[SciPy-Dev] Consensus on the future of integrate.ode

Benny Malengier benny.malengier@gmail....
Mon Sep 9 04:53:16 CDT 2013


2013/9/9 Benny Malengier <benny.malengier@gmail.com>

>
>
>
> 2013/9/8 boyfarrell@gmail.com <boyfarrell@gmail.com>
>
> Hello Juan Luis,
>>
>> Yes, I saw your pull request and this, in part, motivated me to start
>> this discussion. Looks like you put a lot of work into your odeint
>> modifications!
>>
>> I completely agree with you, that ode should be fixed first, then odeint
>> should be a nice interface wrapped around it. integrate.ode becomes a
>> package aimed at people who understand the complexities of solving ODE
>> problems and integrate.odeint is for people who just want an answer.
>>
>> Also, thank you for doing a nice summary, that was really helpful.
>>
>> Remark 1: Backend.
>>
>> I don't think we need to reinvent the wheel, Benny's work looks excellent
>> so I think it make sense to base a new integrate.ode off scikits.odes. It
>> has a nice array of modern solvers, in both C and Fortran.
>>
>
> Thanks for the thumbs up.
> However, odes is only one of 3 implementations, and then the one that
> exposes least of the C solvers. Odes was based originally on the previous
> pysundials which was no longer maintained and was a non-cython wrapper. The
> other implementations are geared towards a specific problem domain though.
>
> One is: https://github.com/casadi/casadi/wiki (LGPL tough)
>
> The other: http://www.jmodelica.org/assimulo (annoying copyright transfer
> contribution license though to a company,http://www.jmodelica.org/page/14)
>
> The non sundials solvers in odes are also not as state of the art as some
> that are added in above two interfaces.
> The problem with above packages is their license and the fact that they
> are packages with parsing language, ..., see eg:
> https://github.com/casadi/casadi/blob/master/examples/python/dae_single_shooting_in_30_lines.py.
>
> Note that you can pass an array of times to sundials at which you want
> output, and then all iteration is done inside sundials, so the point of
> time step outside of sundials is not needed (though in many problems you'll
> want to do stepping controlled in a python loop).
>
>
What would really be interesting is find some way to use the parallel
implementation of sundals in python. Some mapping of a numpy array to the
parallel sundial vector (
https://github.com/bmcage/odes/blob/master/scikits/odes/sundials/nvector/nvector_parallel.h)
would then be needed. Has there ever been work to contruct a parallel aware
array?

Would be nice to find funding for that somewhere

Benny



> Benny
>
>
>> Remark 2 Frontend.
>>
>> We can define a new integrate.ode interface that wraps scikits.odes. It
>> seems that you already have some ideas in that area, mentioning the MATLAB
>> style. I looked at the MATLAB docs just now and spend 20 minutes thinking
>> how this might look if it were more pythonic. You can take a look here,
>> fork your own version to make changes or add comments,
>>
>> https://gist.github.com/danieljfarrell/6482713
>>
>> Best wishes,
>>
>> Dan
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>
>
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