Difference between revisions of "Bugs and fixes"

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(Issues resolved in GEOS-Chem 12.6.0)
(Bugs and fixes lists have now been migrated to Github)
(83 intermediate revisions by the same user not shown)
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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.
 
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 12.6.0 ==
+
== Bugs and fixes lists have now been migrated to Github ==
  
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]], release date TBD.
+
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.
  
{| border=1 cellspacing=0 cellpadding=5
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{| border=1 cellspacing=0 cellpadding=5  
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="200px"|Module or area
+
!Version
!width="675px"|Issue that was resolved
+
!Released
!width="130px"|Git commit ID
+
!colspan="2"|List of bugs and issues (now posted on the listed Github repository)
+
 
 
|-valign="top"
 
|-valign="top"
|Build system
+
|[[GEOS-Chem 12#12.8.0|12.8.0]]
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 
|
 
|
#Remove support for the PGI compiler in both code and makefiles
+
*[https://github.com/geoschem/geos-chem/milestone/7 '''Milestone 12.8.0''' (open issues)]
|
+
*[https://github.com/geoschem/geos-chem/milestone/7?closed=1 '''Milestone 12.8.0''' (closed issues)]
#[https://github.com/geoschem/geos-chem/commit/b711c44516cd170641bece49de13ca764e3961c3 b711c445]
+
  
 
|-valign="top"
 
|-valign="top"
|Diagnostics
+
|[[GEOS-Chem 12#12.7.2|12.7.2]]
|
+
|09 Mar 2020
#Minimize unit conversions when updating diagnostics at the end of every timestep
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
|
+
|[https://github.com/geoschem/geos-chem/milestone/11?closed=1 '''Milestone 12.7.2''']
#[https://github.com/geoschem/geos-chem/commit/cf3b883d816e253a16a57af1a74830cb789c7796 cf3b883d]
+
  
|}
+
|-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''']
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:03, 15 July 2019 (UTC)
+
|-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''']
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.6.3|12.6.3]]
 +
|25 Nov 2019
 +
|[https://github.com/geoschem/gchp geoschem/gchp]
 +
|[https://github.com/geoschem/gchp/milestone/2?closed=1 '''Milestone 12.6.3''']
 +
 
 +
|-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''']
 +
 
 +
|-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''']
 +
 
 +
|-valign="top"
 +
|width="80px"|[[GEOS-Chem 12#12.6.0|12.6.0]]
 +
|width="100px"|18 Oct 2019
 +
|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''']
 +
 
 +
|}
  
 
== Issues resolved in GEOS-Chem 12.5.0 ==
 
== Issues resolved in GEOS-Chem 12.5.0 ==
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!width="200px"|Module or area
 
!width="200px"|Module or area
!width="675px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 
!width="130px"|Git commit ID
 
!width="130px"|Git commit ID
  
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|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
 
!width="200px"|Module or area
 
!width="200px"|Module or area
!width="675px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 
!width="130px"|Git commit ID
 
!width="130px"|Git commit ID
  
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|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
 
!width="200px"|Module or area
 
!width="200px"|Module or area
!width="675px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 
!width="130px"|Git commit ID
 
!width="130px"|Git commit ID
  
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|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
 
!width="200px"|Module or area
 
!width="200px"|Module or area
!width="675px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 
!width="130px"|Git commit ID
 
!width="130px"|Git commit ID
  
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|
 
|
 
#[https://github.com/geoschem/geos-chem/commit/729fd2a7ed79b8a6a4a7fd6231097fbb1c4baf21 729fd2a7]
 
#[https://github.com/geoschem/geos-chem/commit/729fd2a7ed79b8a6a4a7fd6231097fbb1c4baf21 729fd2a7]
#[https://github.com/geoschem/gchp/commit/e4af25f3b893263d1236c3a35c64e2e46f2e78cb 729fd2a7]
+
#[https://github.com/geoschem/gchp/commit/e4af25f3b893263d1236c3a35c64e2e46f2e78cb e4af25f3b]
  
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:42, 15 July 2019 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:06, 16 July 2019 (UTC)
  
 
== Issues resolved in GEOS-Chem 12.3.0 ==
 
== Issues resolved in GEOS-Chem 12.3.0 ==
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|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
 
!width="200px"|Module or area
 
!width="200px"|Module or area
!width="675px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 
!width="130px"|Git commit ID
 
!width="130px"|Git commit ID
  
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#[[HEMCO_versions#Bug_fixes_for_HEMCO_interpolation_algorithm|Bug fixes for the HEMCO interpolation algorithm]]
 
#[[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#Updates from the NASA GEOS development branch|Updates from the NASA GEOS development branch]]
#[[GEOS-Chem_12#Error_reading_restart_file_when_using_a_fixed_emissions_year_in_HEMCO|Add option to always use simulation year for specified fields]]
+
#[[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#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]]
 
#[[HEMCO_versions#Updates to the volcanic emissions extension|Updates to the volcanic emissions extension]]
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|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
 
!width="200px"|Module or area
 
!width="200px"|Module or area
!width="675px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 
!width="130px"|Git commit ID
 
!width="130px"|Git commit ID
  
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|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
 
!width="200px"|Module or area
 
!width="200px"|Module or area
!width="675px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 
!width="130px"|Git commit ID
 
!width="130px"|Git commit ID
  
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{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!width="200px"|Module or area
!width="750px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
 
|Compilation issues
 
|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]]
+
#[[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/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/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]
  
 
|-valign="top"
 
|-valign="top"
 
|Diagnostics
 
|Diagnostics
 
|
 
|
*[[GEOS-Chem_12#Skip_planeflight_observations_outside_a_nested_domain|Skip planeflight observations outside a nested domain]]
+
#[[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]
  
 
|-valign="top"
 
|-valign="top"
 
|Tagged CO simulation
 
|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]]
+
#[[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]
  
 
|-
 
|-
!colspan="2" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
+
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
 
|-valign="top"
 
|-valign="top"
 
|Transport (FvDycore)
 
|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]]
+
#[[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]]) 21:57, 21 December 2018 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:12, 16 July 2019 (UTC)
  
 
== Issues resolved in GEOS-Chem 12.1.0 ==
 
== Issues resolved in GEOS-Chem 12.1.0 ==
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{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!width="200px"|Module or area
!width="750px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
 
|CH4 simulation
 
|CH4 simulation
 
|
 
|
*[[CH4_simulation#Add_fixes_for_seasonal_scale_factors_in_CH4_simulations|Add fixes for seasonal scale factors in CH4 simulations]]
+
#[[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"
 
|-valign="top"
 
|Chemistry and Photolysis
 
|Chemistry and Photolysis
 
|
 
|
*[[#Allow_for_SZA_to_98_degrees_when_getting_photolysis_rates|Allow for SZA to 98 degrees when getting photolysis rates]]
+
#[[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>]]
+
#[[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>]]
 
+
|-valign="top"
+
|CO2 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/commit/d06ae04ad44defd15854a9c4dadd36923dee0498 d06ae04a]
 +
#[https://github.com/geoschem/geos-chem/commit/03e94fed99cf2bb538dfc59ec514690a122b01a9 03e94fed]
  
 
|-valign="top"
 
|-valign="top"
 
|Emissions
 
|Emissions
|Updates and fixes for the CEDS anthropogenic emissions inventory:
+
|
*[[CEDS_anthropogenic_emissions#Add_missing_RCO_sector_to_CEDS_emissions_entries|Add missing RCO sector to CEDS emissions entries]]
+
#[[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#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]]
+
#[[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"]]
HEMCO fixes:
+
#[[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#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#Fix_unit_conversion_in_HCO_UNIT_GetAreaScal|Fix unit conversion in HCO_UNIT_GetAreaScal]]
*[[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"
 
|-valign="top"
 
|PBL Mixing
 
|PBL Mixing
 
|
 
|
*[[Boundary_layer_mixing#Mass_is_not_conserved_when_using_non-local_PBL_mixing|Fix mass conservation in non-local 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="2" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
+
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
 
|-valign="top"
 
|-valign="top"
 
|Emissions (GCHP)
 
|Emissions (GCHP)
 
|
 
|
*[[GEOS-Chem_12#Fix_masked_anthropogenic_emissions_bug_in_GCHP|Fix masking bug to correctly apply anthropogenic emissions]]
+
#[[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]]
+
#[[GEOS-Chem_12#Fix_regional_tile_file_used_for_APEI_inventory_in_GCHP|Remove erroneous 180 degree longitude shift in APEI regridding]]
 +
|
  
 
|-valign="top"
 
|-valign="top"
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|
 
|
 
*Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository
 
*Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository
 +
|
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:04, 21 December 2018 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:12, 16 July 2019 (UTC)
  
 
== Issues resolved in GEOS-Chem 12.0.3 ==
 
== Issues resolved in GEOS-Chem 12.0.3 ==
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{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!width="200px"|Module or area
!width="750px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
!colspan="2" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
+
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
 
|-valign="top"
 
|-valign="top"
 
|Emissions (GCHP)
 
|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_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]]
+
#[[#Fix_bug_in_application_of_CFC_surface_mixing_ratios_in_GCHP|Fix bug in application of CFC surface mixing ratios in GCHP]]
 +
|
  
 
|}
 
|}
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{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!width="200px"|Module or area
!width="750px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
 
|Diagnostics
 
|Diagnostics
 
|
 
|
*[[#Fixed_local-time_averaging_in_ND51_and_ND51b_satellite_timeseries_diagnostics|Fixed local-time averaging in ND51 and ND51b satellite timeseries 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"
 
|-valign="top"
 
|Specialty simulations
 
|Specialty simulations
 
|
 
|
*[[TOMAS_aerosol_microphysics#Fixes_for_missing_biomass_emissions_and_incorrect_aerosol_dry_deposition|Fixes to correct missing BC/OC biomass emissions and incorrect aerosol drydep in TOMAS 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]]
+
#[[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]]) 21:25, 21 December 2018 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:16, 16 July 2019 (UTC)
  
 
== Issues resolved in GEOS-Chem 12.0.1 ==
 
== Issues resolved in GEOS-Chem 12.0.1 ==
Line 457: Line 526:
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!width="200px"|Module or area
!width="750px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
 
|Diagnostics
 
|Diagnostics
 
|
 
|
*[[#Fix typo when registering the State_Chm%SSAlk field|Fix typo when registering the <tt>State_Chm%SSAlk</tt> field]]
+
#[[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]]
+
#[[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"
 
|-valign="top"
 
|Mercury
 
|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]]
+
#[[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"
 
|-valign="top"
 
|Structural updates
 
|Structural updates
 
|
 
|
*Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
+
#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]]
+
#[[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]]
+
#[[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]]
+
#[[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]]) 16:53, 24 August 2018 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:20, 16 July 2019 (UTC)
  
 
== Issues resolved in GEOS-Chem 12.0.0 ==
 
== Issues resolved in GEOS-Chem 12.0.0 ==

Revision as of 17:34, 20 March 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)
12.8.0 TBD geoschem/geos-chem
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)