Difference between revisions of "Bugs and fixes"

Revision as of 16:47, 9 April 2018

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

The bugs and technical issues listed below were resolved in GEOS-Chem v11-02. 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
Chemistry	(v11-02a) Add simplified prod/loss families to KPP to gain computational speedup (v11-02a) Fixes to correct ALK4 lumping issue (v11-02a) Fix bug in CHEM_NIT routine (v11-02a) Fix error in production of SO4s and NITs in SEASALT_CHEM routine (v11-02a) Fix for sulfate production in HET_DROP_CHEM (v11-02a) Fix bugs in sulfate chemistry routines (v11-02c) Add fixes to chemical mechanism to preserve total carbon (v11-02c) Fix bugs for EOH and MGLY following implementation of PAN updates in v11-02a (v11-02d) Fix bug impacting dust radii obtained in RDUST_ONLINE (v11-02d) Fixed IMPN reactions that contributed to high P(Ox) and L(Ox) (v11-02d) Fixed bugs in GLYX, MGLY, IEPOX, and IMAE heterogeneous chemistry (v11-02e) Bug fixes for ISORROPIA II stable mode (v11-02e) Remove MONX from chemical mechanisms (v11-02e) Add MTPO to all full-chemistry simulations (v11-02e) Always use SOA formation from aqueous isoprene uptake (remove input switch) (v11-02e) Fixes for KPP heterogenous chemistry module for halogen chemistry mechanism (v11-02e) Fixes for isoprene SOA for consistency with Marais et al (2016) (v11-02e) Remove UCX 2-D initial boundary conditions option
Cloud convection	(v11-02a) Remove computational bottleneck in the convection module
CO2 simulation	(v11-02b) CO2 emissions unit conversion was not consistent with the new advection pressure
Diagnostics	(v11-02a) Save out PM2.5 diagnostic at STP conditions (v11-02a) Bug fixes in convective flux diagnostics (ND14) (v11-02a) Restore P(OH) in ND22 diagnostic (v11-02a) Make anthropogenic emissions diagnostics 3D (v11-02a) Fix ND65 bugs in tagged CO simulation (v11-02a) Fix bug in ND21 diagnostic indexing for dust species (v11-02b) Always write out ND40 planeflight diagnostic when enabled (v11-02c) Bug fixes for the ND50 timeseries diagnostic (v11-02c) Fix the STE diagnostics and use them in the standard benchmarking procedure (v11-02c) Fix diagnostic bugs in the SOA-SVPOA simulation (v11-02e) Fixes for two new ND21 binary diagnostics introduced in v11-02 (v11-02e} Always use simple SOA in computation of PM2.5 and AOD
Date and time (and related quantities)	(v11-02a) Fixed bug in computation of cosine of solar zenith angle
Dry and wet deposition	(v11-02a) Fix bug in computation of dry deposition aerodynamic resistance Ra (v11-02c) Fix bug in species definitions for marine POA simulation (v11-02e) Fix dust rainout settings to match that of hydrophobic BC (aka BCPO)
Emissions (via HEMCO)	(v11-02a) Update to HEMCO v2.0.004 (v11-02a) Default US emissions to NEI2011 after 2013 (v11-02a) Fixed bug in computation of local time in the HEMCO routine `HCO_GetSuncos` (v11-02a) Fix acetone parameterization in hcox_seaflux_mod.F90 (v11-02a) Change DEP_RESERVOIR time cycling option to C (v11-02c) Now use `YYYYMMDDhhmm` for time stamp values (v11-02c) Add error trap in to avoid a segmentation fault when the DustGinoux extension is turned off (v11-02c) Bug fixes for Hg emissions (v11-02e) Update simple SOA entries in HEMCO_Config.rc to follow MTPA+LIMO+MTPO (v11-02e) Fix bug in HEMCO reference time algorithm
Fixes to facilitate running GEOS-Chem in HPC environments	(v11-02a) Bug fixes for using UCX chemistry in the ESMF environment
Nested-grid simulations	(v11-02a) Fixed typo in nested-grid transport routine `INIT_WINDOW`
Meteorological fields	(v11-02c) Add MERRA2 to `#if` and `#elif` statements where it had been omitted
netCDF and file I/O issues	(v11-02a) Routine `DO_ERR_OUT` now returns a non-zero error code (v11-02a) Enable data compression in netCDF-4 output files (v11-02a) HEMCO diagnostic and restart files now have an unlimited time dimension (v11-02e) Sync GEOS-FP met field files on Harvard FTP with those at Dalhousie
Rn-Pb-Be simulation	(v11-02e) The Rn-Pb-Be simulation now uses 72 vertical levels by default
Structural issues	(v11-02a) Implement ISORROPIA v2.0 as a Fortran module (eliminating `COMMON` blocks) (v11-02a) Bug fix: Specifing `NO_REDUCED=no` now compiles GEOS-Chem for reduced grids (v11-02a) Removed the `COMPILER` variable from `Makefile_header.mk` for a cleaner build sequence (v11-02a) Print the version number to the log file (v11-02a) Removed the `NNPAR` parameter from `CMN_SIZE_mod.F` (v11-02a) Removed obsolete variables `NSOL` and `IDWETD` in the wetdep module (v11-02a) Removed obsolete fields of the `Input_Opt` object (v11-02c) Fixed an incorrect format statement in `input_mod.F` (v11-02e) Reordered IF statement in `sulfate_mod.F` for Fahey & Seinfeld decision algorithm (v11-02e) Change timestep units from minutes to seconds (v11-02e) Remove #ifdefs for UCX and replace with `Input_Opt%LUCX` logical switch
Tagged O3 simulation	(v11-02b) Write initial and final O3 mass to file, to facilitate budget computations
TOMAS aerosol microphysics	(v11-02c) Fixed typo in `wetscav_mod.F` for the TOMAS30 simulation

--Bob Yantosca (talk) 16:47, 9 April 2018 (UTC)

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	Fixed undefined molecular weight of HNO3 in routine SEASALT_CHEM
CH4 simulation	Fix bug in CH4 emissions unit
Chemistry	Adopt the optimal timestep recommendations of Philip et al 2015 Update of PMN + O3 reaction products in globchem.dat file Fix for black carbon in `ucx_mod.F` Modifications to ND20 to archive afternoon P(O3) and L(O3) Bug fix for sea salt alkalinity in `sulfate_mod.F` Bug fix for offline dust aerosols when UCX is on Bug fixes for hydrophobic aerosol properties Fix syntax error in `globchem.dat` for the MOBA + OH —> MOBAOO reaction rate Fixed typo in the ISNOOA + NO2 -> PMN reaction rate in `globchem.dat` Fix for monthly stratospheric P/L rates in HEMCO Fix bug in the GMI stratospheric production rates for HCOOH Fixed incorrect timestamps in the updated GMI HCOOH strat P/L file Fix incorrect species units in routines UCX_NOX and UCX_H2SO4PHOT Fix molecular weight of N2O5 Fix for out-of-bounds error when using the brown carbon option
CO2 simulation	Update CO2 emission files Bug fix: Make sure `nAdvect` is initialized in EMISSCO2
Cloud convection	Correct bug in below cloud average mixing ratio calculation in DO_MERRA_CONVECTION to improve mass balance Resolve very high tracer concentrations in GEOS-FP and MERRA convective scavenging
Compiler / Fortran issues	Compiler issues: Add support for GNU Fortran compiler Fix linker error when using the PGI compiler Additional updates compiling GEOS-Chem with the PGI Fortran compiler Add further fixes for compiling GEOS-Chem with PGI Fortran `TRACEBACK=y` is now the default setting for all simulations Remove offending code that was preventing GEOS-Chem from compiling with Intel Fortran v17 Fortran language issues: Do not nullify local pointers in the same line where they are declared Update flexible precision parameters so that GEOS-Chem can interface with the Beijing Climate Center model Prevent errors caused by uninitialized fields of the `State_Met` object Only allocate certain fields of `State_Chm` for UCX-based simulations Allocate aerosol fields of `State_Chm` only for full-chemistry or aerosol-only simulations Parallelization bug fix for marine POA
Diagnostics	Bug fix for the ND21 diagnostic Bug fix for monoterpenes in ND46 diagnostic Fix units of O1D and O3P in ND43 diagnostic Fix incorrect unit strings for ND65 diagnostic in `diag3.F`
Emissions (via HEMCO)	Fix problem in OTD/LIS lighning redistribution files Fix for reading hourly NEI2011 emissions Use an updated EMEP mask file to prevent zero emissions at 30 N for 2° x 2.5° or higher resolutions Fix an emissions error in the SOA-SVPOA simulation Fixed missing pointer in call to HEMCO routine Hco_CalcVertGrid Correct bug introduced in v11-01e where emissions were disabled in the stratosphere for specialty simulations Fixed bug preventing HEMCO from writing restart files more than once per run Correct bug in units of EDGAR v4.2 SO2 emissions Prevent biofuel emissions from being double counted in EDGAR v4.2 Fix bug in NOx diurnal scale factors Update HEMCO from version 1.1.016 to latest version available Replace RETRO C3H8 emissions with emissions from Xiao et al. Fix for biomass burning diagnostic when QFED emissions are used Prevent seg fault in HEMCO v2.0 caused by Intel Fortran compiler bug
Mercury and POPs simulations	Bug fixes for computing MLD in `ocean_mercury_mod.F` Fix parallelization errors that prevented Hg simulations from passing unit tests Avoid floating-point exception in OCEAN_MERCURY_READ Bug fixes for Arctic Hg updates in v11-01c Correct too-high emissions of Hg2 over China and EU Now call subrouine DO_RED_INPLUME after the HEMCO configuration file is read Avoid floating-point error in routine CHEM_POPGP
Met fields and derived quantities	Incorporate moisture into air quantities, tracer units, and tracer unit conversions Bug fix to update air quantities after specific humidity is updated in non-local PBL mixing Fix to remove moisture signature in dry mixing ratio
netCDF I/O	Migration from bpch to netCDF output file format Improve write speed of netCDF output files GAMAP can now read GEOS-Chem restart files in netCDF format
Photolysis	Fix for TOMS/HEMCO to address strange cycle in OH output Use TOMS ozone for all years when running simulations with GEOS-5 meteorology
Regridding	Bug fix: MAP_A2A now applies periodic boundary conditions only to global data sets during regridding Bug fix for time interpolation in netCDF utility module `ncdf_mod.F90`
RRTMG radiative transfer model	Fix bug that prevents storage of O3 and CH4 RF's Bug fix in RRTMG array sizes Further bug fixes in `rrtmg_transfer_mod.F` Replace nonstandard DLOG function with LOG
Marine POA simulations	Allocate the OCCONV array for marine POA simulations
Radon-Lead-Beryllium simulation	Fix typo in HEMCO extension module `hcox_gc_RnPbBe_mod.F90`
Species database and definitions of physical constants	Remove inconsistencies in the definitions of physical properties of GEOS-Chem species Use proper molecular weights for sea salt aerosols in the dry deposition module Give SO4s and NITs the same molecular weight as SALC 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 Define molecular weight fields of the `Input_Opt` object from the species database Now use consistent physical parameter values throughout GEOS-Chem Now use consistent physical constant declarations
Tagged CO simulation	Now convert OH to the proper units in the tagged CO simulation
Tagged O3 simulation	Bug fix in European grid range for tagged O3 simulation Bug fix for PBLTOP and MTTOP values in tagged O3 simulation
TOMAS aerosol microphysics	Updates to TOMAS Jeagle sea salt extension Add temporary fix to get TOMAS dry deposition to pass unit tests
Various structural updates	Bug fix for custom nested grid in `tpcore_bc_mod.F` Rename `grid_mod.F90` to `gc_grid_mod.F90` GEOS-Chem error messages now advise the user to check the HEMCO log file Print message to log file if OpenMP parallelization is turned off
Wet deposition	Quick fix for low tropospheric 210Pb lifetime against wet deposition Fix bug in GEOS-FP re-evaporation calculation

--Bob Yantosca (talk) 19:57, 23 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	Reduce memory footprint of the stratospheric chemistry module Bug fix in GET_RATES_INTERP Now read corrected stratospheric Bry data via HEMCO
Photolysis	Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution Bug fix for determining when to use TOMS O3 columns Reactivation of Br species photolysis in Fast-JX for tropospheric chemistry simulation Fixed wavelength bin interpolation error in Fast-JX for tropospheric-only simulation Now use proper photolysis input file `org.dat`
NOx-Ox chemistry and nested grid simulations	Modify treatment of N2O5+H2O reaction in calcrate.F Fixed parallelization error in nested grid simulations Fix for high values of O3 dry deposition Remove duplicate GLYX product from RIO2 reaction Bug fix in ND44 drydep diagnostic for sea salt aerosols Implement final recommendation for J(HAC) and J(PAN) Now use updated cross-sections for computing J(ALD2) Resolved technical issues for 0.25° x 0.3125° CH nested simulation Bug fix for planeflight diagnostic when using chemistry timesteps < 15 min Now call the planeflight diagnostic after chemistry, not after emissions Bug fixes for wet scavenging by co-condensation Fixes for bugs in wet deposition when using MERRA meteorology Remove obsolete ISN2 drydep species Fixed typo for BROMOCARB_SEASON in HEMCO configuration files Bug fixes for GEOS-FP nested EU simulation Fixes for wet deposition when using MERRA met fields Fix MEGAN AEF's for sesquiterpenes in the SOA simulation
Specialty simulations	Reactivating dust tracers in TOMAS simulations Prevent sea salt from being emitted over ice in TOMAS Fix for ND61 diagnostic in TOMAS simulations Fixed library linking issue when building GTMM into GEOS-Chem Minor fixes to CH4 simulation for MERRA meteorology Avoid div-by-zero errors in POPs simulation Bug fixes and updates for tagged CO simulation in v9-02 Fixed bug in tagged Hg emissions
HEMCO emissions component	Prevent segmentation fault errors in HEMCO when emissions are turned off Add new functionality into HEMCO Bug fixes for the PARANOX extension in HEMCO Bug fix for regridding of regional data files by HEMCO Prevent array out-of-bounds error if `MEGAN_mono` extension is turned off Restore missing diagnostic: "Biogenic CO from monoterpenes" Additional HEMCO updates made during the v10-01 period of public comment Fixed filename for ICOADS_SHIP in HEMCO configuration files Fix for error in PARANOX caused by improper timestamps of SUNCOS Minor fixes for FINNv1 biomass burning emissions Removing leftover code that was orphaned by HEMCO
Removing computational bottlenecks	Removed array temporaries in the call to the GEOS-4 convection routine Removed array temporaries in the call to the GCAP convection routine Removed array temporaries in subroutine `READ_HG2_PARTITIONING` Reduce time spent in advection driver routine TPCORE_FVDAS
Miscellaneous	Now use correct value of molecular weight for PROPNN tracer Make the netCDF library linking process more portable Fix for optimization error discovered in v10-01h Bug fix for I3 field interpolation Bug fix in gamap_mod.F Bug fixes for the PGI compiler Now use "percent" instead of "%" in data files

--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	Bug fix for updated CAC emissions Bug fix for Br2 emissions Bug fix in regridding of anthro emissions Bug in MEGAN emissions when using MERRA or GEOS-FP Bug fix in nei2005_anthro_mod.F Bug fix in EMIS_STREETS_ANTHRO_05x0666 Bug fixes in biofuel_mod.F and emfossil.F Bug fix for 3-hourly GFED3 emissions Fixed typo in Aerocom volcanic SO2 emissions routine Bug fixes in day-of-week computation Prevent negative emissions over Canada Minor bug fix in TOMAS sulfate emissions Bug fix for NEI2005 SO4 emissions in sulfate_mod.F Prevent LOG(0) error from occurring in soil NOx module Bug fix for biofuels when using RCP scenarios
Dry deposition and wet deposition	Add missing DRYACET to globchem.dat mechanism file Bug fix in Henry's law constant Bug fix in definition of RIP, IEPOX drydep species Bug fix: Do not call PARANOX plume model for offline simulations Fix for parallelization bug in subroutine METERO (in drydep module) Fixed parallelization error in routine DRYFLX (in dry deposition module) Prevent bad drydep flux values from being passed to the soil NOx module Fixed minor bug in AD44 diagnostic in routine DRY DEPOSITION (sea salt aerosols)
Met fields	Correction for GEOS-5 PBL heights Reset NaNs in MOISTQ to zero Convert MERRA and GEOS-FP relative humidity fields to percent after reading from disk Bug fix for declaration of certain GEOS-FP met fields
Computational efficiency	Eliminate inefficient subroutine calls Corrected several floating-point errors Eliminate array temporaries in pjc_pfix_mod.F and pressure_mod.F Eliminate array temporaries in GCAP convection module
Diagnostics	Bug fix in hdf_mod.F Bug fixes in diag48_mod.F Bug fix in ND36 diagnostic when ship emissions are turned off
Specialty simulations (including microphysics)	Bug fixes for tagged CO simulation Bug fixes for nested Hg simulation Bug fix for reading OH file in offline simulations Now include emissions in the aerosol-only simulation when using non-local PBL mixing Avoid error in ISOROPIAII when using offline aerosol simulation Modifications for v9-02 tagged O3 simulation Fixes for wetland emissions in CH4 simulation Reactivate stratospheric P(Ox) in tagged Ox simulation Replace LD65 with LLTROP in tagged_ox_mod.F Several fixes for TOMAS aerosol microphysics Prevent error in POPs simulation when reading global OC
Photolysis	Prevent 0.5 x 0.667 nested grid simulations from crashing when reading TOMS data Add fix to jv_spec_aod.dat file Post-release patch to fix bug in acetone photolysis pressure dependency
Miscellaneous	Additional bug fixes for MAP_A2A regridding Bug fix in grid_mod.F90 Fixed typos in GCAP code Reactivate parallel DO loop in LINOZ_CHEMO3 routine Corrected unit conversion bug when TURBDAY PBL mixing is used Fixes for minor technical issues

--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)

@@ Line 32: / Line 32: @@
 *[[Halogen_chemistry_mechanism#Fixes_in_gckpp_HetRates.F90_following_implementation_in_v11-02d|(v11-02e) Fixes for KPP heterogenous chemistry module for halogen chemistry mechanism]]
 *[[Secondary_organic_aerosols#Fixes_for_isoprene_SOA_for_consistency_with_Marais_et_al._.282016.29|(v11-02e) Fixes for isoprene SOA for consistency with Marais et al  (2016)]]
+*[[UCX_chemistry_mechanism#v11-02|(v11-02e) Remove UCX 2-D initial boundary conditions option]]
 |-valign="top"
@@ Line 107: / Line 108: @@
 *[[Implementation of HEMCO in GEOS-Chem#HEMCO diagnostic and restart files now have an unlimited time dimension|(v11-02a) HEMCO diagnostic and restart files now have an unlimited time dimension]]
 *[[Downloading_GEOS-Chem_source_code_and_data#Inconsistency_in_GEOS-FP_files_at_Harvard_and_Dalhousie_for_July_2013|(v11-02e) Sync GEOS-FP met field files on Harvard FTP with those at Dalhousie]]
+|-valign="top"
+|[[Rn-Pb-Be simulation|Rn-Pb-Be simulation]]
+|
+*[[Rn-Pb-Be_simulation#Vertical_Grid|(v11-02e) The Rn-Pb-Be simulation now uses 72 vertical levels by default]]
 |-valign="top"
@@ Line 120: / Line 126: @@
 *[[GEOS-Chem_v11-02#Fixed_an_incorrect_format_statement_in_input_mod.F|(v11-02c) Fixed an incorrect format statement in <tt>input_mod.F</tt>]]
 *[[Sulfate_aerosols#Add_bug_fix_in_sulfate_mod.F_involving_reorder_IF_statements_for_Fahey_and_Seinfeld_decision_algorithm|(v11-02e) Reordered IF statement in <tt>sulfate_mod.F</tt> for Fahey & Seinfeld decision algorithm]]
-*[[http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v11-02#Change_timestep_units_from_minutes_to_seconds|(v11-02e) Change timestep units from minutes to seconds]]
+*[[GEOS-Chem_v11-02#Change_timestep_units_from_minutes_to_seconds|(v11-02e) Change timestep units from minutes to seconds]]
+*[[UCX_chemistry_mechanism#Remove_UCX_.23ifdefs_and_replace_with_Input_Opt.25LUCX|(v11-02e) Remove #ifdefs for UCX and replace with <tt>Input_Opt%LUCX</tt> logical switch]]
 |-valign="top"
@@ Line 134: / Line 141: @@
 |}
---[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:55, 20 February 2018 (UTC)
+--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:47, 9 April 2018 (UTC)
 == Issues resolved in GEOS-Chem v11-01 ==

Difference between revisions of "Bugs and fixes"

Revision as of 16:47, 9 April 2018

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Issues resolved in GEOS-Chem v11-02

Issues resolved in GEOS-Chem v11-01

Issues resolved in GEOS-Chem v10-01

Issues resolved in GEOS-Chem v9-02

Bugs and fixes in older GEOS-Chem versions

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