Re: [SOSlib-devel] Bug in sensitivity analysis?

[Witold W. <wew...@gm...>]

Reiner,

The meassage:

CVode-- At t =3D 0 and h =3D 1.12418e-06, the corrector
convergence failed repeatedly or with |h| =3D hmin.

1.12418e-06  0 0 0 0 0 0 0 0
1.12418e-06  10  0 0 0 0

I got with only 3 global parameters while with 4 global parmaters (after th=
e
call of the function globalize), but with all other settings the same,
everything is working fine. Not sure what to think about it because it seem=
s
to contradict what you have said before.

The cvodeSettings I am using are:

  CvodeSettings_setTime(settings, 300, 10);
  CvodeSettings_setErrors(settings, 1e-9, 1e-4, 1000);
  CvodeSettings_setStoreResults(settings, 1);
  CvodeSettings_setSensitivity(settings,1);

However, after changing:
CvodeSettings_setTime(settings, 300, 10);

to:
CvodeSettings_setTime(settings, 7.5*200, 200);

And I am just not getting my head around this.

Eryk






Eryk

On 5/11/06, Rainer Machne <ra...@tb...> wrote:
>
> Hi Eryk,
>
> On Thu, 11 May 2006, Witold Wolski wrote:
>
> > Hi Rainer,
> >
> > The point I wanted to make is that I am wondering why depending if I us=
e
> the
> > function globalizeParameter or not prior to integration I am getting
> > different results.
>
> Sorry, I really didn't answer that question!
>
> >> > globalizeParameter(model,"V2","J1");
>
>
> By globalizing two parameters you add them to the cvodeData constants
> (nvalues and nconst increase by two) and thereby request more
> sensitivities from CVODES. Calculating many sensitivities at
> the same time can in some cases significantly decrease the performance or
> even get too much for CVODES and it quits.





`convergence failed' is the usual message when CVODES cannot calculate
> results (timecourses and/or sensitivities) within the requested error
> tolerance.
>
> Unfortunately, the sensitivity error tolerance currently cannot be set,
> but you can try to play with the general tolerances (--error and --rerror=
)
>
> and with the maximum number of internal steps option (--mxstep) or with
> external steps (--printstep).
>
> To solve this, we need to
>
> a) implement a way to select specific parameters for which sensitivities
> are calculated; a quick hack could be a function localizeParameterExcept
> that works on the SBML input model and localizes all global parameters
> except the ones that you want sensititities for.
>
> b) implement error settings for sensitivities
>
>
> Furthermore, we need to write documentation on performance relevant
> settings, such as errors, mxstep etc.
>
>
> Ok?
>
> Rainer
>
>
> >
> > cheers
> > Eryk
> >
> >
> > On 5/10/06, Rainer Machne < ra...@tb...> wrote:
> >>
> >>
> >>
> >> > If I do not call it the output reads:
> >> >
> >> > CVode-- At t =3D 0 and h =3D 1.12418e-06, the corrector
> >> > convergence failed repeatedly or with |h| =3D hmin.
> >> >
> >> > 1.12418e-06  0 0 0 0 0 0 0 0
> >> > 1.12418e-06  10  0 0 0 0
> >>
> >>
> >> The first two lines mean that cvodes has failed for integration with
> >> sensitivity analysis. Thus results and sensitivities were not
> calculated.
> >>
> >> IntegratorInstance_dumpY/PSensitivities
> >>
> >> print first the current time, then the current value of the
> >> variable/parameter, and then the sensitivities to all constants of the
> >> model.
> >>
> >> I have never noticed however that upon failure the current time seems
> to
> >> be the h, which is cvodes' internal timestep. So the sensitivities for
> >> this time h are wrong and the output should look different. Maybe upon
> >> failure cvodeData the time should be reset to the last valid time.
> >>
> >>
> >> Rainer
> >>
> >> On Wed, 10 May 2006, Witold Wolski wrote:
> >>
> >> > Hello,
> >> >
> >> > Depending if I apply globalise parameter or not I am getting
> different
> >> > outputs in the sensitivity analysis.
> >> >
> >> > Given the MAPK.xml
> >> >
> >> > Namely the output of the functions (see attachment)
> >> >
> >> > IntegratorInstance_dumpPSensitivities(integratorInstance,p1);
> >> > IntegratorInstance_dumpYSensitivities(integratorInstance,y1);
> >> >
> >> > differs depedning if
> >> >
> >> > globalizeParameter(model,"V2","J1");
> >> >
> >> > was called.
> >> >
> >> > If I do not call it the output reads:
> >> >
> >> > CVode-- At t =3D 0 and h =3D 1.12418e-06, the corrector
> >> > convergence failed repeatedly or with |h| =3D hmin.
> >> >
> >> > 1.12418e-06  0 0 0 0 0 0 0 0
> >> > 1.12418e-06  10  0 0 0 0
> >> >
> >> > I am working on a very recent cvs checkout.
> >> >
> >> > cheers
> >> >
> >> > Eryk
> >> >
> >>
> >
>