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.
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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.
  
== Numerical noise bug in upbdflx_mod.f ==
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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.
  
=== 12-Jun-2008 ===
+
== Bugs and fixes lists have now been migrated to Github ==
  
'''''Ray Nassar (ray@io.as.harvard.edu) wrote: '''''
+
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.
  
:The run I did last night confirmed that turning off "Use strat O3/NOy BC's" does change O3 and NOx at lower levels so I cannot turn this off for sensitivity tests if comparing to past runs.
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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)
  
:I have tried the debugging approach which you have suggested and it indicates that the problem is coming from the triple loop:
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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)]
  
        DO L = LMIN, LLPAR
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|-valign="top"
        DO J = 1,    JJPAR
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|[[GEOS-Chem 12#12.9.0|12.9.0]]
        DO I = 1,    IIPAR
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|TBD
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
            ! Skip over tropospheric boxes
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|
            IF ( ITS_IN_THE_STRAT( I, J, L ) ) THEN
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*[https://github.com/geoschem/geos-chem/milestone/10 '''Milestone 12.9.0''' (open issues)]
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*[https://github.com/geoschem/geos-chem/milestone/10?closed=1 '''Milestone 12.9.0''' (closed issues)]
              ! PNOY = P(NOy) converted from [v/v/s] to [v/v]
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              PNOY = STRATPNOY(J,L) * DTDYN
+
+
              ! Add [NOx] and [HNO3] to PNOY.
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              ! PNOY is now the total [NOy] concentration
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              PNOY = PNOY + STT(I,J,L,IDTNOX) + STT(I,J,L,IDTHNO3)
+
+
              ! Partition total [NOy] to [NOx], units are [v/v]
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              STT(I,J,L,IDTNOX)  = PNOY * XRATIO(J,L)
+
+
              ! Partition total [NOy] to [HNO3], units are [v/v]
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              STT(I,J,L,IDTHNO3) = PNOY * ( 1d0 - XRATIO(J,L) )
+
+
            ENDIF
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        ENDDO
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        ENDDO
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        ENDDO
+
  
:in the file upbdflx_mod.f. Since <tt>XRATIO</tt> can have a value of zero, it means that numerical noise sometimes makes <tt>1d0 - XRATIO(J,L)</tt> a negative number and then <tt>STT(I,J,L,IDTHNO3)</tt> becomes negative and triggers the error message. For the two instances where the difference is computed, I have now added the lines:
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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)]
  
        ! Ray Nassar (2008-06-11) -------------------------------
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|-valign="top"
        !
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|[[GEOS-Chem 12#12.8.0|12.8.0]]
        ! The kludge below is to deal with errors which result
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|pending
        ! from subtracting 1d0 - XRATIO(J,L). When XRATIO should
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
        ! be equal 1, the binary representation will have a
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|[https://github.com/geoschem/geos-chem/milestone/7?closed=1 '''Milestone 12.8.0''']
        ! finite error making it slightly more or less than 1.
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        ! For XRATIO slightly more than 1, STT(I,J,L,IDTHNO3)<=0
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        ! which triggers a CHECK_STT error message.
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        !
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        if (STT(I,J,L,IDTHNO3) <= 0d0) then
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          STT(I,J,L,IDTHNO3) = 0d0
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        endif
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        !--------------------------------------------------------
+
  
:immediately after the calculation of STT(I,J,L,IDTHNO3) and this fixes the problem!  I think this will have to be fixed in the next version of the code.
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|-valign="top"
 +
|[[GEOS-Chem 12#12.7.2|12.7.2]]
 +
|09 Mar 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/11?closed=1 '''Milestone 12.7.2''']
  
'''''Philippe Le Sager (plesager@seas.as.harvard.edu) wrote:'''''
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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''']
  
:Thanks for catching that. We will put that in the next batch of fixes, maybe simply with a
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|-valign="top"
    MAX( ( 1d0 - XRATIO(J,L) ), 1d-20)
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|[[GEOS-Chem 12#12.7.0|12.7.0]]
:in place of
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|03 Feb 2020
    ( 1d0 - XRATIO(J,L) ),
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
:since we want to have strictly positive concentration in the troposphere and some boxes switch b/w troposphere and stratosphere.
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|[https://github.com/geoschem/geos-chem/milestone/4?closed=1 '''Milestone 12.7.0''']
  
--[[User:Bmy|Bob Y.]] 11:13, 12 June 2008 (EDT)
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|-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''']
  
== Problem w/ ND65 diagnostic and dynamic tropopause ==
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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''']
  
=== 03-Jun-2008 ===
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|-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''']
  
'''''Yuxuan Wang (wang3@fas.harvard.edu) wrote:'''''
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|-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''']
  
:It looks like that it's the dynamic tropopause in v8-01-01 that causes the unrealistically high AD65 values (prod and loss rate of chemical families). When I turn off the dynamic tropopause in input.geos, the model gives AD65 that's reasonable and also comparable to my previous simulations with code version 7.  I took a careful look of tropopause_mod.f, but couldn't find where the problem is.
+
|}
  
:Yuxuan
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== Issues resolved in GEOS-Chem 12.5.0 ==
  
'''''Philippe Le Sager (plesager3@seas.harvard.edu) wrote:'''''
+
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.5.0|GEOS-Chem 12.5.0]], release date TBD.
  
:I think I found the root of your problem with P/L diagnostic. The line 606 (subroutine do_diag_pl, in diag_pl_mod.f) :
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{| border=1 cellspacing=0 cellpadding=5
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|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
          ! Zero each "fake" ND65 prod/loss family for next iteration
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|-valign="top"
          CSPEC(JLOOP,IFAM(N)) = 0.0d0
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|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]
  
:is done too late in the code. Here is the full story:
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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]
  
:At each time step, the CSPEC_FULL array is used to initialize the CSPEC array before entering SMVGEAR. CSPEC_FULL is filled with CSPEC after SMVGEAR. So it should account for the line 606 above, but it does not since the family P/L diagnostic is done after CSPEC_FULL has been updated.
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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 fix is easy. In CHEMDR.F you need to move the call to SAVE_FULL_TROP to the end of the routine, so CSPEC_FULL is updated after the P/L diagnostic. You can look at my: ~phs/Code.current/chemdr.f
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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]
  
:If you could let me know if that fix you problem with a quick run, that would be perfect
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|-valign="top"
:Thanks,
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!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
:-Philippe
+
  
'''''Yuxuan Wang (wang3@fas.harvard.edu) wrote:'''''
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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
 +
|
 +
|}
  
:I just did a one-day test and it worked! P/L diagnostics now are at the right order of magnitude after I turned on the variable tropopause. That's indeed the fix. Thank you!!
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:03, 15 July 2019 (UTC)
:Yuxuan
+
  
This fix will go into the next release of GEOS-Chem.
+
== Issues resolved in GEOS-Chem 12.4.0 ==
  
--[[User:Bmy|Bob Y.]] 16:17, 3 June 2008 (EDT)
+
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.4.0|GEOS-Chem 12.4.0]], release date TBD.
  
== Negative tracer in routine WETDEP because of negative RH ==
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{| border=1 cellspacing=0 cellpadding=5
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|-bgcolor="#CCCCCC"
=== 1-May-2008 ===
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!width="200px"|Module or area
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!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
See this post: [[GEOS-5 issues#Small negative RH value in 20060206.a6.2x25 file]]
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|-valign="top"
 +
|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]
  
Fixes are available at ftp://ftp.as.harvard.edu/pub/exchange/phs/GEOS-Chem-UPDATE/
+
|}
  
--[[User:Plesager|phs]] 16:31, 6 June 2008 (EDT)
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:04, 15 July 2019 (UTC)
  
== Negative tracer in routine WETDEP ==
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== Issues resolved in GEOS-Chem 12.3.2 ==
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=== 17-Apr-2007 ===
+
  
'''''Dylan Millet (dbm@umn.edu) wrote:'''''
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The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.3.2|GEOS-Chem 12.3.2]].
: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.
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:* Platform: Linux cluster
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:* Threads: 8
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:* Version: v7-4-13 out of the box.
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:* GEOS4, 4x5, 30L, full chemistry
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:* IFORT 10.1
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:In Section 6 (No Downward Precip) of wetscav_mod.f, subroutine safety is getting called.
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{| border=1 cellspacing=0 cellpadding=5
    WETDEP - STT < 0 at    1  1  29 for tracer    7 in area   6
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|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
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!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
:(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.
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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]
  
:... By the way, the problem persists when I turn off chemistry altogether.  
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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]
  
'''''Philippe Le Sager (plesager@seas.harvard.edu) replied:'''''
+
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
: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.
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|-valign="top"
 +
|Emissions
 +
|
 +
#Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default
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#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]
  
: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!
+
|}
  
:In other words: the bug happens with IFort 10 and v7-04-13 only.
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:37, 15 July 2019 (UTC)
  
: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.
+
== Issues resolved in GEOS-Chem 12.3.1 ==
  
:... 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.
+
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.3.1|GEOS-Chem 12.3.1]] (release 08 Apr 2019).
  
: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.
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
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.
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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]
  
--[[User:Bmy|Bmy]] 10:38, 17 April 2008 (EDT)
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|-valign="top"
 +
|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]
  
== ISORROPIA and RPMARES ==
+
|}
  
=== 11-Apr-2008 ===
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:06, 16 July 2019 (UTC)
  
Please see the discussion about the bugs & fixes for ISORROPIA and RPMARES on the Code Developer's Forum for [[Aerosol thermodynamical equilibrium]].
+
== Issues resolved in GEOS-Chem 12.3.0 ==
  
== NaN's in SMVGEAR ==
+
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.3.0|GEOS-Chem 12.3.0]] (release date TBD).
  
=== 05-Jul-2007 ===
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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
  
'''''Lok Lamsal (lok.lamsal@fizz.phys.dal.ca)wrote:'''''
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|-valign="top"
:I ran into a problem while running GEOS-4, version v7-04-09, at 2x2.5. The simulation stops on 15th July 2006 with different error messages on two of our machines tuque and beret. One of the error messages on tuque is like this:
+
|Diagnostics / Restart files
 +
|
 +
#[[#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]
  
  sum of rrate = Infinity
+
|-valign="top"
  SMVGEAR: CNEW is NaN!
+
|Emissions
  Species index :            1
+
|
  Grid Box      :         121          15          1
+
#[[HEMCO_versions#Bug_fixes_for_HEMCO_interpolation_algorithm|Bug fixes for the HEMCO interpolation algorithm]]
  STOP in smvgear.f!
+
#[[HEMCO_versions#Updates from the NASA GEOS development branch|Updates from the NASA GEOS development branch]]
      - CLEANUP: deallocating arrays now...
+
#[[HEMCO_versions#Add_option_to_always_use_simulation_year_for_specified_fields|Add option to always use simulation year for specified fields]]
forrtl: severe (174): SIGSEGV, segmentation fault occurred
+
#[[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]
 +
|}
  
:And on beret the message is like this:
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:53, 21 March 2019 (UTC)
  
      - CLEANUP: deallocating arrays now...
+
== Issues resolved in GEOS-Chem 12.2.1 ==
  forrtl: severe (174): SIGSEGV, segmentation fault occurred
+
  Image              PC                Routine            Line
+
  Source
+
  geos_4_nv          400000000059EA10  Unknown              Unknown
+
  Unknown
+
  libguide.so        200000000039C1A0  Unknown              Unknown
+
  Unknown
+
  etc.
+
</pre>
+
  
:The message which is repeated in either case is like this:
+
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).
  
  SMVGEAR: DELT= 9.96E-16 TOO LOW DEC YFAC. KBLK, KTLOOP, NCS, TIME, TIMREMAIN, YFAC, EPS =
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
:Could you suggest me what the problem could be? Just to inform you: while trying to figure out the problem, I noticed from Bastien that he did not have problem on that day with version v7-04-10, which stopped on September 13 2006.
+
|-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]
  
'''''Bob Yantosca (yantosca@seas.harvard.edu) replied:'''''
+
|-valign="top"
:I think there is a division by zero somewhere that is causing SMVGEAR to choke.  It could be a couple of things:
+
|CO2 simulation
 +
|
 +
#[[CO2_simulation#Prevent_double-counting_in_CO2_chemical_source|Fix for CO2 simulation chemical source]]
 +
|
 +
#N/A
  
:(1) Make sure that in your In a6_read_mod.f (routine READ_A6) you have the following code to prevent Q from going to zero. This can make logarithms blow up in other places in the code:
+
|-valign="top"
 +
|TOMAS simulations
 +
|
 +
#[[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]
  
 +
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
          !--------------------------------
+
|-valign="top"
          ! Q: 6-h avg specific humidity
+
|Emissions etc.
          ! (GEOS-4 only)
+
|
          !--------------------------------
+
#[[GEOS-Chem_12#Use_online_sea_flux_emissions_by_default_in_GCHP|Use online sea flux emissions by default in GCHP]]
          CASE ( 'Q' )
+
#[[GEOS-Chem_12#GCHP_uses_outdated_MODIS_files_missing_projection_error_fix|Update MODIS LAI source directory to match GEOS-Chem Classic]]
            READ( IU_A6, IOSTAT=IOS ) XYMD, XHMS, Q3
+
|
            IF ( IOS /= 0 ) CALL IOERROR( IOS, IU_A6, 'read_a6:16' )
+
#[https://github.com/geoschem/gchp/commit/9759d26bcbbb593f6e845a0dc67e1b7bde4b6410 9759d26b]
   
+
#N/A
            IF ( CHECK_TIME( XYMD, XHMS, NYMD, NHMS ) ) THEN
+
                IF ( PRESENT( Q ) ) CALL TRANSFER_3D( Q3, Q )
+
                NFOUND = NFOUND + 1
+
   
+
                ! NOTE: Now set negative Q to a small positive #
+
                ! instead of zero, so as not to blow up logarithms
+
                ! (bmy, 9/8/06)
+
                WHERE ( Q < 0d0 ) Q = 1d-32
+
            ENDIF
+
  
:(2) In fvdas_convect_mod.f, make SMALLEST a smaller number (i.e. 1d-60):
+
|-valign="top"
 +
|Met fields
 +
|
 +
#[[GEOS-Chem_12#Missing_scaling_factors_for_MERRA-2_simulations_with_GCHP|Missing scaling factors for MERRA-2 simulations with GCHP]]
 +
|
 +
#?
  
    !=================================================================
+
|}
    ! MODULE VARIABLES
+
    !=================================================================
+
   
+
    ! Variables
+
    INTEGER            :: LIMCNV              ! Constants
+
    LOGICAL, PARAMETER :: RLXCLM  = .TRUE.
+
    REAL*8,  PARAMETER :: CMFTAU  = 3600.d0
+
    REAL*8,  PARAMETER :: EPS      = 1.0d-13     
+
    REAL*8,  PARAMETER :: GRAV    = 9.8d0
+
    !-------------------------------------------------------
+
    ! Prior to 12/19/06:
+
    ! Make SMALLEST smaller (bmy, 12/19/06)
+
    !REAL*8,  PARAMETER :: SMALLEST = 1.0d-32
+
    !-------------------------------------------------------
+
    REAL*8,  PARAMETER :: SMALLEST = 1.0d-60
+
    REAL*8,  PARAMETER :: TINYALT  = 1.0d-36         
+
    REAL*8,  PARAMETER :: TINYNUM  = 2*SMALLEST
+
  
:(3) In "fvdas_convect_mod.f", avoid division by zero in routine CONVTRAN:
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:03, 15 July 2019 (UTC)
  
            IF ( CDIFR > 1.d-6 ) THEN
+
== Issues resolved in GEOS-Chem 12.2.0 ==
   
+
                ! If the two layers differ significantly.
+
                ! use a geometric averaging procedure
+
                CABV = MAX( CMIX(I,KM1), MAXC*TINYNUM, SMALLEST )
+
                CBEL = MAX( CMIX(I,K),  MAXC*TINYNUM, SMALLEST )
+
  !-----------------------------------------------------------------
+
  !  Prior to 12/19/06:
+
  ! Avoid division by zero (bmy, 12/19/06)
+
  !                  CHAT(I,K) = LOG( CABV / CBEL)
+
  !    &                      /  ( CABV - CBEL)
+
  !    &                      *    CABV * CBEL
+
  !-----------------------------------------------------------------
+
   
+
                ! If CABV-CBEL is zero then set CHAT=SMALLEST
+
                ! so that we avoid div by zero (bmy, 12/19/06)
+
                IF ( ABS( CABV - CBEL ) > 0d0 ) THEN
+
                  CHAT(I,K) = LOG( CABV / CBEL )
+
  &                        /    ( CABV - CBEL )
+
  &                        *      CABV * CBEL
+
                ELSE
+
                  CHAT(I,K) = SMALLEST
+
                ENDIF
+
   
+
            ELSE                         
+
                ! Small diff, so just arithmetic mean
+
                CHAT(I,K) = 0.5d0 * ( CMIX(I,K) + CMIX(I,KM1) )
+
            ENDIF
+
  
:(4) Also I had to rewrite the parallel DO loops in the routine HACK_CONV since this was causing some kind of a memory fault.
+
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).
  
:You may just want to get the most recent version of fvdas_convect_mod.f, which has all of these fixes installed. See:
+
{| 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/exchange/bmy
+
|Diagnostics
  get fvdas_convect_mod.f
+
|
 +
#[[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]
  
:So I would recommend trying to implement these fixes and see if this solves your problem.
+
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
:NOTE: These fixes have been introduced into GEOS-Chem v7-04-10.
+
|-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]]
 +
|
 +
#
 +
|}
  
== regrid_1x1_mod.f ==
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:02, 14 March 2019 (UTC)
  
=== 16 Oct 2007 ===
+
== Issues resolved in GEOS-Chem 12.1.1 ==
  
From Mike Barkley (mbarkley@staffmail.ed.ac.uk)
+
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.
  
<blockquote>
+
{| border=1 cellspacing=0 cellpadding=5
I think I've found an error in the regrid_1x1_mod.f subroutine (attached in the text file):
+
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
<pre>
+
|-valign="top"
SUBROUTINE REGRID_MASS_TO_2x25( I1, J1, L1, IN, I2, J2, OUT )
+
|Compilation issues
</pre>
+
|
 +
#[[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]
  
There is a do loop over longitude with the upper limit defined as the input latitude (J1) instead what should (?) be the output longitude (I2) - I've indicated where this in the program, Which is correct? We didn't notice this until we were running multi-processor 2x2.5 simulations on different servers.
+
|-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]
  
The bug was:
+
|-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]
  
<pre>
+
|-
  !-----------------------
+
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  ! Non-polar latitudes
+
  !-----------------------
+
  DO J = 2, J2-1   
+
    ...         
+
    DO I = 1, J1
+
</pre>
+
  
which needs to be replaced by:
+
|-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]]
 +
|
  
<pre>
+
|}
  !-----------------------
+
  ! Non-polar latitudes
+
  !-----------------------
+
  DO J = 2, J2-1   
+
    ...         
+
    DO I = 1, I1
+
</pre>
+
</blockquote>
+
  
This bug has now been fixed in [[wiki:geos-chem:dev_forum|GEOS-Chem v7-04-13]].
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:12, 16 July 2019 (UTC)
  
== smvgear.f ==
+
== Issues resolved in GEOS-Chem 12.1.0 ==
  
=== 02 Nov 2007 ===
+
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.
  
'''''Bob Yantosca (yantosca@seas.harvard.edu) wrote'''''
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
:Some of you have reported a weird error in SMVGEAR that causes GEOS-Chem simulations to die unexpectedly.  The main symptom of this error is that concentrations of some species (e.g CO) appear to go to zero, while other species (e.g. Ox) seem to reach unphysically high values, all within a single chemistry timestep.  Then the simulation dies shortly thereafter.
+
|-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]
  
:May Fu and Philippe Le Sager have isolated the cause of the problem.  They found that in some instances it is possible (e.g. due to locally low OH) to get into a regime where the first derivative of a species goes very negative during SMVGEAR's internal iteration loop. This then causes the new species concentration to be negative. This can sometimes happen even if the local & global error tolerance checks have passed. Then upon exiting the internal iteration loop, SMVGEAR would automatically reset any negative species concentrations to zero (actually a small positive number like 1e-99).  A species with zero concentration can adversely affect other species within the SMVGEAR solver process.  Furthermore, sometimes these zero concentrations were propagating out of SMVGEAR and into the STT tracer array, which caused problems in other areas of the code.
+
|-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]
  
:May & Philippe implemented a fix into the file "smvgear.f" which does the following: If a negative species concentration value is found during an internal iteration, then we don't set it to zero. We instead reduce the internal iteration timestep and do another iteration (i.e. re-evaluate the Jacobian matrix) to solve for the new species concentration. This process is repeated until SMVGEAR converges onto a non-negative solution. May & Philippe also added an extra error trap to stop the simulation if any negative species concentrations still persist upon exiting the subroutine.  So the entire process should now be more robust.
+
|-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]
  
:You may download the updated "smvgear.f" file from our anonymous FTP site:
+
|-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]
  
<pre>
+
|-valign="top"
  ftp ftp.as.harvard.edu
+
|Tagged CO simulation
  cd pub/geos-chem/patches/v7-04-12
+
|
  get README
+
#[[GEOS-Chem_12#Update_HEMCO_configuration_file_for_tagged_CO_simulation|Update HEMCO configuration file for the tagged CO simulation]]
  get smvgear.f
+
|
</pre>
+
#[https://github.com/geoschem/geos-chem-unittest/commit/02aaad73d32cbd54bba450b0a5b2abce6a5cad5e 02aaad73]
  
:Then copy the "smvgear.f" file to your own source code directory and recompile.  Please see the README file for more information on how to locate the places in "smvgear.f" that were modified.
+
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
:This is not really a "bug" but more of a "design flaw" in the original SMVGEAR package.
+
|-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
 +
|
 +
|}
  
This bug has now been fixed in GEOS-Chem [[wiki:geos-chem:dev_forum|GEOS-Chem v7-04-13]].
+
--[[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)