A strange error while open the biological options

[goodboy]

Hi.
I'm running a realistic application using ROMS coupled with biological modules. I can run the physical parts without any biological modules successfully. It gets blow up when I open any biological modules, such as nemuro, fennel or bio_UMAINE. It blows up because of the large biological value. Whenever I open any biological modules, this problem is always existing. I get troubled why this happens.
The error information is as follows:

Code: Select all

 BIO trouble in DIAG    2052.76815011092        1903.57734389846
   1635.09408393151        377.665606471115        489.688949218299
   1750.68226118927        489.346877783901        3301.98919949652
   883.539902870281        1598.98645016792        377.670002130110
   489.707471734793        1162.85281271295        10001.2588770129
   4409.89532765725
 Found Error: 01   Line: 332      Source: ROMS/Nonlinear/main3d.F
 Found Error: 01   Line: 303      Source: ROMS/Drivers/nl_ocean.h

 Blowing-up: Saving latest model state into  RESTART file
     REASON:

      WRT_RST     - wrote re-start    fields (Index=1,1) in record = 0000003

I have checked out all my forcing, initial, boundary, and climatology file, there isn't any problem. At first, I guess this is the problem of the biological initial value. After I change all the biological initial values to the constant in 3D, this problem also exists. I have tried all the methods to solve this problem, it doesn't work.

Besides, I also tried all the biological modules in the ROMS, all of them blow up because of the same reason.

Before running this realistic application, I have run the ideal upwelling experiment in the bio_toy. It can work well with every biological module. I get puzzled why it can run in the ideal upwelling case and fails to run in my realistic application. Could anyone can help me?

[kate]

The check you are running into is in diag.F:

Code: Select all

IF (maxbio(ibt,ng).gt.max_bio(ibt)) THEN

It looks like you have max_bio set to 10000. Does that make sense for the units you are using? You can change it if 10000 is a valid number for your BGC model. I probably added the check for COSINE, but then kept it for COBALT. For COBALT, typical units are more like 1.e-5 so a value of 10000 is definitely out of bounds.

If you are instead asking how it came that you have such large numbers and they really are out of bounds, that's something else again and you'll have to do some digging yourself.

[wilkin]

Your logfile shows ...

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Tracer Advection Scheme: NLM
 ========================

 Variable               Grid  Horizontal         Vertical
 ---------              ----  ------------       ------------
 temp                     1   HSIMT              Centered4
 salt                     1   HSIMT              Centered4
 NO3                      1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@^@
 NH4                      1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@^@
 SiOH4                    1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@^@
 smallphytoplankton       1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@^@
 diatom                   1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@^@
 microzooplankton         1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@^@
 mesozooplankton          1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@^@
 detritus                 1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@^@
 opal                     1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@^@
 PO4                      1   ^@^@^@^@^@^@^@^@^@^@^@           regu°^@^@^@
 chlorophyll1             1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@p^@^@^@^@^@^@
 chlorophyll2             1   ^@^@^@^@^@^@^@^@^@^@^@        ^@^@^@^@^@^@^@^@^@Pñ
 oxygen                   1   ^@^@^@^@^@^@^@^@^@^@^@        0^A^@^@^@^@ÿÿÿÿÿ
 TIC                      1   ^@^@^@^@^@^@^@^@^@^@^@        ÿÿÿÿÿÿÿÿÿÿÿ
 alkalinity               1   ^@^@^@^@^@^@^@^@^@^@^@        ÿÿÿÿÿÿÿÿÿÿÿ

All you bio tracer advection options are messed up.

Check that you have set advection scheme options in /public/home/rengz/roms/Apps/Lagrangian/run04/bio_UMAINE15.in

This is not the myroms.org trunk code so I can't help any more than this.

[kate]

I haven't used BIO_UMAINE since Hernan changed the advection scheme choices. Good catch, John.

As for my github code, I have stopped updating it because updates can be disruptive and I don't want to spend the time sorting them out. Mark Hadfield is keeping his github code up to date. If you find any of my updates useful, perhaps it's time to bug Hernan to get them into the main branch. I know there are people out there using BIO_UMAINE, for instance.

[goodboy]

Thank you very much, you are right.

It looks like you have max_bio set to 10000. Does that make sense for the units you are using? You can change it if 10000 is a valid number for your BGC model. I probably added the check for COSINE, but then kept it for COBALT. For COBALT, typical units are more like 1.e-5 so a value of 10000 is definitely out of bounds.

I have changed the max_bio to a very large number, such as 100000, it can run successfully. After biological spinups, I can check the model output to judge whether it's right or not.

[goodboy]

All right, it blows up again. Now it's not the issue of this.
I have got errors in ROMS 3.9. Maybe I should use the ROMS 3.8 first in order to find my problems and do my research. I don't want to spend more time on model debugging. Maybe I would bug them to Hadfield after I know the real reason.