12.6.1]]
 +
|28 Oct 2019
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/5?closed=1 '''Milestone 12.6.1''']
  
* [[GEOS-Chem_v8-01-04#Seg fault in GEOS-5 China nested grid simulation|Seg fault in GEOS-5 China nested grid simulation]]
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|-valign="top"
* [[GEOS-Chem_v8-01-04#Error message in partition.f|Error message in partition.f]]
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|width="80px"|[[GEOS-Chem 12#12.6.0|12.6.0]]
* [[GEOS-Chem_v8-01-04#Erroneous O3 diagnostic (ND45)|Erroneous O3 diagnostic (ND45)]]
+
|width="100px"|18 Oct 2019
* [[GEOS-Chem_v8-01-04#Post-Release Patches|Post-Release Patches]]
+
|width="200px"|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|width="400px"|[https://github.com/geoschem/geos-chem/milestone/2?closed=1 '''Milestone 12.6.0''']
  
--[[User:Bmy|Bob Y.]] 09:58, 12 January 2010 (EST)
+
|}
  
== Issues resolved in GEOS-Chem v8-01-03 ==
+
== Issues resolved in GEOS-Chem 12.5.0 ==
  
* [[GEOS-Chem_v8-01-03#TPCORE replaced with version based on GMI model|TPCORE replaced with version based on GMI model]]
+
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.5.0|GEOS-Chem 12.5.0]], release date TBD.
* [[GEOS-Chem_v8-01-03#Output of ND51 does not match output in the ctm.bpch file|Output of ND51 does not match output in the ctm.bpch file]]
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* [[GEOS-Chem_v8-01-03#ND22 (J-value) diagnostic|ND22 (J-value) diagnostic]]
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* [[GEOS-Chem_v8-01-03#ND34 (biofuel emissions) diagnostic|ND34 (biofuel emissions) diagnostic]]
+
* [[GEOS-Chem v8-01-03#Change of location of calls to diagnostics in main.f|Change of location of calls to diagnostics in main.f]]
+
  
== ND05 diagnostic quantities zeroed unexpectedly ==  
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{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
'''''Helen McIntyre (h.macintyre@see.leeds.ac.uk) wrote:'''''
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|-valign="top"
:I'm running the new and old versions of GEOS-Chem, and both seem to not output all the ND05 diagnostics correctly. There are 10 prod/loss diagnostics in this category, but only the 5th, 6th and 7th work. All the rest come out as zero.
+
|Chemistry
 +
|
 +
#[[Stratospheric_chemistry#Bug_fix:_make_sure_stratospheric_BrY_concentrations_are_read_properly_each_month|Bug fix: Make sure stratospheric BrY concentrations are properly read each month]]
 +
#[[FAST-JX_v7.0_photolysis_mechanism#FAST-JX_directory|Add photolysis menu to input.geos for specifying FAST-JX directory]]
 +
#[[GEOS-Chem_12#Corrections_for_CFCs_in_the_chemistry_mechanism|Correction for CFCs in the chemistry mechanism]]
 +
#[[GEOS-Chem_12#Fix_typo_in_CLD_PARAMS_routine_in_gckpp_HetRates.F90|Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/0588a269376e0f1d8c7acd04f4b954402e31a76a 0588a269]
 +
#[https://github.com/geoschem/geos-chem/commit/03e94fed99cf2bb538dfc59ec514690a122b01a9 03e94fed]
 +
#[https://github.com/geoschem/geos-chem/commit/1b9f69f048243cfb59226a69885ef152bfd33441 1b9f69f0]
 +
#[https://github.com/geoschem/geos-chem/commit/95d124e0302d46d64f51ac4ff8db57febb81dda9 95d124e0]
  
:I've had a brief look though the code, and it seems that the ones that work are calculated in one part of the routine (<tt>sulfate_mod.f</tt>), and the zero ones in another (I don't know if this has anything to do with it).
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|-valign="top"
 +
|Diagnostics
 +
|
 +
#[[List_of_diagnostics_archived_to_netCDF_format#Sample_HISTORY.rc_diagnostic_input_file|Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally]]
 +
#[[GEOS-Chem 12#Enable accurate cloud pH diagnostic calculation|Enable accurate cloud pH diagnostic calculation via post-processing ]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/6acd4ce393d9fdc4be8e8a70a532e6391f54b218 6acd4ce3]
 +
#[https://github.com/geoschem/geos-chem/pull/37/commits/1c15e54ad1c4f34ecdbb03266716c992001c8cc5 1c15e54a]
  
:I've just done a 1 day run, with Geos-chem v8-01-01 at 4x5 resolution using GEOS-5 met fields. The old version I'm using is v7-02-04 and I get the same result.
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|-valign="top"
 +
|Structural updates
 +
|
 +
#Add optional capability to compile GEOS-Chem Classic and GCHP using CMake
 +
|
 +
#[https://github.com/geoschem/gchp/pull/27/commits pull/27]
  
:The 'ctm.bpch', 'geos.log' and 'input.geos' files from the v8-01-01 run can be found here: http://homepages.see.leeds.ac.uk/~lechlm/files/
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|-valign="top"
 +
|Emissions
 +
|
 +
#Fixes for GFED4 biomass burning emissions, including:
 +
#*Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year
 +
#*Remove the 27% scaling of POG to POA and emit 1:1 instead
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/3813a6fbd8a016842b16d7daa81f623d3d4edeb6 381386fb]
  
'''''Claire Carouge (ccarouge@seas.harvard.edu) replied:'''''
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|-valign="top"
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
:There are some problems in the calculations. For the 5th element of AD05 (in Fortran notations and not IDL), the diagnostic come from the value of L1 which is calculated line 1529 (v8-01-04):
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|-valign="top"
 +
|Structural updates
 +
|
 +
#Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28
 +
#*Will introuduce faster parallel I/O
 +
#*Will enable full use of gfortran compiler
 +
|
 +
|}
  
    L1    = ( SO20 - SO2_cd + PSO2_DMS(I,J,L) ) * RK1/RK
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:03, 15 July 2019 (UTC)
  
:But on line 1508, we have:
+
== Issues resolved in GEOS-Chem 12.4.0 ==
  
    RK1 = 0.d0
+
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.4.0|GEOS-Chem 12.4.0]], release date TBD.
  
:with the previous comment:
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{| border=1 cellspacing=0 cellpadding=5
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|-bgcolor="#CCCCCC"
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!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
  ! For online runs, SMVGEAR deals w/ this computation,
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|-valign="top"
  ! so we can simply set RK1 = 0 (rjp, bmy, 3/23/03)
+
|Photolysis
 +
|
 +
#[[FAST-JX_v7.0_photolysis_mechanism#Further_fix_added_in_12.4.0|Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2]]
 +
#[[FAST-JX_v7.0_photolysis_mechanism#FAST-JX_directory|Add photolysis menu to input.geos for specifying FAST-JX directory]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/fcd0cfba13d63ee0b94c8fd06d29f6e49156aff6 fcd0cfba]
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/d34a9cd29f1272d85cd1355183ca02373f0b2ee8 d34a9cd2]
  
:So L1 is always 0. I have no idea what RK1 is for, you may have to go into the physics/chemistry behind the code and we are not qualified to help you with it.
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|}
  
:The other values for AD05 are calculated in the routine CHEM_DMS and this routine is only called in an offline aerosol simulation (l. 545 in <tt>sulfate_mod.f</tt>).
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:04, 15 July 2019 (UTC)
  
:So my guess is that the ND05 diagnostic was designed for offline simulations and if you want it for online chemistry, you need to implement it.
+
== Issues resolved in GEOS-Chem 12.3.2 ==
  
 +
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.3.2|GEOS-Chem 12.3.2]].
  
== Output of ND51 does not match output in the ctm.bpch file ==
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{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
Please see [[Previous issues now resolved in v8-01-03#Output of ND51 does not match output in the ctm.bpch file|this discussion]] about an inconsistency between the ND51 diagnostic (<tt>ts_satellite.bpch</tt> file) and the <tt>ctm.bpch</tt> file.
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|-valign="top"
 +
|Chemistry
 +
|
 +
#[[GEOS-Chem 12#Inconsistency in H2402 concentrations in GCHP vs GEOS-Chem Classic|Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic"]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/releases/tag/12.3.2 rel/12.3.2]
  
== Quick fix for GEOS-5 optical depth ==
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|-valign="top"
 +
|Photolysis
 +
|
 +
#[[FAST-JX_v7.0_photolysis_mechanism#Duplicate_entries_for_species_ClNO2_in_FJX_j2j.dat_file|Remove duplicate entry for species ClNO2 in the FJX_j2j.dat file]]
 +
#[[FAST-JX_v7.0_photolysis_mechanism#Species_DHDC_was_not_listed_as_photolyzing_in_the_species_database|Species DHDC was not listed as photolyzing in the GEOS-Chem species database]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/releases/tag/12.3.2 rel/12.3.2]
 +
#[https://github.com/geoschem/gchp/commit/d7c48d144707aa25ac65bb7270466864e0559a0f d7c48d14]
  
Please see the discussion [[GEOS-5_issues#GEOS-5 update and clarification|for a quick fix for the GEOS-5 optical depths]].
+
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
'''''NOTE: if you are using [[GEOS-Chem v8-01-04]] or higher with the [[GEOS-5_issues#Solution|reprocessed GEOS-5 met fields]], then you do not need to use this quick fix.'''''
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|-valign="top"
 +
|Emissions
 +
|
 +
#Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default
 +
#Fix HEMCO diagnostics settings for lightning NO and seasalt emissions
 +
|
 +
#[https://github.com/geoschem/gchp/commit/f6ac477ad7637d7cfc4a6f2d479fd2509ecca9ef f6ac477a]
 +
#[https://github.com/geoschem/gchp/commit/cda5044e9c8430954fc6a0d550553f9f9a80bb33 cda5044e]
  
--[[User:Bmy|Bob Y.]] 16:13, 10 October 2008 (EDT)
+
|}
  
== Bad GEOS-4 A6 met data causing segmentation fault ==
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:37, 15 July 2019 (UTC)
  
'''''Jesse Kenyon (kenyon@duke.edu) wrote:'''''
+
== Issues resolved in GEOS-Chem 12.3.1 ==
  
:In our runs of the GEOS-Chem model using GEOS4 data from 2006, we have run into a corrupt data problem that causes our runs to crash on rundate 20060913. We have been able to isolate this to bad values in the A6 files for the meridional wind (V component). Specifically, it appears two files contain bad data: <tt>20060913.a6.4x5</tt> and <tt>20060915.a6.4x5</tt>. The bad data takes the form of unphysically huge values (e.g. 0.75553E+29), and occurs at many gridboxes on levels 6 and 7 of the 20060913 file and levels 18 and 19 of the 20060915 file.  In both files, the bad data only occur for the 00 hour (06, 12, and 18 hours appear okay).  We also checked the  20060914, 20060916, 20060917, 20060918, and 20060919.a6.4x5 files - they seem okay. A check of the U component wind on 09-13 and 09-15 shows no problems.
+
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.3.1|GEOS-Chem 12.3.1]] (release 08 Apr 2019).
  
:For us, the problem manifested itself as a segmentation fault when trying to access address -21474836 of array qtmp in subroutine xtp in module <tt>tpcore_fdvas_mod.f90</tt>. The address was calculated from xmass which is calculated from wind and pressure in another subroutine (Init_press_fix).  We know some folks at Harvard have been able to get beyond this rundate without crashing and suspect it might be due to a difference in computer system or compiler.
+
{| border=1 cellspacing=0 cellpadding=5
:We have not yet tried running with a "repaired" V wind, so cannot say for sure that there are no other problems in the A6 files besides V (or U which was also checked).
+
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
'''''Philippe Le Sager (plesager@seas.harvard.edu) wrote:'''''
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|-valign="top"
 +
|Diagnostics
 +
|
 +
#[[Planeflight_diagnostic#Planeflight_diagnostic_now_writes_out_data_for_the_last_timestep_of_the_day|Planeflight diagnostic now writes out data for the last timestep of the day]]
 +
#[[List_of_diagnostics_archived_to_netCDF_format#The_JValuesLocalNoon_collection|Fix the netCDF diagnostic for noontime J-values]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/04da94cdbe01c9032904a9f7d14ec3a5aded5aee 04da94cd]
 +
#[https://github.com/geoschem/gchp/commit/f4d43b7ace1d74adc2b8aed1bcd7b4d33a594878 f4d43b7a]
  
:Thanks for reporting the issue. We had the exact same problem with GCAP once and the problem was solved by repairing the met field (a very bad value in U or V). Then Mike and Bastien got the exact same error with GEOS4, on the same day as you. My first idea was to test the met fields but I did not get any bad value. I just did a run with Bastien's inputs, and was not able to reproduce the crash. You just confirmed that the first idea was the good one: a bad met field.
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|-valign="top"
:Since I seem to have a good met field and you do not, I check the met fields on the server this time. And I did find a problem with V for 20060913. Here are the output from test_met.pro (it gives min and max of each met fields):
+
|Structural
 +
|
 +
#[[Stratospheric_chemistry#Do not allocate memory to array MINIT in strat_chem_mod.F90|Do not allocate memory to array MINIT in <tt>strat_chem_mod.F90</tt>]]
 +
#[[GEOS-Chem_12#Declare_State_Met.25AREA_M2_as_2-dimensional.2C_not_3-dimensional|Declare <tt>State_Met%Area_M2</tt> as 2-dimensional, not 3-dimensional]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/729fd2a7ed79b8a6a4a7fd6231097fbb1c4baf21 729fd2a7]
 +
#[https://github.com/geoschem/gchp/commit/e4af25f3b893263d1236c3a35c64e2e46f2e78cb e4af25f3b]
  
    at Harvard (internal disk):
+
|}
    20060913 000000 U            -72.816071    144.557083
+
    20060913 000000 V            -67.133759      61.291386
+
+
    on the server:
+
    20060913 000000 U            -72.816071    144.557083
+
    20060913 000000 V            -67.133759***************
+
  
:All others fields give the exact same min/max. There is a huge or NaN value in the file we put on the server. We do not understand how that happened, since files are simply copied from one location to the other. So we are still investigating the issue, checking the whole archive, and will let you know as soon as we replace it.
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:06, 16 July 2019 (UTC)
  
'''''Bob Yantosca (yantosca@seas.harvard.edu) wrote:'''''
+
== Issues resolved in GEOS-Chem 12.3.0 ==
  
:I have fixed the bad A-6 data for 2006 -- 09/13, 09/14, 09/15, 09/16. For some reason the data in the FTP site was corrupt (bad values in the winds at a couple of GMT times) but the data on our internal disk (behind the firewall) was not.  I just copied the relevant data files over and re-created the TAR file.
+
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.3.0|GEOS-Chem 12.3.0]] (release date TBD).
  
:Please obtain the new TAR file from:
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
  ftp ftp.as.harvard.edu
+
|-valign="top"
  cd pub/geos-chem/data/GEOS_4x5.d/GEOS_4_v4/2006/09
+
|Diagnostics / Restart files
  get 09.tar.gz
+
|
 +
#[[#Further_bug_fix_to_prevent_incorrect_restart_file_output_when_spanning_leap_year_days|Further bug fix for netCDF diagnostics spanning leap years]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/fb093d61b8321834d5f1d9565760e2828138b321 fb093d61]
  
--[[User:Bmy|Bob Y.]] 15:40, 23 September 2008 (EDT)
+
|-valign="top"
 +
|Emissions
 +
|
 +
#[[HEMCO_versions#Bug_fixes_for_HEMCO_interpolation_algorithm|Bug fixes for the HEMCO interpolation algorithm]]
 +
#[[HEMCO_versions#Updates from the NASA GEOS development branch|Updates from the NASA GEOS development branch]]
 +
#[[HEMCO_versions#Add_option_to_always_use_simulation_year_for_specified_fields|Add option to always use simulation year for specified fields]]
 +
#[[HEMCO_versions#Prevent zero emissions for MEGAN_Mono extension species|Prevent zero emissions for MEGAN_Mono extension species]]
 +
#[[HEMCO_versions#Updates to the volcanic emissions extension|Updates to the volcanic emissions extension]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/e947fc8027b75eaa4ff5e22b65f046728b5ee7fb e947fc80]
 +
#[https://github.com/geoschem/geos-chem/commit/7df3fc8eefd47b8835335bd5c48f469d5c7e4385 7df3fc8e]
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/23189032720058b34d7b8140aac52989cfe4c1ee 23189032]
 +
#[https://github.com/geoschem/geos-chem/commit/af86c4ddc10e240662a572d8542292b2d30f5cc7 af86c4dd]
 +
#[https://github.com/geoschem/geos-chem/commit/07c103190221e1d77feaa97dfdd71749767c248a 07c10319]
 +
|}
  
== Too many levels in photolysis code ==
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:53, 21 March 2019 (UTC)
  
The scattering module (OPMIE.f) for Fast-J requires many additional vertical levels. It happens that the limit (NL set in jv_mie.h) can be reached in some situations, causing the program to stop with a "Too many levels in photolysis code.." error message.
+
== Issues resolved in GEOS-Chem 12.2.1 ==
Sometimes you can increase NL to solve the problem.
+
Now a new version of OPMIE.f is available, which still warns you if NL is reached, but works with that limit.
+
  
Before being released into the standard model, you can find the new OPMIE.f at: ftp://ftp.as.harvard.edu/pub/geos-chem/patches/v8-01-01/OPMIE.f
+
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.2.1|GEOS-Chem 12.2.1]] (release date 28 Feb 2019).
+
--[[User:Plesager|phs]] 11:29, 17 June 2008 (EDT)
+
  
This can also be an indication that there may be a problem in your visual optical depths, dust emissions, or aerosol emissions.  Dust and aerosol optical depths are computed from the concentration array STT.  If for some reason you end up emitting too much aerosol or dust (i.e. a unit conversion error), then this will result in an abnormally high dust or aerosol optical depth.  A very high optical depth will cause FAST-J to want to keep adding points to the Gaussian quadrature in OPMIE.f.  You can get into a situation where the number of points that FAST-J wants to add is greater than the array parameter NL (it may want to add thousands of points!).
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
Therefore, if you encounter this type of error, it is a good idea to doublecheck your aerosol & dust emissions to make sure that the monthly and annual totals are reasonable.
+
|-valign="top"
 +
|Diagnostics / Restart files
 +
|
 +
#[[GEOS-Chem 12#Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days|Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/ca68f508b956a24663cf49722b437c638e9e9c6f ca68f508]
  
--[[User:Bmy|Bob Y.]] 11:03, 26 June 2008 (EDT)
+
|-valign="top"
 +
|CO2 simulation
 +
|
 +
#[[CO2_simulation#Prevent_double-counting_in_CO2_chemical_source|Fix for CO2 simulation chemical source]]
 +
|
 +
#N/A
  
== Negative tracer in routine WETDEP because of negative RH ==
+
|-valign="top"
+
|TOMAS simulations
See this post: [[GEOS-5 issues#Small negative RH value in 20060206.a6.2x25 file]]
+
|
 +
#[[TOMAS_aerosol_microphysics#Restore_DST1.2C_DST2.2C_DST3.2C_and_DST4_in_TOMAS_simulations|Restore DST1, DST2, DST3, and DST4 in TOMAS simulations]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/5ed3e9cf3bdccfd7b144b5d768e64d0059357a7b 5ed3e9cf]
  
Fixes are available at [ftp://ftp.as.harvard.edu/pub/geos-chem/patches/v8-01-01/ ftp://ftp.as.harvard.edu/pub/geos-chem/patches/v8-01-01].
+
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
--[[User:Plesager|phs]] 16:31, 6 June 2008 (EDT)
+
|-valign="top"
 +
|Emissions etc.
 +
|
 +
#[[GEOS-Chem_12#Use_online_sea_flux_emissions_by_default_in_GCHP|Use online sea flux emissions by default in GCHP]]
 +
#[[GEOS-Chem_12#GCHP_uses_outdated_MODIS_files_missing_projection_error_fix|Update MODIS LAI source directory to match GEOS-Chem Classic]]
 +
|
 +
#[https://github.com/geoschem/gchp/commit/9759d26bcbbb593f6e845a0dc67e1b7bde4b6410 9759d26b]
 +
#N/A
  
== Negative tracer in routine WETDEP ==
+
|-valign="top"
+
|Met fields
'''''Dylan Millet (dbm@umn.edu) wrote:'''''
+
|
:I'm having a run die consistently at the same time (October 1, 2005; first time step of the month) in large-scale wetdep, with an STT element < 0.
+
#[[GEOS-Chem_12#Missing_scaling_factors_for_MERRA-2_simulations_with_GCHP|Missing scaling factors for MERRA-2 simulations with GCHP]]
:* Platform: Linux cluster
+
|
:* Threads: 8
+
#?
:* Version: v7-4-13 out of the box.
+
:* GEOS4, 4x5, 30L, full chemistry
+
:* IFORT 10.1
+
  
:In Section 6 (No Downward Precip) of wetscav_mod.f, subroutine safety is getting called.
+
|}
    WETDEP - STT < 0 at    1  1  29 for tracer    7 in area    6
+
  
:(First of all it seems odd to do wetdep for L=29, this is 63 km up).  Have you seen anything like this?  I ran for the whole year starting Jan 1 successfully until this point.
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:03, 15 July 2019 (UTC)
  
:... By the way, the problem persists when I turn off chemistry altogether.
+
== Issues resolved in GEOS-Chem 12.2.0 ==
  
'''''Philippe Le Sager (plesager@seas.harvard.edu) replied:'''''
+
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.2.0|GEOS-Chem 12.2.0]] (release date 19 Feb 2019).
  
:I used your restart file and the same input.geos (w/ chemistry on and off). My code went thru without problem.  I tried both Sun Studio and Ifort 9 compilers, and the later on two different machines (altix and ceres). I used v7-04-13 and v8-01-01. I never reproduced your error.
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
:We just got the new Ifort 10, and tried it too. I run v8-01-01 without an error. But when I tried v7-04-13, I finally reproduced your error, with the exact same negative values!
+
|-valign="top"
 +
|Diagnostics
 +
|
 +
#[[GEOS-Chem_12#Fix_bug_in_stratosperic_aerosol_surface_area_netcdf_diagnostics|Fix bug in stratospheric aerosol surface area in netCDF diagnostics]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/e4fecf01c87aa76169751c6e0a515ee717573121 e4fecf01]
  
:In other words: the bug happens with IFort 10 and v7-04-13 only.
+
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
:Also, have a look at this [[Aerosol_thermodynamical_equilibrium#ISORROPIA|recent development]].  This is not the reason for your bug (I tried v8 w/ ifort 10 and isorropia -like v7-04-13- and it did not crash), but using RPMARES instead of Isorropia may be a way to fix it.
+
|-valign="top"
 +
|Restart files
 +
|
 +
#[[GEOS-Chem_12#GCHP_Bug_fix:_use_checkpoint_output_file_as_subsequent_run_restart|GCHP bug fix: Use checkpoint output as the subsequent restart file]]
 +
|
 +
#
 +
|}
  
:... More about the Ifort 10 / v7-04-13 issue.  When I wanted to debug with TotalView, I could not reproduce the bug anymore.... because I simply suppress any optimization.  So, I did more test and found that if the default -O2 optimization is used, GEOS-Chem crashes.  But it works fine with -O1. It is hard to tell what happens, since only the emissions step is done between reading the restart file and the crash.
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:02, 14 March 2019 (UTC)
  
:Bob and I will further test Ifort 10 for optimization on our machines. Maybe we will find something... For the time being, you may have to switch to -O1, at least for the run that crashes. You will find the optimization flag at the beginning of the Makefile.ifort.
+
== Issues resolved in GEOS-Chem 12.1.1 ==
  
Long story short: This appears to be an optimization issue with IFORT 10 and v7-04-13.  Upgrading to [[GEOS-Chem_versions_under_development#v8-01-01|GEOS-Chem v8-01-01]] should solve this problem.
+
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.1.1|GEOS-Chem 12.1.1]], which was released on 13 Dec 2018.
  
--[[User:Bmy|Bmy]] 10:38, 17 April 2008 (EDT)
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
== ISORROPIA and RPMARES ==
+
|-valign="top"
 +
|Compilation issues
 +
|
 +
#[[GEOS-Chem_12#Always_enable_BCPH_TPBC_to_allow_saving_out_BC_files_in_global_simulations|Always enable BPCH_TPBC to allow saving out BC files in global simulations]]
 +
#[https://github.com/geoschem/geos-chem/commit/096ad29d02afbdba64a5dd138df0c976ddee3140 Add hco_interface_mod.o to list of dependencies for get_met_mod.o and only compile get_met_mod.F90 and flexgrid_mod.F90 for GEOS-Chem "Classic"]
 +
#[https://github.com/geoschem/geos-chem/commit/f9b2f19593afeaa396ff3ee3d315148d5a6f8600 Add flexgrid_read_mod.o to list of dependencies for hcoi_gc_main_mod.o]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/072ec9d61580105bcfa755081bc5d238e1b3f60d 072ec9d6]
 +
#[https://github.com/geoschem/geos-chem/commit/096ad29d02afbdba64a5dd138df0c976ddee3140 096ad29d]
 +
#[https://github.com/geoschem/geos-chem/commit/f9b2f19593afeaa396ff3ee3d315148d5a6f8600 f9b2f195]
  
Please see the discussion about the bugs & fixes for ISORROPIA and RPMARES on the Code Developer's Forum for [[Aerosol thermodynamical equilibrium]].
+
|-valign="top"
 +
|Diagnostics
 +
|
 +
#[[GEOS-Chem_12#Skip_planeflight_observations_outside_a_nested_domain|Skip planeflight observations outside a nested domain]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/f6f90fd404cae1f911277f27f7a4fcb15b3bb039 f6f90fd4]
  
Also, if you are trying to run an aerosol-only simulation, then please see [[Aerosol thermodynamical equilibrium#Bug in sulfate_mod.f caused by switch to RPMARES|this discussion about a bug that manifested itself only after switching from ISORROPIA to RPMARES]].
+
|-valign="top"
 +
|Tagged CO simulation
 +
|
 +
#[[Tagged CO simulation#Do not multiply emission timestep by 60|Bug fix for tagged CO: don't multiply emissions timestep by 60]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/8a1b078e337edfa5fdfb0a5d9ca636b6d0c0634a 8a1b078e]
  
--[[User:Bmy|Bob Y.]] 10:44, 26 June 2008 (EDT)
+
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
 +
 
 +
|-valign="top"
 +
|Transport (FvDycore)
 +
|
 +
#[[GEOS-Chem_12#GCHP_transport_fix_to_prevent_instant_propagation_from_troposphere_to_stratosphere|GCHP transport fix to prevent instant propagation from troposphere to stratosphere]]
 +
|
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:12, 16 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.1.0 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], which was released on 26 Nov 2018.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
 +
 
 +
|-valign="top"
 +
|CH4 simulation
 +
|
 +
#[[CH4_simulation#Add_fixes_for_seasonal_scale_factors_in_CH4_simulations|Add fixes for seasonal scale factors in CH4 simulations]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/6f48d04570ea616a0c39f8dd02c2c902e6183393 6f48d045]
 +
 
 +
|-valign="top"
 +
|Chemistry and Photolysis
 +
|
 +
#[[FAST-JX_v7.0_photolysis_mechanism#Allow_for_SZA_to_98_degrees_when_getting_photolysis_rates|Allow for SZA to 98 degrees when getting photolysis rates]]
 +
#[[GEOS-Chem_v11-02#Code_cleanup_suggestions|Move Fast-JX .dat files from the <tt>geos-chem-unittest</tt> repository to <tt>gcgrid/ExtData</tt>]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/d06ae04ad44defd15854a9c4dadd36923dee0498 d06ae04a]
 +
#[https://github.com/geoschem/geos-chem/commit/03e94fed99cf2bb538dfc59ec514690a122b01a9 03e94fed]
 +
 
 +
|-valign="top"
 +
|Emissions
 +
|
 +
#[[CEDS_anthropogenic_emissions#Add_missing_RCO_sector_to_CEDS_emissions_entries|Add missing RCO sector to CEDS emissions entries]]
 +
#[[CEDS_anthropogenic_emissions#Include_CEDS_ship_emissions|Include CEDS ship emissions as default global ship emissions inventory]]
 +
#[[CEDS_anthropogenic_emissions#Reduce_file_size_for_CEDS_inventory|Reduce file size for CEDS inventory]]
 +
#[[Implementation_of_HEMCO_in_GEOS-Chem#Bug_fix:_Read_data_with_the_.22E.22_cycle_flag_just_once|HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic"]]
 +
#[[Implementation_of_HEMCO_in_GEOS-Chem#Add_fix_for_collapsing_model_levels_to_reduced_grid|Add fix for collapsing model levels to reduced grid]]
 +
#[[Implementation_of_HEMCO_in_GEOS-Chem#Fix_unit_conversion_in_HCO_UNIT_GetAreaScal|Fix unit conversion in HCO_UNIT_GetAreaScal]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/642dd0af874e9ddfa87d096158a61f1d9f9c0fe6 642dd0af]
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/e71d0d6754faeed0adcfc9ed94846677551337f3 e71d0d67]
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/20451cb47bf8dace9b9fc7878bca6720b6fe3a56 20451cb4]
 +
#[https://github.com/geoschem/geos-chem/commit/3f62e74954136cbbabda166a453cbd3811689ac4 3f62e749]
 +
#[https://github.com/geoschem/geos-chem/commit/820b8d7d9b25a50f79cf6688a359c9dcc91d8c2b 820b8d7d]
 +
#[https://github.com/geoschem/geos-chem/commit/7dfd99da3d750046dc08478978b3f2cbd0a31018 7dfd99da]
 +
 
 +
|-valign="top"
 +
|PBL Mixing
 +
|
 +
#[[Boundary_layer_mixing#Mass_is_not_conserved_when_using_non-local_PBL_mixing|Fix mass conservation in non-local PBL mixing]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/57c75178c4f9b809c5abca5e3b236c3db7889669 57c75178]
 +
 
 +
|-valign="top"
 +
|Tagged CO simulation
 +
|
 +
#[[GEOS-Chem_12#Update_HEMCO_configuration_file_for_tagged_CO_simulation|Update HEMCO configuration file for the tagged CO simulation]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/02aaad73d32cbd54bba450b0a5b2abce6a5cad5e 02aaad73]
 +
 
 +
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
 +
 
 +
|-valign="top"
 +
|Emissions (GCHP)
 +
|
 +
#[[GEOS-Chem_12#Fix_masked_anthropogenic_emissions_bug_in_GCHP|Fix masking bug to correctly apply anthropogenic emissions]]
 +
#[[GEOS-Chem_12#Fix_regional_tile_file_used_for_APEI_inventory_in_GCHP|Remove erroneous 180 degree longitude shift in APEI regridding]]
 +
|
 +
 
 +
|-valign="top"
 +
|Structural (GCHP)
 +
|
 +
*Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository
 +
|
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:12, 16 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.0.3 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.0.3|GEOS-Chem 12.0.3]], which was released on 16 Oct 2018.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
 +
 
 +
|-valign="top"
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
 +
 
 +
|-valign="top"
 +
|Emissions (GCHP)
 +
|
 +
#[[#Fix_incorrect_run_configuration_for_offline_sea_salt_emissions_in_GCHP|Fix incorrect run configuration for offline sea salt emissions in GCHP]]
 +
#[[#Fix_bug_in_application_of_CFC_surface_mixing_ratios_in_GCHP|Fix bug in application of CFC surface mixing ratios in GCHP]]
 +
|
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:01, 21 December 2018 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.0.2 ==
 +
 
 +
The bugs and technical issues listed below were be resolved in [[GEOS-Chem 12#12.0.2|GEOS-Chem 12.0.2]], which was released on 10 Oct 2018.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
 +
 
 +
|-valign="top"
 +
|Diagnostics
 +
|
 +
#[[GEOS-Chem 12#Fixed_local-time_averaging_in_ND51_and_ND51b_satellite_timeseries_diagnostics|Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/14b29d3df84994a9251dd9b2fb0082b75c4affbc 14b29d3d]
 +
 
 +
|-valign="top"
 +
|Specialty simulations
 +
|
 +
#[[TOMAS_aerosol_microphysics#Fixes_for_missing_biomass_emissions_and_incorrect_aerosol_dry_deposition|Correct missing BC/OC biomass emissions and aerosol drydep in TOMAS simulations]]
 +
#[[CO2_simulation#CO2_emissions_are_double_counted|Avoid double-counting of emissions in the CO2 simulation]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/6a944b929764b6e1e7d22f0fd396a3d1515f71dc 6a944b92]
 +
#[https://github.com/geoschem/geos-chem/commit/8320e73d06d94b3e39dd0440f6eb0b1cf3fa0e98 8320e73d]
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:16, 16 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.0.1 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.0.1|GEOS-Chem 12.0.1]], which was released on 24 Aug 2018.
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
 +
 
 +
|-valign="top"
 +
|Diagnostics
 +
|
 +
#[[GEOS-Chem 12#Fix typo when registering the State_Chm%SSAlk field|Fix typo when registering the <tt>State_Chm%SSAlk</tt> field]]
 +
#[[Sulfate aerosols#Fix mis-indexing in the ND05 diagnostic|Fix mis-indexing in the ND05 diagnostic]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/55d1687384bcd1e0091cf96ad42fed4fa69cb450 55d16873]
 +
#[https://github.com/geoschem/geos-chem/commit/8e118c0e00403edac7f8d91a7c68c1144a0e64a6 8e118c0e]
 +
 
 +
|-valign="top"
 +
|Mercury
 +
|
 +
#[[Mercury#Restore_biomass_emissions_and_do_not_double_count_anthropogenic_emissions|Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/e1e6668b901a49e82e78302bc83e03271af011b0 e1e6668b]
 +
 
 +
|-valign="top"
 +
|Structural updates
 +
|
 +
#Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
 +
#[[GEOS-Chem_Makefile_Structure#Add a more robust test for netCDF-Fortran in Makefile_header.mk|Add a more robust test for netCDF-Fortran in Makefile_header.mk]]
 +
#[[GNU_Fortran_compiler#Compiliation_issues_with_GNU_Fortran_8.2.0|Fix compilation issues encountered with GNU Fortran 8.2.0]]
 +
#[[Intel_Fortran_Compiler#Compilation_issues_with_Intel_Fortran_18|Fix compilation issues encountered with Intel Fortran 18]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/ff7b0c3c73faafa1fdbebaf163178d0a7d224af7 ff7b0c3c]
 +
#[https://github.com/geoschem/geos-chem/commit/a4d550552ecd3a4e2a9dc0b2b63f79500d7eae10 a4d55055]
 +
#[https://github.com/geoschem/geos-chem/commit/e0959563c23b9fe19d9a4e064be846b10cafbc63 e0959563]
 +
#[https://github.com/geoschem/geos-chem/commit/9833fff44cc1b12b41306140dbbd653004c71b54 9833fff4]
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:20, 16 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.0.0 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]], which was released on 10 Aug 2018.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="250px"|Module or area
 +
!width="750px"|Issue that was resolved
 +
 
 +
|-valign="top"
 +
|Aerosols
 +
|
 +
*[[GEOS-Chem_12#Fix_issues_in_complexSOA_and_complexSOA_SVPOA_restart_files|Fix issues in complexSOA and complexSOA_SVPOA restart files]]
 +
 
 +
|-valign="top"
 +
|Chemistry
 +
|
 +
*[[Stratospheric_chemistry#Disable_STE_calculation_printed_to_log_file|Disable STE calculation printed to log file]]
 +
*[[Linoz_stratospheric_ozone_chemistry#Turn_on_Synoz_when_Linoz_is_set_to_false_in_input.geos|Turn on Synoz when Linoz is set to false in input.geos]]
 +
*[[GEOS-Chem_12#Remove_duplicate_C3HI_spectrum_in_FJX_spec.dat_and_FJX_j2j.dat|Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat]]
 +
*[[GEOS-Chem 12#Add PH2O2 to the default list of prod/loss families in the KPP mechanisms|Add P(H2O2) to the default list of prod/loss families in the KPP mechanisms]]
 +
*[[GEOS-Chem_12#Bug_fix_for_liquid_water_content_in_gckpp_HetRates.F90|Bug fix for liquid water content in gckpp_Hetrates.F90]]
 +
*[[GEOS-Chem_12#Fixed_typo_in_call_to_GAMMA_HOBr_AER|Fixed typo in call to GAMMA_HOBr_AER (in KPP module gckpp_HetRates.F90)]]
 +
*[[Organics_Working_Group#Add_missing_Criegee_intermediate_reaction|Add missing Criegee intermediate reaction]]
 +
*[[GEOS-Chem_12#Bug_fix_for_CH4_boundary_conditions|Bug fix for CH4 boundary conditions]]
 +
*[[FlexChem#FlexChem bug fix: do not zero ACTA, EOH, HCOOH|Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations]]
 +
 
 +
|-valign="top"
 +
|Diagnostics
 +
|
 +
*[[GEOS-Chem 12#Fixed typo that prevented PM2.5 from being archived to netCDF output|Fixed typo that prevented PM2.5 from being archived to netCDF output]]
 +
*[[Planeflight_diagnostic#Stop_with_error_if_the_plane_type_is_not_specified_in_Planeflight.dat|Planeflight diagnostic fix: Stop with error if the plane type is not specified in Planeflight.dat]]
 +
*[[#Bug fix for reference time in netCDF diagnostic files|Bug fix for reference time in netCDF diagnostic files]]
 +
 
 +
|-valign="top"
 +
|Emissions
 +
|
 +
*[[Lightning_NOx_emissions#Limit_flash_rate_density_in_hcox_lightnox_mod.F90|Limit flash rate density in hcox_lightnox_mod.F90]]
 +
*[[GEOS-Chem_12#Add_entries_to_HEMCO_Config.rc_for_SOAP_and_pFe_in_CEDS_inventory|Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory]]
 +
*[[Trash_burning_emissions#Avoid_double_counting_trash_emissions|Turn off TRASH emissions by default to avoid double counting]]
 +
*Update to HEMCO v2.1.007, which includes minor updates:
 +
*#[[Implementation of HEMCO in GEOS-Chem#Fixed_error_in_HEMCO_.22exact.22_time_option|Fixed error in HEMCO "exact" cycling option]]
 +
*#[[Implementation of HEMCO in GEOS-Chem#Stop with error if multiple containers have the same name|Stop with error if multiple containers have the same name]]
 +
*#[[Implementation of HEMCO in GEOS-Chem#Bug fix for distributing emissions in the vertical dimension|Bug fix for distributing emissions in the vertical dimension]]
 +
*#[[Implementation of HEMCO in GEOS-Chem#Add extra error checks in HEMCO standalone module|Add extra error checks in HEMCO standalone module]]
 +
*#[[Implementation of HEMCO in GEOS-Chem#Remove null string character from netCDF unit string|Remove null string character from netCDF unit string for GEOS-Chem "Classic" simulations]]
 +
*#[[Implementation_of_HEMCO_in_GEOS-Chem#Bug fix for HEMCO soil NOx error with ifort 17|Bug fix for HEMCO soil NOx error with ifort 17]]
 +
*Correct issues when specifying [[DICE-Africa anthropogenic emissions inventory|DICE-Africa emissions]]:
 +
*#[[DICE-Africa_anthropogenic_emissions_inventory#Avoid_double-counting_between_DICE-Africa_and_other_inventories|Avoid double-counting between DICE-Africa and other inventories]]
 +
*#[[DICE-Africa_anthropogenic_emissions_inventory#Use_unique_names_for_DICE-Africa_entries_in_HEMCO_Config.rc|Use unique names for DICE-Africa entries in the <tt>HEMCO_Config.rc</tt> file]]
 +
*Updates for [[QFED biomass burning emissions]]:
 +
*#[[QFED biomass burning emissions#Update to QFED v2.5r1|Update to QFED v2.5r1]]
 +
*#[[QFED_biomass_burning_emissions#Fix_QFED_files_for_2016.2F10.2F13|Fix QFED v2.4r6 files for 2016/10/13]]
 +
*[[GEOS-Chem 12#Avoid double counting CEDS and GEIA NH3 biofuel emissions|Avoid double counting CEDS and GEIA NH3 biofuel emissions]]
 +
*[[Ship_emissions#Fix_bug_in_ARCTAS_SHIP_SO2_scale_factors|Bug fix for ARCTAS_SHIP in <tt>HEMCO_Config.rc</tt> files]]
 +
 
 +
|-valign="top"
 +
|Specialty simulations
 +
|
 +
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_fixes_for_RRTMG_in_v11-02|Bug fixes for v11-02 simulations using the RRTMG radiative transfer model]]
 +
 
 +
|-valign="top"
 +
|Structural updates
 +
|
 +
*Initial structural updates to interface GEOS-Chem into WRF
 +
*Now always declare the netCDF time variable with an unlimited dimension
 +
 
 +
|}
 +
 
 +
== Issues resolved in GEOS-Chem v11-01 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem v11-01]].  Also be sure to visit [[Known issues caused by compiler bugs|our ''Known issues caused by compiler bugs'' wiki page]] for a list of compiler-related issues and workarounds.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="250px"|Module or area
 +
!width="750px"|Issue that was resolved
 +
 
 +
|-valign="top"
 +
|[[Aerosol-only simulation]]
 +
|
 +
*[[Aerosol-only_simulation#Fixed_undefined_molecular_weight_of_HNO3_in_routine_SEASALT_CHEM|Fixed undefined molecular weight of HNO3 in routine SEASALT_CHEM]]
 +
 
 +
|-valign="top"
 +
|[[CH4 simulation]]
 +
|
 +
*[[CH4_simulation#Fix_bug_in_CH4_emissions|Fix bug in CH4 emissions unit]]
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem chemistry mechanisms|Chemistry]]
 +
|
 +
*[[Centralized_chemistry_time_step#Optimal_Configuration|Adopt the optimal timestep recommendations of Philip et al 2015]]
 +
*[[GEOS-Chem_v11-01#Update_of_PMN_.2B_O3_reaction_products_in_globchem.dat_file|Update of PMN + O3 reaction products in globchem.dat file]]
 +
*[[UCX_chemistry_mechanism#Fix_for_black_carbon_in_ucx_mod.F|Fix for black carbon in <tt>ucx_mod.F</tt>]]
 +
*[[GEOS-Chem_v11-01#Modifications_to_ND20_to_archive_afternoon_P.28O3.29_and_L.28O3.29|Modifications to ND20 to archive afternoon P(O3) and L(O3)]]
 +
*[[Sulfate_aerosols#Bug_fix_for_sea_salt_alkalinity_in_sulfate_mod.F|Bug fix for sea salt alkalinity in <tt>sulfate_mod.F</tt>]]
 +
*[[GEOS-Chem_v10-01#Bug_fix_for_offline_dust_aerosols_when_UCX_is_on|Bug fix for offline dust aerosols when UCX is on]]
 +
*[[Mineral_dust_aerosols#Bug_fixes_for_hydrophobic_aerosol_properties|Bug fixes for hydrophobic aerosol properties]]
 +
*[[New_isoprene_scheme#Syntax_error_in_globchem.dat_file_for_MOBA_reaction_rate|Fix syntax error in <tt>globchem.dat</tt> for the MOBA + OH —> MOBAOO reaction rate]]
 +
*[[New_isoprene_scheme#Bug_in_reaction_ISNOOA_.2B_NO2_in_globchem.dat|Fixed typo in the ISNOOA + NO2 -> PMN reaction rate in <tt>globchem.dat</tt>]]
 +
*[[Stratospheric_chemistry#Fix_for_monthly_stratospheric_P.2FL_rates_in_HEMCO|Fix for monthly stratospheric P/L rates in HEMCO]]
 +
*[[Stratospheric_chemistry#Bug_in_the_GMI_stratospheric_production_rates_for_HCOOH|Fix bug in the GMI stratospheric production rates for HCOOH]]
 +
**[[Stratospheric_chemistry#Fixed_incorrect_timestamps_in_the_newest_HCOOH_prod.2Floss_file|Fixed incorrect timestamps in the updated GMI HCOOH strat P/L file]]
 +
*[[FlexChem#Incorrect_species_units_used_in_routines_UCX_NOX_and_UCX_H2SO4PHOT|Fix incorrect species units in routines UCX_NOX and UCX_H2SO4PHOT]]
 +
*[[GEOS-Chem_v11-01#Fix_molecular_weight_of_N2O5|Fix molecular weight of N2O5]]
 +
*[[Aerosol_optical_properties#Fix_for_TITLEAAt_out-of-bounds_error|Fix for out-of-bounds error when using the brown carbon option]]
 +
 
 +
|-valign="top"
 +
|[[CO2 simulation]]
 +
|
 +
*[[CO2_simulation#Additional_Update_and_Bug_Fix|Update CO2 emission files]]
 +
*[[CO2_simulation#Bug_fix:_Make_sure_nAdvect_is_initialized_in_EMISSCO2|Bug fix: Make sure <tt>nAdvect</tt> is initialized in EMISSCO2]]
 +
 
 +
|-valign="top"
 +
|[[Cloud convection]]
 +
|
 +
*[[Cloud_convection#Fixed bug in DO_MERRA_CONVECTION affecting mass conservation|Correct bug in below cloud average mixing ratio calculation in DO_MERRA_CONVECTION to improve mass balance]]
 +
*[[Cloud_convection#Resolve_very_high_tracer_concentrations_in_MERRA_and_GEOS-FP_convective_scavenging|Resolve very high tracer concentrations in GEOS-FP and MERRA convective scavenging]]
 +
 
 +
|-valign="top"
 +
|Compiler / Fortran issues
 +
|Compiler issues:
 +
*[[GNU Fortran compiler|Add support for GNU Fortran compiler]]
 +
*[[PGI Fortran compiler#File_Linking_Error|Fix linker error when using the PGI compiler]]
 +
*[[PGI Fortran compiler#Updates_for_GEOS-Chem_v11-01|Additional updates compiling GEOS-Chem with the PGI Fortran compiler]]
 +
*[[PGI Fortran compiler#Updates_for_GEOS-Chem_v11-01|Add further fixes for compiling GEOS-Chem with PGI Fortran]]
 +
*[[GEOS-Chem_Makefile_Structure#TRACEBACK.3Dy_is_now_the_default_setting|<tt>TRACEBACK=y</tt> is now the default setting for all simulations]]
 +
*[[Intel_Fortran_Compiler#Cannot_compile_GEOS-Chem_v10-01_with_Intel_Fortran_Compiler_v17|Remove offending code that was preventing GEOS-Chem from compiling with Intel Fortran v17]]
 +
 
 +
Fortran language issues:
 +
*[[GEOS-Chem_v11-01#Do_not_nullify_local_pointers_in_the_same_line_where_they_are_declared|Do not nullify local pointers in the same line where they are declared]]
 +
*[[Flexible_precision_in_GEOS-Chem#Update_KIND_parameters_to_facilitate_interface_with_the_Beijing_Climate_Center_model|Update flexible precision parameters so that GEOS-Chem can interface with the Beijing Climate Center model]]
 +
*[[GEOS-Chem v11-01#Prevent errors caused by uninitialized fields of the State_Met object|Prevent errors caused by uninitialized fields of the <tt>State_Met</tt> object]]
 +
*[[UCX_chemistry_mechanism#Only_allocate_certain_fields_of_State_Chm_for_UCX-based_simulations|Only allocate certain fields of <tt>State_Chm</tt> for UCX-based simulations]]
 +
*[[GEOS-Chem v11-01#Allocate aerosol fields of State_Chm only for full-chemistry or aerosol-only simulations|Allocate aerosol fields of <tt>State_Chm</tt> only for full-chemistry or aerosol-only simulations]]
 +
*[[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|Parallelization bug fix for marine POA]]
 +
 
 +
|-valign="top"
 +
|[[List of diagnostics for v11-01|Diagnostics]]
 +
|
 +
*[[GEOS-Chem_v11-01#Bug_fixes_for_the_ND21_diagnostic|Bug fix for the ND21 diagnostic]]
 +
*[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Bug_fix_for_monoterpenes_in_ND46_diagnostic|Bug fix for monoterpenes in ND46 diagnostic]]
 +
*[[GEOS-Chem_v11-01#Fix_units_of_O1D_and_O3P_in_ND43_diagnostic|Fix units of O1D and O3P in ND43 diagnostic]]
 +
*[[GEOS-Chem_v11-01#Fix_incorrect_unit_strings_for_ND65_diagnostic_in_diag3.F|Fix incorrect unit strings for ND65 diagnostic in <tt>diag3.F</tt>]]
 +
 
 +
|-valign="top"
 +
|[[HEMCO data directories|Emissions (via HEMCO)]]
 +
|
 +
*[[Lightning_NOx_emissions#Correct_problem_in_OTD-LIS_local_redistribution_files|Fix problem in OTD/LIS lighning redistribution files]]
 +
*[[GEOS-Chem_v10-01#Fix_for_reading_hourly_NEI2011_emissions|Fix for reading hourly NEI2011 emissions]]
 +
*[[EMEP_European_anthropogenic_emissions#Zero_EMEP_emissions_at_30N_for_2x25_and_higher_resolutions|Use an updated EMEP mask file to prevent zero emissions at 30 N for 2&deg; x 2.5&deg; or higher resolutions]]
 +
*[[Secondary_organic_aerosols#Incorrect_concentrations_in_SOA-SVPOA_simulation|Fix an emissions error in the SOA-SVPOA simulation]]
 +
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fixed_missing_pointer_in_call_to_HCO_CalcVertGrid|Fixed missing pointer in call to HEMCO routine Hco_CalcVertGrid]]
 +
*[[Implementation_of_HEMCO_in_GEOS-Chem#Enable_emissions_in_the_stratosphere_for_specialty_simulations|Correct bug introduced in v11-01e where emissions were disabled in the stratosphere for specialty simulations]]
 +
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fix_bug_preventing_HEMCO_from_writing_restart_files_more_than_once_per_run|Fixed bug preventing HEMCO from writing restart files more than once per run]]
 +
*[[EDGAR_v4.2_anthropogenic_emissions#Correct_bug_in_units_of_EDGAR_v4.2_SO2_emissions|Correct bug in units of EDGAR v4.2 SO2 emissions]]
 +
*[[EDGAR_v4.2_anthropogenic_emissions#Prevent_biofuel_emissions_from_being_double_counted|Prevent biofuel emissions from being double counted in EDGAR v4.2]]
 +
*[[Scale_factors_for_anthropogenic_emissions#Bug_fix_for_NOx_diurnal_scale_factors|Fix bug in NOx diurnal scale factors]]
 +
*[[Implementation_of_HEMCO_in_GEOS-Chem|Update HEMCO from version 1.1.016 to latest version available]]
 +
*[[Implementation_of_RETRO_Anthropogenic_Emissions#RETRO_anthropogenic_propane_emissions_are_too_low|Replace RETRO C3H8 emissions with emissions from Xiao et al.]]
 +
*[[QFED_biomass_burning_emissions#Biomass_burning_emissions_diagnostic_is_zero_when_QFED_is_used|Fix for biomass burning diagnostic when QFED emissions are used]]
 +
*[[HEMCO#Update:_Preventing_seg_fault_in_HEMCO_v2.0_caused_by_compiler_bug|Prevent seg fault in HEMCO v2.0 caused by Intel Fortran compiler bug]]
 +
 
 +
|-valign="top"
 +
|[[Mercury]] and [[POPs simulation|POPs]] simulations
 +
|
 +
*[[Mercury#Hg_ocean_MLD_bug_fixes|Bug fixes for computing MLD in <tt>ocean_mercury_mod.F</tt>]]
 +
*[[Mercury#Parallelization_bug_fixes_for_GEOS-5_Hg_simulations|Fix parallelization errors that prevented Hg simulations from passing unit tests]]
 +
*[[Mercury#Avoid_floating-point_exception_in_OCEAN_MERCURY_READ|Avoid floating-point exception in OCEAN_MERCURY_READ]]
 +
*[[Mercury#Bug_Fixes_to_v11-01c_Hg_Updates|Bug fixes for Arctic Hg updates in v11-01c]]
 +
*[[Mercury#Correct_too-high_emissions_of_Hg2_over_China_and_EU|Correct too-high emissions of Hg2 over China and EU]]
 +
*[[Mercury#Now_call_DO_RED_INPLUME_after_the_HEMCO_configuration_file_is_read|Now call subrouine DO_RED_INPLUME after the HEMCO configuration file is read]]
 +
*[[POPs_simulation#Avoid_floating-point_exception_in_routine_CHEM_POPGP|Avoid floating-point error in routine CHEM_POPGP]]
 +
 
 +
|-valign="top"
 +
|Met fields and derived quantities
 +
|
 +
*[[Air_Quantity_Updates_for_v11-01|Incorporate moisture into air quantities, tracer units, and tracer unit conversions]]
 +
*[[GEOS-Chem_species_units#Updating_Air_Quantities|Bug fix to update air quantities after specific humidity is updated in non-local PBL mixing]]
 +
*[[GEOS-Chem_v11-01#Incorrect_incorporation_of_moisture_in_GEOS-Chem_air_quantities|Fix to remove moisture signature in dry mixing ratio]]
 +
 
 +
|-valign="top"
 +
|[[Preparing data files for use with HEMCO#The COARDS netCDF standard|netCDF I/O]]
 +
|
 +
*[[GEOS-Chem_Output_Files#NetCDF_File_Format|Migration from bpch to netCDF output file format]]
 +
*[[GEOS-Chem_Output_Files#Improve_write_speed_of_netCDF_output_files|Improve write speed of netCDF output files]]
 +
*[[GEOS-Chem_Output_Files#GAMAP_can_now_read_GEOS-Chem_restart_files_in_netCDF_format|GAMAP can now read GEOS-Chem restart files in netCDF format]]
 +
 
 +
|-valign="top"
 +
|[[FAST-JX_v7.0_photolysis_mechanism|Photolysis]]
 +
|
 +
*[[FAST-JX_v7.0_photolysis_mechanism#Fix_for_TOMS_to_address_strange_cycle_in_OH_output|Fix for TOMS/HEMCO to address strange cycle in OH output]]
 +
*[[FAST-JX_v7.0_photolysis_mechanism#Use_TOMS_ozone_for_all_years_when_running_simulations_with_GEOS-5|Use TOMS ozone for all years when running simulations with GEOS-5 meteorology]]
 +
 
 +
|-valign="top"
 +
|[[Regridding in GEOS-Chem|Regridding]]
 +
|
 +
*[[Regridding_in_GEOS-Chem#Bug_fix:_MAP_A2A_now_only_uses_periodic_BCs_for_global_data|Bug fix: MAP_A2A now applies periodic boundary conditions only to global data sets during regridding]]
 +
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fixed_bug_in_time_interpolation_in_ncdf_mod.F90|Bug fix for time interpolation in netCDF utility module <tt>ncdf_mod.F90</tt>]]
 +
 
 +
|-valign="top"
 +
|[[Coupling_GEOS-Chem_with_RRTMG|RRTMG radiative transfer model]]
 +
|
 +
*[[Coupling_GEOS-Chem_with_RRTMG#Fix_bug_that_prevents_storage_of_O3_and_CH4_RFs|Fix bug that prevents storage of O3 and CH4 RF's]]
 +
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_in_RRTMG_array_sizes|Bug fix in RRTMG array sizes]]
 +
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_fixes_in_rrtmg_rad_transfer_mod.F|Further bug fixes in <tt>rrtmg_transfer_mod.F</tt>]]
 +
*[[Coupling_GEOS-Chem_with_RRTMG#Replace_nonstandard_DLOG_function_with_LOG|Replace nonstandard DLOG function with LOG]]
 +
 
 +
|-valign="top"
 +
|Marine POA simulations
 +
|
 +
*[[Aerosol_emissions#Bug_fix:_Allocate_the_OCCONV_array_for_marine_POA_simulations|Allocate the OCCONV array for marine POA simulations]]
 +
 
 +
|-valign="top"
 +
|[[Rn-Pb-Be simulation|Radon-Lead-Beryllium simulation]]
 +
|
 +
*[[Rn-Pb-Be_simulation#Typo_in_HEMCO_extension_module_hcox_gc_RnPbBe_mod.F90|Fix typo in HEMCO extension module <tt>hcox_gc_RnPbBe_mod.F90</tt>]]
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem species database|Species database]] and [[Physical_constants|definitions of physical constants]]
 +
|
 +
*[[Physical_properties_of_GEOS-Chem_species#Discrepancies_found_in_the_dry_deposition_module|Remove inconsistencies in the definitions of physical properties of GEOS-Chem species]]
 +
*[[Sea_salt_aerosols#Molecular_weight_discrepancy_in_drydep_mod.F|Use proper molecular weights for sea salt aerosols in the dry deposition module]]
 +
*[[Sulfate_aerosols#Give_SO4s_and_NITs_the_same_molecular_weight_as_SALC|Give SO4s and NITs the same molecular weight as SALC]]
 +
*[[Mineral_dust_aerosols#Now_treat_DST2-DST4_as_coarse_mode_in_wet_scavenging|Now treat DST2-DST4 as coarse mode in wet scavenging]]
 +
**NOTE: This also will apply to dust uptake tracers DSTAL2-4, NITD2-4, SO4D2-4
 +
*[[GEOS-Chem_species_database#Defining_molecular_weight_fields_of_the_Input_Opt_object_from_the_species_database|Define molecular weight fields of the <tt>Input_Opt</tt> object from the species database]]
 +
*[[Physical_constants|Now use consistent physical parameter values throughout GEOS-Chem]]
 +
*[[Physical_constants|Now use consistent physical constant declarations]]
 +
 
 +
|-valign="top"
 +
|[[Tagged CO simulation]]
 +
|
 +
*[[Tagged_CO_simulation#OH_is_now_converted_to_the_proper_units_after_being_read_from_HEMCO|Now convert OH to the proper units in the tagged CO simulation]]
 +
 
 +
|-valign="top"
 +
|[[Tagged O3 simulation]]
 +
|
 +
*[[GEOS-Chem_v10-01#Bug_in_European_grid_range_for_tagged_Ox_simulation|Bug fix in European grid range for tagged O3 simulation]]
 +
*[[GEOS-Chem_v10-01#Bug_fix_for_PBLTOP_and_MTTOP_values_in_tagged_ozone_simulation|Bug fix for PBLTOP and MTTOP values in tagged O3 simulation]]
 +
 
 +
|-valign="top"
 +
|[[TOMAS aerosol microphysics]]
 +
|
 +
*[[TOMAS_aerosol_microphysics#Updates_to_TOMAS_Jeagle_sea_salt_extension|Updates to TOMAS Jeagle sea salt extension]]
 +
*[[TOMAS_aerosol_microphysics#Add_temporary_fix_to_get_TOMAS_dry_deposition_to_pass_unit_tests|Add temporary fix to get TOMAS dry deposition to pass unit tests]]
 +
 
 +
|-valign="top"
 +
|Various structural updates
 +
|
 +
*[[GEOS-Chem_v11-01#Bug_fix_for_custom_grid_in_tpcore_bc_mod.F|Bug fix for custom nested grid in <tt>tpcore_bc_mod.F</tt>]]
 +
*[[GEOS-Chem v11-01#Rename_grid_mod.F90_to_gc_grid_mod.F90|Rename <tt>grid_mod.F90</tt> to <tt>gc_grid_mod.F90</tt>]]
 +
*[[GEOS-Chem v11-01#Error message output now advises users to check the HEMCO log file|GEOS-Chem error messages now advise the user to check the HEMCO log file]]
 +
*[[GEOS-Chem_v11-01#Print_message_to_log_file_if_OpenMP_parallelization_is_turned_off|Print message to log file if OpenMP parallelization is turned off]]
 +
 
 +
|-valign="top"
 +
|[[Wet deposition]]
 +
|
 +
*[[Wet_deposition#Low_tropospheric_210Pb_lifetime_against_deposition_in_v11-01b|Quick fix for low tropospheric 210Pb lifetime against wet deposition]]
 +
*[[Wet_deposition#Fix_bug_in_GEOS-FP_re-evaporation_calculation|Fix bug in GEOS-FP re-evaporation calculation]]
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:57, 23 January 2017 (UTC)
 +
 
 +
== Bugs and fixes in older GEOS-Chem versions ==
 +
 
 +
For a complete list of bugs and fixes in older GEOS-Chem versions, please see:
 +
 
 +
*[[Bugs and fixes in GEOS-Chem v9, v10, and v11]]
 +
*[[Bugs and fixes in GEOS-Chem v7 and v8]]
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:47, 2 January 2019 (UTC)

Revision as of 15:25, 3 April 2020

On this page we list the GEOS-Chem specific bugs and issues that users have recently encountered, and how to fix them.

Please also be sure to visit our Common GEOS-Chem error messages wiki page for more general information about some frequently encountered errors. Also visit our Currently unresolved issues in GEOS-Chem and Known issues caused by compiler bugs wiki pages for more information about unresolved issues.

Bugs and fixes lists have now been migrated to Github

We have been migrating bug reports to our GEOS-Chem issue tracker, which is located on our Github repository: https://github.com/geoschem/geos-chem/issues/. We recommend that you also look through both the open and closed issues on this page, as your issue might be listed there.

Version Released List of bugs and issues (now posted on the listed Github repository)
13.0.0 TBD geoschem/geos-chem
12.9.0 TBD geoschem/geos-chem
12.8.1 TBD geoschem/geos-chem
12.8.0 pending geoschem/geos-chem Milestone 12.8.0
12.7.2 09 Mar 2020 geoschem/geos-chem Milestone 12.7.2
12.7.1 19 Feb 2020 geoschem/geos-chem Milestone 12.7.1
12.7.0 03 Feb 2020 geoschem/geos-chem Milestone 12.7.0
12.6.3 25 Nov 2019 geoschem/gchp Milestone 12.6.3
12.6.2 15 Nov 2019 geoschem/geos-chem Milestone 12.6.2
12.6.1 28 Oct 2019 geoschem/geos-chem Milestone 12.6.1
12.6.0 18 Oct 2019 geoschem/geos-chem Milestone 12.6.0

Issues resolved in GEOS-Chem 12.5.0

The bugs and technical issues listed below will be resolved GEOS-Chem 12.5.0, release date TBD.

Module or area Issue that was resolved Git commit ID
Chemistry
  1. Bug fix: Make sure stratospheric BrY concentrations are properly read each month
  2. Add photolysis menu to input.geos for specifying FAST-JX directory
  3. Correction for CFCs in the chemistry mechanism
  4. Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90
  1. 0588a269
  2. 03e94fed
  3. 1b9f69f0
  4. 95d124e0
Diagnostics
  1. Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally
  2. Enable accurate cloud pH diagnostic calculation via post-processing
  1. 6acd4ce3
  2. 1c15e54a
Structural updates
  1. Add optional capability to compile GEOS-Chem Classic and GCHP using CMake
  1. pull/27
Emissions
  1. Fixes for GFED4 biomass burning emissions, including:
    • Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year
    • Remove the 27% scaling of POG to POA and emit 1:1 instead
  1. 381386fb
Fixes affecting GCHP only:
Structural updates
  1. Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28
    • Will introuduce faster parallel I/O
    • Will enable full use of gfortran compiler

--Bob Yantosca (talk) 17:03, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.4.0

The bugs and technical issues listed below will be resolved GEOS-Chem 12.4.0, release date TBD.

Module or area Issue that was resolved Git commit ID
Photolysis
  1. Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2
  2. Add photolysis menu to input.geos for specifying FAST-JX directory
  1. fcd0cfba
  2. d34a9cd2

--Bob Yantosca (talk) 17:04, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.2

The bugs and technical issues listed below will be resolved GEOS-Chem 12.3.2.

Module or area Issue that was resolved Git commit ID
Chemistry
  1. Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic"
  1. rel/12.3.2
Photolysis
  1. Remove duplicate entry for species ClNO2 in the FJX_j2j.dat file
  2. Species DHDC was not listed as photolyzing in the GEOS-Chem species database
  1. rel/12.3.2
  2. d7c48d14
Fixes affecting GCHP only:
Emissions
  1. Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default
  2. Fix HEMCO diagnostics settings for lightning NO and seasalt emissions
  1. f6ac477a
  2. cda5044e

--Bob Yantosca (talk) 16:37, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.1

The bugs and technical issues listed below were resolved GEOS-Chem 12.3.1 (release 08 Apr 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Planeflight diagnostic now writes out data for the last timestep of the day
  2. Fix the netCDF diagnostic for noontime J-values
  1. 04da94cd
  2. f4d43b7a
Structural
  1. Do not allocate memory to array MINIT in strat_chem_mod.F90
  2. Declare State_Met%Area_M2 as 2-dimensional, not 3-dimensional
  1. 729fd2a7
  2. e4af25f3b

--Bob Yantosca (talk) 20:06, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.0

The bugs and technical issues listed below were resolved GEOS-Chem 12.3.0 (release date TBD).

Module or area Issue that was resolved Git commit ID
Diagnostics / Restart files
  1. Further bug fix for netCDF diagnostics spanning leap years
  1. fb093d61
Emissions
  1. Bug fixes for the HEMCO interpolation algorithm
  2. Updates from the NASA GEOS development branch
  3. Add option to always use simulation year for specified fields
  4. Prevent zero emissions for MEGAN_Mono extension species
  5. Updates to the volcanic emissions extension
  1. e947fc80
  2. 7df3fc8e
  3. 23189032
  4. af86c4dd
  5. 07c10319

--Bob Yantosca (talk) 15:53, 21 March 2019 (UTC)

Issues resolved in GEOS-Chem 12.2.1

The bugs and technical issues listed below were resolved GEOS-Chem 12.2.1 (release date 28 Feb 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics / Restart files
  1. Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days
  1. ca68f508
CO2 simulation
  1. Fix for CO2 simulation chemical source
  1. N/A
TOMAS simulations
  1. Restore DST1, DST2, DST3, and DST4 in TOMAS simulations
  1. 5ed3e9cf
Fixes affecting GCHP only:
Emissions etc.
  1. Use online sea flux emissions by default in GCHP
  2. Update MODIS LAI source directory to match GEOS-Chem Classic
  1. 9759d26b
  2. N/A
Met fields
  1. Missing scaling factors for MERRA-2 simulations with GCHP
  1. ?

--Bob Yantosca (talk) 17:03, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.2.0

The bugs and technical issues listed below were resolved GEOS-Chem 12.2.0 (release date 19 Feb 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fix bug in stratospheric aerosol surface area in netCDF diagnostics
  1. e4fecf01
Fixes affecting GCHP only:
Restart files
  1. GCHP bug fix: Use checkpoint output as the subsequent restart file

--Bob Yantosca (talk) 20:02, 14 March 2019 (UTC)

Issues resolved in GEOS-Chem 12.1.1

The bugs and technical issues listed below were resolved in GEOS-Chem 12.1.1, which was released on 13 Dec 2018.

Module or area Issue that was resolved Git commit ID
Compilation issues
  1. Always enable BPCH_TPBC to allow saving out BC files in global simulations
  2. Add hco_interface_mod.o to list of dependencies for get_met_mod.o and only compile get_met_mod.F90 and flexgrid_mod.F90 for GEOS-Chem "Classic"
  3. Add flexgrid_read_mod.o to list of dependencies for hcoi_gc_main_mod.o
  1. 072ec9d6
  2. 096ad29d
  3. f9b2f195
Diagnostics
  1. Skip planeflight observations outside a nested domain
  1. f6f90fd4
Tagged CO simulation
  1. Bug fix for tagged CO: don't multiply emissions timestep by 60
  1. 8a1b078e
Fixes affecting GCHP only:
Transport (FvDycore)
  1. GCHP transport fix to prevent instant propagation from troposphere to stratosphere

--Bob Yantosca (talk) 14:12, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.1.0

The bugs and technical issues listed below were resolved in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.

Module or area Issue that was resolved Git commit ID
CH4 simulation
  1. Add fixes for seasonal scale factors in CH4 simulations
  1. 6f48d045
Chemistry and Photolysis
  1. Allow for SZA to 98 degrees when getting photolysis rates
  2. Move Fast-JX .dat files from the geos-chem-unittest repository to gcgrid/ExtData
  1. d06ae04a
  2. 03e94fed
Emissions
  1. Add missing RCO sector to CEDS emissions entries
  2. Include CEDS ship emissions as default global ship emissions inventory
  3. Reduce file size for CEDS inventory
  4. HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic"
  5. Add fix for collapsing model levels to reduced grid
  6. Fix unit conversion in HCO_UNIT_GetAreaScal
  1. 642dd0af
  2. e71d0d67
  3. 20451cb4
  4. 3f62e749
  5. 820b8d7d
  6. 7dfd99da
PBL Mixing
  1. Fix mass conservation in non-local PBL mixing
  1. 57c75178
Tagged CO simulation
  1. Update HEMCO configuration file for the tagged CO simulation
  1. 02aaad73
Fixes affecting GCHP only:
Emissions (GCHP)
  1. Fix masking bug to correctly apply anthropogenic emissions
  2. Remove erroneous 180 degree longitude shift in APEI regridding
Structural (GCHP)
  • Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository

--Bob Yantosca (talk) 15:12, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.3

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.3, which was released on 16 Oct 2018.

Module or area Issue that was resolved Git commit ID
Fixes affecting GCHP only:
Emissions (GCHP)
  1. Fix incorrect run configuration for offline sea salt emissions in GCHP
  2. Fix bug in application of CFC surface mixing ratios in GCHP

--Bob Yantosca (talk) 22:01, 21 December 2018 (UTC)

Issues resolved in GEOS-Chem 12.0.2

The bugs and technical issues listed below were be resolved in GEOS-Chem 12.0.2, which was released on 10 Oct 2018.

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics
  1. 14b29d3d
Specialty simulations
  1. Correct missing BC/OC biomass emissions and aerosol drydep in TOMAS simulations
  2. Avoid double-counting of emissions in the CO2 simulation
  1. 6a944b92
  2. 8320e73d

--Bob Yantosca (talk) 19:16, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.1

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.1, which was released on 24 Aug 2018.

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fix typo when registering the State_Chm%SSAlk field
  2. Fix mis-indexing in the ND05 diagnostic
  1. 55d16873
  2. 8e118c0e
Mercury
  1. Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions
  1. e1e6668b
Structural updates
  1. Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
  2. Add a more robust test for netCDF-Fortran in Makefile_header.mk
  3. Fix compilation issues encountered with GNU Fortran 8.2.0
  4. Fix compilation issues encountered with Intel Fortran 18
  1. ff7b0c3c
  2. a4d55055
  3. e0959563
  4. 9833fff4

--Bob Yantosca (talk) 19:20, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.0

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.0, which was released on 10 Aug 2018.

Module or area Issue that was resolved
Aerosols
Chemistry
Diagnostics
Emissions
Specialty simulations
Structural updates
  • Initial structural updates to interface GEOS-Chem into WRF
  • Now always declare the netCDF time variable with an unlimited dimension

Issues resolved in GEOS-Chem v11-01

The bugs and technical issues listed below were resolved in GEOS-Chem v11-01. Also be sure to visit our Known issues caused by compiler bugs wiki page for a list of compiler-related issues and workarounds.

Module or area Issue that was resolved
Aerosol-only simulation
CH4 simulation
Chemistry
CO2 simulation
Cloud convection
Compiler / Fortran issues Compiler issues:

Fortran language issues:

Diagnostics
Emissions (via HEMCO)
Mercury and POPs simulations
Met fields and derived quantities
netCDF I/O
Photolysis
Regridding
RRTMG radiative transfer model
Marine POA simulations
Radon-Lead-Beryllium simulation
Species database and definitions of physical constants
Tagged CO simulation
Tagged O3 simulation
TOMAS aerosol microphysics
Various structural updates
Wet deposition

--Bob Yantosca (talk) 19:57, 23 January 2017 (UTC)

Bugs and fixes in older GEOS-Chem versions

For a complete list of bugs and fixes in older GEOS-Chem versions, please see:

--Bob Yantosca (talk) 20:47, 2 January 2019 (UTC)