sbmlsolver-devel

[SOSlib-devel] Bug in sensitivity analysis?

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

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 = 0 and h = 1.12418e-06, the corrector
convergence failed repeatedly or with |h| = 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

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

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

> If I do not call it the output reads:
>
> CVode-- At t = 0 and h = 1.12418e-06, the corrector
> convergence failed repeatedly or with |h| = 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 = 0 and h = 1.12418e-06, the corrector
> convergence failed repeatedly or with |h| = 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
>

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

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

Hi Rainer,

The point I wanted to make is that I am wondering why depending if I use th=
e
function globalizeParameter or not prior to integration I am getting
different results.

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
> >
>

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

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

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 use 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 = 0 and h = 1.12418e-06, the corrector
>> > convergence failed repeatedly or with |h| = 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 = 0 and h = 1.12418e-06, the corrector
>> > convergence failed repeatedly or with |h| = 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
>> >
>> 
>

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
> >> >
> >>
> >
>

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

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

Hi,

Sorry, I have forgotten a sentence in the last e-mail.

However, after changing:

CvodeSettings_setTime(settings, 300, 10);
to:
CvodeSettings_setTime(settings, 7.5*200, 200);

The sensitivities are computed ....

I am just not getting my head around this.

Eryk

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

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

Hi,

> CvodeSettings_setTime(settings, 7.5*200, 200);

The success of CVODES integration really depends on the number of 
printsteps because the error tolerances are used separately for each 
printstep. Errors can accumulate and cause numerical instabilities that 
CVODES cannot handle.

The behaviour you described in the previous emails, that CVODES 
convergence fails with less parameters and succeeds with more parameters 
is really strange.

I cannot explain this, but currently couldn't think of any bug that causes 
this. To find out if it is a SOSlib bug, we could try to change the input 
file, i.e. localize/globalize the parameters by hand and see what happens.

It might be some problem of the algorithm. Maybe 
you can play with the error tolerances and printsteps. If that succeeds 
that we could be sure that it's not a SOSlib bug.

Rainer


On Thu, 11 May 2006, Witold Wolski wrote:

> Hi,
>
> Sorry, I have forgotten a sentence in the last e-mail.
>
> However, after changing:
>
> CvodeSettings_setTime(settings, 300, 10);
> to:
> CvodeSettings_setTime(settings, 7.5*200, 200);
>
> The sensitivities are computed ....
>
> I am just not getting my head around this.
>
> Eryk
>

[SOSlib-devel] sbmlsolver in a c++ program

[Stefan M. <ste...@oe...>]

hi!

i would like to use the SOSlib in a c++ program. using
#include <sbmlsolver/odeSolver.h>
works fine with the compiler, but not with the linker. Using
extern "C" { #include <sbmlsolver/odeSolver.h> }
the compiler gives the error: template with C linkage

does anybody know what i can do about this?

cheers,
stefan.

p.s. the exact error message:
In file included from /usr/include/c++/3.3.5/iosfwd:46,
                 from /usr/local/include/sbml/SBMLDocument.h:62,
                 from /usr/local/include/sbml/SBMLTypes.h:56,
                 from /home/stefan/local/include/sbmlsolver/odeSolver.h:40,
                 from adj_sensitivity.cpp:43:
/usr/include/c++/3.3.5/x86_64-suse-linux/bits/c++locale.h:70: error: template
   with C linkage

[SOSlib-devel] Re: sbmlsolver in a c++ program

[Stefan M. <ste...@oe...>]

hi!

xtof solved the problem.
the extern "C" statement is not necessary in the c++ file.
it is already included in the SOSlib headers.

in processAST.h there was an error: the definitions of
indexAST
simplifyAST
AST_dump
ASTNode_getSymbols
ASTNode_containsTime
have to be inside the extern "C" statement.

thanks,
stefan.


Am Freitag 12 Mai 2006 11:37 schrieben Sie:
> hi!
>
> i would like to use the SOSlib in a c++ program. using
> #include <sbmlsolver/odeSolver.h>
> works fine with the compiler, but not with the linker. Using
> extern "C" { #include <sbmlsolver/odeSolver.h> }
> the compiler gives the error: template with C linkage
>
> does anybody know what i can do about this?
>
> cheers,
> stefan.
>
> p.s. the exact error message:
> In file included from /usr/include/c++/3.3.5/iosfwd:46,
>                  from /usr/local/include/sbml/SBMLDocument.h:62,
>                  from /usr/local/include/sbml/SBMLTypes.h:56,
>                  from /home/stefan/local/include/sbmlsolver/odeSolver.h:40,
>                  from adj_sensitivity.cpp:43:
> /usr/include/c++/3.3.5/x86_64-suse-linux/bits/c++locale.h:70: error:
> template with C linkage