sbmlsolver-discuss — support and discussion for the SBML ODE Solver Library

[SOSlib-discuss] SBML Solver 1.6.0 under Cygwin (fwd)

[John L. <jl...@he...>]

We are attempting to build SBMLSolver 1.6.0 under Cygwin 1.5 and are 
encountering errors during configure's detection of SBML. We've built libsbml 
2.3.4 and Xerces 2.7.0 from source  We are using the following configure 
command:
./configure --with-libsbml=/cygdrive/g/public//cygwin/libsbml-2_3_4/ 
--with-sundials=/cygdrive/g/public/cygwin/sundials-2_1_1/

We are getting errors along the lines of:

cygdrive/g/public//cygwin/libsbml-2_3_4//include/sbml 
-L/cygdrive/g/public/cygwin/libxerces2_7_0/
lib -Wl,-rpath,/cygdrive/g/public//cygwin/libsbml-2_3_4//lib 
-L/cygdrive/g/public//cygwin/libsbml-
2_3_4//lib conftest.c  -lxerces-c -lsbml >&5
/cygdrive/g/public//cygwin/libsbml-2_3_4//lib/libsbml.a(SBMLReader.o): In 
function `_ZNSsC1IPcEET_
S1_RKSaIcE':
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/basic_string.tcc:(.text+0x11): 
undefined refere
nce to `xercesc_2_7::XMLString::transcode(unsigned short const*)'
/usr/lib/gcc/i686-pc-cygwin/3.4.4/include/c++/bits/basic_string.tcc:(.text+0x3e): 
undefined refere
nce to `xercesc_2_7::XMLString::release(char**)'
/cygdrive/g/public//cygwin/libsbml-2_3_4//lib/libsbml.a(SBMLReader.o): In 
function `_Z16XMLReader_
createPN11xercesc_2_714DefaultHandlerE':
//biocoreserver1/jlegato/cygwin/libsbml-2.3.4/src/sbml/SBMLReader.cpp:113: 
undefined reference to
`___gxx_personality_sj0'

(Compressed Full log attached)

Does anyone have any insights into what is going wrong?

Thanks

John
---
Contractor

Re: [SOSlib-discuss] tcc-based online compilation, increasing SOSlib performance

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

Hi,

now also the forward sensitivity function can be compiled. In CVS now.

Performance for forward sensitivity calculation is roughly 8-fold!

However, there is a problem with using multiple code instances in TCC - 
they can be used but cause a segmentation fault when the second instance 
is freed.

We need two code instances because sensitivity function can change 
between subsequent solver runs, but the ODE and Jacobi stay the same. So 
until I get a response by the TCC people, whether this will be solved 
soon or whether anyone has a patch, I will leave it like this to avoid 
unnecessary TCC allocations/compilations. If TCC can't be patched soon, 
we can either
a) have an additional sensitivity compilation option, so the leak can be 
avoided but still compilation for ODE/Jacobi functions used
or
b) also re-compile the ODE/Jacobi function for each new sensitivity run

So please watch out: there are memory leaks because currently, the 
sensitivity code is not freed after usage!

Rainer

Rainer Machne wrote:
> Hi Everyone,
> 
> Great news:
> 
> as recently several people started to use SOSlib on supercomputing 
> clusters, we were motivated to go into the code again and optimize.
> 
> Christoph and me went through Andrew Finney's old code for online 
> compilation of the right-hand side functions passed to CVODES (including 
> command-line calls etc.).
> 
> So I just managed to get the same code running under Linux using the 
> Tiny C Compiler as a library and the very cool TCC online compilation:
> 
>    tcc_compile_string(TCCState *s, char *sourceCode);
> 
> 
> So far it works only for the one bottle-neck function that evaluates 
> ODEs (and not e.g. for jacobi evaluation or sensitivity stuff).
> 
> But that already brings significant performance gains! E.g. for the 
> example model MAPK.xml, integrating to time 100000 in 1000 steps:
> 
> without compilation:  2.13 seconds
> with tcc compilation: 0.53 seconds
> 
> A strange effect is that at higher error tolerances and long integration 
> times the results start to differ. We need to check where the different 
> round-offs etc. are made. At lower tolerances the results are exactly 
> the same.
> 
> 
> The new code is in CVS now. Linking to TCC is optional, so everything 
> else should still work as before.
> 
> Caveat: TCC so far only works on 32-bit architecture, and thus all 
> libraries (sundials, xerces/expat, libsbml and soslib) must also be 
> compiled and run on 32-bit machines.
> 
> So we can only hope that TCC will soon be available for x86_64, 
> otherwise we could still implement command-line calls, like for the 
> Windows version (where back then tcc didn't work as a library).
> (TCC can be run on 64-bit but only with -m32 options and asfaik it's not 
> possible to have a mixed architecture code in on tool).
> 
> 
> TCC is available from http://fabrice.bellard.free.fr/tcc/
> 
> However, I used Robert Landley's fork because I couldn't compile the 
> original, and he seems to be the only one still working on it:
> 
> http://landley.net/code/tinycc
> 
> It should work with both ... in principle.
> 
> 
> So if that all works (with all rhs functions), I think there are not 
> much more possibilities to get faster, i.e. to make better use of 
> SUNDIALS from arbitrary ODE models.
> 
> We can only include the usual reaction network analysis, i.e. mass 
> conservation analysis, to get rid of unnecessary ODEs etc. However, I 
> guess, that won't bring very much gain, because the lost equation is 
> similar to a still existing one which still needs to be solved by 
> CVODES. Maybe "fast reaction analysis" would have some potential?
> 
> So, I think we are close to becoming as fast as possible.
> 
> Well, there'd probably still be possibilities with model-specific 
> "preconditioning" and such stuff about which I don't know much. Feel 
> free to propose your ideas :)
> 
> Rainer
> 
> 
> 
> -------------------------------------------------------------------------
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[SOSlib-discuss] tcc-based online compilation, increasing SOSlib performance

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

Hi Everyone,

Great news:

as recently several people started to use SOSlib on supercomputing 
clusters, we were motivated to go into the code again and optimize.

Christoph and me went through Andrew Finney's old code for online 
compilation of the right-hand side functions passed to CVODES (including 
command-line calls etc.).

So I just managed to get the same code running under Linux using the 
Tiny C Compiler as a library and the very cool TCC online compilation:

   tcc_compile_string(TCCState *s, char *sourceCode);


So far it works only for the one bottle-neck function that evaluates 
ODEs (and not e.g. for jacobi evaluation or sensitivity stuff).

But that already brings significant performance gains! E.g. for the 
example model MAPK.xml, integrating to time 100000 in 1000 steps:

without compilation:  2.13 seconds
with tcc compilation: 0.53 seconds

A strange effect is that at higher error tolerances and long integration 
times the results start to differ. We need to check where the different 
round-offs etc. are made. At lower tolerances the results are exactly 
the same.


The new code is in CVS now. Linking to TCC is optional, so everything 
else should still work as before.

Caveat: TCC so far only works on 32-bit architecture, and thus all 
libraries (sundials, xerces/expat, libsbml and soslib) must also be 
compiled and run on 32-bit machines.

So we can only hope that TCC will soon be available for x86_64, 
otherwise we could still implement command-line calls, like for the 
Windows version (where back then tcc didn't work as a library).
(TCC can be run on 64-bit but only with -m32 options and asfaik it's not 
possible to have a mixed architecture code in on tool).


TCC is available from http://fabrice.bellard.free.fr/tcc/

However, I used Robert Landley's fork because I couldn't compile the 
original, and he seems to be the only one still working on it:

http://landley.net/code/tinycc

It should work with both ... in principle.


So if that all works (with all rhs functions), I think there are not 
much more possibilities to get faster, i.e. to make better use of 
SUNDIALS from arbitrary ODE models.

We can only include the usual reaction network analysis, i.e. mass 
conservation analysis, to get rid of unnecessary ODEs etc. However, I 
guess, that won't bring very much gain, because the lost equation is 
similar to a still existing one which still needs to be solved by 
CVODES. Maybe "fast reaction analysis" would have some potential?

So, I think we are close to becoming as fast as possible.

Well, there'd probably still be possibilities with model-specific 
"preconditioning" and such stuff about which I don't know much. Feel 
free to propose your ideas :)

Rainer

Re: [SOSlib-discuss] SOSlib as shared library

[John L. <jl...@he...>]

Hi Rainer,

Yes it usually is that easy. I'll see if I can do that and send out a 
patch. I know we'll need it for the Java bindings.


John

On Thu, 10 May 2007, Rainer Machne wrote:

> Hi John,
>
>>  Does Soslib by default generate only static libs?
>
> I am forwarding this also to the list because it might be of general interest.
>
> Yes currently it only creates a static lib. Actually I don't know how we 
> could make a shared lib but a quick google search indicated that it just 
> requires additional flags during compilation like
>
> -shared -soname,libmean.so.1 -o libmean.so.1.0.1
>
> Is it really that easy? Does anyone know?
>
> Rainer
>

---
Contractor

Re: [SOSlib-discuss] SOSlib as shared library

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

Hi John,

 >  Does Soslib by default generate only static libs?

I am forwarding this also to the list because it might be of general 
interest.

  Yes currently it only creates a static lib. Actually I don't know how 
we could make a shared lib but a quick google search indicated that it 
just requires additional flags during compilation like

-shared -soname,libmean.so.1 -o libmean.so.1.0.1

Is it really that easy? Does anyone know?

Rainer

John Legato wrote:
>  Does Soslib by default generate only static libs? We'll need shared for 
> Java bindings. I looked in the  installed directory as well as the src 
> and all I found was the static version (libODES.a).  An ldd on odeSolver 
> seems to confirm that it was staticly linked:
> 
> [jlegato@biocore21 SBML_odeSolver-1.6.0]$ ldd odeSolver/odeSolver
>         libsbml.so => /usr/local/libsbml2/lib/libsbml.so (0xb7f68000)
>         libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0442f000)
>         libxerces-c.so.27 => not found
>         libm.so.6 => /lib/tls/libm.so.6 (0x005df000)
>         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00c6f000)
>         libc.so.6 => /lib/tls/libc.so.6 (0x004b2000)
>         /lib/ld-linux.so.2 (0x00499000)
>         libxerces-c.so.27 => not found
> 
> (The Xerces not found can be ignored when I ran that my LD_LIBRARY_PATH 
> was off)
> 
> Thanks
> 
> John

Re: [SOSlib-discuss] ode solver allows for negative concentrations?

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

> Such errors (in mass conservation) are very common in modeling, and thus 
> it is actually a frequently used quality check to see if a model 
> produces negative concentrations.

Maybe a small feature that might be useful in SOSlib:

We could include an option "CheckNegativeConcentrations" which will lead 
to either a warning or a break of integration. Might be useful during 
modeling.

R

Re: [SOSlib-discuss] ode solver allows for negative concentrations?

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

Hi Phillip,

I CCed this to the discuss list, because the question is asked more often.

> I've gotten the sbml ode solver up and running and noticed some curious 
> results. I'm printing out time courses for a simple uni uni reactions 
> with only two species, A and B. By 10 seconds, the output indicates a 
> negative concentrations for species A - which is of course non physical 
> behavior.
> 
> Is there some switch so that I can keep the solver from giving me 
> negative concentrations?

No, there is no such switch.

There are two ways you can get negative concentrations:

1)  The model is wrong:
A correct model of a chemical reaction network model should always obey 
the fundamental law of "mass conservation" and never produce negative 
concentrations!

An irreversible reaction:

A -> B; k * A
dA/dt = -k * A
dB/dt = k * A

If A get's zero, then the rate get's zero and thus A can never decrease 
below 0.

If you choose a kinetic law like e.g. "k", then of course A can get 
negative. However, this doesn't make any sense in chemical kinetics, and 
you would need some justification for such a kinetic law. Such a 
justification could e.g. be the A is assumed to be buffered and always 
constant. In this case A will also never decrease below 0, of course.

Such errors (in mass conservation) are very common in modeling, and thus 
it is actually a frequently used quality check to see if a model 
produces negative concentrations.

2) Numerical instabilities, too high error tolerances
If you are sure that the model is correct, then that's what probably 
happens. You can set very low error tolerances, e.g.

--error 1e-30 --rerror 1e-14

but you should play around with these to find good settings. If the 
solver is getting problems with too low tolerance, then set a higher

--mxstep 1e9

to give the solver more time to solve the problematic region.

Hope that helped,
Rainer

[SOSlib-discuss] implement variable compartments

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

Hi Everyone,

A related problem to the one from the previous email (species in 
substance units):

Currently SOSlib can not handle variable compartments (just as e.g. 
copasi and MathSBML).

For this case ALL ODEs need to be formulated in substance rather than 
substance/volume units, and species in concentration units will need 
additional assignment rules to map their values from the ODE variables, 
and this will probably involve significant changes to the code.


To have ODEs in substance units we only need to leave out the division 
by the compartment, as the kinetic laws in SBML are already in 
substance/time units.

Instead of (current) ODEs:

1) for X in substance units:
dX/dt = stoichiometry * kineticLaw(X)

2) for X in substance/volume:
dX/dt = stoichiometry * kineticLaw(X) / volume

we will have:

1) for X in substance units, as above:
dX/dt = stoichiometry * kineticLaw(X)

2) for X in substance/volume:
dX_amount /dt = stoichiometry * kineticLaw(X)
X = X_amount / volume

where X_amount is an internal variable we need to define and X is 
defined by a new internal assignment rule.

Does anyone see any problems with above approach?

Rainer

[SOSlib-discuss] accounting for species in substance units

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

Hi Everyone,

SOSlib code starts to live again a bit.

We have just recently found out that we didn't account for species that 
are defined with HasOnlySubstanceUnits == true, or which live in a 
compartment with SpatialDimension == 0.

In both cases, the units of the species in all equations of the model 
are in substance instead of concentration (substance/volume) units.

ODEs for such species change from:
dX/dt = stoichiometry * kineticLaw(X) / volume
to:
dX/dt = stoichiometry * kineticLaw(X)

While I have never seen such a model, it is possible in SBML. It should 
work now with SOSlib but I couldn't test it, because I don't know any 
model which has such species. If anyone knows about such models (doesn't 
have to be in SBML), please send me a link or reference, so I can test it.

We still solve 100 out of 113 semantic test suite models correctly, so 
nothing should have changed for usual models. The new code is at 
sourceforge CVS now.

Rainer

Re: [SOSlib-discuss] drawJacoby and drawSense

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

Hi Will,

> Error: Layout was not done.  Missing layout plugins?

This error message doesn't come from SOSlib, so I guess it comes from 
graphviz. I have never seen it.

Which version of graphviz are you using? Maybe we have a version conflict. 
But then probably also the compilation itself should have failed. Very 
strange. Mhm, does the problem only appear when using these functions from 
Java, or already from the C versions?

Great, that you are interested in the graphviz plugin :) That's my 
personal favorite tool to quickly view the network structure and the 
relevant feedback cycles in the ODE model (although the name drawJacoby is 
wrong and should be drawJacobian) :)

Anyways, you write that you have succeeded with using SOSlib from Java. 
Great news! We had a request for Java bindings just yesterday.
Would you be willing to share the Java bindings?

Rainer

On Fri, 27 Apr 2007, Will Norman wrote:

> I have everything working from Java now except these functions.
>
> I have graphviz, and link it when compiling, but when I run an example I get 
> this error message:
>
> Error: Layout was not done.  Missing layout plugins?
>
> Any idea what may be causing this, or any possible solutions?
>
> Thanks,
>
> Will
>

Re: [SOSlib-discuss] [SOSlib-devel] SOSlib Java bindings? (fwd)

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

---------- Forwarded message ----------
Date: Fri, 27 Apr 2007 12:21:59 +0200
From: Christoph Flamm <xt...@tb...>
To: John Legato <jl...@he...>
Cc: sbm...@li...
Subject: Re: [SOSlib-devel] [SOSlib-discuss] SOSlib Java bindings?

hi john,

the Perl bindings of SOSlib are not functional at the moment. the idea for
the bindings is to generate them in a semi automatic fashion using Swig
(http://www.swig.org/), which allows to generate bindings for many
different languages like Java, Python, Perl, ... with one interface
file. (libsbml is a very good example which follows this strategy)

the problem with Swig is that it does not support all the features equally
well for the various languages. While Java and Python are equally well
supported by Swig, this is not the case for Perl.

another basic question is if only the high level API of SOSlib should be
accessible via the bindings, or if every function which is in the
SOSlib should have be bindings.

our time frame to fix the Perl bindings is around June to July, and we will
definitely use Swig for that.

so if you want to develop Java bindings I would suggest to use Swig for
that purpose. it would be also very kind if you could contribute the Java
bindings to SOSlib or parts of them once you have developed them.

if you need any help concerning binding generation using Swig, please don't
hesitate to contact me.

=;) xtof

-- 
Christoph Flamm
Institut fuer Theoretische Chemie | email: xt...@tb...
Universitaet Wien                 | phone: ++43-1-4277-527-39
Waehringerstrasse 17/3/308        | fax:   ++43-1-4277-527-93
A-1090 Wien, Austria              | www: http://www.tbi.univie.ac.at/~xtof

John Legato writes:
  > Hi,
  >
  > We would like to leverage the capabilities of SOSlib from a Java
  > application we are developing called  QBT (Quantitative Biology Tool).
  > Do Java bindings for SOSlib exist? How were the Perl bindings generated?
  > Would it be reasonable for us to take a similar approach using Java?
  >
  > Thanks
  >
  > John

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[SOSlib-discuss] drawJacoby and drawSense

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

I have everything working from Java now except these functions.

I have graphviz, and link it when compiling, but when I run an example I 
get this error message:

Error: Layout was not done.  Missing layout plugins?

Any idea what may be causing this, or any possible solutions?

Thanks,

Will

[SOSlib-discuss] SOSlib Java bindings?

[John L. <jl...@he...>]

Hi,

We would like to leverage the capabilities of SOSlib from a Java 
application we are developing called  QBT (Quantitative Biology Tool). 
Do Java bindings for SOSlib exist? How were the Perl bindings generated? 
Would it be reasonable for us to take a similar approach using Java?

Thanks

John


---
Contractor

Re: [SOSlib-discuss] [Fwd: Re: Configure problem]

[Colin G. <c.g...@nc...>]

Hi Rainer,

Rainer Machne wrote:
> Hi Colin,
>
> The version required for SOSlib is Sundials v.2.1.1 released in May 2005.
>
> Is this the problem?
>   
Yes, that's the problem.

Thanks

Colin
> Rainer
>
>
> Colin Gillespie wrote:
>   
>> Dear All,
>>
>> I'm trying to install ODE-solver, but I'm having configuration problems 
>> - it can't find sundials.
>>
>> I've tried the last few versions of sundials and ODEsolver 1.6 & 1.7 and 
>> get the same error.
>>
>>  >$ ./configure --with-libsbml=/data/ncsg3/libsbml/ 
>> --with-sundials=/data/ncsg3/sundials/
>> <snip>
>> checking for correct functioning of SBML... yes
>> checking correct functioning of SUNDIALS... no:
>>                    CFLAGS=-g -O2 -Wno-unknown-pragmas -Wall -ansi 
>> -std=iso9899:1990 -I/data/ncsg3/sundials//include
>>                    LDFLAGS= -L/data/ncsg3/sundials//lib
>>                    LIBS=-lsundials_kinsol -lsundials_cvodes 
>> -lsundials_nvecserial -lsundials_shared -lm -lstdc++
>> configure: error: Can not link to SUNDIALS Library
>>  > $ ls /data/ncsg3/sundials
>> bin  include  lib
>>  > $ ls /data/ncsg3/sundials/lib/
>> libsundials_cvode.a    libsundials_fida.a            
>> libsundials_fnvecserial.a   libsundials_nvecparallel.a
>> libsundials_cvode.la   libsundials_fida.la           
>> libsundials_fnvecserial.la  libsundials_nvecparallel.la
>> libsundials_cvodes.a   libsundials_fkinsol.a         
>> libsundials_ida.a           libsundials_nvecserial.a
>> libsundials_cvodes.la  libsundials_fkinsol.la        
>> libsundials_ida.la          libsundials_nvecserial.la
>> libsundials_fcvode.a   libsundials_fnvecparallel.a   libsundials_kinsol.a
>> libsundials_fcvode.la  libsundials_fnvecparallel.la  libsundials_kinsol.la
>>
>> Any ideas?
>>
>> I have installed ODE solver in the past with no problem.
>>
>> Cheers
>>
>> Colin
>>
>>
>>     
>
>
>
> -------------------------------------------------------------------------
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> Download DB2 Express C - the FREE version of DB2 express and take
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>   

-- 
Dr Colin Gillespie
http://www.mas.ncl.ac.uk/~ncsg3/

[SOSlib-discuss] [Fwd: Re: Configure problem]

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

Hi Colin,

Maybe you have updated your Sundials version?

Sundials has changed its interfaces, and SOSlib is still using the old
version. We will wait for their next release to update (was recommended
by the Sundials folks).

The version required for SOSlib is Sundials v.2.1.1 released in May 2005.

Is this the problem?

Rainer


Colin Gillespie wrote:
> Dear All,
> 
> I'm trying to install ODE-solver, but I'm having configuration problems 
> - it can't find sundials.
> 
> I've tried the last few versions of sundials and ODEsolver 1.6 & 1.7 and 
> get the same error.
> 
>  >$ ./configure --with-libsbml=/data/ncsg3/libsbml/ 
> --with-sundials=/data/ncsg3/sundials/
> <snip>
> checking for correct functioning of SBML... yes
> checking correct functioning of SUNDIALS... no:
>                    CFLAGS=-g -O2 -Wno-unknown-pragmas -Wall -ansi 
> -std=iso9899:1990 -I/data/ncsg3/sundials//include
>                    LDFLAGS= -L/data/ncsg3/sundials//lib
>                    LIBS=-lsundials_kinsol -lsundials_cvodes 
> -lsundials_nvecserial -lsundials_shared -lm -lstdc++
> configure: error: Can not link to SUNDIALS Library
>  > $ ls /data/ncsg3/sundials
> bin  include  lib
>  > $ ls /data/ncsg3/sundials/lib/
> libsundials_cvode.a    libsundials_fida.a            
> libsundials_fnvecserial.a   libsundials_nvecparallel.a
> libsundials_cvode.la   libsundials_fida.la           
> libsundials_fnvecserial.la  libsundials_nvecparallel.la
> libsundials_cvodes.a   libsundials_fkinsol.a         
> libsundials_ida.a           libsundials_nvecserial.a
> libsundials_cvodes.la  libsundials_fkinsol.la        
> libsundials_ida.la          libsundials_nvecserial.la
> libsundials_fcvode.a   libsundials_fnvecparallel.a   libsundials_kinsol.a
> libsundials_fcvode.la  libsundials_fnvecparallel.la  libsundials_kinsol.la
> 
> Any ideas?
> 
> I have installed ODE solver in the past with no problem.
> 
> Cheers
> 
> Colin
> 
> 

[SOSlib-discuss] Configure problem

[Colin G. <c.g...@nc...>]

Dear All,

I'm trying to install ODE-solver, but I'm having configuration problems 
- it can't find sundials.

I've tried the last few versions of sundials and ODEsolver 1.6 & 1.7 and 
get the same error.

 >$ ./configure --with-libsbml=/data/ncsg3/libsbml/ 
--with-sundials=/data/ncsg3/sundials/
<snip>
checking for correct functioning of SBML... yes
checking correct functioning of SUNDIALS... no:
                   CFLAGS=-g -O2 -Wno-unknown-pragmas -Wall -ansi 
-std=iso9899:1990 -I/data/ncsg3/sundials//include
                   LDFLAGS= -L/data/ncsg3/sundials//lib
                   LIBS=-lsundials_kinsol -lsundials_cvodes 
-lsundials_nvecserial -lsundials_shared -lm -lstdc++
configure: error: Can not link to SUNDIALS Library
 > $ ls /data/ncsg3/sundials
bin  include  lib
 > $ ls /data/ncsg3/sundials/lib/
libsundials_cvode.a    libsundials_fida.a            
libsundials_fnvecserial.a   libsundials_nvecparallel.a
libsundials_cvode.la   libsundials_fida.la           
libsundials_fnvecserial.la  libsundials_nvecparallel.la
libsundials_cvodes.a   libsundials_fkinsol.a         
libsundials_ida.a           libsundials_nvecserial.a
libsundials_cvodes.la  libsundials_fkinsol.la        
libsundials_ida.la          libsundials_nvecserial.la
libsundials_fcvode.a   libsundials_fnvecparallel.a   libsundials_kinsol.a
libsundials_fcvode.la  libsundials_fnvecparallel.la  libsundials_kinsol.la

Any ideas?

I have installed ODE solver in the past with no problem.

Cheers

Colin


-- 
Dr Colin Gillespie
http://www.mas.ncl.ac.uk/~ncsg3/

Re: [SOSlib-discuss] [Fwd: Re: Difficulty compiling]

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

Hi Phillip,

sorry, actually the sbml.m4 file wasn't the right thing to exchange,
it's not used, if you already have a configure file.

I have just tested the new configure file, and it doesn't work.

In the current development version, we do not have these tests anymore!
So you could try the development version.

a) either check out this version via anonymous CVS from sourceforge, as
described here: http://sourceforge.net/cvs/?group_id=139893
b) download todays snapshot of the 1.7.0-beta version from
http://www.tbi.univie.ac.at/~raim/odeSolver/download/SBML_odeSolver-1.7.0.tar.gz

Please let us know, if this works for you. If not, we can still
hand-edit the configure file of the 1.6.0 version for you (remove the
tests that don't work).

BTW, what is Falcon? Have never heard of this.

Rainer

Phillip Tabor wrote:
> The sbml.m4 file was a no-go. To further complicate matters, it will be 
> impossible to update expr or bash on these systems. Is there something 
> else we can do?
> 
> On 4/17/07, *Rainer Machne* <ra...@tb... 
> <mailto:ra...@tb...>> wrote:
> 
> 
>     Hi Phillip,
> 
>     I remembered that we also had this configure bug once. Christoph
>     suggested:
> 
>     "yes, this is a configure bug which is fixed in the cvs version of
>     SOSlib. a quick fix would be to just replace the config/sbml.m4 file
>     with the one from the cvs repository.
> 
>     =;) xtof"
> 
>     I have attached the new sbml.m4 file (but haven't tested it with the old
>     release). Maybe you can backup your file and try this one. Just run
>     ./configure again with the attached file in folder config/
> 
>     Please, let us know, if that (or updating expr and test) helped.
> 
>     Thanks,
>     Rainer
> 
> 
>     Phillip Tabor wrote:
>      > Hello,
>      >
>      > while attempting to compile the sbml ode solver library on our
>     machines,
>      > the following error crops up:
>      >
>      > Jim, Phil,
>      >
>      > This is the error message I'm getting when building SBML ODE on
>     Falcon.
>      > I rebuilt everything with the GNU compilers just to be sure we
>     were on
>      > the same footing with everything:
>      >
>      > checking for SBML Library Version... expr: syntax error
>      > expr: syntax error
>      > expr: syntax error
>      > ./configure: line 4175: test: -eq: unary operator expected
>      > configure: found SBML Library Version
>      > checking correct functioning of SBML... no:
>      >                   CFLAGS=-g -O2
>     -I/app/moes/platform/opteron.hp/include
>      > -I/app/moes/platform/opteron.hp/include/sbml
>      >                   LDFLAGS=
>     -Wl,-rpath,/app/moes/platform/opteron.hp/lib
>      > -L/app/moes/platform/opteron.hp/lib
>      >                   LIBS= -lxerces-c -lsbml
>      > configure: error: Can not link to SBML Library:
>      >                  Please, make sure to use libSBML version >= 2.3.2
>      >
>      > I've already sent the config.log. I'm pretty certain it's a configure
>      > file issue, but I haven't been able to track it down just yet.
>      >
>      >
>      > Has anyone encountered anything similar? Is this perhaps user
>     error (our
>      > tech guy is working on it for me)?
>      >
>      >
>      >
>     ------------------------------------------------------------------------
> 
>      >
>      >
>     -------------------------------------------------------------------------
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>      > Download DB2 Express C - the FREE version of DB2 express and take
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> 
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> 
> 

[SOSlib-discuss] [Fwd: Re: Difficulty compiling]

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

Hi Phillip,

I remembered that we also had this configure bug once. Christoph suggested:

"yes, this is a configure bug which is fixed in the cvs version of
SOSlib. a quick fix would be to just replace the config/sbml.m4 file
with the one from the cvs repository.

=;) xtof"

I have attached the new sbml.m4 file (but haven't tested it with the old
release). Maybe you can backup your file and try this one. Just run
./configure again with the attached file in folder config/

Please, let us know, if that (or updating expr and test) helped.

Thanks,
Rainer


Phillip Tabor wrote:
> Hello,
> 
> while attempting to compile the sbml ode solver library on our machines, 
> the following error crops up:
> 
> Jim, Phil,
> 
> This is the error message I'm getting when building SBML ODE on Falcon. 
> I rebuilt everything with the GNU compilers just to be sure we were on 
> the same footing with everything:
> 
> checking for SBML Library Version... expr: syntax error
> expr: syntax error
> expr: syntax error
> ./configure: line 4175: test: -eq: unary operator expected
> configure: found SBML Library Version
> checking correct functioning of SBML... no:
>                   CFLAGS=-g -O2 -I/app/moes/platform/opteron.hp/include 
> -I/app/moes/platform/opteron.hp/include/sbml
>                   LDFLAGS= -Wl,-rpath,/app/moes/platform/opteron.hp/lib 
> -L/app/moes/platform/opteron.hp/lib
>                   LIBS= -lxerces-c -lsbml
> configure: error: Can not link to SBML Library:
>                  Please, make sure to use libSBML version >= 2.3.2
> 
> I've already sent the config.log. I'm pretty certain it's a configure 
> file issue, but I haven't been able to track it down just yet.
> 
> 
> Has anyone encountered anything similar? Is this perhaps user error (our 
> tech guy is working on it for me)?
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> sbmlsolver-discuss mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss

Re: [SOSlib-discuss] Difficulty compiling

[Akira F. <fu...@bi...>]

Hi,

At Mon, 16 Apr 2007 09:15:52 -0400,
"Phillip Tabor" <pt...@gm...> wrote:
> This is the error message I'm getting when building SBML ODE on Falcon. I
> rebuilt everything with the GNU compilers just to be sure we were on the same
> footing with everything:
> 
> checking for SBML Library Version... expr: syntax error
> expr: syntax error
> expr: syntax error

This error occurs when the "expr" command is bit old than expected.
Please try to install new version of "expr".

> ./configure: line 4175: test: -eq: unary operator expected

This also happens depending on your "test" command. Usually, the
"test" command is a built-in command of your shell (sh, bash, zsh,
etc.)  This error will be solved by installing newer version of sh,
bash, etc.

Hope this helps,
-- 
Akira Funahashi, Ph.D.| Assistant Professor, Dept. of Biosciences
[fu...@bi...] | and Informatics, Keio Univ.

[SOSlib-discuss] Difficulty compiling

[Phillip T. <pt...@gm...>]

Hello,

while attempting to compile the sbml ode solver library on our machines, the
following error crops up:

Jim, Phil,

This is the error message I'm getting when building SBML ODE on Falcon. I
rebuilt everything with the GNU compilers just to be sure we were on the
same footing with everything:

checking for SBML Library Version... expr: syntax error
expr: syntax error
expr: syntax error
./configure: line 4175: test: -eq: unary operator expected
configure: found SBML Library Version
checking correct functioning of SBML... no:
                  CFLAGS=-g -O2 -I/app/moes/platform/opteron.hp/include
-I/app/moes/platform/opteron.hp/include/sbml
                  LDFLAGS= -Wl,-rpath,/app/moes/platform/opteron.hp/lib
-L/app/moes/platform/opteron.hp/lib
                  LIBS= -lxerces-c -lsbml
configure: error: Can not link to SBML Library:
                 Please, make sure to use libSBML version >= 2.3.2

I've already sent the config.log. I'm pretty certain it's a configure file
issue, but I haven't been able to track it down just yet.


Has anyone encountered anything similar? Is this perhaps user error (our
tech guy is working on it for me)?

Re: [SOSlib-discuss] Regarding inputting of kinetic rate constants

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

Hi Roy and Phillip,

You might even get better performance, if you use the integration 
routines at a finer level via the odeModel and integratorInstance 
interface functions.

At this level, you can create both the internal odeModel (derived from 
the SBML input) and the SUNDIALS integrator instance only once, and run 
as many integrations as you like.
The function IntegratorInstance_setVariableValue allows you to set any 
parameters or variables in between (also during) the integration runs.

This level would save you a lot of memory allocation and general 
performance.

You can use Andrew Finney's ParameterScanner.c program in the example 
folder of the SOSlib distribution as a template for your own program, or 
just use it as a commandline tool if you are happy with its output.

It's usage is described at
  http://www.tbi.univie.ac.at/~raim/odeSolver/doc/app.html#param

If you are interested, I can help you changing the output of 
ParameterScanner.c to your requirements. Currently it only gives the 
results of the chosen variable at some specified end-time of 
integration, and that in gnuplot format. Would you need the whole 
time-courses?

Also, if you want to analyze local parameters of kinetic laws, you will 
need to "globalize" these parameters before calling any SOSlib 
functions, because SOSlib only treats global parameters as constants of 
the ODE model, while locals are replaced during ODE construction.
However, we also have such a globalizeParemter function, internally in 
release 1.6.0, but that can easily be "externalized" so you can use it 
in your application (or just copy/paste it :) ).

For the next release we plan much better support for such parameter 
scans also for the main commandline tool, as we realize that this is the 
most widely used application for SOSlib.

Rainer



Roy Wollman wrote:
> Hi Phillip,
> 
> Did you consider using it as a library instead of using the command line 
> utility?
> An example of a library usage that changes a parameter can be found:
> 
> http://www.csc.fi/english/research/sciences/bioscience/programs/sysbio/parameterChange.c
> 
> It will be almost the exact thing to change initial conditions, without 
> parsing the xml file.
> 
> Roy
> 
> 
> Phillip Tabor wrote:
>> Hello,
>>
>> I am attempting to use the odeSolver commandline tool and I'd like to 
>> know if there is a way to input the initial rate constants as an 
>> array. In other words, does the program have to parse the .xml file at 
>> every iteration, or is there a way to override this and simply pass it 
>> an array of numbers to be assigned as rates to the odes?
>>
>> I am attempting to use the software to fit kinetic rate constants with 
>> an evolutionary algorithm. This requires many executions of the 
>> program, and having to parse the .xml file on each run will add a 
>> considerable amount of overhead to the execution time.
>>
>>
>> ------------------------------------------------------------------------
>>
>> -------------------------------------------------------------------------
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to share your
>> opinions on IT & business topics through brief surveys-and earn cash
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>> ------------------------------------------------------------------------
>>
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>> sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss
>>   
> 
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
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> _______________________________________________
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[SOSlib-discuss] Hot pictures of paris hilton nude

[Nude jennajameson.c. <sbm...@li...>]

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Re: [SOSlib-discuss] Regarding inputting of kinetic rate constants

[Roy W. <rwo...@uc...>]

Hi Phillip,

Did you consider using it as a library instead of using the command line 
utility?
An example of a library usage that changes a parameter can be found:

http://www.csc.fi/english/research/sciences/bioscience/programs/sysbio/parameterChange.c

It will be almost the exact thing to change initial conditions, without 
parsing the xml file.

Roy


Phillip Tabor wrote:
> Hello,
>
> I am attempting to use the odeSolver commandline tool and I'd like to 
> know if there is a way to input the initial rate constants as an 
> array. In other words, does the program have to parse the .xml file at 
> every iteration, or is there a way to override this and simply pass it 
> an array of numbers to be assigned as rates to the odes?
>
> I am attempting to use the software to fit kinetic rate constants with 
> an evolutionary algorithm. This requires many executions of the 
> program, and having to parse the .xml file on each run will add a 
> considerable amount of overhead to the execution time.
>
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> ------------------------------------------------------------------------
>
> _______________________________________________
> sbmlsolver-discuss mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss
>   

[SOSlib-discuss] Regarding inputting of kinetic rate constants

[Phillip T. <pt...@gm...>]

Hello,

I am attempting to use the odeSolver commandline tool and I'd like to know
if there is a way to input the initial rate constants as an array. In other
words, does the program have to parse the .xml file at every iteration, or
is there a way to override this and simply pass it an array of numbers to be
assigned as rates to the odes?

I am attempting to use the software to fit kinetic rate constants with an
evolutionary algorithm. This requires many executions of the program, and
having to parse the .xml file on each run will add a considerable amount of
overhead to the execution time.

[SOSlib-discuss] Hot pictures of Britiney Speers

[<Fr...@Br...>]

<style>

(He's away on business, and his wife is out all day at work, and I'm
guessing neither of them has much of a clue of the right way to go
about it, any more than I do really)


>

<!

I have checked the Default Time Zone setting for the 
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settings. Every where it is configured to use GMT-06.00 - 
Central Time (US & Canada). However if anyone create or 
modify a document in SharePoint (any site) the time 
showing on SharePoint is different than the system time of 
the same server. Suppose if the current time on the server 
clock is 2.34 AM, then the modified document time on the 
SharePoint would be 1.34 AM. 



>

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appropriate forum for asking support questions. 

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In our past parking deal, OUT NORTH agreed not to have events on
Sunday so that churchgoers could use our lot during daytime and
evening services. Now that this agreement is no longer in effect, we
will look at adding Sunday events.
Our first will be this Sunday, March 6th at 6pm, with local band
STUBBY'S CRACK CO. headlining a concert of work by young musicians as
part of our Alaska Artist Access program. Details will be available
online later this week; low-price tickets will be sold at the door
only, and earplugs will be available for purchase>

Actually, looks like I screwed up the placement anyways, and the slave 
goes on the end.

Jim, you probably don't have to worry about it either way.
I know I shouldn't bitch, and that this is proof that resources are 
needed, like volunteers, and that I should volunteer, but I just 
can't do it right now. It was just too hard on my heart seeing 
first hand what goes on. I salute all of the volunteers in rescue 
groups that do this stuff on a regular basis and make a difference.
Groeten en knuffels van ICY aan iedereen van nltest!

En ja het gaat goed maar haar....
Nog steeds wel RSI, maar wel langzaam minderend....

-- 
Dolfy
- Webstek : - Nieuwsgroep : 
-  (Ook bereikbaar via groupsgoogle
- Rain... Is that what you call this? I like it.' (Aeryn Sun - Farscape)

Can anyone recommend a maroon shade, particularly an OPI one?  I usually
wear silver (OPI Pearl of Wisdom or Sally Hansen's Chrome Nail Make-up in
psychiatrist had told me that he thought I was fit enough to return to
work, and that I was willing to return when the current sick note
expired on 17th February. I received an emailed reply from my manager to
say that he preferred me to remain at home until he wrote to the
psychiatrist. To be precise, his email said: "I would much prefer it,

Bonjour,

Je vais effectuer ce soir ma premiere photo du ciel profond avec mon
Arcane 180 F/D 6.
Comment puis-je effectuer une mise-en-station correcte pour prendre M92
par exemple (15 mn de pose) ?
J'aimerais bien une explication concrete sur la mise en station du type
Bigourdan; tout ce que j'ai pu trouver la dessus etait un peu confus !

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