[SciPy-Dev] Adding new wrappers (dassl, daspk version 2, cvode version 2.7.0) to scipy.integrate?

Geoff Oxberry goxberry@gmail....
Thu Jun 21 19:57:01 CDT 2012


Johan,

Assimulo indeed does many of the things I've mentioned in the post. I have had trouble installing Assimulo on my machine, so I haven't had a chance to test the software myself, but it is one candidate project that I believe does a lot of things well (there is a lot of documentation, there are organizations that back the software, and there are interfaces to many ODE and DAE solvers).

It does not have a permissive (that is, BSD or MIT/X11 or similar) license, which means that other Python package developers may have trouble using it in their work. For instance, licensing issues are one reason my colleagues decided to roll-their-own DASSL wrapper.

For my work right now, that's not a problem at all, because I'm not building a library; I just want to release the source code of my case studies so that others can reproduce my results. But I think when it would be beneficial to the computational science community to have these sorts of wrappers in SciPy, because they are so useful in the types of simulations Benny mentions in his scikits.odes README (solving ODEs arising from method of lines discretizations of PDEs) and in other types of problems (combustion chemistry, control problems with fast and slow time scales). In turn, developers and researchers working in these application areas would be able to use SciPy to build applications and other software libraries, increasing SciPy's user base.

Geoff

On Jun 21, 2012, at 6:09 PM, Johan Åkesson wrote:

> 
> Geoff Oxberry <goxberry <at> gmail.com> writes:
> 
>> 
>> I posted a feature request ticket (#1678,
> http://projects.scipy.org/scipy/ticket/1678) about this on
>> the SciPy Dev Wiki, and Ralf Gommers suggested that I follow up on the
> scipy-dev mailing list.
>> 
>> To recap the gist of my ticket, there are problems for which DVODE (currently
> wrapped in
>> scipy.integrate.ode) are inadequate, such as in computational combustion. It
> would be helpful to
>> researchers in combustion to wrap updated numerical integration libraries
> (such as DASSL, DASPK, and
>> CVODE); DAE solver wrappers would also be very helpful (technically, DASSL and
> DASPK are DAE solvers, but
>> one thing at a time here).
>> 
>> Since some of these wrappers already exist in scikits.odes, would it be
> possible to merge them into
>> scipy.integrate.ode? If so, in the process, could the Sundials wrappers also
> be updated to operate with
>> Sundials version 2.5.0 instead of Sundials version 2.4.0? The newest version
> of Sundials contains only
>> minor changes to the API (a few integer arguments are changed to long integers
> to accommodate larger
>> problem sizes), and several bugs are fixed.
>> 
>> There have been many e-mails on the Sundials-users mailing list requesting a
> good, well-maintained and
>> supported Python interface to Sundials with a reputable institution behind it.
> It looks like
>> scikits.odes is the best-maintained Python interface out there, since
> pysundials and python-sundials
>> are no longer maintained, and the Assimulo documentation uses some
> nomenclature that is nonstandard in
>> numerical analysis (which makes me doubt the software). Furthermore, I know
> that users in the combustion
>> community, frustrated with this situation, have implemented their own wrappers
> to such solvers (see for
>> instance, https://github.com/jwallen/PyDAS, written by a colleague of mine).
>> 
>> I am willing to help with this effort after I graduate (I am in the process of
> finishing my PhD) in a few months.
>> 
>> Geoff
>> 
> 
> Hi Geoff,
> 
> I'm involved in the Assimulo development, and since Assimulo is mentioned in the
> post, I'd like to contribute some comments to the discussion. I think that
> Assimulo matches well the requirements mentioned in Geoff's post. The project is
> backed by an environment where departments at Lund University, Sweden, (notably
> the Center for Mathematical Sciences (www.maths.lth.se) and the Lund Center for
> Control of Complex Systems (www.lccc.lth.se)) collaborates with Modelon, a
> Lund-based company in the simulation and optimization industry. The project
> benefits from a mix contributions from academic research, ensuring sound
> numerics, and industrial applications, ensuring scalability to real world
> problems. The institutions involved in the development are committed to long
> term development and maintenance, which is one of the key differentiators to
> ensure quality in OSS projects.
> 
> From early on, the goal of the Assimulo project has been to provide an easy to
> use and well documented front-end to a variety of integration algorithms – in
> addition to the Sundials solvers, we recently added interfaces to Hairer's
> Dopri5 and Radau codes, ODASSL and the Glimda solver. Additional solvers are
> planned for inclusion in the future. There was a publication recently that talks
> about Assimulo at the 2nd Joint International Conference on Multibody System
> Dynamics: http://www.control.lth.se/Publication/and_etal2012imsd.html.
> 
> Through the Python-package PyFMI (www.pyfmi.org), Assimulo is conveniently
> connected to a wide range of state of the art tools for physical modeling,
> including AMESim, Dymola, JModelica.org, OpenModelica and SimulationX. The PyFMI
> package is based on the Functional Mock-up Interface Standard
> (www.fmi-standard.org), which is supported by a wide range of simulation tools.
> 
> All input on how to improve Assimulo is very welcome!
> 
> Best regards
> /Johan
> 
> 
> 
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