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sys-bio / tellurium

Python Environment for Modeling and Simulating Biological Systems
http://tellurium.analogmachine.org/
Apache License 2.0
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This model crashes roadrunner #65

Closed hsauro closed 8 years ago

hsauro commented 8 years ago

This model crashes roadruner, why?

import tellurium as te r = te.loada (''' J0: A -> D; A*0.05

A = 100 D = 0 ''')

result = r.gillespie (0, 10) r.plot (result)

runfile('C:/Users/hsauro/Documents/untitled2.py', wdir='C:/Users/hsauro/Documents') Traceback (most recent call last):

File "", line 1, in runfile('C:/Users/hsauro/Documents/untitled2.py', wdir='C:/Users/hsauro/Documents')

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 711, in runfile execfile(filename, namespace)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 79, in execfile exec(compile(scripttext, filename, 'exec'), glob, loc)

File "C:/Users/hsauro/Documents/untitled2.py", line 10, in result = r.gillespie (0, 10)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\tellurium\tellurium.py", line 400, in gillespie prev = r.integrator.name

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\roadrunner\roadrunner.py", line 4136, in getattr return Solver.getValue(self, name)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\roadrunner\roadrunner.py", line 3986, in getValue return _roadrunner.Solver_getValue(self, key)

RuntimeError: Solver::getValue: invalid key: name

0u812 commented 8 years ago

I didn't know we had a method called gillespie. Is it necessary to support this method for legacy code, or can we remove it? I ask because I'd much rather have users use the standard solver API:

r.setIntegrator('gillespie')
r.simulate(0,10)

On 12/22/2015 10:44 AM, Herbert Sauro wrote:

This model crashes roadruner, why?

import tellurium as te r = te.loada (''' J0: A -> D; A*0.05

A = 100 D = 0 ''')

result = r.gillespie (0, 10) r.plot (result)

runfile('C:/Users/hsauro/Documents/untitled2.py', wdir='C:/Users/hsauro/Documents') Traceback (most recent call last):

File "", line 1, in runfile('C:/Users/hsauro/Documents/untitled2.py', wdir='C:/Users/hsauro/Documents')

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 711, in runfile execfile(filename, namespace)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 79, in execfile exec(compile(scripttext, filename, 'exec'), glob, loc)

File "C:/Users/hsauro/Documents/untitled2.py", line 10, in result = r.gillespie (0, 10)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\tellurium\tellurium.py", line 400, in gillespie prev = r.integrator.name

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\roadrunner\roadrunner.py", line 4136, in getattr return Solver.getValue(self, name)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\roadrunner\roadrunner.py", line 3986, in getValue return _roadrunner.Solver_getValue(self, key)

RuntimeError: Solver::getValue: invalid key: name

— Reply to this email directly or view it on GitHub https://github.com/sys-bio/tellurium/issues/65.

0u812 commented 8 years ago

Just saw the email with Jacob, I guess we have to support this. It's a real menace that we have all these different ways of doing the same thing...

On 12/22/2015 10:47 AM, Kyle Medley wrote:

I didn't know we had a method called gillespie. Is it necessary to support this method for legacy code, or can we remove it? I ask because I'd much rather have users use the standard solver API:

r.setIntegrator('gillespie')
r.simulate(0,10)

On 12/22/2015 10:44 AM, Herbert Sauro wrote:

This model crashes roadruner, why?

import tellurium as te r = te.loada (''' J0: A -> D; A*0.05

A = 100 D = 0 ''')

result = r.gillespie (0, 10) r.plot (result)

runfile('C:/Users/hsauro/Documents/untitled2.py', wdir='C:/Users/hsauro/Documents') Traceback (most recent call last):

File "", line 1, in runfile('C:/Users/hsauro/Documents/untitled2.py', wdir='C:/Users/hsauro/Documents')

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 711, in runfile execfile(filename, namespace)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 79, in execfile exec(compile(scripttext, filename, 'exec'), glob, loc)

File "C:/Users/hsauro/Documents/untitled2.py", line 10, in result = r.gillespie (0, 10)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\tellurium\tellurium.py", line 400, in gillespie prev = r.integrator.name

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\roadrunner\roadrunner.py", line 4136, in getattr return Solver.getValue(self, name)

File "C:\Tellurium-Winpython\python-2.7.10\lib\site-packages\roadrunner\roadrunner.py", line 3986, in getValue return _roadrunner.Solver_getValue(self, key)

RuntimeError: Solver::getValue: invalid key: name

— Reply to this email directly or view it on GitHub https://github.com/sys-bio/tellurium/issues/65.

hsauro commented 8 years ago

Yes we need to support r.gillespie, its documented, see:

http://sys-bio.github.io/roadrunner/python_docs/api_reference.html?highlight=gillespie#RoadRunner.RoadRunner.gillespie

Added issue to roadrunner