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.
  
== Too many levels in photolysis code ==
+
== Bugs and fixes lists have now been migrated to Github ==
  
The scattering module (OPMIE.f) for Fast-J requires many additional vertical levels. It happens that the limit (NL set in jv_mie.h) can be reached in some situations, causing the program to stop with a "Too many levels in photolysis code.." error message.
+
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.
Sometimes you can increase NL to solve the problem.
+
Now a new version of OPMIE.f is available, which still warns you if NL is reached, but works with that limit.
+
  
Before being released into the standard model, you can find the new OPMIE.f at: ftp://ftp.as.harvard.edu/pub/exchange/phs/GEOS-Chem-UPDATE/
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=== GEOS-Chem 13 ===
+
--[[User:Plesager|phs]] 11:29, 17 June 2008 (EDT)
+
  
This can also be an indication that there may be a problem in your visual optical depths, dust emissions, or aerosol emissions.  Dust and aerosol optical depths are computed from the concentration array STT.  If for some reason you end up emitting too much aerosol or dust (i.e. a unit conversion error), then this will result in an abnormally high dust or aerosol optical depth.  A very high optical depth will cause FAST-J to want to keep adding points to the Gaussian quadrature in OPMIE.f.  You can get into a situation where the number of points that FAST-J wants to add is greater than the array parameter NL (it may want to add thousands of points!).
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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)
  
Therefore, if you encounter this type of error, it is a good idea to doublecheck your aerosol & dust emissions to make sure that the monthly and annual totals are reasonable.
+
|-valign="top"
 +
|[[GEOS-Chem_model_development_priorities#13.3.0|13.3.0]]
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/19 '''Milestone 13.3.0''']
  
--[[User:Bmy|Bob Y.]] 11:03, 26 June 2008 (EDT)
+
|-valign="top"
 +
|[[GEOS-Chem_model_development_priorities#13.2.0|13.2.0]]
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/18 '''Milestone 13.2.0''']
  
== Mis-labeling of SOA quantities in carbon_mod.f ==
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|-valign="top"
 +
|[[GEOS-Chem 13.1.0|13.1.0]]
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/17 '''Milestone 13.1.0''']
  
'''''Colette Heald (heald@atmos.colostate.edu) wrote:'''''
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|-valign="top"
 +
|[[GEOS-Chem 13.0.2|13.0.2]]
 +
|12 Apr 2021
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/21?closed=1 '''Milestone 13.0.2''']
  
:I noticed previously that the parameters in (routine) <tt>SOA_PARA</tt> were confusingly ordered, but it's only today that I realized that in fact they are mis-labeled as well. The actual numbers are all perfectly correct but they should correspond to the information in Tables 3 and 4 for the categories of Table 1 of the [http://www.as.harvard.edu/ctm/geos/wiki_docs/ChungSeinfeld2002_JGR.pdf Chung and Seinfeld (2002) paper.] I have re-organized the code & comments for clarity (lines 1875-1939), they should read as:
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|-valign="top"
 +
|[[GEOS-Chem 13.0.1|13.0.1]]
 +
|23 Mar 2021
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/20?closed=1 '''Milestone 13.0.1''']
  
      ! Average of ALPHA-PINENE, BETA-PINENE, SABINENE, D3-CARENE
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|-valign="top"
      RALPHA(1,1) = 0.067d0           
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|width="80px"|[[GEOS-Chem 13.0.0|13.0.0]]
      RALPHA(2,1) = 0.35425d0
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|width="100px"|18 Mar 2021
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|width="200px"|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
      ! LIMONENE
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|width="400px"|[https://github.com/geoschem/geos-chem/milestone/8?closed=1 '''Milestone 13.0.0''']
      RALPHA(1,2) = 0.239d0
+
      RALPHA(2,2) = 0.363d0
+
+
      ! Average of TERPINENES and TERPINOLENE
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      RALPHA(1,3) = 0.0685d0
+
      RALPHA(2,3) = 0.2005d0
+
+
      ! Average of MYRCENE, LINALOOL, TERPINENE-4-OL, OCIMENE
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      RALPHA(1,4) = 0.06675d0
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      RALPHA(2,4) = 0.135d0
+
+
      ! Average of BETA-CARYOPHYLLENE and and ALPHA-HUMULENE
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      RALPHA(1,5) = 1.0d0
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      RALPHA(2,5) = 0.0d0
+
+
      ! Using BETA-PINENE for all species for NO3 oxidation
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      ! Data from Table 4 of Griffin, et al., JGR 104 (D3): 3555-3567 (1999)
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      RALPHA(3,:) = 1.d0         
+
+
      ! Here we define some alphas for isoprene (dkh, bmy, 5/22/06)
+
+
      ! high NOX  [Kroll et al, 2005]
+
      !RALPHA(1,6) = 0.264d0
+
      !RALPHA(2,6) = 0.0173d0
+
      !RALPHA(3,6) = 0d0
+
+
      ! low NOX  [Kroll et al, 2006; Henze and Seinfeld, 2006]
+
      RALPHA(1,6) = 0.232d0
+
      RALPHA(2,6) = 0.0288d0
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      RALPHA(3,6) = 0d0
+
+
      !=================================================================
+
      ! Equilibrium gas-particle partition coefficients of
+
      ! semi-volatile compounds [ug-1 m**3]
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      !=================================================================
+
+
      ! Average of ALPHA-PINENE, BETA-PINENE, SABINENE, D3-CARENE
+
      KOM(1,1) = 0.1835d0
+
      KOM(2,1) = 0.004275d0
+
+
      ! LIMONENE
+
      KOM(1,2) = 0.055d0
+
      KOM(2,2) = 0.0053d0
+
+
      ! Average of TERPINENES and TERPINOLENE
+
      KOM(1,3) = 0.133d0
+
      KOM(2,3) = 0.0035d0
+
+
      ! Average of MYRCENE, LINALOOL, TERPINENE-4-OL, OCIMENE
+
      KOM(1,4) = 0.22375d0
+
      KOM(2,4) = 0.0082d0
+
+
      ! Average of BETA-CARYOPHYLLENE and and ALPHA-HUMULENE
+
      KOM(1,5) = ( 0.04160d0 + 0.0501d0 ) / 2.d0
+
      KOM(2,5) = 0.0d0
+
+
      ! NOT APPLICABLE -- using BETA-PINENE for all species
+
      ! Data from Table 4 of Griffin, et al., JGR 104 (D3): 3555-3567 (1999)
+
      KOM(3,:) = 0.0163d0
+
  
'''''Bob Yantosca (heald@atmos.colostate.edu) wrote:'''''
+
|}
  
:We will put this in the next update of the code.  Thanks!
+
=== GEOS-Chem 12 ===
  
--[[User:Bmy|Bob Y.]] 10:11, 13 June 2008 (EDT)
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!Version
 +
!Released
 +
!colspan="2"|List of bugs and issues (now posted on the listed Github repository)
  
== Numerical noise bug in upbdflx_mod.f ==
+
|-valign="top"
 +
|[[GEOS-Chem 12#12.9.3|12.9.3]]
 +
|06 Aug 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/16?closed=1 '''Milestone 12.9.3''']
  
'''''Ray Nassar (ray@io.as.harvard.edu) wrote: '''''
+
|-valign="top"
 +
|[[GEOS-Chem 12#12.9.2|12.9.2]]
 +
|24 Jul 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/15?closed=1 '''Milestone 12.9.2''']
  
: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.
+
|-valign="top"
 +
|[[GEOS-Chem 12#12.9.1|12.9.1]]
 +
|17 Jul 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/14?closed=1 '''Milestone 12.9.1''']
  
:I have tried the debugging approach which you have suggested and it indicates that the problem is coming from the triple loop:
+
|-valign="top"
 +
|[[GEOS-Chem 12#12.9.0|12.9.0]]
 +
|17 Jul 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/10?closed=1 '''Milestone 12.9.0''']
  
        DO L = LMIN, LLPAR
+
|-valign="top"
        DO J = 1,    JJPAR
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|[[GEOS-Chem 12#12.8.2|12.8.2]]
        DO I = 1,    IIPAR
+
|27 May 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
            ! Skip over tropospheric boxes
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|[https://github.com/geoschem/geos-chem/milestone/13?closed=1 '''Milestone 12.8.2''']
            IF ( ITS_IN_THE_STRAT( I, J, L ) ) THEN
+
+
              ! PNOY = P(NOy) converted from [v/v/s] to [v/v]
+
              PNOY = STRATPNOY(J,L) * DTDYN
+
+
              ! Add [NOx] and [HNO3] to PNOY.
+
              ! PNOY is now the total [NOy] concentration
+
              PNOY = PNOY + STT(I,J,L,IDTNOX) + STT(I,J,L,IDTHNO3)
+
+
              ! Partition total [NOy] to [NOx], units are [v/v]
+
              STT(I,J,L,IDTNOX)  = PNOY * XRATIO(J,L)
+
+
              ! Partition total [NOy] to [HNO3], units are [v/v]
+
              STT(I,J,L,IDTHNO3) = PNOY * ( 1d0 - XRATIO(J,L) )
+
+
            ENDIF
+
        ENDDO
+
        ENDDO
+
        ENDDO
+
  
:in the file upbdflx_mod.f. Since <tt>XRATIO</tt> can have a value of one, 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:
+
|-valign="top"
 +
|[[GEOS-Chem 12#12.8.1|12.8.1]]
 +
|21 May 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/12?closed=1 '''Milestone 12.8.1''']
  
        ! Ray Nassar (2008-06-11) -------------------------------
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|-valign="top"
        !
+
|[[GEOS-Chem 12#12.8.0|12.8.0]]
        ! The kludge below is to deal with errors which result
+
|04 Mar 2020
        ! from subtracting 1d0 - XRATIO(J,L). When XRATIO should
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
        ! be equal 1, the binary representation will have a
+
|[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
+
        ! 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
+
        !--------------------------------------------------------
+
  
: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.
+
|-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
+
|-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
+
|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.
+
|[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''']
  
'''''Yuxuan Wang (wang3@fas.harvard.edu) wrote:'''''
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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''']
  
: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.
+
|-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''']
  
:Yuxuan
+
|}
  
'''''Philippe Le Sager (plesager3@seas.harvard.edu) wrote:'''''
+
== Bugs and fixes in older GEOS-Chem versions ==
  
: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) :
+
For a complete list of bugs and fixes in older GEOS-Chem versions, please see:
  
          ! Zero each "fake" ND65 prod/loss family for next iteration
+
*[[Bugs and fixes in GEOS-Chem 12.0.0 to 12.5.0]]
          CSPEC(JLOOP,IFAM(N)) = 0.0d0
+
*[[Bugs and fixes in GEOS-Chem v9, v10, and v11]]
 +
*[[Bugs and fixes in GEOS-Chem v7 and v8]]
  
:is done too late in the code. Here is the full story:
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:23, 22 March 2021 (UTC)
 
+
: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.
+
 
+
:The fix is easy. In <tt>chemdr.f</tt> 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
+
 
+
:If you could let me know if that fix you problem with a quick run, that would be perfect
+
:Thanks,
+
:-Philippe
+
 
+
'''''Yuxuan Wang (wang3@fas.harvard.edu) wrote:'''''
+
 
+
: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!!
+
:Yuxuan
+
 
+
This fix will go into the next release of GEOS-Chem.
+
 
+
--[[User:Bmy|Bob Y.]] 16:17, 3 June 2008 (EDT)
+
 
+
== Negative tracer in routine WETDEP because of negative RH ==
+
+
See this post: [[GEOS-5 issues#Small negative RH value in 20060206.a6.2x25 file]]
+
 
+
Fixes are available at [ftp://ftp.as.harvard.edu/pub/geos-chem/patches/v8-01-01/ pub/geos-chem/patches/v8-01-01].
+
 
+
--[[User:Plesager|phs]] 16:31, 6 June 2008 (EDT)
+
 
+
== Negative tracer in routine WETDEP ==
+
+
'''''Dylan Millet (dbm@umn.edu) wrote:'''''
+
:I'm having a run die consistently at the same time (October 1, 2005; first time step of the month) in large-scale wetdep, with an STT element < 0.
+
:* Platform: Linux cluster
+
:* Threads: 8
+
:* Version: v7-4-13 out of the box.
+
:* GEOS4, 4x5, 30L, full chemistry
+
:* IFORT 10.1
+
 
+
:In Section 6 (No Downward Precip) of wetscav_mod.f, subroutine safety is getting called.
+
    WETDEP - STT < 0 at    1  1  29 for tracer    7 in area    6
+
 
+
:(First of all it seems odd to do wetdep for L=29, this is 63 km up).  Have you seen anything like this?  I ran for the whole year starting Jan 1 successfully until this point.
+
 
+
:... By the way, the problem persists when I turn off chemistry altogether.
+
 
+
'''''Philippe Le Sager (plesager@seas.harvard.edu) replied:'''''
+
 
+
: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.
+
 
+
: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.
+
 
+
: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.
+
 
+
:... 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.
+
 
+
: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.
+
 
+
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.
+
 
+
--[[User:Bmy|Bmy]] 10:38, 17 April 2008 (EDT)
+
 
+
== ISORROPIA and RPMARES ==
+
 
+
Please see the discussion about the bugs & fixes for ISORROPIA and RPMARES on the Code Developer's Forum for [[Aerosol thermodynamical equilibrium]].
+
 
+
Also, if you are trying to run an aerosol-only simulation, then please see [[Aerosol thermodynamical equilibrium#Bug in sulfate_mod.f caused by switch to RPMARES|this discussion about a bug that manifested itself only after switching from ISORROPIA to RPMARES]].
+
 
+
--[[User:Bmy|Bob Y.]] 10:44, 26 June 2008 (EDT)
+

Latest revision as of 13:56, 14 April 2021

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

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.

GEOS-Chem 13

Version Released List of bugs and issues (now posted on the listed Github repository)
13.3.0 TBD geoschem/geos-chem Milestone 13.3.0
13.2.0 TBD geoschem/geos-chem Milestone 13.2.0
13.1.0 TBD geoschem/geos-chem Milestone 13.1.0
13.0.2 12 Apr 2021 geoschem/geos-chem Milestone 13.0.2
13.0.1 23 Mar 2021 geoschem/geos-chem Milestone 13.0.1
13.0.0 18 Mar 2021 geoschem/geos-chem Milestone 13.0.0

GEOS-Chem 12

Version Released List of bugs and issues (now posted on the listed Github repository)
12.9.3 06 Aug 2020 geoschem/geos-chem Milestone 12.9.3
12.9.2 24 Jul 2020 geoschem/geos-chem Milestone 12.9.2
12.9.1 17 Jul 2020 geoschem/geos-chem Milestone 12.9.1
12.9.0 17 Jul 2020 geoschem/geos-chem Milestone 12.9.0
12.8.2 27 May 2020 geoschem/geos-chem Milestone 12.8.2
12.8.1 21 May 2020 geoschem/geos-chem Milestone 12.8.1
12.8.0 04 Mar 2020 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

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) 14:23, 22 March 2021 (UTC)