Difference between revisions of "Bugs and fixes"

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(Issues resolved in GEOS-Chem v11-01)
(Issues resolved in GEOS-Chem v11-01)
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|[[GEOS-Chem chemistry mechanisms|Chemistry]]
 
|[[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]]
 
*[[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>]]
 
*[[UCX_chemistry_mechanism#Fix_for_black_carbon_in_ucx_mod.F|Fix for black carbon in <tt>ucx_mod.F</tt>]]
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|Structural updates
 
|Structural updates
 
|
 
|
 +
Compilers:
 +
*[[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#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]]
 +
 +
Diagnostics:
 
*[[GEOS-Chem_v11-01#Bug_fixes_for_the_ND21_diagnostic|Bug fix for the ND21 diagnostic]]
 
*[[GEOS-Chem_v11-01#Bug_fixes_for_the_ND21_diagnostic|Bug fix for the ND21 diagnostic]]
*[[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>]]
 
 
*[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Bug_fix_for_monoterpenes_in_ND46_diagnostic|Bug fix for monoterpenes in ND46 diagnostic]]
 
*[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Bug_fix_for_monoterpenes_in_ND46_diagnostic|Bug fix for monoterpenes in ND46 diagnostic]]
*[[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|Parallelization bug fix for marine POA]]
+
 
*[[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]];
+
Fixes for Fortran issues:
*[[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]];
+
*[[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]]
+
*[[PGI Fortran compiler#Updates_for_GEOS-Chem_v11-01|Add further fixes for compiling GEOS-Chem with PGI Fortran]]
+
*[[Centralized_chemistry_time_step#Optimal_Configuration|Adopt the optimal timestep recommendations of Philip et al 2015]]
+
 
*[[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]]
 
*[[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]]
*[[PGI Fortran compiler#Updates_for_GEOS-Chem_v11-01|Additional updates compiling GEOS-Chem with the PGI Fortran compiler]]
 
*[[Physical_constants|Now use consistent physical constant declarations]]
 
*[[GEOS-Chem_Output_Files#NetCDF_File_Format|Migration from bpch to netCDF output file format]]
 
*[[GNU Fortran compiler|Add support for GNU Fortran compiler]]
 
 
*[[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]]
 
*[[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]]
 
*[[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]]
 
*[[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]]
 
*[[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]]
*[[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>]]
+
*[[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|Parallelization bug fix for marine POA]]
*[[GEOS-Chem_Makefile_Structure#TRACEBACK.3Dy_is_now_the_default_setting|<tt>TRACEBACK=y</tt> is now the default setting for all simulations]]
+
 
*[[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]]
+
I/O:
 +
*[[GEOS-Chem_Output_Files#NetCDF_File_Format|Migration from bpch to netCDF output file format]]
 +
 
 +
Species database / 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]]
  
 
Regridding:
 
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]]
 
*[[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>]]
 
*[[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>]]
 +
 +
Other:
 +
*[[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]]
  
 
|-valign="top"
 
|-valign="top"
 
|[[Wet deposition]]
 
|[[Wet deposition]]
 
|
 
|
*[[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
 
 
*[[Wet_deposition#Low_tropospheric_210Pb_lifetime_against_deposition_in_v11-01b|Quick fix for low tropospheric 210Pb lifetime against 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]]
 
*[[Wet_deposition#Fix_bug_in_GEOS-FP_re-evaporation_calculation|Fix bug in GEOS-FP re-evaporation calculation]]
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|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:49, 4 January 2017 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:12, 10 January 2017 (UTC)
  
 
== Issues resolved in GEOS-Chem v10-01 ==
 
== Issues resolved in GEOS-Chem v10-01 ==

Revision as of 22:12, 10 January 2017

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 wiki page to see a list of unresolved issues by GEOS-Chem version (and if they have been fixed in subsequent releases).

Issues resolved in GEOS-Chem v11-02

TBD

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
Chemistry
Cloud convection
Emissions (via HEMCO)
Met fields and derived quantities
RRTMG radiative transfer model
Photolysis
Specialty simulations Aerosol-only

CO2

CH4

Marine POA

Mercury

POPs

Radon-Lead-Beryllium

RRTMG

Tagged CO

Tagged O3

TOMAS Microphysics

Structural updates

Compilers:

Diagnostics:

Fixes for Fortran issues:

I/O:

Species database / physical constants:

Regridding:

Other:

Wet deposition

--Bob Yantosca (talk) 22:12, 10 January 2017 (UTC)

Issues resolved in GEOS-Chem v10-01

The following bugs and/or technical issues were resolved in GEOS-Chem v10-01. 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
Stratospheric chemistry module
Photolysis
NOx-Ox chemistry and nested grid simulations
Specialty simulations
HEMCO emissions component
Removing computational bottlenecks
Miscellaneous

--Bob Y. (talk) 20:56, 26 October 2015 (UTC)

Issues resolved in GEOS-Chem v9-02

The following bugs and/or technical issues were resolved in GEOS-Chem v9-02. 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
Emissions
Dry deposition and wet deposition
Met fields
Computational efficiency
Diagnostics
Specialty simulations (including microphysics)
Photolysis
Miscellaneous

--Bob Y. (talk) 21:00, 26 October 2015 (UTC)

Bugs and fixes in older GEOS-Chem versions

For a complete list of bugs and fixes in older GEOS-Chem versions, please see our Bugs and fixes prior to v9-02 wiki page.

--Bob Y. 17:40, 16 April 2015 (EDT) --Bob Y. 14:11, 20 May 2014 (EDT)