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From: Michele M. <mat...@eb...> - 2009-04-20 09:25:59
|
Hello list, I modified the SessionManager class so it doesn't change always the directory, but it has a true/false switch to do it. Patch attached (against the last revision of the svn) Default is False. (Not as normal) Cheers, Michele |
|
From: Moriyoshi K. <mo...@sf...> - 2009-04-05 02:35:18
|
This eventually turned out to be a problem in ecel3-session-manager script, rather than the session manager modules. Try ecell-3.1.107rc4 to see if it works. -- moriyoshi 2009/3/31 giuseppe aprea <apr...@gm...>: > Hallo, > I am using the ecell release 3.1.107rc3 and I have some problem in > running ecell3-session-manager. > > I send you just an example code. > > When I try to run the attached scripts (ecell3-session-manager esm.py) > I get the following error: > > Traceback (most recent call last): > File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager", > line 278, in <module> > sys.exit( main( sys.argv ) ) > File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager", > line 271, in main > aConsole.loadScript( anEsmFile, aParameters ) > File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager", > line 89, in loadScript > execfile( esmfile, aContext ) > File "esm.py", line 14, in <module> > class RCGA: > TypeError: Error when calling the metaclass bases > __metaclass__() takes exactly 3 arguments (4 given) > > > unfortunately I am not a very skilled python programmer but I think > that the problem is triggered when I try to run sessions > from my own class in the script esm.py (if I run everything from the > main function it runs fine). Is there a workaround to > keep the program structure and avoid the error? > > Thanks, > > giuseppe > > ------------------------------------------------------------------------------ > > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users > > |
|
From: giuseppe a. <apr...@gm...> - 2009-04-01 07:17:37
|
I don't know if it can help but I noticed that if I change
class myClass: -----> class myClass(object):
the code doesn't show:
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 278, in <module>
sys.exit( main( sys.argv ) )
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 271, in main
aConsole.loadScript( anEsmFile, aParameters )
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 89, in loadScript
execfile( esmfile, aContext )
File "esm.py", line 14, in <module>
class myClass:
TypeError: Error when calling the metaclass bases
__metaclass__() takes exactly 3 arguments (4 given)
It seems all method not
involving arguments (other than self) work fine, except
if I write them as "self.method()" (instead "method()"
alone works)
Unfortunately that is not enough. The error I when I use
sessionmanager methods with arguments is:
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 278, in <module>
sys.exit( main( sys.argv ) )
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 271, in main
aConsole.loadScript( anEsmFile, aParameters )
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 89, in loadScript
execfile( esmfile, aContext )
File "esm.py", line 74, in <module>
main()
File "esm.py", line 70, in main
ga.go()
File "esm.py", line 64, in go
for ajob in
getSystemProxy().jobs:getSystemProxy().getSessionProxy(ajob).clear()
RuntimeError: dictionary changed size during iteration
Has anybody any idea about a workaround to use all methods?
thanks
giuseppe
2009/3/31 yuri matsuzaki <yu...@e-...>:
> Works fine with 3.1.106 but failed with 3.1.107rc3.
> The directory structure of session manager script
> looks a lot different between 3.1.106 and 3.1.107rc1.
> Might this have something to do with the problem?
> I have not traced the problem further. Any ideas anyone?
>
> Yuri
>
> 2009/3/31 giuseppe aprea <apr...@gm...>:
>> Hallo,
>> I am using the ecell release 3.1.107rc3 and I have some problem in
>> running ecell3-session-manager.
>>
>> I send you just an example code.
>>
>> When I try to run the attached scripts (ecell3-session-manager esm.py)
>> I get the following error:
>>
>> Traceback (most recent call last):
>> File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
>> line 278, in <module>
>> sys.exit( main( sys.argv ) )
>> File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
>> line 271, in main
>> aConsole.loadScript( anEsmFile, aParameters )
>> File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
>> line 89, in loadScript
>> execfile( esmfile, aContext )
>> File "esm.py", line 14, in <module>
>> class RCGA:
>> TypeError: Error when calling the metaclass bases
>> __metaclass__() takes exactly 3 arguments (4 given)
>>
>>
>> unfortunately I am not a very skilled python programmer but I think
>> that the problem is triggered when I try to run sessions
>> from my own class in the script esm.py (if I run everything from the
>> main function it runs fine). Is there a workaround to
>> keep the program structure and avoid the error?
>>
>> Thanks,
>>
>> giuseppe
>
|
|
From: yuri m. <yu...@e-...> - 2009-03-31 06:06:32
|
Works fine with 3.1.106 but failed with 3.1.107rc3. The directory structure of session manager script looks a lot different between 3.1.106 and 3.1.107rc1. Might this have something to do with the problem? I have not traced the problem further. Any ideas anyone? Yuri 2009/3/31 giuseppe aprea <apr...@gm...>: > Hallo, > I am using the ecell release 3.1.107rc3 and I have some problem in > running ecell3-session-manager. > > I send you just an example code. > > When I try to run the attached scripts (ecell3-session-manager esm.py) > I get the following error: > > Traceback (most recent call last): > File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager", > line 278, in <module> > sys.exit( main( sys.argv ) ) > File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager", > line 271, in main > aConsole.loadScript( anEsmFile, aParameters ) > File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager", > line 89, in loadScript > execfile( esmfile, aContext ) > File "esm.py", line 14, in <module> > class RCGA: > TypeError: Error when calling the metaclass bases > __metaclass__() takes exactly 3 arguments (4 given) > > > unfortunately I am not a very skilled python programmer but I think > that the problem is triggered when I try to run sessions > from my own class in the script esm.py (if I run everything from the > main function it runs fine). Is there a workaround to > keep the program structure and avoid the error? > > Thanks, > > giuseppe |
|
From: giuseppe a. <apr...@gm...> - 2009-03-30 17:27:10
|
Hallo,
I am using the ecell release 3.1.107rc3 and I have some problem in
running ecell3-session-manager.
I send you just an example code.
When I try to run the attached scripts (ecell3-session-manager esm.py)
I get the following error:
Traceback (most recent call last):
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 278, in <module>
sys.exit( main( sys.argv ) )
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 271, in main
aConsole.loadScript( anEsmFile, aParameters )
File "/afs/.enea.it/project/cresco/LA2/cresco_sp21_bionet/soft/cresco1x/bin/ecell3-session-manager",
line 89, in loadScript
execfile( esmfile, aContext )
File "esm.py", line 14, in <module>
class RCGA:
TypeError: Error when calling the metaclass bases
__metaclass__() takes exactly 3 arguments (4 given)
unfortunately I am not a very skilled python programmer but I think
that the problem is triggered when I try to run sessions
from my own class in the script esm.py (if I run everything from the
main function it runs fine). Is there a workaround to
keep the program structure and avoid the error?
Thanks,
giuseppe
|
|
From: giuseppe a. <apr...@gm...> - 2009-02-07 21:27:46
|
Hi Moriyoshi,
thanks for your help. Since your answer I guess I missed something about
ecell's internal ode machinery.
Actually I set up Processes and em files thinking that the total delta for
each variable is the sum of the velocities of the processes for which it has
a +1 entry. I'll make an example: in my em file I have 4 processes entries
".........
Process ODE1Process( ODE1 )
{
mu1 0.303;
n1 3.5938;
n2 2.213;
ks1 22.836;
ks2 0.234;
sm1 90.11;
sm2 10.11;
a1 3.19;
a2 0.97;
VariableReferenceList[X1 Variable:.:BIOMASS 1]
[X3 Variable:.:NUTRIENT -1]
[X4 Variable:.:INHIBITOR -1];
}
Process ODE2Process( ODE2 )
{
mu1 0.303;
n1 3.5938;
n2 2.213;
ks1 22.836;
ks2 0.234;
sm1 90.11;
sm2 10.11;
a1 3.19;
a2 0.97;
k1 0.008;
k2 0.034;
VariableReferenceList[X1 Variable:.:BIOMASS -1]
[X2 Variable:.:PHA 1]
[X3 Variable:.:NUTRIENT -1]
[X4 Variable:.:INHIBITOR -1];
}
Process ODE3Process( ODE3 )
{
mu1 0.303;
n1 3.5938;
n2 2.213;
ks1 22.836;
ks2 0.234;
sm1 90.11;
sm2 10.11;
a1 3.19;
a2 0.97;
alp 0.48;
gam 0.0348;
VariableReferenceList[X1 Variable:.:BIOMASS -1]
[X3 Variable:.:NUTRIENT 1]
[X4 Variable:.:INHIBITOR -1];
}
Process ODE4Process( ODE4 )
{
mu1 0.303;
n1 3.5938;
n2 2.213;
ks1 22.836;
ks2 0.234;
sm1 90.11;
sm2 10.11;
a1 3.19;
a2 0.97;
yRS2 16.7;
mS2 0.0000045;
VariableReferenceList[X1 Variable:.:BIOMASS -1]
[X3 Variable:.:NUTRIENT -1]
[X4 Variable:.:INHIBITOR 1];
}
.........."
As far as I understood the four DELTAs were:
DELTA[X1]=velocity[PROCESS1]
DELTA[X2]=velocity[PROCESS2]
DELTA[X3]=velocity[PROCESS3]
DELTA[X4]=velocity[PROCESS4]
And I would have got t the initial ODE system.
But from your words and your second file I guess the answer is that my em file
gives:
DELTA[X1]=velocity[PROCESS1]-velocity[PROCESS2]-velocity[PROCESS3]-velocity[PROCESS4]
DELTA[X2]=velocity[PROCESS2]
DELTA[X3]=-velocity[PROCESS1]-velocity[PROCESS2]+velocity[PROCESS3]-velocity[PROCESS4]
DELTA[X4]=-velocity[PROCESS1]-velocity[PROCESS2]-velocity[PROCESS3]+velocity[PROCESS4]
(But in this case I would have missed not just a "-1" entry).
Now I have changed every "-1" with "0" and the results are the same of matlab.
It was a stupid error since I would have recognized that those species
acted like enzymes.
thanks a lot for your help (as always).
g
2009/2/6 Moriyoshi Koizumi <mo...@sf...>:
> On Fri, Feb 6, 2009 at 12:51 AM, giuseppe aprea
> <apr...@gm...> wrote:
>
>> I guess ecell will associate ODE2Process' velocity to X2 Variable (PHA).
>> Is that right?
>
> Right, X2 is accumulated according to the value of the ODE2Process's activity.
>
>> Now I have 2 problems:
>>
>> - during compilation I get los of warnings of the kind:
>> "/usr/include/ecell-3.1/libecs/Entity.hpp:73: warning: comparison with
>> string literal results in unspecified behaviour"
>> I don't really understand if I am doing some fatal error in the code,
>> anyway I successfully get my .so objacts. Can I ignore this warning?
>
> Those warnings are basically harmless, but it was addressed in the
> newer releases. Give 3.1.107rc2 a try.
>
>> - if I compare the results with matlab ones they are quite different
>> both quantitatively (~20%) and qualitatively after "only" 60 sec.
>
> You apparently specified an wrong coeffient (-1). Each process denotes
> a flux, so variables given with negative coefficients have negative
> deltas.
>
>> By the way, does anybody know if there is some documentation about
>> Stepper settings (timestep, tolerance) or about how to make your own Stepper?
>
> Assuming you took a look at the E-Cell manual, there has been no
> comprehensive document known that elaborates on Stepper
> specifications. Sorry.
>
> By the way, you can write such simple equations with
> ExpressionFluxProcess'es. Attached is a version rewritten with them.
>
> Regards,
> Moriyoshi
>
|
|
From: Moriyoshi K. <mo...@sf...> - 2009-02-06 12:38:27
|
It seems I sent you a wrong version of the model file. Try this one instead. -- moriyoshi On Fri, Feb 6, 2009 at 7:07 PM, Moriyoshi Koizumi <mo...@sf...> wrote: > On Fri, Feb 6, 2009 at 12:51 AM, giuseppe aprea > <apr...@gm...> wrote: > >> I guess ecell will associate ODE2Process' velocity to X2 Variable (PHA). >> Is that right? > > Right, X2 is accumulated according to the value of the ODE2Process's activity. > >> Now I have 2 problems: >> >> - during compilation I get los of warnings of the kind: >> "/usr/include/ecell-3.1/libecs/Entity.hpp:73: warning: comparison with >> string literal results in unspecified behaviour" >> I don't really understand if I am doing some fatal error in the code, >> anyway I successfully get my .so objacts. Can I ignore this warning? > > Those warnings are basically harmless, but it was addressed in the > newer releases. Give 3.1.107rc2 a try. > >> - if I compare the results with matlab ones they are quite different >> both quantitatively (~20%) and qualitatively after "only" 60 sec. > > You apparently specified an wrong coeffient (-1). Each process denotes > a flux, so variables given with negative coefficients have negative > deltas. > >> By the way, does anybody know if there is some documentation about >> Stepper settings (timestep, tolerance) or about how to make your own Stepper? > > Assuming you took a look at the E-Cell manual, there has been no > comprehensive document known that elaborates on Stepper > specifications. Sorry. > > By the way, you can write such simple equations with > ExpressionFluxProcess'es. Attached is a version rewritten with them. > > Regards, > Moriyoshi > |
|
From: Moriyoshi K. <mo...@sf...> - 2009-02-06 12:32:32
|
Hi, Coincidentially I hit the same problem and that was fixed in the second release candidate :) http://downloads.sourceforge.net/ecell/ecell-3.1.107rc2.tar.bz2 Anyway, thanks for the report. -- moriyoshi On Fri, Feb 6, 2009 at 7:02 PM, Michele Mattioni <mat...@eb...> wrote: > Hy Moriyoshi, > > E-cell compile well, but when I tried to save the data I found a runtime problem > > Traceback (most recent call last): > File "/usr/local/bin/ecell3-session", line 234, in <module> > main() > File "/usr/local/bin/ecell3-session", line 229, in main > aConsole.loadScript( anEssFile, aParameters ) > File "/usr/local/bin/ecell3-session", line 56, in loadScript > execfile( ecsFile, aContext ) > File "/home/mattions/Work/model/MSN/Time_scales/trunk/sandbox/lu_ex.py", > line 51, in <module> > aDataFile.save(aVariableName + ".ecd") > File "/usr/local/lib/python2.5/site-packages/ecell/ECDDataFile.py", > line 91, in save > TableIO.writeArray( self.theFileName, self.theData, 1 ) > NameError: global name 'TableIO' is not defined > > The way to come over that is to change the import in the file ECDDataFile.py > from > > import ecell.TableIO > > to > > import ecell.TableIO as TableIO > > Cheers, > Michele. > > On Thu, Feb 5, 2009 at 11:31 AM, Moriyoshi Koizumi <mo...@sf...> wrote: >> Sorry, it seems I uploaded wrong files. Please try this one: >> >> http://chaperone.e-cell.org/downloads/ecell-3.1.107rc1.tar.bz2 >> >> -- moriyoshi >> >> >> >> On Thu, Feb 5, 2009 at 5:02 PM, Michele Mattioni <mat...@eb...> wrote: >>> Dear Moriyoshi, >>> >>> this is the error that I've got with this release: >>> >>> copying ecell/__init__.py -> build/lib.linux-i686-2.5/ecell >>> copying ecell/StepperStub.py -> build/lib.linux-i686-2.5/ecell >>> copying ecell/convertSBMLFunctions.py -> build/lib.linux-i686-2.5/ecell >>> error: package directory 'ecell/SessionManager' does not exist >>> make[4]: *** [all-local] Error 1 >>> make[4]: Leaving directory >>> `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell/pyecell' >>> make[3]: *** [all-recursive] Error 1 >>> make[3]: Leaving directory >>> `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell' >>> make[2]: *** [all] Error 2 >>> make[2]: Leaving directory >>> `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell' >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1' >>> make: *** [all] Error 2 >>> >>> Thanks for the reply. >>> >>> >>> On Thu, Feb 5, 2009 at 7:00 AM, Moriyoshi Koizumi <mor...@gm...> wrote: >>>> Hi, >>>> >>>> Sorry for keeping you waiting. >>>> >>>> Could you please try out the latest release 3.1.107rc1? >>>> You can download it from the following location: >>>> >>>> http://downloads.sourceforge.net/ecell/ecell-3.1.107rc1.tar.bz2 >>>> >>>> Thanks, >>>> Moriyoshi >>>> >>>> On Fri, Jan 30, 2009 at 8:01 PM, Michele Mattioni <mat...@eb...> wrote: >>>>> Dear list, >>>>> >>>>> I'm trying to compile E-Cell from the source, because I'm running >>>>> Ubuntu Intrepid Ibex but the compilation fail with this error: >>>>> >>>>> make[5]: Entering directory >>>>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' >>>>> /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H >>>>> -I. -I.. -I.. -I../.. -I/home/mattions/Work/progs/ecell/ecell-3.1.106 >>>>> -I../../libltdl -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2 >>>>> -Wno-pmf-conversions -MT PropertySlot.lo -MD -MP -MF >>>>> .deps/PropertySlot.Tpo -c -o PropertySlot.lo PropertySlot.cpp >>>>> g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../.. >>>>> -I/home/mattions/Work/progs/ecell/ecell-3.1.106 -I../../libltdl >>>>> -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2 -Wno-pmf-conversions >>>>> -MT PropertySlot.lo -MD -MP -MF .deps/PropertySlot.Tpo -c >>>>> PropertySlot.cpp -fPIC -DPIC -o .libs/PropertySlot.o >>>>> In file included from PropertyInterface.hpp:38, >>>>> from PropertySlot.cpp:38: >>>>> PropertySlot.hpp:305: error: declaration of 'typedef class >>>>> libecs::ConcretePropertySlot<T, SlotType_> >>>>> libecs::LoadSaveConcretePropertySlot<T, >>>>> SlotType_>::ConcretePropertySlot' >>>>> PropertySlot.hpp:155: error: changes meaning of 'ConcretePropertySlot' >>>>> from 'class libecs::ConcretePropertySlot<T, SlotType_>' >>>>> In file included from PropertyInterface.hpp:39, >>>>> from PropertySlot.cpp:38: >>>>> PropertySlotProxy.hpp:166: error: declaration of 'typedef class >>>>> libecs::PropertySlot<T> >>>>> libecs::ConcretePropertySlotProxy<T>::PropertySlot' >>>>> PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from >>>>> 'class libecs::PropertySlot<T>' >>>>> In file included from PropertySlot.cpp:38: >>>>> PropertyInterface.hpp:92: error: declaration of 'typedef class >>>>> libecs::PropertySlot<T> libecs::PropertyInterface<T>::PropertySlot' >>>>> PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from >>>>> 'class libecs::PropertySlot<T>' >>>>> make[5]: *** [PropertySlot.lo] Error 1 >>>>> make[5]: Leaving directory >>>>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' >>>>> make[4]: *** [all-recursive] Error 1 >>>>> make[4]: Leaving directory >>>>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' >>>>> make[3]: *** [all-recursive] Error 1 >>>>> make[3]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell' >>>>> make[2]: *** [all] Error 2 >>>>> make[2]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell' >>>>> make[1]: *** [all-recursive] Error 1 >>>>> make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106' >>>>> make: *** [all] Error 2 >>>>> >>>>> >>>>> Do you know how to fix it? >>>>> Or can you provide debs also for this release of ubuntu? >>>>> >>>>> Regards, >>>>> Michele >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.net email is sponsored by: >>>>> SourcForge Community >>>>> SourceForge wants to tell your story. >>>>> http://p.sf.net/sfu/sf-spreadtheword >>>>> _______________________________________________ >>>>> Ecell-users mailing list >>>>> Ece...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/ecell-users >>>>> >>>> >>> >> > |
|
From: Moriyoshi K. <mo...@sf...> - 2009-02-06 10:07:17
|
On Fri, Feb 6, 2009 at 12:51 AM, giuseppe aprea <apr...@gm...> wrote: > I guess ecell will associate ODE2Process' velocity to X2 Variable (PHA). > Is that right? Right, X2 is accumulated according to the value of the ODE2Process's activity. > Now I have 2 problems: > > - during compilation I get los of warnings of the kind: > "/usr/include/ecell-3.1/libecs/Entity.hpp:73: warning: comparison with > string literal results in unspecified behaviour" > I don't really understand if I am doing some fatal error in the code, > anyway I successfully get my .so objacts. Can I ignore this warning? Those warnings are basically harmless, but it was addressed in the newer releases. Give 3.1.107rc2 a try. > - if I compare the results with matlab ones they are quite different > both quantitatively (~20%) and qualitatively after "only" 60 sec. You apparently specified an wrong coeffient (-1). Each process denotes a flux, so variables given with negative coefficients have negative deltas. > By the way, does anybody know if there is some documentation about > Stepper settings (timestep, tolerance) or about how to make your own Stepper? Assuming you took a look at the E-Cell manual, there has been no comprehensive document known that elaborates on Stepper specifications. Sorry. By the way, you can write such simple equations with ExpressionFluxProcess'es. Attached is a version rewritten with them. Regards, Moriyoshi |
|
From: Michele M. <mat...@eb...> - 2009-02-06 10:02:55
|
Hy Moriyoshi,
E-cell compile well, but when I tried to save the data I found a runtime problem
Traceback (most recent call last):
File "/usr/local/bin/ecell3-session", line 234, in <module>
main()
File "/usr/local/bin/ecell3-session", line 229, in main
aConsole.loadScript( anEssFile, aParameters )
File "/usr/local/bin/ecell3-session", line 56, in loadScript
execfile( ecsFile, aContext )
File "/home/mattions/Work/model/MSN/Time_scales/trunk/sandbox/lu_ex.py",
line 51, in <module>
aDataFile.save(aVariableName + ".ecd")
File "/usr/local/lib/python2.5/site-packages/ecell/ECDDataFile.py",
line 91, in save
TableIO.writeArray( self.theFileName, self.theData, 1 )
NameError: global name 'TableIO' is not defined
The way to come over that is to change the import in the file ECDDataFile.py
from
import ecell.TableIO
to
import ecell.TableIO as TableIO
Cheers,
Michele.
On Thu, Feb 5, 2009 at 11:31 AM, Moriyoshi Koizumi <mo...@sf...> wrote:
> Sorry, it seems I uploaded wrong files. Please try this one:
>
> http://chaperone.e-cell.org/downloads/ecell-3.1.107rc1.tar.bz2
>
> -- moriyoshi
>
>
>
> On Thu, Feb 5, 2009 at 5:02 PM, Michele Mattioni <mat...@eb...> wrote:
>> Dear Moriyoshi,
>>
>> this is the error that I've got with this release:
>>
>> copying ecell/__init__.py -> build/lib.linux-i686-2.5/ecell
>> copying ecell/StepperStub.py -> build/lib.linux-i686-2.5/ecell
>> copying ecell/convertSBMLFunctions.py -> build/lib.linux-i686-2.5/ecell
>> error: package directory 'ecell/SessionManager' does not exist
>> make[4]: *** [all-local] Error 1
>> make[4]: Leaving directory
>> `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell/pyecell'
>> make[3]: *** [all-recursive] Error 1
>> make[3]: Leaving directory
>> `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell'
>> make[2]: *** [all] Error 2
>> make[2]: Leaving directory
>> `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell'
>> make[1]: *** [all-recursive] Error 1
>> make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1'
>> make: *** [all] Error 2
>>
>> Thanks for the reply.
>>
>>
>> On Thu, Feb 5, 2009 at 7:00 AM, Moriyoshi Koizumi <mor...@gm...> wrote:
>>> Hi,
>>>
>>> Sorry for keeping you waiting.
>>>
>>> Could you please try out the latest release 3.1.107rc1?
>>> You can download it from the following location:
>>>
>>> http://downloads.sourceforge.net/ecell/ecell-3.1.107rc1.tar.bz2
>>>
>>> Thanks,
>>> Moriyoshi
>>>
>>> On Fri, Jan 30, 2009 at 8:01 PM, Michele Mattioni <mat...@eb...> wrote:
>>>> Dear list,
>>>>
>>>> I'm trying to compile E-Cell from the source, because I'm running
>>>> Ubuntu Intrepid Ibex but the compilation fail with this error:
>>>>
>>>> make[5]: Entering directory
>>>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs'
>>>> /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H
>>>> -I. -I.. -I.. -I../.. -I/home/mattions/Work/progs/ecell/ecell-3.1.106
>>>> -I../../libltdl -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2
>>>> -Wno-pmf-conversions -MT PropertySlot.lo -MD -MP -MF
>>>> .deps/PropertySlot.Tpo -c -o PropertySlot.lo PropertySlot.cpp
>>>> g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../..
>>>> -I/home/mattions/Work/progs/ecell/ecell-3.1.106 -I../../libltdl
>>>> -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2 -Wno-pmf-conversions
>>>> -MT PropertySlot.lo -MD -MP -MF .deps/PropertySlot.Tpo -c
>>>> PropertySlot.cpp -fPIC -DPIC -o .libs/PropertySlot.o
>>>> In file included from PropertyInterface.hpp:38,
>>>> from PropertySlot.cpp:38:
>>>> PropertySlot.hpp:305: error: declaration of 'typedef class
>>>> libecs::ConcretePropertySlot<T, SlotType_>
>>>> libecs::LoadSaveConcretePropertySlot<T,
>>>> SlotType_>::ConcretePropertySlot'
>>>> PropertySlot.hpp:155: error: changes meaning of 'ConcretePropertySlot'
>>>> from 'class libecs::ConcretePropertySlot<T, SlotType_>'
>>>> In file included from PropertyInterface.hpp:39,
>>>> from PropertySlot.cpp:38:
>>>> PropertySlotProxy.hpp:166: error: declaration of 'typedef class
>>>> libecs::PropertySlot<T>
>>>> libecs::ConcretePropertySlotProxy<T>::PropertySlot'
>>>> PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from
>>>> 'class libecs::PropertySlot<T>'
>>>> In file included from PropertySlot.cpp:38:
>>>> PropertyInterface.hpp:92: error: declaration of 'typedef class
>>>> libecs::PropertySlot<T> libecs::PropertyInterface<T>::PropertySlot'
>>>> PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from
>>>> 'class libecs::PropertySlot<T>'
>>>> make[5]: *** [PropertySlot.lo] Error 1
>>>> make[5]: Leaving directory
>>>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs'
>>>> make[4]: *** [all-recursive] Error 1
>>>> make[4]: Leaving directory
>>>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs'
>>>> make[3]: *** [all-recursive] Error 1
>>>> make[3]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell'
>>>> make[2]: *** [all] Error 2
>>>> make[2]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell'
>>>> make[1]: *** [all-recursive] Error 1
>>>> make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106'
>>>> make: *** [all] Error 2
>>>>
>>>>
>>>> Do you know how to fix it?
>>>> Or can you provide debs also for this release of ubuntu?
>>>>
>>>> Regards,
>>>> Michele
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by:
>>>> SourcForge Community
>>>> SourceForge wants to tell your story.
>>>> http://p.sf.net/sfu/sf-spreadtheword
>>>> _______________________________________________
>>>> Ecell-users mailing list
>>>> Ece...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/ecell-users
>>>>
>>>
>>
>
|
|
From: giuseppe a. <apr...@gm...> - 2009-02-05 15:51:27
|
Dear all,
I am giuseppe and I am using IE-Cell SE Version 3.1.106 on kubuntu 8.04.
I am experiencing some problems in implementig new processes.
I am trying to use ecell as an ode solver: the differential equations are:
pow1a=(ks3/x(3))^n3;
pow1b=(ks4/x(4))^n4;
pow2a=(x(3)/sm3)^a3;
pow2b=(x(4)/sm4)^a4;
mu=mu1*(1/(1+pow1a))*(1/(1+pow1b))*(1-pow2a)*(1-pow2b)
dx(1)dt = mu*x(1)
dx(2)dt = ((k1*mu)+k2)*x(1)
dx(3)dt = -((alp*mu)+gam)*x(1)
dx(4)dt = -((mu/yRS2)+mS2)*x(1)
where ks3,ks4,n3,n4,sm3,sm4,a3,a4,mu1,k1,k2,alp,gam,yRS2,mS2
are numerical parameters; they keep the same value throughout the
computation. I wrote 4 new processes (which are attached); one for
each equation. As far as I understand ona can use ecell to as an ode
solver once given a process for each equation. the system should
assign to each "1" entry in the VariableReferenceList the proper
velocity in the following way. Given this entry in .em file:
...........
Process ODE2Process( ODE2 )
{
mu1 0.303;
n1 3.5938;
n2 2.213;
ks1 22.836;
ks2 0.234;
sm1 90.11;
sm2 10.11;
a1 3.19;
a2 0.97;
k1 0.008;
k2 0.034;
VariableReferenceList[X1 Variable:.:BIOMASS -1]
[X2 Variable:.:PHA 1]
[X3 Variable:.:NUTRIENT -1]
[X4 Variable:.:INHIBITOR -1];
}
...........
I guess ecell will associate ODE2Process' velocity to X2 Variable (PHA).
Is that right?
Now I have 2 problems:
- during compilation I get los of warnings of the kind:
"/usr/include/ecell-3.1/libecs/Entity.hpp:73: warning: comparison with
string literal results in unspecified behaviour"
I don't really understand if I am doing some fatal error in the code,
anyway I successfully get my .so objacts. Can I ignore this warning?
- if I compare the results with matlab ones they are quite different
both quantitatively (~20%) and qualitatively after "only" 60 sec.
By the way, does anybody know if there is some documentation about
Stepper settings (timestep, tolerance) or about how to make your own Stepper?
Many Thanks in advance,
Giuseppe
|
|
From: Moriyoshi K. <mo...@sf...> - 2009-02-05 12:20:54
|
Sorry, it seems I uploaded wrong files. Please try this one: http://chaperone.e-cell.org/downloads/ecell-3.1.107rc1.tar.bz2 -- moriyoshi On Thu, Feb 5, 2009 at 5:02 PM, Michele Mattioni <mat...@eb...> wrote: > Dear Moriyoshi, > > this is the error that I've got with this release: > > copying ecell/__init__.py -> build/lib.linux-i686-2.5/ecell > copying ecell/StepperStub.py -> build/lib.linux-i686-2.5/ecell > copying ecell/convertSBMLFunctions.py -> build/lib.linux-i686-2.5/ecell > error: package directory 'ecell/SessionManager' does not exist > make[4]: *** [all-local] Error 1 > make[4]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell/pyecell' > make[3]: *** [all-recursive] Error 1 > make[3]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell' > make[2]: *** [all] Error 2 > make[2]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1/ecell' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.107rc1' > make: *** [all] Error 2 > > Thanks for the reply. > > > On Thu, Feb 5, 2009 at 7:00 AM, Moriyoshi Koizumi <mor...@gm...> wrote: >> Hi, >> >> Sorry for keeping you waiting. >> >> Could you please try out the latest release 3.1.107rc1? >> You can download it from the following location: >> >> http://downloads.sourceforge.net/ecell/ecell-3.1.107rc1.tar.bz2 >> >> Thanks, >> Moriyoshi >> >> On Fri, Jan 30, 2009 at 8:01 PM, Michele Mattioni <mat...@eb...> wrote: >>> Dear list, >>> >>> I'm trying to compile E-Cell from the source, because I'm running >>> Ubuntu Intrepid Ibex but the compilation fail with this error: >>> >>> make[5]: Entering directory >>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' >>> /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H >>> -I. -I.. -I.. -I../.. -I/home/mattions/Work/progs/ecell/ecell-3.1.106 >>> -I../../libltdl -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2 >>> -Wno-pmf-conversions -MT PropertySlot.lo -MD -MP -MF >>> .deps/PropertySlot.Tpo -c -o PropertySlot.lo PropertySlot.cpp >>> g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../.. >>> -I/home/mattions/Work/progs/ecell/ecell-3.1.106 -I../../libltdl >>> -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2 -Wno-pmf-conversions >>> -MT PropertySlot.lo -MD -MP -MF .deps/PropertySlot.Tpo -c >>> PropertySlot.cpp -fPIC -DPIC -o .libs/PropertySlot.o >>> In file included from PropertyInterface.hpp:38, >>> from PropertySlot.cpp:38: >>> PropertySlot.hpp:305: error: declaration of 'typedef class >>> libecs::ConcretePropertySlot<T, SlotType_> >>> libecs::LoadSaveConcretePropertySlot<T, >>> SlotType_>::ConcretePropertySlot' >>> PropertySlot.hpp:155: error: changes meaning of 'ConcretePropertySlot' >>> from 'class libecs::ConcretePropertySlot<T, SlotType_>' >>> In file included from PropertyInterface.hpp:39, >>> from PropertySlot.cpp:38: >>> PropertySlotProxy.hpp:166: error: declaration of 'typedef class >>> libecs::PropertySlot<T> >>> libecs::ConcretePropertySlotProxy<T>::PropertySlot' >>> PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from >>> 'class libecs::PropertySlot<T>' >>> In file included from PropertySlot.cpp:38: >>> PropertyInterface.hpp:92: error: declaration of 'typedef class >>> libecs::PropertySlot<T> libecs::PropertyInterface<T>::PropertySlot' >>> PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from >>> 'class libecs::PropertySlot<T>' >>> make[5]: *** [PropertySlot.lo] Error 1 >>> make[5]: Leaving directory >>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' >>> make[4]: *** [all-recursive] Error 1 >>> make[4]: Leaving directory >>> `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' >>> make[3]: *** [all-recursive] Error 1 >>> make[3]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell' >>> make[2]: *** [all] Error 2 >>> make[2]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell' >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106' >>> make: *** [all] Error 2 >>> >>> >>> Do you know how to fix it? >>> Or can you provide debs also for this release of ubuntu? >>> >>> Regards, >>> Michele >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by: >>> SourcForge Community >>> SourceForge wants to tell your story. >>> http://p.sf.net/sfu/sf-spreadtheword >>> _______________________________________________ >>> Ecell-users mailing list >>> Ece...@li... >>> https://lists.sourceforge.net/lists/listinfo/ecell-users >>> >> > |
|
From: Moriyoshi K. <mor...@gm...> - 2009-02-05 07:00:05
|
Hi, Sorry for keeping you waiting. Could you please try out the latest release 3.1.107rc1? You can download it from the following location: http://downloads.sourceforge.net/ecell/ecell-3.1.107rc1.tar.bz2 Thanks, Moriyoshi On Fri, Jan 30, 2009 at 8:01 PM, Michele Mattioni <mat...@eb...> wrote: > Dear list, > > I'm trying to compile E-Cell from the source, because I'm running > Ubuntu Intrepid Ibex but the compilation fail with this error: > > make[5]: Entering directory > `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' > /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H > -I. -I.. -I.. -I../.. -I/home/mattions/Work/progs/ecell/ecell-3.1.106 > -I../../libltdl -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2 > -Wno-pmf-conversions -MT PropertySlot.lo -MD -MP -MF > .deps/PropertySlot.Tpo -c -o PropertySlot.lo PropertySlot.cpp > g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../.. > -I/home/mattions/Work/progs/ecell/ecell-3.1.106 -I../../libltdl > -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2 -Wno-pmf-conversions > -MT PropertySlot.lo -MD -MP -MF .deps/PropertySlot.Tpo -c > PropertySlot.cpp -fPIC -DPIC -o .libs/PropertySlot.o > In file included from PropertyInterface.hpp:38, > from PropertySlot.cpp:38: > PropertySlot.hpp:305: error: declaration of 'typedef class > libecs::ConcretePropertySlot<T, SlotType_> > libecs::LoadSaveConcretePropertySlot<T, > SlotType_>::ConcretePropertySlot' > PropertySlot.hpp:155: error: changes meaning of 'ConcretePropertySlot' > from 'class libecs::ConcretePropertySlot<T, SlotType_>' > In file included from PropertyInterface.hpp:39, > from PropertySlot.cpp:38: > PropertySlotProxy.hpp:166: error: declaration of 'typedef class > libecs::PropertySlot<T> > libecs::ConcretePropertySlotProxy<T>::PropertySlot' > PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from > 'class libecs::PropertySlot<T>' > In file included from PropertySlot.cpp:38: > PropertyInterface.hpp:92: error: declaration of 'typedef class > libecs::PropertySlot<T> libecs::PropertyInterface<T>::PropertySlot' > PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from > 'class libecs::PropertySlot<T>' > make[5]: *** [PropertySlot.lo] Error 1 > make[5]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' > make[4]: *** [all-recursive] Error 1 > make[4]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs' > make[3]: *** [all-recursive] Error 1 > make[3]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell' > make[2]: *** [all] Error 2 > make[2]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106' > make: *** [all] Error 2 > > > Do you know how to fix it? > Or can you provide debs also for this release of ubuntu? > > Regards, > Michele > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users > |
|
From: Michele M. <mat...@eb...> - 2009-01-30 11:01:35
|
Dear list,
I'm trying to compile E-Cell from the source, because I'm running
Ubuntu Intrepid Ibex but the compilation fail with this error:
make[5]: Entering directory
`/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs'
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H
-I. -I.. -I.. -I../.. -I/home/mattions/Work/progs/ecell/ecell-3.1.106
-I../../libltdl -I/usr/include -g -O2 -Wno-pmf-conversions -g -O2
-Wno-pmf-conversions -MT PropertySlot.lo -MD -MP -MF
.deps/PropertySlot.Tpo -c -o PropertySlot.lo PropertySlot.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../..
-I/home/mattions/Work/progs/ecell/ecell-3.1.106 -I../../libltdl
-I/usr/include -g -O2 -Wno-pmf-conversions -g -O2 -Wno-pmf-conversions
-MT PropertySlot.lo -MD -MP -MF .deps/PropertySlot.Tpo -c
PropertySlot.cpp -fPIC -DPIC -o .libs/PropertySlot.o
In file included from PropertyInterface.hpp:38,
from PropertySlot.cpp:38:
PropertySlot.hpp:305: error: declaration of 'typedef class
libecs::ConcretePropertySlot<T, SlotType_>
libecs::LoadSaveConcretePropertySlot<T,
SlotType_>::ConcretePropertySlot'
PropertySlot.hpp:155: error: changes meaning of 'ConcretePropertySlot'
from 'class libecs::ConcretePropertySlot<T, SlotType_>'
In file included from PropertyInterface.hpp:39,
from PropertySlot.cpp:38:
PropertySlotProxy.hpp:166: error: declaration of 'typedef class
libecs::PropertySlot<T>
libecs::ConcretePropertySlotProxy<T>::PropertySlot'
PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from
'class libecs::PropertySlot<T>'
In file included from PropertySlot.cpp:38:
PropertyInterface.hpp:92: error: declaration of 'typedef class
libecs::PropertySlot<T> libecs::PropertyInterface<T>::PropertySlot'
PropertySlot.hpp:94: error: changes meaning of 'PropertySlot' from
'class libecs::PropertySlot<T>'
make[5]: *** [PropertySlot.lo] Error 1
make[5]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell/libecs'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106/ecell'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.106'
make: *** [all] Error 2
Do you know how to fix it?
Or can you provide debs also for this release of ubuntu?
Regards,
Michele
|
|
From: Koichi T. <sh...@sf...> - 2008-08-10 23:59:15
|
Mozo, Can you get a patch from Kaizu for the bug caught by the assertion when you have time after the ICSB stuff is done? Koichi > Hi Koichi, > > I cannot handle this problem right now since I'm way busy making stuff > for ICSB 2008. Would you mind taking care of this instead of me? > > Thanks, > Moriyoshi > > On Mon, Aug 11, 2008 at 4:17 AM, Koichi Takahashi <sh...@sf...> wrote: >> Hi Lu, >> >> Thanks for the report. >> >> Moriyoshi will follow up, but he'll need to know what kind of >> model you tried to run. How many processes/variables >> did you have? Also, make sure all steppers have >> at least one variable/process connected. >> >> Koichi >> >> >> >>> Hi >>> >>> I got the following assertion when I run the model. >>> >>> python: /usr/include/boost/multi_array/base.hpp:136: : Assertion >>> `size_type(idx - index_bases[0]) < extents[0]' failed. >>> Aborted >>> >>> Could the developer explain to me what does this mean, please? >>> >>> Could it possible because I only included PythonProcess in my model? >>> >>> Best wishes and wish to hearing from you soon >>> >>> yours Lu >>> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Ecell-users mailing list >> Ece...@li... >> https://lists.sourceforge.net/lists/listinfo/ecell-users >> > > > |
|
From: Koichi T. <sh...@sf...> - 2008-08-10 23:57:44
|
PassiveStepper does nothing unless it is interrupted
by another Stepper. Therefore, a model with only
a PassiveStepper does nothing, too. You can use
DiscreteTimeStepper to check if your process is working
correctly, and then add the main part of the model
with ODEStepper or DiscreteEventStepper, and connect
it to PassiveStepper, if necessary.
Koichi
> Hi
>
> The attachment is a very simple model that only contains one
> PythonProcess, doing an assignment.
> But I can not get correct number for totCa.
> Could you please check for me, which part is wrong?
>
> Best Wishes and wish to hearing from you soon.
>
> Lu
>
>
>> Hi
>>
>> Thank you so much for reply.
>> Finally, I figured out the problem. (Thank you for your reminder)
>> It is because I add one stepper which is not used by any of the processes
>> I listed. Thus the system gives this assertion.
>>
>> Thank you again for help.
>>
>> Best Wishes
>> Lu
>>
>>
>>> Hi Lu,
>>>
>>> Thanks for the report.
>>>
>>> Moriyoshi will follow up, but he'll need to know what kind of
>>> model you tried to run. How many processes/variables
>>> did you have? Also, make sure all steppers have
>>> at least one variable/process connected.
>>>
>>> Koichi
>>>
>>>
>>>
>>>> Hi
>>>>
>>>> I got the following assertion when I run the model.
>>>>
>>>> python: /usr/include/boost/multi_array/base.hpp:136: : Assertion
>>>> `size_type(idx - index_bases[0]) < extents[0]' failed.
>>>> Aborted
>>>>
>>>> Could the developer explain to me what does this mean, please?
>>>>
>>>> Could it possible because I only included PythonProcess in my model?
>>>>
>>>> Best wishes and wish to hearing from you soon
>>>>
>>>> yours Lu
>>>>
>>
>> --
>> Lu Li
>> PhD student in Computational Neurobiology
>> EMBL-European Bioinformatics Institute
>> Cambridge, UK
>> . .' '. _
>> . . . (_\
>> . . . -{{((|8<
>> ' . . ' ' . . ' (_/
>>
>
>
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Ecell-users mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-users
|
|
From: Moriyoshi K. <mo...@sf...> - 2008-08-10 23:31:48
|
Hi Koichi, I cannot handle this problem right now since I'm way busy making stuff for ICSB 2008. Would you mind taking care of this instead of me? Thanks, Moriyoshi On Mon, Aug 11, 2008 at 4:17 AM, Koichi Takahashi <sh...@sf...> wrote: > Hi Lu, > > Thanks for the report. > > Moriyoshi will follow up, but he'll need to know what kind of > model you tried to run. How many processes/variables > did you have? Also, make sure all steppers have > at least one variable/process connected. > > Koichi > > > >> Hi >> >> I got the following assertion when I run the model. >> >> python: /usr/include/boost/multi_array/base.hpp:136: : Assertion >> `size_type(idx - index_bases[0]) < extents[0]' failed. >> Aborted >> >> Could the developer explain to me what does this mean, please? >> >> Could it possible because I only included PythonProcess in my model? >> >> Best wishes and wish to hearing from you soon >> >> yours Lu >> > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users > -- Moriyoshi Koizumi <mor...@gm...> (also reachable on <mo...@sf...>) |
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From: Koichi T. <sh...@sf...> - 2008-08-10 22:22:19
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Hi Lu, Thanks for the report again. Mozo, This is a user unfriendly design and has to be improved asap. Kaizu is aware of the problem and he could make a suggestion as to how the code should be modified. thanks, Koichi > Hi > > Thank you so much for reply. > Finally, I figured out the problem. (Thank you for your reminder) > It is because I add one stepper which is not used by any of the processes > I listed. Thus the system gives this assertion. > > Thank you again for help. > > Best Wishes > Lu > > >> Hi Lu, >> >> Thanks for the report. >> >> Moriyoshi will follow up, but he'll need to know what kind of >> model you tried to run. How many processes/variables >> did you have? Also, make sure all steppers have >> at least one variable/process connected. >> >> Koichi >> >> >> >>> Hi >>> >>> I got the following assertion when I run the model. >>> >>> python: /usr/include/boost/multi_array/base.hpp:136: : Assertion >>> `size_type(idx - index_bases[0]) < extents[0]' failed. >>> Aborted >>> >>> Could the developer explain to me what does this mean, please? >>> >>> Could it possible because I only included PythonProcess in my model? >>> >>> Best wishes and wish to hearing from you soon >>> >>> yours Lu >>> > > |
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From: Lu L. <lu...@eb...> - 2008-08-10 22:04:08
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Hi
The attachment is a very simple model that only contains one
PythonProcess, doing an assignment.
But I can not get correct number for totCa.
Could you please check for me, which part is wrong?
Best Wishes and wish to hearing from you soon.
Lu
> Hi
>
> Thank you so much for reply.
> Finally, I figured out the problem. (Thank you for your reminder)
> It is because I add one stepper which is not used by any of the processes
> I listed. Thus the system gives this assertion.
>
> Thank you again for help.
>
> Best Wishes
> Lu
>
>
>> Hi Lu,
>>
>> Thanks for the report.
>>
>> Moriyoshi will follow up, but he'll need to know what kind of
>> model you tried to run. How many processes/variables
>> did you have? Also, make sure all steppers have
>> at least one variable/process connected.
>>
>> Koichi
>>
>>
>>
>>> Hi
>>>
>>> I got the following assertion when I run the model.
>>>
>>> python: /usr/include/boost/multi_array/base.hpp:136: : Assertion
>>> `size_type(idx - index_bases[0]) < extents[0]' failed.
>>> Aborted
>>>
>>> Could the developer explain to me what does this mean, please?
>>>
>>> Could it possible because I only included PythonProcess in my model?
>>>
>>> Best wishes and wish to hearing from you soon
>>>
>>> yours Lu
>>>
>>
>
>
> --
> Lu Li
> PhD student in Computational Neurobiology
> EMBL-European Bioinformatics Institute
> Cambridge, UK
> . .' '. _
> . . . (_\
> . . . -{{((|8<
> ' . . ' ' . . ' (_/
>
--
Lu Li
PhD student in Computational Neurobiology
EMBL-European Bioinformatics Institute
Cambridge, UK
. .' '. _
. . . (_\
. . . -{{((|8<
' . . ' ' . . ' (_/ |
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From: Lu L. <lu...@eb...> - 2008-08-10 21:43:11
|
Hi
Thank you so much for reply.
Finally, I figured out the problem. (Thank you for your reminder)
It is because I add one stepper which is not used by any of the processes
I listed. Thus the system gives this assertion.
Thank you again for help.
Best Wishes
Lu
> Hi Lu,
>
> Thanks for the report.
>
> Moriyoshi will follow up, but he'll need to know what kind of
> model you tried to run. How many processes/variables
> did you have? Also, make sure all steppers have
> at least one variable/process connected.
>
> Koichi
>
>
>
>> Hi
>>
>> I got the following assertion when I run the model.
>>
>> python: /usr/include/boost/multi_array/base.hpp:136: : Assertion
>> `size_type(idx - index_bases[0]) < extents[0]' failed.
>> Aborted
>>
>> Could the developer explain to me what does this mean, please?
>>
>> Could it possible because I only included PythonProcess in my model?
>>
>> Best wishes and wish to hearing from you soon
>>
>> yours Lu
>>
>
--
Lu Li
PhD student in Computational Neurobiology
EMBL-European Bioinformatics Institute
Cambridge, UK
. .' '. _
. . . (_\
. . . -{{((|8<
' . . ' ' . . ' (_/
|
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From: Koichi T. <sh...@sf...> - 2008-08-10 19:17:26
|
Hi Lu, Thanks for the report. Moriyoshi will follow up, but he'll need to know what kind of model you tried to run. How many processes/variables did you have? Also, make sure all steppers have at least one variable/process connected. Koichi > Hi > > I got the following assertion when I run the model. > > python: /usr/include/boost/multi_array/base.hpp:136: : Assertion > `size_type(idx - index_bases[0]) < extents[0]' failed. > Aborted > > Could the developer explain to me what does this mean, please? > > Could it possible because I only included PythonProcess in my model? > > Best wishes and wish to hearing from you soon > > yours Lu > |
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From: Lu L. <lu...@eb...> - 2008-08-10 18:26:25
|
Hi I got the following assertion when I run the model. python: /usr/include/boost/multi_array/base.hpp:136: : Assertion `size_type(idx - index_bases[0]) < extents[0]' failed. Aborted Could the developer explain to me what does this mean, please? Could it possible because I only included PythonProcess in my model? Best wishes and wish to hearing from you soon yours Lu -- Lu Li PhD student in Computational Neurobiology EMBL-European Bioinformatics Institute Cambridge, UK |
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From: giuseppe a. <apr...@gm...> - 2008-05-13 12:58:55
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hallo,
I am trying to convert the attached simple sbml models to eml format
using ecell3-sbml2eml.
Although the models are extremely simple I get an error:
> ecell3-sbml2eml BIOMD0000000005.xml
Traceback (most recent call last):
File "/usr/local/bin/ecell3-sbml2eml", line 99, in <module>
anEml = convertSBML2EML( aSbmlString )
File "/usr/local/lib/python2.5/site-packages/ecell/convertSBML2EML.py",
line 45, in convertSBML2EML
theModel = SBML_Model( aSBMLDocument, aSBMLModel )
File "/usr/local/lib/python2.5/site-packages/ecell/convertSBMLFunctions.py",
line 136, in __init__
self.CompartmentList = getCompartment( aSBMLmodel )
File "/usr/local/lib/python2.5/site-packages/ecell/SbmlFunctions.py",
line 49, in getCompartment
NumCompartment = theList.getNumItems()
File "/usr/local/lib/python2.5/site-packages/libsbml/libsbml.py",
line 7517, in <lambda>
__getattr__ = lambda self, name: _swig_getattr(self,
ListOfCompartments, name)
File "/usr/local/lib/python2.5/site-packages/libsbml/libsbml.py",
line 35, in _swig_getattr
raise AttributeError,name
AttributeError: getNumItems
> ecell3-sbml2eml BIOMD0000000006.xml
Traceback (most recent call last):
File "/usr/local/bin/ecell3-sbml2eml", line 99, in <module>
anEml = convertSBML2EML( aSbmlString )
File "/usr/local/lib/python2.5/site-packages/ecell/convertSBML2EML.py",
line 45, in convertSBML2EML
theModel = SBML_Model( aSBMLDocument, aSBMLModel )
File "/usr/local/lib/python2.5/site-packages/ecell/convertSBMLFunctions.py",
line 136, in __init__
self.CompartmentList = getCompartment( aSBMLmodel )
File "/usr/local/lib/python2.5/site-packages/ecell/SbmlFunctions.py",
line 49, in getCompartment
NumCompartment = theList.getNumItems()
File "/usr/local/lib/python2.5/site-packages/libsbml/libsbml.py",
line 7517, in <lambda>
__getattr__ = lambda self, name: _swig_getattr(self,
ListOfCompartments, name)
File "/usr/local/lib/python2.5/site-packages/libsbml/libsbml.py",
line 35, in _swig_getattr
raise AttributeError,name
AttributeError: getNumItems
I am using ecell-3.1.106 and libsbml-3.1.1 . Otherwise, if I use
ecell-3.1.105 and 2.3.4 I don't get errors
but it just "translate" processes and not metabolites
Any idea?
thanks,
giuseppe
|
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From: giuseppe a. <apr...@gm...> - 2008-05-12 16:12:27
|
Hi everybody, my problem is about using ecell3-model-editor. I am using ecell-3.1.106 on kubuntu 8.04 (hardy, 64bit). Installation was fine without errors. When I try to launch ecell3-model-editor I get a double "Segmentation fault" record on the terminal. Nevertheless the application starts and seems to work properly. I wonder why I got that fault messages. Another problem is when I try to get a layout starting with the .eml file only. I have a .eml file describing a quite complicated model and i would just like to generate a layout from it and then do some modifications using the graphical tools. First of all the application seems not to be able to generate a layout only for the selected SYSTEM and not the ones in/under it. The second problem is that if you try to modify the layout and save it, you can do it but then, when you try to reload your modified model you have lost your layout. Is this behaviour correct? Finally I wonder if there is a way to have a wider space to draw metabolic pathways in ecell3-model-editor. Many thanks, Giuseppe |
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From: Koichi T. <sh...@e-...> - 2008-03-20 02:09:47
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Hi Lu,
1. Expression string in an ExpressionFluxProcess represents a flux.
Therefore, your expression means a zero-th order flux.
> da/dt = -K^2 and db/dt = K^2
2. In E-Cell, It is the user's responsibility to ensure unit
consistency.
3. This is a biochemistry question, rather than a software question.
Your expression is Kch [C1]^2 / (K1 + [C1]^2) ( [C2] - [C1] ).
It seems like to have a form of a Hill equation multiplied by
a concentration gradient. If Kch really has the unit [1/s], there
must be an additional factor that converts the unit of the second
term (concentration difference) to the same [1/s]. How you do this
depends on what you want to model. If you assume it is
linearly dependent on the concentration difference,
you can replace ([C2]-[C1]) with something like lambda ([C2]-[C1]).
Lambda must have a unit [1/M].
4. Expression processes are continuous processes, therefore
a continuous Stepper is necessary to integrate them.
We recommend ODEStepper for practically all types of ODE models.
Koichi
> Hi Moriyoshi and Yuri
>
> Thank you very much, yes I think ExpressionFluxProcess will be helpful.
> But I have several questions:
>
> 1. ExpressionFluxProcess represents a customized reaction rate or it
> directly presents flux?
> e.g.
> Process ExpressionFluxProcess(a2b)
> {
> k 33;
> Expression "K^2";
> VariableReferenceList [S0 Variable:/cell:a -1][P0 Variable:/cell:b 1]
> }
>
> Then, if we only consider this one reaction, which of the following
> expression is correct?
> da/dt = -K^2[a] and db/dt = K^2[a]
> or
> da/dt = -K^2 and db/dt = K^2
>
> 2. Since the unit for Expression must be "number/second" instead of
> "concentration/second", if, in the expression, the MolarConc of some
> variables are used, I must multiply self.getSuperSystem().sizeN_A once, in
> order to inform the system that I changed the unit?
> I just wonder how e-cell do this consistency check ?
> If under some circumstances, I need to multiply the size twice.....can
> e-cell detect it?
>
> 3 In the case of multi-compartment model, in which way I can indicate that
> I multiplied correct compartment/compartments?
> e.g.
> Process ExpressionFluxProcess(Ca_ER2Cytosol)
> {
> Kch 3;
> K1 2;
> Expression "(Kch*C1.MolarConc^2/(K1^2+C1.MolarConc^2)) *
> (C2.MolarConc-C1.MolarConc)"; #this expression is wrong since I haven't
> multiply any compartment size!#
> VariableReferenceList [C1 Variable:/cytosol:Ca 1][C2 Variable:/ER:Ca -1];
> }
>
> * in this example I want to represent ER release Ca to cytosol.
> the first part of this expression,
> Kch*C1.MolarConc^2/(K1^2+C1.MolarConc^2) should have no unit problem,
> since the unit for Kch is per-second, and the unit for K1 is
> concentration.
> However, for the second part C2.MolarConc-C1.MolarConc, I should convert
> its unit into Number instead of concentration. Which compartment size, and
> what kind of expression I should use here.
>
> 4 which stepper I should use for ExpressioFluxProcess?
> should it must be a continuous stepper?
> Can I use ODEstepper?
>
>
> I am looking forward to your reply.
> Thank you very much !
>
> yours Lu
>
>
>> Hi,
>>
>> In which sence did you say "directly" ? Sounds like
>> it's ExpressionFluxProcess that fits to your case; did
>> you try it yet?
>>
>> Moriyoshi
>>
>>
>> 2008/3/18, Lu Li <lu...@eb...>:
>>> Hello
>>>
>>> I wonder in e-cell, can I directly set up ODE for some species?
>>> And these species, even can play a role in some reactions, their flux
>>> will not be influenced by these reactions?
>>>
>>> I am looking forward to your reply.
>>>
>>> Best Wishes
>>> yours Lu Li
>>> --
>>> Lu Li
>>> PhD student in Computational Neurobiology
>>> EMBL-European Bioinformatics Institute, Cambridge, UK
>>>
>>> -------------------------------------------------------------------------
>>> This SF.net email is sponsored by: Microsoft
>>> Defy all challenges. Microsoft(R) Visual Studio 2008.
>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>>> _______________________________________________
>>> Ecell-users mailing list
>>> Ece...@li...
>>> https://lists.sourceforge.net/lists/listinfo/ecell-users
>>>
>>
>> --
>> Moriyoshi Koizumi <mor...@gm...>
>> (also reachable on <mo...@sf...>)
>>
>
>
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