Denitrification in Fennel model

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Tomasz
Posts: 22
Joined: Tue Oct 07, 2008 11:27 am
Location: Marine Institute, Ireland

Denitrification in Fennel model

#1 Post by Tomasz » Thu Jan 06, 2011 11:02 am

Hi,

When switching off DENITRIFICATION in the Fennel model and leaving the DIAGNOSTICS_BIO switched on, the model crashes with not a very informative 'Segmentation fault...' error message. It works fine when DIAGNOSTICS_BIO is also switched off. Does anyone know what causes the problem?

I did not run too many tests to investigate this issue. Other BIOLOGY-related switches that I am using are here:
/* Biology */
#define BIOLOGY
#define BIO_FENNEL

#if defined BIO_FENNEL || defined ECOSIM || \
defined NPZD_POWELL || defined NEMURO
# define ANA_BIOLOGY
# define ANA_SPFLUX
# define ANA_BPFLUX
# undef DIAGNOSTICS_BIO
#endif

#ifdef BIO_FENNEL
# define CARBON
# define OXYGEN
# define OCMIP_OXYGEN_SC
# undef DENITRIFICATION
# define BIO_SEDIMENT
# define TALK_PROGNOSTIC

and the system is x86_64, intel 10.1.015

I don't think I will be spending much time investigating this issue, but if I find out anything I will post it here.

Regards,
Tomasz

kfennel
Posts: 33
Joined: Thu Jun 12, 2003 6:55 pm
Location: Dalhousie University

Re: Denitrification in Fennel model

#2 Post by kfennel » Fri Jan 07, 2011 1:25 pm

Most likely the model is trying to write a diagnostic term related to denitrification that doesn't exist because denitrification is switched off. I would check the logic in the DIAGNOSTICS_BIO portion at the end of the biology subroutine (the section dealing with sediment fluxes).

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