Re: [SOSlib-devel] Parameters with undefined values in odeSolver

[Rainer M. <ra...@tb...>]

Hi Michael,

Two patch files for the bug you observed can be found in the attachment.

Basically, one needs to avoid the dangerous

* Parameter_createWith(.... Parameter_getValue ...)

for params, species and compartments in odeConstruct.c,
(the code which constructs a new internal SBML model, in which reactions 
are replaced by rate rules (i.e. ODEs))

and not use

* Parameter_getValue

in cvodedata.c,
(when writing initial values (ODE variables) or constants (ODE parameters) 
to the data structure used by the integrator.)

When no value is available, a fatal error is stored, and
IntegratorInstance_create(...) returns NULL.

This patch doesn't care however, if a parameter that is defined by an 
assignment rule (a in our example) does not have a value, as this value 
would be overruled by the assignment anyways. I think, this should be 
correct.


The output of our command-line program now should be:

odeSolver/odeSolver valtest.xml 
Fatal Error     20000   No value found for parameter b
Exit 1


Rainer




On Tue, 6 Jun 2006, Michael Hucka wrote:

> You're welcome, but thank you for creating the most
> excellent SBML ODE Solver!
>
> MH
>
>  raim> Hi Michael
>  >>
>  >> It sounds like the short-term solution is for SOSlib to
>  >> implement this:
>  >>
>  BB> ... the value returned by getValue() should *not* be
>  BB> used / trusted if isSetValue() returns false
>  BB> (zero)....
>  >>
>  >> The long-term solution is that libsbml 3 will
>  >> incorporate a check.
>  >>
>  >> Is that correct?
>  raim>
>  raim> Yes, I will try to find out where our code needs to
>  raim> be fixed and post detailed instructions for changing
>  raim> 1.6.0 code on our website.
>  raim>
>  raim> Unfortunately, we don't have a separate CVS branch
>  raim> for bugfixes of the current release, so the CVS will
>  raim> only contain the bugfix for the current development
>  raim> version of the code.
>  raim>
>  raim> Thanks again for finding and reporting this quite
>  raim> serious bug!
>  raim>
>  raim> Rainer
>  raim>
>  raim>
>  raim> On Thu, 1 Jun 2006, Michael Hucka wrote:
>  raim>
>  raim>
>  raim>
>  raim>
>  raim>
>  raim>
>  raim>
>  >>
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