ecell-devel Mailing List for E-Cell System

Didn't include the result of the first test, here:

Test 1 (closest to your problematic configuration, I don't have gcc-3.4.1):
python 2.3.4 -> gcc-3.4.0
boost 1.31 -> gcc-3.3.3
ecell cvs -> gcc-3.3.3
result: ok

Hello Eric,

Here are some of my tests, in all configurations both libstdc++ 3.3.3 
and 3.4.0 are available.

Test 1 (closest to your problematic configuration, I don't have gcc-3.4.1):
python 2.3.4 -> gcc-3.4.0
boost 1.31 -> gcc-3.3.3
ecell cvs -> gcc-3.3.3
result:

Test 2:
python 2.3.4 -> gcc-3.3.3
boost 1.31 -> gcc-3.4.0
ecell cvs -> gcc-3.4.0
result: ok

Test 3:
python 2.3.4 -> gcc-3.4.0
boost 1.31 -> gcc-3.4.0
ecell cvs -> gcc-3.4.0
result: ok

I think your problem could be related to unavailability of both versions 
3.3 and 3.4 of libstdc++, or the changes in gcc-3.4.1 compared to 
gcc-3.4.0. Sorry can't help you much.

satya

Hi Eric,


- Did you do 'make clean' when changing the compiler?
  It is safe to do so.

- If you did, please try this:

  ECELL_DEBUG=1 ecell3-session -f LTD.eml

  at the gdb prompt, type 'bt', and you get the traceback.
  Show us the trace so that we can try to figure out what the problem
  is.

-sha




> I compiled ecell3 cvs (and also 3.1.102) under Mandrake cooker
> (development version) with gcc 3.3 (I posted I had a problem with the
> latest gcc-3.4, but this seems related to a known bug).
> 
> Compilation is working, but application crashes when trying to load an
> .eml file with:
> $ gecell -f sample/LTD/LTD.eml
> PyECS: SIGSEGV. Invalid memory reference.
> 
> The Python version on Mandrake cooker is actually 2.3.4. If I downgrade to
> the Python 2.3.3 packages (that are in Mandrake 10 stable release), it
> works.
> 
> Has anyone else observed problems with Python 2.3.4 ?
> 
> Eric
> 
> 
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-- 
Kouichi Takahashi, PhD,
E-Cell Project,
Institute for Advanced Biosciences,
Keio University, Japan.
http://www.sfc.keio.ac.jp/~shafi

I compiled ecell3 cvs (and also 3.1.102) under Mandrake cooker
(development version) with gcc 3.3 (I posted I had a problem with the
latest gcc-3.4, but this seems related to a known bug).

Compilation is working, but application crashes when trying to load an
.eml file with:
$ gecell -f sample/LTD/LTD.eml
PyECS: SIGSEGV. Invalid memory reference.

The Python version on Mandrake cooker is actually 2.3.4. If I downgrade to
the Python 2.3.3 packages (that are in Mandrake 10 stable release), it
works.

Has anyone else observed problems with Python 2.3.4 ?

Eric

> Anyway, I still have compilation problems with ecell3 cvs :
> Entity.hpp:72: error: invalid use of ' libecs::Entity::setName' to form a
> pointer-to-member-function.  Use a qualified-id.

Ok, looks like you are hitting a bug in gcc34-CVS.
See this page: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=15875
Seems like the fix is submitted as of 6/10, and gcc-3.4.1 release
will include that.   
I don't know if your gcc34-CVS that came with Mandrake-cooker is built
after 6/10.    Please try it again with the released version of gcc341.

Here is the latest GCC status report:
http://gcc.gnu.org/ml/gcc/2004-06/msg00991.html

> I wish to maintain an ecell3 package for
> Mandrake too. 

That's great!    Takeshi Sakurada (sakurada at sfc.keio.ac.jp) is
maintaining spec files for Fedora and Redhat.   Get a boilerplate from
him.


-sha

>
> ok, after a struggle, ecell CVS is now gcc34-ready without breaking
> compatibility with gcc33.
>
> boost-1.31 compiles fine with gcc3.4 too (Eric, what boost version
> did you use?).  Satya helped me to check that ecell+gcc3.4+boost-1.31
> works correctly on Linux.
>
>
> Aside from this, we found a problem in the GUI session monitor that
> prevents variable traces to show up on TracerWindows.   Maybe gabor
> will create a patch really soon.
>
>
> -sha
>

Hi Takahashi

Sorry for this late answer, I was away for a couple of days.
I still have problems with gcc-3.4.
After having used a LFS machine that was not satisfactory, I went back to
Mandrake, using the development version (cooker) which has the advantage
to include a good rpm manager and also very recent software versions, and
is used by a lab we work with. I wish to maintain an ecell3 package for
Mandrake too. Ecell used to compile perfectly on Mandrake 10 and also
cooker, until they switched to gcc-3.4.1 (cvs version).

I am in contact with the libboost maintainer for Mandrake , and will try
to sort out the problem with libboost_python. For the moment I use a
previous version of libboost_python.so.

Anyway, I still have compilation problems with ecell3 cvs (20040618) :

 g++ -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../.. -I/usr/include
-I/usr/local/src/ecell3 -I../../libltdl -g -O2 -MT ProcessMaker.lo -MD
-MP -MF .deps/ProcessMaker.Tpo -c ProcessMaker.cpp  -fPIC -DPIC -o
.libs/ProcessMaker.o
In file included from Process.hpp:40,
                 from ProcessMaker.hpp:34,
                 from ProcessMaker.cpp:31:
Entity.hpp: In static member function `static void
libecs::Entity::initializePropertyInterface(libecs::Type2Type<TT>)':
Entity.hpp:72: error: invalid use of ' libecs::Entity::setName' to form a
pointer-to-member-function.  Use a qualified-id.
Entity.hpp:72: error: invalid use of ' libecs::Entity::getName' to form a
pointer-to-member-function.  Use a qualified-id.
In file included from Variable.hpp:39,
                 from VariableReference.hpp:35,
                 from Process.hpp:41,
                 from ProcessMaker.hpp:34,
                 from ProcessMaker.cpp:31:
System.hpp: In static member function `static void
libecs::System::initializePropertyInterface(libecs::Type2Type<TT>)':
System.hpp:69: error: invalid use of ' libecs::System::setStepperID' to
form a pointer-to-member-function.  Use a qualified-id.
System.hpp:69: error: invalid use of ' libecs::System::getStepperID' to
form a pointer-to-member-function.  Use a qualified-id.
System.hpp:71: error: invalid use of ' libecs::System::getSize' to form a
pointer-to-member-function.  Use a qualified-id.
In file included from VariableReference.hpp:35,
                 from Process.hpp:41,
                 from ProcessMaker.hpp:34,
                 from ProcessMaker.cpp:31:
Variable.hpp: In static member function `static void
libecs::Variable::initializePropertyInterface(libecs::Type2Type<TT>)':
Variable.hpp:69: error: invalid use of ' libecs::Variable::setValue' to
form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:69: error: invalid use of ' libecs::Variable::getValue' to
form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:69: error: invalid use of ' libecs::Variable::loadValue' to
form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:69: error: invalid use of ' libecs::Variable::saveValue' to
form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:75: error: invalid use of ' libecs::Variable::getFixed' to
form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:77: error: invalid use of '
libecs::Variable::getTotalVelocity' to form a pointer-to-member-function. 
Use a qualified-id.
Variable.hpp:79: error: invalid use of ' libecs::Variable::getVelocity' to
form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:83: error: invalid use of ' libecs::Variable::setMolarConc'
to form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:83: error: invalid use of ' libecs::Variable::getMolarConc'
to form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:83: error: invalid use of ' libecs::Variable::loadMolarConc'
to form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:92: error: invalid use of ' libecs::Variable::setNumberConc'
to form a pointer-to-member-function.  Use a qualified-id.
Variable.hpp:92: error: invalid use of ' libecs::Variable::getNumberConc'
to form a pointer-to-member-function.  Use a qualified-id.
In file included from ProcessMaker.hpp:34,
                 from ProcessMaker.cpp:31:
Process.hpp: In static member function `static void
libecs::Process::initializePropertyInterface(libecs::Type2Type<TT>)':
Process.hpp:75: error: invalid use of '
libecs::Process::setVariableReferenceList' to form a
pointer-to-member-function.  Use a qualified-id.
Process.hpp:75: error: invalid use of '
libecs::Process::getVariableReferenceList' to form a
pointer-to-member-function.  Use a qualified-id.
Process.hpp:75: error: invalid use of '
libecs::Process::setVariableReferenceList' to form a
pointer-to-member-function.  Use a qualified-id.
Process.hpp:75: error: invalid use of '
libecs::Process::saveVariableReferenceList' to form a
pointer-to-member-function.  Use a qualified-id.
Process.hpp:81: error: invalid use of ' libecs::Process::setPriority' to
form a pointer-to-member-function.  Use a qualified-id.
Process.hpp:81: error: invalid use of ' libecs::Process::getPriority' to
form a pointer-to-member-function.  Use a qualified-id.
Process.hpp:82: error: invalid use of ' libecs::Process::setStepperID' to
form a pointer-to-member-function.  Use a qualified-id.
Process.hpp:82: error: invalid use of ' libecs::Process::getStepperID' to
form a pointer-to-member-function.  Use a qualified-id.
Process.hpp:84: error: invalid use of ' libecs::Process::setActivity' to
form a pointer-to-member-function.  Use a qualified-id.
Process.hpp:84: error: invalid use of ' libecs::Process::getActivity' to
form a pointer-to-member-function.  Use a qualified-id.
Process.hpp:85: error: invalid use of ' libecs::Process::getIsContinuous'
to form a pointer-to-member-function.  Use a qualified-id.
make[5]: *** [ProcessMaker.lo] Erreur 1
make[5]: Leaving directory `/usr/local/src/ecell3/ecell/libecs'
make[4]: *** [all-recursive] Erreur 1
make[4]: Leaving directory `/usr/local/src/ecell3/ecell/libecs'
make[3]: *** [all-recursive] Erreur 1
make[3]: Leaving directory `/usr/local/src/ecell3/ecell'
make[2]: *** [all] Erreur 2
make[2]: Leaving directory `/usr/local/src/ecell3/ecell'
make[1]: *** [all-recursive] Erreur 1
make[1]: Leaving directory `/usr/local/src/ecell3'
make: *** [all] Erreur 2


Hope this is informative.
Eric.

I fixed the problem with the GUI tracer and check into
CVS.
Gabor

--- Kouichi Takahashi <sh...@sf...> wrote: > 
> ok, after a struggle, ecell CVS is now gcc34-ready
> without breaking
> compatibility with gcc33.
> 
> boost-1.31 compiles fine with gcc3.4 too (Eric, what
> boost version
> did you use?).  Satya helped me to check that
> ecell+gcc3.4+boost-1.31
> works correctly on Linux.
> 
> 
> Aside from this, we found a problem in the GUI
> session monitor that
> prevents variable traces to show up on
> TracerWindows.   Maybe gabor
> will create a patch really soon.
> 
> 
> -sha
> 
> 
> 
>
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HI,
is it the one that Kaizu reported to me?
I have fixed it already and checked into CVS
yesterday.
Gabor

--- Kouichi Takahashi <sh...@sf...> wrote: > 
> ok, after a struggle, ecell CVS is now gcc34-ready
> without breaking
> compatibility with gcc33.
> 
> boost-1.31 compiles fine with gcc3.4 too (Eric, what
> boost version
> did you use?).  Satya helped me to check that
> ecell+gcc3.4+boost-1.31
> works correctly on Linux.
> 
> 
> Aside from this, we found a problem in the GUI
> session monitor that
> prevents variable traces to show up on
> TracerWindows.   Maybe gabor
> will create a patch really soon.
> 
> 
> -sha
> 
> 
> 
>
-------------------------------------------------------
> This SF.Net email is sponsored by The 2004
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> Conference, June 28 - July 1 at the Moscone Center
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ok, after a struggle, ecell CVS is now gcc34-ready without breaking
compatibility with gcc33.

boost-1.31 compiles fine with gcc3.4 too (Eric, what boost version
did you use?).  Satya helped me to check that ecell+gcc3.4+boost-1.31
works correctly on Linux.


Aside from this, we found a problem in the GUI session monitor that
prevents variable traces to show up on TracerWindows.   Maybe gabor
will create a patch really soon.


-sha

Hi,

Thanks for the report.

Satya is correct. The current E-Cell3 CVS is not gcc34-clean yet.
I think it's my job, and I'm going to sort things out for that.

It is given bug ID #971569 in sourceforge.
Sorry for the low priority (4).  This is due to our main target
OSes(FC1/2)'s still sticking to gcc 3.3.   
Is there anyone who wants this immediately?  If not I'm going to
do this within a week or so.



-sha




> I have tried compiling E-Cell CVS previously with gcc 3.4. It is not a 
> gcc problem, it is as a result of some changes in gcc with C++ codes. 
> You can solve the problem below by appending "this->" to the undeclared 
> identifiers, for example:
> this->theAllocator
> 
> However, I must say that after solving this problem, you will be further 
> faced with other compilation errors. I gave up after trying sometime as 
> I couldn't allocate much time into this.
> 
> satya
> 
> 
> >I updated my 'Linux from scratch' machine to the latest 3.4.1 (preversion
> >0.3) gcc and experience compilation issues. I know you may not want to
> >support cvs versions of libraries, but this may be interesting if this bug
> >is still there with the next release of gcc. Is it strictly a gcc problem
> >?
> >Hre is the error :
> >
> >make[5]: Entering directory `/usr/local/src/ecell3/ecell/libecs'
> >if /bin/sh ../libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I.. -I..
> > -I../.. -I/usr/include -I/usr/local/src/ecell3 -I../../libltdl    -g -O2 
> >-MT libecs.lo -MD -MP -MF ".deps/libecs.Tpo" -c -o libecs.lo libecs.cpp; \
> >then mv -f ".deps/libecs.Tpo" ".deps/libecs.Plo"; else rm -f
> >".deps/libecs.Tpo"; exit 1; fi
> > g++ -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../.. -I/usr/include
> >-I/usr/local/src/ecell3 -I../../libltdl -g -O2 -MT libecs.lo -MD -MP -MF
> >.deps/libecs.Tpo -c libecs.cpp  -fPIC -DPIC -o .libs/libecs.o
> >In file included from ../../dmtool/ModuleMaker.hpp:40,
> >                 from libecs.cpp:31:
> >../../dmtool/DynamicModule.hpp: In constructor `SharedDynamicModule<Base,
> >DMAllocator>::SharedDynamicModule(const std::string&)':
> >../../dmtool/DynamicModule.hpp:221: error: `theAllocator' undeclared
> >(first use this function)
> >../../dmtool/DynamicModule.hpp:221: error: (Each undeclared identifier is
> >reported only once for each function it appears in.)
> >In file included from libecs.cpp:31:
> >../../dmtool/ModuleMaker.hpp: In member function `void
> >SharedModuleMaker<T, DMAllocator>::loadModule(const std::string&)':
> >../../dmtool/ModuleMaker.hpp:327: error: `theModuleMap' undeclared (first
> >use this function)
> >make[5]: *** [libecs.lo] Erreur 1
> >
> >Thank you for any advice.
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by the new InstallShield X.
> >>From Windows to Linux, servers to mobile, InstallShield X is the
> >one installation-authoring solution that does it all. Learn more and
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> >
> >
> >  
> >
> 
> 
> 
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-- 
Kouichi Takahashi, PhD,
E-Cell Project,
Institute for Advanced Biosciences,
Keio University, Japan.
http://www.sfc.keio.ac.jp/~shafi

Hi,

I have tried compiling E-Cell CVS previously with gcc 3.4. It is not a 
gcc problem, it is as a result of some changes in gcc with C++ codes. 
You can solve the problem below by appending "this->" to the undeclared 
identifiers, for example:
this->theAllocator

However, I must say that after solving this problem, you will be further 
faced with other compilation errors. I gave up after trying sometime as 
I couldn't allocate much time into this.

satya


>I updated my 'Linux from scratch' machine to the latest 3.4.1 (preversion
>0.3) gcc and experience compilation issues. I know you may not want to
>support cvs versions of libraries, but this may be interesting if this bug
>is still there with the next release of gcc. Is it strictly a gcc problem
>?
>Hre is the error :
>
>make[5]: Entering directory `/usr/local/src/ecell3/ecell/libecs'
>if /bin/sh ../libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I.. -I..
> -I../.. -I/usr/include -I/usr/local/src/ecell3 -I../../libltdl    -g -O2 
>-MT libecs.lo -MD -MP -MF ".deps/libecs.Tpo" -c -o libecs.lo libecs.cpp; \
>then mv -f ".deps/libecs.Tpo" ".deps/libecs.Plo"; else rm -f
>".deps/libecs.Tpo"; exit 1; fi
> g++ -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../.. -I/usr/include
>-I/usr/local/src/ecell3 -I../../libltdl -g -O2 -MT libecs.lo -MD -MP -MF
>.deps/libecs.Tpo -c libecs.cpp  -fPIC -DPIC -o .libs/libecs.o
>In file included from ../../dmtool/ModuleMaker.hpp:40,
>                 from libecs.cpp:31:
>../../dmtool/DynamicModule.hpp: In constructor `SharedDynamicModule<Base,
>DMAllocator>::SharedDynamicModule(const std::string&)':
>../../dmtool/DynamicModule.hpp:221: error: `theAllocator' undeclared
>(first use this function)
>../../dmtool/DynamicModule.hpp:221: error: (Each undeclared identifier is
>reported only once for each function it appears in.)
>In file included from libecs.cpp:31:
>../../dmtool/ModuleMaker.hpp: In member function `void
>SharedModuleMaker<T, DMAllocator>::loadModule(const std::string&)':
>../../dmtool/ModuleMaker.hpp:327: error: `theModuleMap' undeclared (first
>use this function)
>make[5]: *** [libecs.lo] Erreur 1
>
>Thank you for any advice.
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by the new InstallShield X.
>>From Windows to Linux, servers to mobile, InstallShield X is the
>one installation-authoring solution that does it all. Learn more and
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>_______________________________________________
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>https://lists.sourceforge.net/lists/listinfo/ecell-devel
>
>
>  
>

I updated my 'Linux from scratch' machine to the latest 3.4.1 (preversion
0.3) gcc and experience compilation issues. I know you may not want to
support cvs versions of libraries, but this may be interesting if this bug
is still there with the next release of gcc. Is it strictly a gcc problem
?
Hre is the error :

make[5]: Entering directory `/usr/local/src/ecell3/ecell/libecs'
if /bin/sh ../libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I.. -I..
 -I../.. -I/usr/include -I/usr/local/src/ecell3 -I../../libltdl    -g -O2 
-MT libecs.lo -MD -MP -MF ".deps/libecs.Tpo" -c -o libecs.lo libecs.cpp; \
then mv -f ".deps/libecs.Tpo" ".deps/libecs.Plo"; else rm -f
".deps/libecs.Tpo"; exit 1; fi
 g++ -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../.. -I/usr/include
-I/usr/local/src/ecell3 -I../../libltdl -g -O2 -MT libecs.lo -MD -MP -MF
.deps/libecs.Tpo -c libecs.cpp  -fPIC -DPIC -o .libs/libecs.o
In file included from ../../dmtool/ModuleMaker.hpp:40,
                 from libecs.cpp:31:
../../dmtool/DynamicModule.hpp: In constructor `SharedDynamicModule<Base,
DMAllocator>::SharedDynamicModule(const std::string&)':
../../dmtool/DynamicModule.hpp:221: error: `theAllocator' undeclared
(first use this function)
../../dmtool/DynamicModule.hpp:221: error: (Each undeclared identifier is
reported only once for each function it appears in.)
In file included from libecs.cpp:31:
../../dmtool/ModuleMaker.hpp: In member function `void
SharedModuleMaker<T, DMAllocator>::loadModule(const std::string&)':
../../dmtool/ModuleMaker.hpp:327: error: `theModuleMap' undeclared (first
use this function)
make[5]: *** [libecs.lo] Erreur 1

Thank you for any advice.

.desc files for storing interface specification of dms are
temporary makeshifts.   The design which is not fully implemented
yet is that shared object files (.so) have that 'dm info' and the
frontend gets the information through pyecs API.

Gabor was forced to create such a mechanism as I have not been able
to spend time to design details and code it.   (Sorry gabor..)

The plan is the real dminfo mechanism should be implemented before
version 3.2.


BTY I think there is no agreed plan for versoin 3.1.103, but I guess
we should keep making monthly or bimonthly releases before 3.2.  
The software is still in beta.

-sha



> ModelEditor is looking for classname.desc files in
> ecell/dm directory. such a file should be created for
> PassiveStepper class. it is actually little more than
> the list of properties and the default values for
> properties in the class. there are a lot of examples
> as we created .desc files for all classes that were
> available in dm directory in April.
> I can create the desc file for passivestepper and any
> other new classes , when are you going to release new
> packages? ( either windows or fedora)
> Gabor
> 
>  --- Lei Zhou <lz...@uf...> wrote: > Thanks,
> Takeshi-san.
> > 
> >  >What kind of problems you got with the  
> > PassiveStepper? If you don't
> > mind,
> >  >put the error message or some details.
> > 
> > I could not find the PassiveStepper from list of
> > steppers provided by
> > the ModelEditor.  I was told that I could still use
> > it with EM file.
> > 
> > -lei
> > 
> > 
> >
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-- 
Kouichi Takahashi, PhD,
E-Cell Project,
Institute for Advanced Biosciences,
Keio University, Japan.
http://www.sfc.keio.ac.jp/~shafi

Hi Lei.

I write sample code that hybrid system mixing passive stepper with
differential/discrete steppers.

this is here:

Stepper FixedODE1Stepper( DE1 )
{
	# no property
}

Stepper PassiveStepper( Passive )
{
	# no property
}

System System( / )
{
	StepperID	DE1;

	Variable Variable( SIZE )
	{
		Value	1e-18;
	}

	Variable Variable( S )
	{
		Value	1000000;
	}
	
	Variable Variable( P )
	{
		Value	0;
	}
	
	Variable Variable( E )
	{
		Value	1000;
	}

	Variable Variable( N )
	{
		Value	1000;
	}

	
	Process MichaelisUniUniFluxProcess( E1 )
	{
		VariableReferenceList	[ S0 :.:S -1 ]
 					[ P0 :.:P 1 ]
					[ C0 :.:E 0 ];
		KmS	1;
		KcF	10;
	}

	Process BisectionRapidEquilibriumProcess( E2 )
	{
		StepperID	Passive;

		Keq	1;

		VariableReferenceList	[ S0 :.:P -1 ]
					[ P0 :.:N 1 ];
	}
	
}

BisectionRapidEquilibriumProcess is rapid-equilibrium reaction.
In This Model, BisectionRapidEquilibriumProcess maintains the ratio,
that is 1 in this model, of P to N.

After DE1(FixedODE1Stepper)is called, PassiveStepper is called.

thank you.

-- Kitayama Tomoya

On Tue, 08 Jun 2004 01:47:40 -0400
"Lei Zhou" <lz...@uf...> wrote:

> Thanks, Takeshi-san.
> 
>  >What kind of problems you got with the   PassiveStepper? If you don't
> mind,
>  >put the error message or some details.
> 
> I could not find the PassiveStepper from list of steppers provided by
> the ModelEditor.  I was told that I could still use it with EM file.
> 
> -lei
> 

ModelEditor is looking for classname.desc files in
ecell/dm directory. such a file should be created for
PassiveStepper class. it is actually little more than
the list of properties and the default values for
properties in the class. there are a lot of examples
as we created .desc files for all classes that were
available in dm directory in April.
I can create the desc file for passivestepper and any
other new classes , when are you going to release new
packages? ( either windows or fedora)
Gabor

 --- Lei Zhou <lz...@uf...> wrote: > Thanks,
Takeshi-san.
> 
>  >What kind of problems you got with the  
> PassiveStepper? If you don't
> mind,
>  >put the error message or some details.
> 
> I could not find the PassiveStepper from list of
> steppers provided by
> the ModelEditor.  I was told that I could still use
> it with EM file.
> 
> -lei
> 
> 
>
-------------------------------------------------------
> This SF.Net email is sponsored by: GNOME Foundation
> Hackers Unite!  GUADEC: The world's #1 Open Source
> Desktop Event.
> GNOME Users and Developers European Conference,
> 28-30th June in Norway
> http://2004/guadec.org
> _______________________________________________
> Ecell-devel mailing list
> Ece...@li...
>
https://lists.sourceforge.net/lists/listinfo/ecell-devel 


	
	
		
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Thanks, Takeshi-san.

 >What kind of problems you got with the   PassiveStepper? If you don't
mind,
 >put the error message or some details.

I could not find the PassiveStepper from list of steppers provided by
the ModelEditor.  I was told that I could still use it with EM file.

-lei

Hi Lei,
I'm sorry the delay.

> PassiveStepper is described in the user manual but is not available as
> a stepper class in the 3.102 version.

What kind of problems you got with the PassiveStepper? If you don't mind,
put the error message or some details.

> Has anyone tried hybrid system mixing passive stepper with
> differential/discrete steppers.  An example will be much appreciated.
> 
> -lei

I think Tomoya Kitayama has some experiences about this issue. Tomoya, could
you get into this discussion?


-Takeshi

Dear Takeshi:

PassiveStepper is described in the user manual  but is not available as
a stepper class in the 3.102 version.  

Has anyone tried hybrid system mixing passive stepper with
differential/discrete steppers.  An example will be much appreciated.

-lei

-----------------------------------------------------------------------------------
Lei Zhou  (B.Med.  Ph.D.)
Assistant Professor
Department of Molecular Genetics and Microbiology
Member, UF Shands Cancer Center
College of Medicine
University of Florida
PO Box 100232
Gainesville, FL 32610
Tel:(352) 392-6079 (o)
http://www.mgm.ufl.edu/faculty/lzhou.htm
For FedEX only:
ARB, R4-136
1600 SW Archer Road,
Gainesville, FL 32610

Dear E-Cell users,


We are pleased to announce the availability of version 3.1.102 of E-Cell
Simulation Environment.  


All users are recommended to upgrade to the latest version.
Although we plan some more beta releases before the stable
version 3.2, we believe the software is reaching a fairly
usable state for many simulation projects.   For features
that are considered criteria of release of version 3.2 and 
missing from the current version, please visit this page
and look for items with priorities higher than six:
http://sourceforge.net/tracker/?atid=534673&group_id=72485&func=browse


Improvements introduced in this version include the followings:

  * Model editor with pathway view (still under active development).
  * Importing SBML Level 2 documents with libSBML installed.
  * Support for differential-algebraic equations is now fairly stable.
  * Mainline branch can now compile on Microsoft Windows.
  * Lots of minor enhancements and bugfixes.


See here for full changelog:
http://sourceforge.net/project/shownotes.php?group_id=72485&release_id=24235
4

Visit the following URL for more information on downloading
and installation:
http://ecell.sourceforge.net/download.html

Report bugs and request new features on this mailing list or
bug/feature request trackers on http://ecell.sf.net/.


Best regards,
---
Takeshi Sakurada
E-Cell Project
Keio University, Japan.