Denitrification in Fennel model

[Tomasz]

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]

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).