ecell-users Mailing List for E-Cell System

Dear Yasuhiro,

Thank you for your reply.
However, while running "make" for ecell3.1, I got the following error

--
...(I only displayed the part when error start)
make[5]: Entering directory 
`/home/luli/bin/ecell-ecell3-ed9c78e-ecell3.1source/ecell/libecs'
/bin/bash ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. 
-I.. -I..  -I../.. -I/home/luli/bin/ecell-ecell3-ed9c78e-ecell3.1source 
-I../../libltdl  -I/usr/include -g -O2 -g -O2 -MT libecs.lo -MD -MP -MF 
.deps/libecs.Tpo -c -o libecs.lo libecs.cpp
mv -f .deps/libecs.Tpo .deps/libecs.Plo
mv: cannot stat `.deps/libecs.Tpo': No such file or directory
...
-- 

Cheers
Lu

On 20/03/12 06:21, Yasuhiro Naito wrote:
> Dear Lu,
>
> Another way is downgrading E-cell to ver 3.1.x.
>
> You can download the latest version of E-Cell 3.1.x from GitHub [ecell/ecell3 branch:ecell-3.1].
> https://github.com/ecell/ecell3/tree/ecell-3.1 (ZIP download)
>
> You should run ./autogen.sh before ./configure .
> I installed it just now on the latest Ubuntu, and successfully run the model including PythonProcess.
>
> We are sorry for the inconvenience.
>
> Regards,
> Yasuhiro
>
>
> On 2012/03/20, at 11:21, Yasuhiro Naito wrote:
>
>> Dear Lu,
>>
>> I'm not a developer but a modeler with E-Cell project.
>> As you pointed out, both of PythonFluxProcess and PythonProcess in ver 3.2.x don't work correctly at present. E-Cell3 developers work to fix the problems.
>> Temporarily, I use custom Processes wrote in C++ instead of using Python(Flux)Process.
>> Some built-in Processes such as MichaelisUniUniFluxProces (/ecell/dm/MichaelisUniUniFluxProcess.cpp) are good samples to develop custom Process.
>>
>> Regards
>> Yasuhiro
>>
>>
>> On 2012/03/20, at 2:56, luli wrote:
>>
>>> Dear ECell3 developers,
>>>
>>> I just installed ecell-3.2.3pre2, however, encountering the following
>>> problems.
>>>
>>> 1) PythonFluxProcess does not allow any "attribute" appear in the
>>> expression.
>>> For instance:
>>>
>>>     Process PythonFluxProcess( test )
>>>     {
>>>         k    0.5;
>>>         StepperID    DE1;
>>>         Expression    "k*S1.MolarConc*self.getSuperSystem().SizeN_A";
>>>         VariableReferenceList     [S1 Variable:/Spine:A] [P1
>>> Variable:/Spine:B];
>>>     }
>>>
>>> When running ecell3-session..... ecell gives AttributeError, complaining
>>> that there is no MolarConc attribute.
>>>
>>> 2) PythonProcess does not allo any "attribute" appear in the expression
>>> either.
>>>
>>> Could you give an explanation please.
>>>
>>> BTW, the Ecell user manual is very incomplete and out of date (the last
>>> modification is June 30th 2006).
>>> Is it possible to update this manual, since ECell becomes more and more
>>> popular now?
>>>
>>> Cheers
>>> Lu
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF email is sponsosred by:
>>> Try Windows Azure free for 90 days Click Here
>>> http://p.sf.net/sfu/sfd2d-msazure
>>> _______________________________________________
>>> Ecell-users mailing list
>>> Ece...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ecell-users

Dear Lu,

Another way is downgrading E-cell to ver 3.1.x.

You can download the latest version of E-Cell 3.1.x from GitHub [ecell/ecell3 branch:ecell-3.1].
https://github.com/ecell/ecell3/tree/ecell-3.1 (ZIP download)

You should run ./autogen.sh before ./configure .
I installed it just now on the latest Ubuntu, and successfully run the model including PythonProcess.

We are sorry for the inconvenience.

Regards,
Yasuhiro


On 2012/03/20, at 11:21, Yasuhiro Naito wrote:

> Dear Lu,
> 
> I'm not a developer but a modeler with E-Cell project.
> As you pointed out, both of PythonFluxProcess and PythonProcess in ver 3.2.x don't work correctly at present. E-Cell3 developers work to fix the problems.
> Temporarily, I use custom Processes wrote in C++ instead of using Python(Flux)Process.
> Some built-in Processes such as MichaelisUniUniFluxProces (/ecell/dm/MichaelisUniUniFluxProcess.cpp) are good samples to develop custom Process.
> 
> Regards
> Yasuhiro
> 
> 
> On 2012/03/20, at 2:56, luli wrote:
> 
>> Dear ECell3 developers,
>> 
>> I just installed ecell-3.2.3pre2, however, encountering the following 
>> problems.
>> 
>> 1) PythonFluxProcess does not allow any "attribute" appear in the 
>> expression.
>> For instance:
>> 
>>    Process PythonFluxProcess( test )
>>    {
>>        k    0.5;
>>        StepperID    DE1;
>>        Expression    "k*S1.MolarConc*self.getSuperSystem().SizeN_A";
>>        VariableReferenceList     [S1 Variable:/Spine:A] [P1 
>> Variable:/Spine:B];
>>    }
>> 
>> When running ecell3-session..... ecell gives AttributeError, complaining 
>> that there is no MolarConc attribute.
>> 
>> 2) PythonProcess does not allo any "attribute" appear in the expression 
>> either.
>> 
>> Could you give an explanation please.
>> 
>> BTW, the Ecell user manual is very incomplete and out of date (the last 
>> modification is June 30th 2006).
>> Is it possible to update this manual, since ECell becomes more and more 
>> popular now?
>> 
>> Cheers
>> Lu
>> 
>> 
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here 
>> http://p.sf.net/sfu/sfd2d-msazure
>> _______________________________________________
>> Ecell-users mailing list
>> Ece...@li...
>> https://lists.sourceforge.net/lists/listinfo/ecell-users
> 

Dear Lu,

I'm not a developer but a modeler with E-Cell project.
As you pointed out, both of PythonFluxProcess and PythonProcess in ver 3.2.x don't work correctly at present. E-Cell3 developers work to fix the problems.
Temporarily, I use custom Processes wrote in C++ instead of using Python(Flux)Process.
Some built-in Processes such as MichaelisUniUniFluxProces (/ecell/dm/MichaelisUniUniFluxProcess.cpp) are good samples to develop custom Process.

Regards
Yasuhiro


On 2012/03/20, at 2:56, luli wrote:

> Dear ECell3 developers,
> 
> I just installed ecell-3.2.3pre2, however, encountering the following 
> problems.
> 
> 1) PythonFluxProcess does not allow any "attribute" appear in the 
> expression.
> For instance:
> 
>     Process PythonFluxProcess( test )
>     {
>         k    0.5;
>         StepperID    DE1;
>         Expression    "k*S1.MolarConc*self.getSuperSystem().SizeN_A";
>         VariableReferenceList     [S1 Variable:/Spine:A] [P1 
> Variable:/Spine:B];
>     }
> 
> When running ecell3-session..... ecell gives AttributeError, complaining 
> that there is no MolarConc attribute.
> 
> 2) PythonProcess does not allo any "attribute" appear in the expression 
> either.
> 
> Could you give an explanation please.
> 
> BTW, the Ecell user manual is very incomplete and out of date (the last 
> modification is June 30th 2006).
> Is it possible to update this manual, since ECell becomes more and more 
> popular now?
> 
> Cheers
> Lu
> 
> 
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here 
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> Ecell-users mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-users

Dear ECell3 developers,

I just installed ecell-3.2.3pre2, however, encountering the following 
problems.

1) PythonFluxProcess does not allow any "attribute" appear in the 
expression.
For instance:

     Process PythonFluxProcess( test )
     {
         k    0.5;
         StepperID    DE1;
         Expression    "k*S1.MolarConc*self.getSuperSystem().SizeN_A";
         VariableReferenceList     [S1 Variable:/Spine:A] [P1 
Variable:/Spine:B];
     }

When running ecell3-session..... ecell gives AttributeError, complaining 
that there is no MolarConc attribute.

2) PythonProcess does not allo any "attribute" appear in the expression 
either.

Could you give an explanation please.

BTW, the Ecell user manual is very incomplete and out of date (the last 
modification is June 30th 2006).
Is it possible to update this manual, since ECell becomes more and more 
popular now?

Cheers
Lu

Dear Yasuhiro,

The problem listed in my previous e-mail has been solved by setting 
LD_LIBRARY_PATH to my local folder where Ecell has been installed 
(thanks to Michele Mattioni).

Cheers
Lu

On 19/03/12 15:38, luli wrote:
> Dear Yasuhiro,
>
> Thank you very much for your reply.
> It seems ecell-3.2.3pre2 can be compiled, following the following commands:
> ./configure --prefix=[myLocalFolder]
> make
> make install
>
> However, when I use ecell3-session to run a model (for instance,
> ecell3-session run.py), I got the following error message:
>
> Traceback (most recent call last):
>     File "../bin/ecell3.2.3pre2/bin/ecell3-session", line 9, in<module>
>       import ecell.ecs
>     File
> "/home/luli/bin/ecell3.2.3pre2/lib/python2.7/site-packages/ecell/ecs.py", line
> 28, in<module>
>       import ecell._ecs
> ImportError: libecs.so.2: cannot open shared object file: No such file
> or directory
>
>
> Could your please give some advice to fix this?
>
> The linux distribution I am using is: Ubuntu 11.10 (Oneiric Ocelot).
>
> Best Regards
> Lu
>
> On 18/03/12 16:37, Yasuhiro Naito wrote:
>> Dear Lu,
>>
>> Thank you for the report.
>>
>> Could you try ecell-3.2.3pre2? E-Cell 3.2.2 has some incompatibilities with recent boost C++ library.
>> The source code of ecell-3.2.3pre2 is available at following:
>> https://github.com/ecell/ecell3/downloads
>>
>> Please let me know your LINUX distribution and version. We'd like to reproduce your situation.
>>
>> Regards,
>>
>> -----
>> Yasuhiro Naito
>> Institute for Advanced Biosciences, Keio University
>>
>>
>>> I am trying to install the latest Ecell (3.2.2), but unsuccessfully.
>>>
>>> First of all, your repository of pre-built packages (for debian and
>>> ubuntu) is down.
>>>
>>> Secondly, I tried to install the source from both sourceForge and
>>> GitHub. During "make", I obtained the following logs:
>>
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>> _______________________________________________
>> Ecell-users mailing list
>> Ece...@li...
>> https://lists.sourceforge.net/lists/listinfo/ecell-users
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> Ecell-users mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-users

Dear Yasuhiro,

Thank you very much for your reply.
It seems ecell-3.2.3pre2 can be compiled, following the following commands:
./configure --prefix=[myLocalFolder]
make
make install

However, when I use ecell3-session to run a model (for instance, 
ecell3-session run.py), I got the following error message:

Traceback (most recent call last):
   File "../bin/ecell3.2.3pre2/bin/ecell3-session", line 9, in <module>
     import ecell.ecs
   File 
"/home/luli/bin/ecell3.2.3pre2/lib/python2.7/site-packages/ecell/ecs.py", line 
28, in <module>
     import ecell._ecs
ImportError: libecs.so.2: cannot open shared object file: No such file 
or directory


Could your please give some advice to fix this?

The linux distribution I am using is: Ubuntu 11.10 (Oneiric Ocelot).

Best Regards
Lu

On 18/03/12 16:37, Yasuhiro Naito wrote:
> Dear Lu,
>
> Thank you for the report.
>
> Could you try ecell-3.2.3pre2? E-Cell 3.2.2 has some incompatibilities with recent boost C++ library.
> The source code of ecell-3.2.3pre2 is available at following:
> https://github.com/ecell/ecell3/downloads
>
> Please let me know your LINUX distribution and version. We'd like to reproduce your situation.
>
> Regards,
>
> -----
> Yasuhiro Naito
> Institute for Advanced Biosciences, Keio University
>
>
>> I am trying to install the latest Ecell (3.2.2), but unsuccessfully.
>>
>> First of all, your repository of pre-built packages (for debian and
>> ubuntu) is down.
>>
>> Secondly, I tried to install the source from both sourceForge and
>> GitHub. During "make", I obtained the following logs:
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> Ecell-users mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-users

Dear Lu,

Thank you for the report.

Could you try ecell-3.2.3pre2? E-Cell 3.2.2 has some incompatibilities with recent boost C++ library.
The source code of ecell-3.2.3pre2 is available at following:
https://github.com/ecell/ecell3/downloads

Please let me know your LINUX distribution and version. We'd like to reproduce your situation.

Regards,

-----
Yasuhiro Naito
Institute for Advanced Biosciences, Keio University

> I am trying to install the latest Ecell (3.2.2), but unsuccessfully.
> 
> First of all, your repository of pre-built packages (for debian and
> ubuntu) is down.
> 
> Secondly, I tried to install the source from both sourceForge and
> GitHub. During "make", I obtained the following logs:

Dear Lu,

Thank you for the report.

Could you try ecell-3.2.3pre2? E-Cell 3.2.2 has some incompatibilities with recent boost C++ library.
The source code of ecell-3.2.3pre2 is available at following:
https://github.com/ecell/ecell3/downloads

Please let me know your LINUX distribution and version. We'd like to reproduce your situation.

Regards,

-----
Yasuhiro Naito
Institute for Advanced Biosciences, Keio University


> I am trying to install the latest Ecell (3.2.2), but unsuccessfully.
> 
> First of all, your repository of pre-built packages (for debian and
> ubuntu) is down.
> 
> Secondly, I tried to install the source from both sourceForge and
> GitHub. During "make", I obtained the following logs:

Hi,

I am trying to install the latest Ecell (3.2.2), but unsuccessfully.

First of all, your repository of pre-built packages (for debian and 
ubuntu) is down.

Secondly, I tried to install the source from both sourceForge and 
GitHub. During "make", I obtained the following logs:
---
make  all-recursive
make[1]: Entering directory `/home/luli/bin/ecell-3.2.2'
Making all in libltdl
make[2]: Entering directory `/home/luli/bin/ecell-3.2.2/libltdl'
make  all-am
make[3]: Entering directory `/home/luli/bin/ecell-3.2.2/libltdl'
/bin/bash ./libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H 
-I.     -g -O2 -c -o ltdl.lo ltdl.c
/bin/bash ./libtool --tag=CC   --mode=link gcc  -g -O2   -o libltdlc.la  
ltdl.lo -ldl
make[3]: Leaving directory `/home/luli/bin/ecell-3.2.2/libltdl'
make[2]: Leaving directory `/home/luli/bin/ecell-3.2.2/libltdl'
Making all in dmtool
make[2]: Entering directory `/home/luli/bin/ecell-3.2.2/dmtool'
make  all-am
make[3]: Entering directory `/home/luli/bin/ecell-3.2.2/dmtool'
make[3]: Leaving directory `/home/luli/bin/ecell-3.2.2/dmtool'
make[2]: Leaving directory `/home/luli/bin/ecell-3.2.2/dmtool'
Making all in ecell
make[2]: Entering directory `/home/luli/bin/ecell-3.2.2/ecell'
make  all-recursive
make[3]: Entering directory `/home/luli/bin/ecell-3.2.2/ecell'
Making all in libecs
make[4]: Entering directory `/home/luli/bin/ecell-3.2.2/ecell/libecs'
Making all in scripting
make[5]: Entering directory 
`/home/luli/bin/ecell-3.2.2/ecell/libecs/scripting'
/bin/bash ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H 
-I. -I../.. -I.. -I../.. -I/home/luli/bin/ecell-3.2.2 
-I../../../libltdl  -I/usr/include -g -O2 -g -O2 -MT 
ExpressionCompiler.lo -MD -MP -MF .deps/ExpressionCompiler.Tpo -c -o 
ExpressionCompiler.lo ExpressionCompiler.cpp
mv -f .deps/ExpressionCompiler.Tpo .deps/ExpressionCompiler.Plo
mv: cannot stat `.deps/ExpressionCompiler.Tpo': No such file or directory
make[5]: *** [ExpressionCompiler.lo] Error 1
make[5]: Leaving directory 
`/home/luli/bin/ecell-3.2.2/ecell/libecs/scripting'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/luli/bin/ecell-3.2.2/ecell/libecs'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/luli/bin/ecell-3.2.2/ecell'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/luli/bin/ecell-3.2.2/ecell'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/luli/bin/ecell-3.2.2'
make: *** [all] Error 2
--

It seems that the .deps/ExpressionCompiler.Tpo can not be generated....

Could you please give some advice and help?

Best Regards
Lu