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

[SOSlib-devel] todo for next release

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

Hi Friends,

here a rough todo list for the next release ... at least some of the 
stuff below should be done before the next release. If you have 
preferences/opions or want to add things feel free:

Functionality:
General:
* odeSolverBatch (use Eryk's code)
* assignment rule ordering (also consider DAE systems/IDA solver extension)
* variable compartments, ODEs in amounts
* online compilation
* exact event detection
-> Rainer and Xtof

Text-based input files for:
** reaction network: Vienna Reaction library
** ODE system: xppaut format
-> Xtof

Sens. Analysis output:
* Direct Lyapunov Exponent analysis
* Fisher Information Matrix
-> James and Stefan :-) ???

Dependencies:
* libSBML 3
* Sundials 2.3.0
-> Rainer and Xtof

Pending:
* Test suite ??
** Functionality
** Performance

Configure:
* malloc.h
* -R/-rpath switch
* general refactoring!!
-> Rainer and Xtof

[SOSlib-devel] [ sbmlsolver-Bugs-1387998 ] getopt and Solaris 9

[SourceForge.net <no...@so...>]

Bugs item #1387998, was opened at 2005-12-22 13:52
Message generated for change (Comment added) made by chfl
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Category: autotools compilation
Group: None
>Status: Closed
Resolution: None
Priority: 5
Private: No
Submitted By: t_aho (t_aho)
Assigned to: Nobody/Anonymous (nobody)
Summary: getopt and Solaris 9

Initial Comment:
getopt cannot be found automatically in Solaris 9.  
  
sbmlsolver/SBML_odeSolver-1.6.0> make   
...   
options.c:7:20: getopt.h: No such file or directory   
...   
   
getopt has problems with portability. See e.g.   
http://www.thedotin.net/maillists/coldsync-hackers/msg01314.html   
  
Here is a workaround:  
   
Download the needed getopt files, e.g. from   
http://www.molpopgen.org/krthornt/gccSolaris/   
Compile them   
sbmlsolver/SBML_odeSolver-1.6.0/odeSolver> gcc   
--pedantic -c getopt.c   
sbmlsolver/SBML_odeSolver-1.6.0/odeSolver> gcc   
--pedantic -c getopt1.c   
   
Add the created object files to the linking by 
modifying   
odeSolver/Makefile and odeSolver/Makefile.in:   
   
am_odeSolver_OBJECTS = main.$(OBJEXT) commandLine.  
$(OBJEXT) \   
       options.$(OBJEXT) printModel.$(OBJEXT)   
interactive.$(OBJEXT) \   
       getopt1.$(OBJEXT) getopt.$(OBJEXT)   
   

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

>Comment By: Christoph Flamm (chfl)
Date: 2006-11-23 12:27

Message:
Logged In: YES 
user_id=1113720
Originator: NO

added gnu getopt long source for compatibility reasons with solaris.

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[SOSlib-devel] [ sbmlsolver-Bugs-1420489 ] libSBML with expat

[SourceForge.net <no...@so...>]

Bugs item #1420489, was opened at 2006-01-31 14:39
Message generated for change (Comment added) made by chfl
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Category: autotools compilation
Group: None
>Status: Closed
Resolution: None
Priority: 5
Private: No
Submitted By: Rainer Machne (raimc)
Assigned to: Nobody/Anonymous (nobody)
Summary: libSBML with expat

Initial Comment:
LOPEZ GARCIA DE LOMANA, ADRIAN
has reported that configure and make don't work for
libSBML installation with the Expat instead of the
Xerces-c XML library.

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

`-lxerces-c'

in the files:

configure
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.


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

>Comment By: Christoph Flamm (chfl)
Date: 2006-11-23 12:13

Message:
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Originator: NO

added configure dispatch between xerces-c and expat.

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

Comment By: Rainer Machne (raimc)
Date: 2006-06-08 15:10

Message:
Logged In: YES 
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The same replacement needs to be done for the src directory

src/Makefile.am
src/Makefile.in



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[SOSlib-devel] [ sbmlsolver-Bugs-1575411 ] configure fails under Mac OS 10.4

[SourceForge.net <no...@so...>]

Bugs item #1575411, was opened at 2006-10-11 18:49
Message generated for change (Comment added) made by chfl
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Category: autotools compilation
Group: None
>Status: Closed
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: configure fails under Mac OS 10.4

Initial Comment:
There are several issues compiling SOSlib under Mac OS X:

The configure script does not correctly indentify the version of the 
installed SBML library. Replacing the filename suffix ".so" by ".dylib" in 
library file names in lines 4146 and 4148 is a possible workaround.

Even after that, the configure script fails:

configure: found SBML Library Version 2.3.4
checking correct functioning of SBML... no:
                   CFLAGS=-g -O2 -I/usr/local/include -I/usr/local/include/
sbml
                   LDFLAGS=-L/sw/lib  -L/usr/local/lib
                   LIBS= -lxerces-c -lsbml
configure: error: Can not link to SBML Library:
                  Please, make sure to use libSBML version >= 2.3.2

System information: Mac OS 10.4.8, libSBML 2.3.4 built with expat


Bug submitted by Hendrik Fuss <fu...@ul...>

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

>Comment By: Christoph Flamm (chfl)
Date: 2006-11-23 12:11

Message:
Logged In: YES 
user_id=1113720
Originator: NO

removed libSBML version check from the configure process. added configure
dispatch between xerces-c and expat.

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Re: [SOSlib-devel] [SOSlib-discuss] Altering the parameters of an ODE object.

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

Dear Dr. Fernando,

I just realized that you might want to change local parameters given in 
kinetic laws:
No, this is currently not possible, as local parameters are replaced 
with their values during construction of the odeModel. SOSlib only keeps 
parameters of the global parameter list as odeModel parameters. You 
would need to `globalize' local parameters of your model yourself, via 
libSBML.

In the SOSlib file src/odeSolver.c you will find an example how to do 
that, the function:

static int globalizeParameter(Model_t *m, char *id, char *rid)

at line 309 of the 1.6.0 release, where id is the parameter ID and rid 
is the ID of the reaction, where this local parameter is defined and used.

We are currently not handling local parameters explicitly because it is 
much easier to do this via libSBML before passing a model to SOSlib, but 
we don't want to change an applications' input model. But I will think 
about offering our globalizeParameter function for the SOSlib API. You 
could do this by hand, if you want: Just move the function declaration 
to src/sbmlsolver/odeSolver.h and remove the `static'.

Rainer



Rainer Machne wrote:
> Dear Dr. Fernando,
> 
> yes you can change any parameter or variable (in SBML: global 
> parameters, species, compartments) between iterative integration runs 
> and even during an integration (e.g. to handle external events).
> 
> First, you need to get a pointer to structure variableIndex_t for your 
> parameter from the odeModel structure:
> 
> odeModel = ODEModel_createFromFile("model.xml");
> vi = ODEModel_getVariableIndex(odeModel, "paramX");
>    /* where paramX is the SBML ID of the parameter you want to set */
> 
> Then you can use this variableIndex to get or set the value of this 
> parameter or variable via the integratorInstance:
> 
> IntegratorInstance_setVariableValue(ii, vi, 55);
> 
> There is one caveat with this function:
> 
> If you run multiple integrations wiht one integratorInstance, you need 
> to do an
> IntegratorInstance_reset(ii);
> before the next integration run, and this will reset your initial 
> conditions and parameters to the original values in the input SBML file!
> And thus, currently the setVariableValue function MUST be called AFTER 
> the reset function! (We hope to provide additional reset functions with 
> the next release, which keep current or manually reset values.)
> 
> See
> http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__variableIndex.html
> for functions to get the variableIndex from the odeModel, and
> http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__integrator.html#ga25
> for setting variable/parameter values in the integrator.
> 
> See
> examples/ChangingIntegratorInstance.c
> for an example program which changes variables during an integration.
> 
> Please, keep asking if anything is unclear.
> 
> Thanks,
> Rainer
> 
> 
> 
> SourceForge.net wrote:
> 
>>Support Requests item #1597040, was opened at 2006-11-15 07:00
>>Message generated for change (Tracker Item Submitted) made by Item Submitter
>>You can respond by visiting: 
>>https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
>>
>>Please note that this message will contain a full copy of the comment thread,
>>including the initial issue submission, for this request,
>>not just the latest update.
>>Category: None
>>Group: None
>>Status: Open
>>Priority: 5
>>Private: No
>>Submitted By: Nobody/Anonymous (nobody)
>>Assigned to: Nobody/Anonymous (nobody)
>>Summary: Altering the parameters of an ODE object. 
>>
>>Initial Comment:
>>Is there any way of altering the rate constants once an SBML file has been read in? This is quite important for using evolutionary algorithms, because a significant amount of time is wasted reading the new SBML file into the ODEsolver. 
>>
>>Yours, 
>>Dr. C. Fernando 
>>Birmingham University 
>>UK. 
>>
>>
>>----------------------------------------------------------------------
>>
>>You can respond by visiting: 
>>https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
>>
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Re: [SOSlib-devel] [SOSlib-discuss] [ sbmlsolver-Support Requests-1597040 ] Altering the parameters of an ODE object.

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

Dear Dr. Fernando,

yes you can change any parameter or variable (in SBML: global 
parameters, species, compartments) between iterative integration runs 
and even during an integration (e.g. to handle external events).

First, you need to get a pointer to structure variableIndex_t for your 
parameter from the odeModel structure:

odeModel = ODEModel_createFromFile("model.xml");
vi = ODEModel_getVariableIndex(odeModel, "paramX");
   /* where paramX is the SBML ID of the parameter you want to set */

Then you can use this variableIndex to get or set the value of this 
parameter or variable via the integratorInstance:

IntegratorInstance_setVariableValue(ii, vi, 55);

There is one caveat with this function:

If you run multiple integrations wiht one integratorInstance, you need 
to do an
IntegratorInstance_reset(ii);
before the next integration run, and this will reset your initial 
conditions and parameters to the original values in the input SBML file!
And thus, currently the setVariableValue function MUST be called AFTER 
the reset function! (We hope to provide additional reset functions with 
the next release, which keep current or manually reset values.)

See
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__variableIndex.html
for functions to get the variableIndex from the odeModel, and
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__integrator.html#ga25
for setting variable/parameter values in the integrator.

See
examples/ChangingIntegratorInstance.c
for an example program which changes variables during an integration.

Please, keep asking if anything is unclear.

Thanks,
Rainer



SourceForge.net wrote:
> Support Requests item #1597040, was opened at 2006-11-15 07:00
> Message generated for change (Tracker Item Submitted) made by Item Submitter
> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
> 
> Please note that this message will contain a full copy of the comment thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: None
> Group: None
> Status: Open
> Priority: 5
> Private: No
> Submitted By: Nobody/Anonymous (nobody)
> Assigned to: Nobody/Anonymous (nobody)
> Summary: Altering the parameters of an ODE object. 
> 
> Initial Comment:
> Is there any way of altering the rate constants once an SBML file has been read in? This is quite important for using evolutionary algorithms, because a significant amount of time is wasted reading the new SBML file into the ODEsolver. 
> 
> Yours, 
> Dr. C. Fernando 
> Birmingham University 
> UK. 
> 
> 
> ----------------------------------------------------------------------
> 
> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
> 
> -------------------------------------------------------------------------
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[SOSlib-devel] [ sbmlsolver-Support Requests-1597041 ] Altering the parameters of an ODE object 2

[SourceForge.net <no...@so...>]

Support Requests item #1597041, was opened at 2006-11-15 07:00
Message generated for change (Tracker Item Submitted) made by Item Submitter
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Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Altering the parameters of an ODE object 2 

Initial Comment:
Is there any way of altering the rate constants once an SBML file has been read in? This is quite important for using evolutionary algorithms, because a significant amount of time is wasted reading the new SBML file into the ODEsolver. 

Yours, 
Dr. C. Fernando 
Birmingham University 
UK. 


PLEASE reply to ct...@su...


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[SOSlib-devel] [ sbmlsolver-Support Requests-1597040 ] Altering the parameters of an ODE object.

[SourceForge.net <no...@so...>]

Support Requests item #1597040, was opened at 2006-11-15 07:00
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Altering the parameters of an ODE object. 

Initial Comment:
Is there any way of altering the rate constants once an SBML file has been read in? This is quite important for using evolutionary algorithms, because a significant amount of time is wasted reading the new SBML file into the ODEsolver. 

Yours, 
Dr. C. Fernando 
Birmingham University 
UK. 


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Re: [SOSlib-devel] [SOSlib-discuss] SBML ODE Solver SWIG Bindings

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

Hi Will,

No, unfortunately nobody is currently working on SWIG bindings. It is a 
bit work to do it for C and requires that the code is written in some 
special convention. I hope that we actually use this (or a close) C 
convention because the SOSlib code was initially strongly influenced by 
libSBML's first versions, which were in SWIG-readable C. That's 
unfortunately all I currently know (?) about SWIG bindings. If you could 
contribute anything towards SWIG or other bindings, you'd be my hero :-) 
and would of course be accurately credited at the website and docs.

The CellDesigner team is using a self-made SOSlib Java wrapper, but only 
for the high-level interface functions (SBML_odeSolver(...)). Maybe they 
can provide some hints.

cheers,
Rainer



On Thu, 2 Nov 2006, Will Norman wrote:

> My name is Will Norman and I am working on my Master's Thesis in
> Computer Science at Clemson University.  I am very interested in using
> the SBML ODE Solver library in a Java application.  I see in the
> development roadmap that altering the API to better accomidate SWIG
> bindings is a future enhancement for the library.  Has anyone had any
> luck getting SWIG to work, or does anyone have any tips for doing so.
> If anyone has any suggestions I would really appreciate it.  If I get
> things going I will certainly share my work with the community.
>
>
> Thank you,
>
> Will Norman
>
> -------------------------------------------------------------------------
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[SOSlib-devel] [SOSlib-discuss] SBML ODE Solver SWIG Bindings

[Will N. <jw...@cl...>]

My name is Will Norman and I am working on my Master's Thesis in 
Computer Science at Clemson University.  I am very interested in using 
the SBML ODE Solver library in a Java application.  I see in the 
development roadmap that altering the API to better accomidate SWIG 
bindings is a future enhancement for the library.  Has anyone had any 
luck getting SWIG to work, or does anyone have any tips for doing so.  
If anyone has any suggestions I would really appreciate it.  If I get 
things going I will certainly share my work with the community.


Thank you,

Will Norman

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Re: [SOSlib-devel] [SOSlib-discuss] how to compile SBML ODESolver library under Mac OS X

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

Hi Hendrik,

Sorry for the late reply. I just came back from the ICSB in Tokyo where I=
=20
was quite busy and had only limited access to internet.

Thank you very much for the instructions! I hope we can make installation=
=20
on Mac OS and other systems easier with the next release. Your=20
instructions will help.

I hope SOSlib works fine for you. There is not much (or no) activity=20
on the discuss list. Although we have ca. 500 downloads and no of many=20
projects using SOSlib, noone subscribed to the list and we get almost no=20
feedback. If you have any requests or suggestions, please write us!

Thanks,
Rainer




On Wed, 11 Oct 2006, Hendrik Fuss wrote:

> Hi everyone,
>
> one of the older threads in the archive was about problems running
> configure under Linux. After a long day, I managed to compile SOSlib
> under Mac OS 10.4 and thought I'd share this brief how-to with you.
>
> 1. As mentioned in requirements you need SUNDIALS 2.1.1 and *NOT* the
> latest version. I can confirm version 2.2.0 does NOT work.
>
> 2. Configure sundials with "./configure --prefix=3D/usr/local", make
> and make install as usual
>
> 3. Change to SBML_odeSolver directory. If you compiled libSBML with
> expat rather than xerces, the configure script needs modification.
> Run the following command:
>
> perl -p -i~ -e 's/-lxerces-c/-lexpat/g;' examples/Makefile.in
> examples/Makefile.am odeSolver/Makefile.am odeSolver/Makefile.in
> configure
>
> 4. Configure should now run smoothly
>
> 5. On my system, make threw an error in the very last linking step,
> saying that it couldn't find libexpat, even though /sw/lib was
> included in the LDFLAGS environment variable. I simply linked the
> file manually by just adding -L/sw/lib to the gcc command line.
>
> Done. make install worked fine for me. Hope this was helpful.
>
> Hendrik
>
> --
> Hendrik Fu=DF
> PhD student
> Systems Biology Research Group
>
> University of Ulster, School of Biomedical Sciences
> Cromore Road, Coleraine, BT52 1SA, Northern Ireland
>
>
>
>
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>

[SOSlib-devel] [SOSlib-discuss] how to compile SBML ODESolver library under Mac OS X

[Hendrik F. <fu...@ul...>]

Hi everyone,

one of the older threads in the archive was about problems running  =

configure under Linux. After a long day, I managed to compile SOSlib  =

under Mac OS 10.4 and thought I'd share this brief how-to with you.

1. As mentioned in requirements you need SUNDIALS 2.1.1 and *NOT* the  =

latest version. I can confirm version 2.2.0 does NOT work.

2. Configure sundials with "./configure --prefix=3D/usr/local", make  =

and make install as usual

3. Change to SBML_odeSolver directory. If you compiled libSBML with  =

expat rather than xerces, the configure script needs modification.  =

Run the following command:

perl -p -i~ -e 's/-lxerces-c/-lexpat/g;' examples/Makefile.in  =

examples/Makefile.am odeSolver/Makefile.am odeSolver/Makefile.in  =

configure

4. Configure should now run smoothly

5. On my system, make threw an error in the very last linking step,  =

saying that it couldn't find libexpat, even though /sw/lib was  =

included in the LDFLAGS environment variable. I simply linked the  =

file manually by just adding -L/sw/lib to the gcc command line.

Done. make install worked fine for me. Hope this was helpful.

Hendrik

--
Hendrik Fu=DF
PhD student
Systems Biology Research Group

University of Ulster, School of Biomedical Sciences
Cromore Road, Coleraine, BT52 1SA, Northern Ireland




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Re: [SOSlib-devel] [SOSlib-discuss] problem installing on linux

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

Hi Ivan,

the problem is, that the structure of the sundials library changed between
suite version 2.1.1 and suite version 2.2.0 in particular the
libsundials_shared.a library vanished from the sundials suite. this causes
some restructuring of the SBML Ode Solver which is planned to get done
around the end of october.

please use sundials suite version 2.1.1 (the previouse release) in the mean
time until we have upgraded SBML Ode Solver to the new sundials suite.

there is no need to install the old sundials package globally you can
specify the location of your local build of the sundilas library (e.g. in
directory /WHEREEVER/sundials) with the SBML Ode Solver configure option
--with-sundials=/WHEREEVER/sundials

=;) xtof

Ivan Merelli writes:
 > Dear all,
 > 
 > we have a nasty problem with the installation on linux (Fedora Core 5)
 > of the SBML Ode Solver. I have installed libsbml version 2.3.4 and
 > sundials 2.2.0 (but I tried even with the version 2.4). 
 > 
 > The problem is that there is no way to pass the ./configure step of the
 > installation because of this error:
 > 
 > checking correct functioning of SUNDIALS CVODE... no:
 >                    CFLAGS=-g -O2 -I/usr/local/include
 >                    LDFLAGS= -L/usr/local/lib
 >                    LIBS= -lsundials_kinsol -lsundials_cvodes
 > -lsundials_cvode -lsundials_nvecserial -lsundials_shared -lm
 > configure: error: Can not link to SUNDIALS CVODE Library
 > 
 > I tried to specify in different ways the path of the library, that are
 > correctly installed in /usr/lib. There is anyone who has been able to
 > install SBML ode Solver on linux?
 > 
 > Ivan
 > 
 > 
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Re: [SOSlib-devel] [SOSlib-discuss] problem installing on linux

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

Hi Ivan,

> we have a nasty problem with the installation on linux (Fedora Core 5)
> of the SBML Ode Solver. I have installed libsbml version 2.3.4 and
> sundials 2.2.0 (but I tried even with the version 2.4).

Unfortunately the new sundials version is not backwards compatible and we 
just realized that a few weeks ago but forgot to indicate it at our 
website. SOSlib is currently built for Sundials 2.1.1. The next 
official release of SOSlib will change to the upcoming next Sundials 
release.

We use Fedora ourselves, so installation should be no problem with the 
correct Sundials version!

Rainer




On Wed, 4 Oct 2006, Ivan Merelli wrote:

> Dear all,
>
> we have a nasty problem with the installation on linux (Fedora Core 5)
> of the SBML Ode Solver. I have installed libsbml version 2.3.4 and
> sundials 2.2.0 (but I tried even with the version 2.4).
>
> The problem is that there is no way to pass the ./configure step of the
> installation because of this error:
>
> checking correct functioning of SUNDIALS CVODE... no:
>                   CFLAGS=-g -O2 -I/usr/local/include
>                   LDFLAGS= -L/usr/local/lib
>                   LIBS= -lsundials_kinsol -lsundials_cvodes
> -lsundials_cvode -lsundials_nvecserial -lsundials_shared -lm
> configure: error: Can not link to SUNDIALS CVODE Library
>
> I tried to specify in different ways the path of the library, that are
> correctly installed in /usr/lib. There is anyone who has been able to
> install SBML ode Solver on linux?
>
> Ivan
>
>
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Re: [SOSlib-devel] Manipulating initial concentrations.

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

Just was not shure. No problem than.
Thanks/

Just was not sure, if it also applies to initial conditions or global
parameters only.

cheers
Eryk

On 10/5/06, Rainer Machne <ra...@tb...> wrote:
> On Thu, 5 Oct 2006, W Eryk Wolski wrote:
>
> > Hi,
> >
> > In addition to changing parameters as shown in the example   ParameterScanner.c
> > using the function IntegratorInstance_setVariableValue I would like to
> > be able to change the initialAmount.
>
> Yes you can use this function.
>
> > Suggestions please.
>
> What is the problem?
>
> Rainer
>
> >
> > Eryk
> >
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> >
>

Re: [SOSlib-devel] Manipulating initial concentrations.

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

On Thu, 5 Oct 2006, W Eryk Wolski wrote:

> Hi,
>
> In addition to changing parameters as shown in the example   ParameterScanner.c
> using the function IntegratorInstance_setVariableValue I would like to
> be able to change the initialAmount.

Yes you can use this function.

> Suggestions please.

What is the problem?

Rainer

>
> Eryk
>
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Re: [SOSlib-devel] Problem compiling cvs checkout from today.

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

I have just commited a new processAST.c with new names aCosh, aSinh and 
aTanh. Now it shouldn't give conflicts with tgmath.h anymore.

R

On Wed, 4 Oct 2006, W Eryk Wolski wrote:

> Hi,
>
> Checked out SBML_odeSolver and have run:
>
> ./autogen.sh
> ./configure --prefix=/home/witek/opt/sbmlodesolve
> --with-libsbml=/home/witek/opt/libsbml2.3.4
> --with-sundials=/home/witek/opt/sundials
> make
>
> but getting the following compilation errors:
>
>
> if gcc -DHAVE_CONFIG_H -I. -I. -I../src/sbmlsolver
> -I/home/witek/opt/sundials/include
> -I/home/witek/opt/libsbml2.3.4/include
> -I/home/witek/opt/libsbml2.3.4/include/sbml
> -I/home/witek/opt/libsbml2.3.4/include
> -I/home/witek/opt/libsbml2.3.4/include/sbml/sbml -I.     -MT
> processAST.o -MD -MP -MF ".deps/processAST.Tpo" -c -o processAST.o
> processAST.c; \
>        then mv -f ".deps/processAST.Tpo" ".deps/processAST.Po"; else
> rm -f ".deps/processAST.Tpo"; exit 1; fi
> processAST.c:69: error: static declaration of 'acosh' follows
> non-static declaration
> processAST.c:74: error: static declaration of 'asinh' follows
> non-static declaration
> processAST.c:79: error: static declaration of 'atanh' follows
> non-static declaration
> make[1]: *** [processAST.o] Error 1
> make[1]: Leaving directory
> `/home/witek/devel/cpp/odesolver/sos4/SBML_odeSolver/src'
> make: *** [all-recursive] Error 1
>
> I am posting because I assumed that in the repository only version
> which do compile should be checked in.
>
> cheers
>
> Eryk
>
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Re: [SOSlib-devel] Problem compiling cvs checkout from today.

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

Hi Eryk,

you had the same problem a while ago, in July, see emails there. It seems 
your system includes tgmath.h which is not ISO-C90 compatible. We can 
probably avoid this problem by either checking in configure scripts for 
existing definitions or just rename the hand-made functions in 
processAST.c

Rainer

On Wed, 4 Oct 2006, W Eryk Wolski wrote:

> Hi,
>
> Checked out SBML_odeSolver and have run:
>
> ./autogen.sh
> ./configure --prefix=/home/witek/opt/sbmlodesolve
> --with-libsbml=/home/witek/opt/libsbml2.3.4
> --with-sundials=/home/witek/opt/sundials
> make
>
> but getting the following compilation errors:
>
>
> if gcc -DHAVE_CONFIG_H -I. -I. -I../src/sbmlsolver
> -I/home/witek/opt/sundials/include
> -I/home/witek/opt/libsbml2.3.4/include
> -I/home/witek/opt/libsbml2.3.4/include/sbml
> -I/home/witek/opt/libsbml2.3.4/include
> -I/home/witek/opt/libsbml2.3.4/include/sbml/sbml -I.     -MT
> processAST.o -MD -MP -MF ".deps/processAST.Tpo" -c -o processAST.o
> processAST.c; \
>        then mv -f ".deps/processAST.Tpo" ".deps/processAST.Po"; else
> rm -f ".deps/processAST.Tpo"; exit 1; fi
> processAST.c:69: error: static declaration of 'acosh' follows
> non-static declaration
> processAST.c:74: error: static declaration of 'asinh' follows
> non-static declaration
> processAST.c:79: error: static declaration of 'atanh' follows
> non-static declaration
> make[1]: *** [processAST.o] Error 1
> make[1]: Leaving directory
> `/home/witek/devel/cpp/odesolver/sos4/SBML_odeSolver/src'
> make: *** [all-recursive] Error 1
>
> I am posting because I assumed that in the repository only version
> which do compile should be checked in.
>
> cheers
>
> Eryk
>
> -------------------------------------------------------------------------
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[SOSlib-devel] [SOSlib-discuss] problem installing on linux

[Ivan M. <iva...@it...>]

Dear all,

we have a nasty problem with the installation on linux (Fedora Core 5)
of the SBML Ode Solver. I have installed libsbml version 2.3.4 and
sundials 2.2.0 (but I tried even with the version 2.4). 

The problem is that there is no way to pass the ./configure step of the
installation because of this error:

checking correct functioning of SUNDIALS CVODE... no:
                   CFLAGS=-g -O2 -I/usr/local/include
                   LDFLAGS= -L/usr/local/lib
                   LIBS= -lsundials_kinsol -lsundials_cvodes
-lsundials_cvode -lsundials_nvecserial -lsundials_shared -lm
configure: error: Can not link to SUNDIALS CVODE Library

I tried to specify in different ways the path of the library, that are
correctly installed in /usr/lib. There is anyone who has been able to
install SBML ode Solver on linux?

Ivan


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[SOSlib-devel] Please move globalize and localizeParameter to the api interface.

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

Hi,

Would it be please possible ot move the functions

static int globalizeParameter(Model_t *, char *id, char *rid);
static int localizeParameter(Model_t *, char *id, char *rid);

to the API interface please? If possible, It would be very practical to me.

Thanks
Eryk

[SOSlib-devel] Manipulating initial concentrations.

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

Hi,

In addition to changing parameters as shown in the example   ParameterScanner.c
using the function IntegratorInstance_setVariableValue I would like to
be able to change the initialAmount.

Suggestions please.

Eryk

[SOSlib-devel] Problem compiling cvs checkout from today.

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

Hi,

Checked out SBML_odeSolver and have run:

./autogen.sh
./configure --prefix=/home/witek/opt/sbmlodesolve
--with-libsbml=/home/witek/opt/libsbml2.3.4
--with-sundials=/home/witek/opt/sundials
make

but getting the following compilation errors:


if gcc -DHAVE_CONFIG_H -I. -I. -I../src/sbmlsolver
-I/home/witek/opt/sundials/include
-I/home/witek/opt/libsbml2.3.4/include
-I/home/witek/opt/libsbml2.3.4/include/sbml
-I/home/witek/opt/libsbml2.3.4/include
-I/home/witek/opt/libsbml2.3.4/include/sbml/sbml -I.     -MT
processAST.o -MD -MP -MF ".deps/processAST.Tpo" -c -o processAST.o
processAST.c; \
        then mv -f ".deps/processAST.Tpo" ".deps/processAST.Po"; else
rm -f ".deps/processAST.Tpo"; exit 1; fi
processAST.c:69: error: static declaration of 'acosh' follows
non-static declaration
processAST.c:74: error: static declaration of 'asinh' follows
non-static declaration
processAST.c:79: error: static declaration of 'atanh' follows
non-static declaration
make[1]: *** [processAST.o] Error 1
make[1]: Leaving directory
`/home/witek/devel/cpp/odesolver/sos4/SBML_odeSolver/src'
make: *** [all-recursive] Error 1

I am posting because I assumed that in the repository only version
which do compile should be checked in.

cheers

Eryk

Re: [SOSlib-devel] piecewise ... (fwd)

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

Hi Andrew,

the bug described below by Nicolas seems related with the processEvents 
code in IntegratorInstance_updateData.

You had replaced the update of assignment rules with the code that is 
only executed if engine->processEvents is true (1).

Then assignmentsBeforeEvents and assignmentAfterEvents are executed 
there. However, it seems that these do not involve the reaction 
assignment rules!! That seems to underly the problem that Nicolas 
describes. If I evaluate all assignment rules in the updateData function 
the results seem to be OK, again.

Where would be the best way to fix this without removing this 
optimization of assignment rule ?

Rainer






Rainer Machne wrote:
> Hi All,
> 
> for the record, and for anyone interested in bug fixing :), i forward 
> this email to the list.
> 
> Again or still, we seem to have a piecewise bug. The reason for the 
> strange behaviour described by Nicolas below is unclear.
> 
> A piecewise expression used in an assignment rule contains the "time". 
> The respective expression seems to be set true at time 57... while it 
> should only become true at time 60.
> 
> The only suspicion I have is that the assignment rule is not updated 
> correctly and that the rule still has some value which it took in an 
> internal CVODE evaluation when it internally was already at time 60 for 
> evaluating f.
> Andrew, is it possible that your priority for assignment rule evaluation 
> doesn't account for rules that contain "time"?
> 
> I will look at it next week but maybe you have an idea.
> 
> Rainer
> 
> 
> ---------- Forwarded message ----------
> Date: Tue, 12 Sep 2006 18:03:20 +0100 (BST)
> From: Nicolas Le Novere <le...@eb...>
> To: ra...@tb...
> Subject: piecewise ...
> 
> Dear Rainer,
> 
> We are still working on the problematic model that led us to ask-you
> to modify SBMLodeSolver for piecewise functions (we are doing other
> things as well, don't worry :-)
> 
> I attach a model that should be fine. I tested it without rule, and
> with only the assignment rule for Sstar. In both case, the model
> worked perfectly. Now, with the piecewise function (only one piece for
> the moment), we encounter all kinds of problems:
> 
> For some reason, at t=57, Sstar jumps from 0.012 to 14.45, the value
> it will take after the piecewise jump for calcium at t>60. But the
> calcium is still unchanged!
> 
> Then, after t=60, even if Sstar increased 0.012 to 14.45, the
> reactions involving it remain unchanged, until t=62.44.
> 
> Is-it a problem of output only? Is-it a problem in the patching of
> SBMLodeSolver?
> 
> I join the SBML and the output of
> 
> odeSolver -w --time 100 --printstep 1000 
> dAlcantara_Bidirectional_Plasticity_CorrectedOnePiece.xml
> 
> (renamed .clean to go through the mail filters)
> 
> 

Re: [SOSlib-devel] New Sensitivity Analysis and Matrix Construction

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

Hi,

of course there were some inconsistencies (between approximation and use 
of analytic matrices) and bugs that needed to be fixed. In CVS now.

Rainer

Rainer Machne wrote:
> Dear All,
> 
> New files are in CVS with the following 2 updates:
> 
> Now sensitity can be calculated for both, parameters and initial 
> conditions and the calling application can select parameters and 
> variables via cvodeSettings.
> 
> Note, that matrix construction was moved from cvodeSolver.c and 
> sensSolver.c to cvodeData.c.
> 
> We have 2 new important (non-API!) functions:
> 
> 1) CvodeData_initializeSensitivities
> and
> 2) CvodeData_createMatrices
> 
> which need to be called in this order from CvodeData_initialize, and thus only 
> when (re)setting an integrator freshly (to time 0 of the forward problem) 
> before a new integration.
> 
> I think the code has become a little bit better segmented into 
> functionally coherent pieces. I hope the changed position of matrix 
> construction doesn't cause any unforseen problems.
> 
> The adjoint module will be updated accordingly by James and Stefan soon.
> 
> 
> Rainer
> 
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[SOSlib-devel] New Sensitivity Analysis and Matrix Construction

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

Dear All,

New files are in CVS with the following 2 updates:

Now sensitity can be calculated for both, parameters and initial 
conditions and the calling application can select parameters and 
variables via cvodeSettings.

Note, that matrix construction was moved from cvodeSolver.c and 
sensSolver.c to cvodeData.c.

We have 2 new important (non-API!) functions:

1) CvodeData_initializeSensitivities
and
2) CvodeData_createMatrices

which need to be called in this order from CvodeData_initialize, and thus only 
when (re)setting an integrator freshly (to time 0 of the forward problem) 
before a new integration.

I think the code has become a little bit better segmented into 
functionally coherent pieces. I hope the changed position of matrix 
construction doesn't cause any unforseen problems.

The adjoint module will be updated accordingly by James and Stefan soon.


Rainer