sbmlsolver-devel — developer's email list for the SBML ODE Solver Library

Re: [SOSlib-devel] building SBML ODE Solver for AIX - can I use expat?[Scanned]

[Andrew F. <af...@ph...>]

Rainer

I managed to substitute expat for xerces

But I still can't link to libsbml in the config.log
(attached)
I get the following:

---------------------------------

configure:4155: checking correct functioning of SBML
configure:4185: gcc -o conftest -g -O2
-I/hpc/home/finneya/programs/include
-Wl,-rpath,/hpc/home/finneya/programs/lib
-L/hpc/home/finneya/programs/lib conftest.c  -lexpat -lsbml >&5
ld: 0706-012 The -p flag is not recognized.
ld: 0706-012 The -a flag is not recognized.
ld: 0706-012 The -t flag is not recognized.
ld: 0706-012 The -h flag is not recognized.
collect2: ld returned 255 exit status
configure:4191: $? =3D 1
configure: failed program was:
| /* confdefs.h.  */
|=20
| #define PACKAGE_NAME "odeSolver"
| #define PACKAGE_TARNAME "SBML_odeSolver"
| #define PACKAGE_VERSION "1.5.0"
| #define PACKAGE_STRING "odeSolver 1.5.0"
| #define PACKAGE_BUGREPORT "{raim,xtof}@tbi.univie.ac.at"
| #define PACKAGE "SBML_odeSolver"
| #define VERSION "1.5.0"
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| /* end confdefs.h.  */
| #include <sbml/SBMLTypes.h>
| int
| main ()
| {
| SBMLReader_t *sr; sr =3D SBMLReader_create(); SBMLReader_free(sr);
|   ;
|   return 0;
| }
configure:4220: result: no:
                   CFLAGS=3D-g -O2 -I/hpc/home/finneya/programs/include
                   LDFLAGS=3D -Wl,-rpath,/hpc/home/finneya/programs/lib
-L/hpc/home/finneya/programs/lib
                   LIBS=3D -lexpat -lsbml
configure:4228: error: Can not link to SBML Library:
		  Please, make sure to use libSBML version >=3D 2.3.2

------------------

It looks as if the loader (ld) isn't performing as expected :-(

what's the -rpath supposed to do?

yours Andrew
=20

> -----Original Message-----
> From: Rainer Machne [mailto:ra...@tb...]=20
> Sent: 08 June 2006 14:13
> To: Andrew Finney
> Cc: SOSlib Development
> Subject: Re: building SBML ODE Solver for AIX - can I use=20
> expat?[Scanned]
>=20
> Hi Andrew
>=20
> Unfortunately we completely forgot about libSBML with expat.
>=20
> There is a bug report in sourceforge with short instructions.
> http://sourceforge.net/tracker/index.php?func=3Ddetail&aid=3D14204
> 89&group_id=3D139893&atid=3D744811
>=20
>=20
> Copied from there, with slight corrections:
>=20
> This bug can temporarily be solved simply by replacing all=20
> occurences of
>=20
> `-lxerces-c'
>=20
> in the files:
>=20
> configure
> src/Makefile.am
> src/Makefile.in
> examples/Makefile.am
> examples/Makefile.in
> odeSolver/Makefile.am
> odeSolver/Makefile.in
>=20
> with `-lexpat'
>=20
> e.g. by usind sed:
>=20
> sed 's/xerces-c/expat/g' configure >configure.new mv=20
> configure.new configure
>=20
> for all above files.
>=20
>=20
> I tried it once and it worked! Please let me know if you suceed!
>=20
> Rainer
>=20
>=20
>=20
> On Thu, 8 Jun 2006, Andrew Finney wrote:
>=20
> > Rainer
> >
> > I'm trying to build SOS on AIX
> >
> > for some reason I'm having problems linking with xerces for that=20
> > platform
> >
> > Is there a way to configure SOS to use expat?
> >
> > Andrew
> >
>=20

Re: [SOSlib-devel] building SBML ODE Solver for AIX - can I use expat?

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

Hi Andrew

Unfortunately we completely forgot about libSBML with expat.

There is a bug report in sourceforge with short instructions.
http://sourceforge.net/tracker/index.php?func=detail&aid=1420489&group_id=139893&atid=744811


Copied from there, with slight corrections:

This bug can temporarily be solved simply by replacing
all occurences of

`-lxerces-c'

in the files:

configure
src/Makefile.am
src/Makefile.in
examples/Makefile.am
examples/Makefile.in
odeSolver/Makefile.am
odeSolver/Makefile.in

with `-lexpat'

e.g. by usind sed:

sed 's/xerces-c/expat/g' configure >configure.new
mv configure.new configure

for all above files.


I tried it once and it worked! Please let me know if you suceed!

Rainer



On Thu, 8 Jun 2006, Andrew Finney wrote:

> Rainer
>
> I'm trying to build SOS on AIX
>
> for some reason I'm having problems linking with xerces for that
> platform
>
> Is there a way to configure SOS to use expat?
>
> Andrew
>

[SOSlib-devel] building SBML ODE Solver for AIX - can I use expat?

[Andrew F. <af...@ph...>]

Rainer

I'm trying to build SOS on AIX

for some reason I'm having problems linking with xerces for that
platform

Is there a way to configure SOS to use expat?

Andrew

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

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

ok, sorry.

here is a proper patch file.

r


On Wed, 7 Jun 2006, Rainer Machne wrote:

> 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>
>>  >>
>>  >> -------------------------------------------------------
>>  >> All the advantages of Linux Managed Hosting--Without
>>  >> the Cost and Risk!  Fully trained technicians. The
>>  >> highest number of Red Hat certifications in the hosting
>>  >> industry. Fanatical Support. Click to learn more
>>  >> 
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642
>>  >> _______________________________________________
>>  >> sbmlsolver-devel mailing list
>>  >> sbm...@li...
>>  >> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>>  >>
>> 
>> 
>> 
>> _______________________________________________
>> sbmlsolver-devel mailing list
>> sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>

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>
>  >>
>  >> -------------------------------------------------------
>  >> All the advantages of Linux Managed Hosting--Without
>  >> the Cost and Risk!  Fully trained technicians. The
>  >> highest number of Red Hat certifications in the hosting
>  >> industry. Fanatical Support. Click to learn more
>  >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642
>  >> _______________________________________________
>  >> sbmlsolver-devel mailing list
>  >> sbm...@li...
>  >> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>  >>
>
>
>
> _______________________________________________
> sbmlsolver-devel mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>

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

[Michael H. <mh...@ca...>]

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>
  >>
  >> -------------------------------------------------------
  >> All the advantages of Linux Managed Hosting--Without
  >> the Cost and Risk!  Fully trained technicians. The
  >> highest number of Red Hat certifications in the hosting
  >> industry. Fanatical Support. Click to learn more
  >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642
  >> _______________________________________________
  >> sbmlsolver-devel mailing list
  >> sbm...@li...
  >> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
  >>

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

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

Hi Michael

>
> It sounds like the short-term solution is for SOSlib to
> implement this:
>
>  BB> ... the value returned by getValue() should
>  BB> *not* be used / trusted if isSetValue() returns false
>  BB> (zero)....
>
> The long-term solution is that libsbml 3 will incorporate a
> check.
>
> Is that correct?

Yes, I will try to find out where our code needs to be fixed and post 
detailed instructions for changing 1.6.0 code on our website.

Unfortunately, we don't have a separate CVS branch for bugfixes of the 
current release, so the CVS will only contain the bugfix for the current 
development version of the code.

Thanks again for finding and reporting this quite serious bug!

Rainer


On Thu, 1 Jun 2006, Michael Hucka wrote:







>
> -------------------------------------------------------
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat certifications in
> the hosting industry. Fanatical Support. Click to learn more
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642
> _______________________________________________
> sbmlsolver-devel mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>

[SOSlib-devel] Re: Possible problem behavior w.r.t. assignment rules

[Michael H. <mh...@ca...>]

Sorry, I realize now that particular case is something that
falls into the "overdetermined system" set of conditions in
SBML.  So it is in fact something that's known, and it's
discussed on the validation wiki, but there's just not a
check for this in libsbml yet.

MH

[SOSlib-devel] Possible problem behavior w.r.t. assignment rules

[Michael H. <mh...@ca...>]

Hi,

Harish Dharuri encountered an interesting result with a
model (attached).  The model actually contains an error:
there is both an assignment rule and a reaction referencing
species "S".  This is technically invalid in SBML L2v1 and
L2v2 unless the species is labeled as a boundary species.

The interesting thing is that SOSlib actually simulates
this, and produces an expected result.  We didn't realize
the SBML was in error until Harish spotted it a moment ago.

LibSBML doesn't appear to have a validation rule to catch
this, which surprises me, because this aspect of SBML has
been around for a long time.  This is probably why SOSlib
doesn't report it as an error.  We'll file this as a bug to
fix in libsbml.

MH

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

[Michael H. <mh...@ca...>]

Rainer and Ben,

It sounds like the short-term solution is for SOSlib to
implement this:

  BB> ... the value returned by getValue() should
  BB> *not* be used / trusted if isSetValue() returns false
  BB> (zero)....

The long-term solution is that libsbml 3 will incorporate a
check.

Is that correct?

MH

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

[Ben B. <ben...@jp...>]

Hi Rainer, Mike,

Parameters are stored as C doubles so they need to store *some* value  
even when they're not set.  This value is set to NaN if you call  
unsetValue(), but when an SBML Parameter structure is first created /  
initialized, it's apparently zero.  Sorry, this is an implementation  
inconsistency on my part.

That said, the value returned by getValue() should *not* be used /  
trusted if isSetValue() returns false (zero).  LibSBML can't stop a  
programmer from calling getValue() (unless it throws an exception,  
but this wouldn't work for the C API).

This error should be caught by XML Schema validation, which is one  
reason why we never added a check to libSBML 2.  LibSBML 3 performs  
the check, since one of its design goals is to subsume all XML Schema  
checks.

Thanks.

Ben


On May 29, 2006, at 2:37 AM, Rainer Machne wrote:

> The non-constant parameters a and b in the example file have no  
> initial value, but are interpreted as 0 by SOSlib.
>
> I have attached a simple example program, which I compiled with  
> libsbml 2.3.4, probably from a version that was updated from CVS on  
> Feb 14 this year.
>
> It shows that Parameter_getValue returns 0 for both parameters even  
> though Parameter_isSetValue correctly returns "no" for both  
> parameters.
> No errors are reported by the consistency check.
>
>
> It is quite some bug in SOSlib.
> Unfortunately, we didn't think earlier of this problem.
>
> So I'd have some questions to start repairing SOSlib:
>
> Does this happen on purpose, i.e. is 0 the default value to return,  
> if no value is set?
>
> For which other values (species, compartments) does this happen?
>
> and:
>
> Should there be a test in the consistency check?

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

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

sorry, this is the test program that also does the consistency check.
r

On Mon, 29 May 2006, Rainer Machne wrote:

> Hi Michael and Ben
>
> Michael had reported a mis-behaviour of SOSlib in the email below.
>
> The non-constant parameters a and b in the example file have no initial 
> value, but are interpreted as 0 by SOSlib.
>
> I have attached a simple example program, which I compiled with libsbml 
> 2.3.4, probably from a version that was updated from CVS on Feb 14 this year.
>
> It shows that Parameter_getValue returns 0 for both parameters even though 
> Parameter_isSetValue correctly returns "no" for both parameters.
> No errors are reported by the consistency check.
>
>
> It is quite some bug in SOSlib.
> Unfortunately, we didn't think earlier of this problem.
>
> So I'd have some questions to start repairing SOSlib:
>
> Does this happen on purpose, i.e. is 0 the default value to return, if no 
> value is set?
>
> For which other values (species, compartments) does this happen?
>
> and:
>
> Should there be a test in the consistency check?
>
> Thanks
> Rainer
>
>
>
>
>
> On Wed, 24 May 2006, Michael Hucka wrote:
>
>> Hi guys,
>> 
>> Harish has been using odeSolver to test models during
>> curation and has bumped into the following behavior.  If you
>> have a model that has a parameter with an undefined value,
>> odeSolver doesn't complain, and seems to assume a value of 0
>> for the parameter.  The attached model demonstrates this
>> behavior for parameter 'b'.
>> 
>> Unless I'm misunderstanding something, I think this is an
>> error.  Missing values in an SBML model should be considered
>> as unknown and a software tool should acquire the value from
>> an external source (such as asking the user).  I checked the
>> online documentation but couldn't find mention of whether
>> there is a way to tell odeSolver to behave differently in
>> this situation.
>> 
>> Please don't take this as criticism!  I think odeSolver is
>> outstanding and the online facilities are terrific :-).  We
>> merely wanted to point out this issue, and ask if our
>> understanding is in fact correct about what's going on.
>> 
>> Best regards,
>> MH
>

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

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

Hi Michael and Ben

Michael had reported a mis-behaviour of SOSlib in the email below.

The non-constant parameters a and b in the example file have no 
initial value, but are interpreted as 0 by SOSlib.

I have attached a simple example program, which I compiled with 
libsbml 2.3.4, probably from a version that was updated from CVS on Feb 14 
this year.

It shows that Parameter_getValue returns 0 for both parameters even though 
Parameter_isSetValue correctly returns "no" for both parameters.
No errors are reported by the consistency check.


It is quite some bug in SOSlib.
Unfortunately, we didn't think earlier of this problem.

So I'd have some questions to start repairing SOSlib:

Does this happen on purpose, i.e. is 0 the default value to return, if no 
value is set?

For which other values (species, compartments) does this happen?

and:

Should there be a test in the consistency check?

Thanks
Rainer





On Wed, 24 May 2006, Michael Hucka wrote:

> Hi guys,
>
> Harish has been using odeSolver to test models during
> curation and has bumped into the following behavior.  If you
> have a model that has a parameter with an undefined value,
> odeSolver doesn't complain, and seems to assume a value of 0
> for the parameter.  The attached model demonstrates this
> behavior for parameter 'b'.
>
> Unless I'm misunderstanding something, I think this is an
> error.  Missing values in an SBML model should be considered
> as unknown and a software tool should acquire the value from
> an external source (such as asking the user).  I checked the
> online documentation but couldn't find mention of whether
> there is a way to tell odeSolver to behave differently in
> this situation.
>
> Please don't take this as criticism!  I think odeSolver is
> outstanding and the online facilities are terrific :-).  We
> merely wanted to point out this issue, and ask if our
> understanding is in fact correct about what's going on.
>
> Best regards,
> MH
>

RE: [SOSlib-devel] please summarize latest changes[Scanned]

[Andrew F. <af...@ph...>]

Rainer

you wrote:

> After your last commit I have just repaired the simple event=20
> handling in integratorInstance.c and cvodedata.c, as=20
> discussed with you before.
> Maybe that is breaking your model?  You mentioned back then,=20
> that you might get problems.

Yes, I have not tried commenting these out but I think this is the cause
:-(

Don't worry this is our problem really I'll have to put in some option
to work around it like "CrudeEventSemantics".

yours Andrew=20

> -----Original Message-----
> From: Rainer Machne [mailto:ra...@tb...]=20
> Sent: 24 May 2006 17:18
> To: Andrew Finney
> Cc: SOSlib Development
> Subject: Re: [SOSlib-devel] please summarize latest changes[Scanned]
>=20
>=20
> > The latest source breaks our large model.
> > Can people summarize the changes that have been checked in=20
> recently...
>=20
> I am just looking at the online CVS at sourceforge=20
> http://sbmlsolver.cvs.sourceforge.net/sbmlsolver/SBML_odeSolve
> r/src/?sortby=3Ddate#dirlist
>=20
> After your last commit I have just repaired the simple event=20
> handling in integratorInstance.c and cvodedata.c, as=20
> discussed with you before.
> Maybe that is breaking your model?  You mentioned back then,=20
> that you might get problems.
>=20
>=20
> My other changes are the declaration for the local functions=20
> in integratorInstance.c and some editing towards the style convention.
>=20
> Stefan has made some changes, of which I don't know yet, if=20
> they might break anything. To find out maybe you can try the=20
> files before his commit (download from online CVS e.g.)
>=20
>=20
> Rainer
>=20
>=20
>=20
> > Has the accurate event detection been checked in?
>=20
> No.
>=20
> On Wed, 24 May 2006,
> Andrew Finney wrote:
>=20
> > Folks
> >
> > The latest source breaks our large model.
> > Can people summarize the changes that have been checked in=20
> recently...
> >
> > Has the accurate event detection been checked in?
> >
> > yours Andrew
> >
> >
> > -------------------------------------------------------
> > All the advantages of Linux Managed Hosting--Without the=20
> Cost and Risk!
> > Fully trained technicians. The highest number of Red Hat=20
> > certifications in the hosting industry. Fanatical Support. Click to=20
> > learn more=20
> >=20
> http://sel.as-us.falkag.net/sel?cmd___________________________________
> > ____________
> > sbmlsolver-devel mailing list
> > sbm...@li...
> > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
> >
>=20

Re: [SOSlib-devel] please summarize latest changes

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

> The latest source breaks our large model.
> Can people summarize the changes that have been checked in recently...

I am just looking at the online CVS at sourceforge
http://sbmlsolver.cvs.sourceforge.net/sbmlsolver/SBML_odeSolver/src/?sortby=date#dirlist

After your last commit I have just repaired the simple event handling in 
integratorInstance.c and cvodedata.c, as discussed with you before.
Maybe that is breaking your model?  You mentioned back then, that you 
might get problems.


My other changes are the declaration for the local functions in 
integratorInstance.c and some editing towards the style convention.

Stefan has made some changes, of which I don't know yet, if they might 
break anything. To find out maybe you can try the files before his commit 
(download from online CVS e.g.)


Rainer



> Has the accurate event detection been checked in?

No.

On Wed, 24 May 2006, 
Andrew Finney wrote:

> Folks
>
> The latest source breaks our large model.
> Can people summarize the changes that have been checked in recently...
>
> Has the accurate event detection been checked in?
>
> yours Andrew
>
>
> -------------------------------------------------------
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> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>

Re: [SOSlib-devel] Indenting still screwed up

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

Hi Andrew

I planned to pretty print all files together and then submit them, but 
haven't done yet. So everything still looks the same as people had 
submitted it.

I think I can start working on my SOSlib todo list next week. So I could 
dp this as a first thing before starting to write any new code and submit 
it all together. However, browsing the online CVS will not be very 
informative because the last commit comments will be lost. Should I do it 
anyways?

Rainer

On Wed, 24 May 2006, Andrew Finney wrote:

> Folks
>
> Is anyone else seeing screwed up indents of C code?
>
> Please make sure editors are set to insert 2 spaces
> on a tab i.e. 2 spaces are inserted when you press the tab
> key.  This should also apply to automatically inserted
> tabs created by pretty printing or formatting operations
> as well.  If not please disable them.
>
> Large parts of my latest checkout look like garbage.
>
> It might be worth doing some experiments to see what's
> causing this problem.
>
> I have set my editor to use 2 space indenting
> there may be some 4 space indents left over...
>
> Andrew
>
>
> -------------------------------------------------------
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat certifications in
> the hosting industry. Fanatical Support. Click to learn more
> http://sel.as-us.falkag.net/sel?cmd_______________________________________________
> sbmlsolver-devel mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>

[SOSlib-devel] Indenting still screwed up

[Andrew F. <af...@ph...>]

Folks

Is anyone else seeing screwed up indents of C code?

Please make sure editors are set to insert 2 spaces
on a tab i.e. 2 spaces are inserted when you press the tab
key.  This should also apply to automatically inserted
tabs created by pretty printing or formatting operations
as well.  If not please disable them.

Large parts of my latest checkout look like garbage.

It might be worth doing some experiments to see what's
causing this problem.

I have set my editor to use 2 space indenting
there may be some 4 space indents left over...

Andrew

[SOSlib-devel] please summarize latest changes

[Andrew F. <af...@ph...>]

Folks

The latest source breaks our large model.
Can people summarize the changes that have been checked in recently...

Has the accurate event detection been checked in?

yours Andrew

[SOSlib-devel] SF cvs service online again

[Christoph F. <xt...@tb...>]

hi all,

the SourceForge cvs server is online again!

unfortunately they changed the host ot the cvs repository from
cvs.sourceforge.net to sbmlsolver.cvs.sourceforge.net, which basically
means either to do a fresh checkout of the sources

cvs -d:ext:YOU...@sb...:/cvsroot/sbmlsolver co SBML_odeSolver

and merging your local changes from the old checkout into the new
checkout by hand (tedious!)

OR

recursively change all CVS/Root files in your local checkout to the
new host:

find . -name Root -exec sed -i -e's/@cvs/@sbmlsolver.cvs/' {} \;

for anonymous checkout with read permissions only use

cvs -d:pserver:ano...@sb...:/cvsroot/sbmlsolver co SBML_odeSolver

=;) xtof

-- 
Christoph Flamm
Bioinformatik, Inst.f.Informatik, Univ.Leipzig, Germany
  www: http://www.tbi.univie.ac.at/~xtof
phone: ++49 341 97-16688 fax: ++49 341 97-16709
email: xt...@bi...
smail: Haertelstrasse 16-18, D-04107 Leipzig, Germany

[SOSlib-devel] [SOSlib-discuss] Problem with odeSolver (fwd)

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

Hi

just for the record, see the following C++ problems and solution:

---------- Forwarded message ----------
Date: Tue, 16 May 2006 13:04:36 +0100
From: Vladislav V Vyshemirsky <vv...@dc...>
To: sbm...@li...
Subject: [SOSlib-discuss] Problem with odeSolver

Dear developers of odeSolver,

I have found a problem in the library sources from the last release.
It is impossible to compile the library with the sources using C++.

The problem is in sbmlsolver/odeSolver.h file.
Line number 95 should be changed from
extern "C" {
to
}

Seems to be just a typo.

Kind regards,
Vladislav Vyshemirsky.
--
Vladislav Vyshemirsky
Bioinformatics Research Centre
Department of Computing Science
University of Glasgow
tel: 0141-330 8751
fax: 0141-330 8627
http://www.brc.dcs.gla.ac.uk/~vlad

[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

[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

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
>

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?

[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
> >> >
> >>
> >
>