[SciPy-User] faster expm

Alex Leach - Gmail beamesleach@gmail....
Thu Nov 8 17:19:45 CST 2012


Great news guys. The Expokit author, Professor Roger Sidje, is perfectly happy 
for Expokit to be used in SciPy. He just likes to keep a tab on things, for 
appraisals and such like. 

His full response, and my original message, is below:-

Alex,

Thanks for your interest.

Please note that the wording of the license is merely a way to keep
track of where it is used rather than an attempt to restrict its
usage.

The license is simple -- any other open/closed source can use the
software any way they want.

All the license does is to allow me to know/have a bullet point in
those end-of-year activity reports for the powers that be, telling
that the software is found useful.

I have had similar requests in the past re:GPL. All I say is, feel
free to use/modify the software any way you want. This e-mail of yours
is exactly the kind of expression-of-interest indicated (even for use
in a commercial setting).

Because I have moved from UQ (in Australia) to UA (in the USA), making
changes to Expokit won't be convenient for a while. Please consider
this response as a plain acknowledgment that Expokit can be
embedded/released under GPL. You can add the following in the meantime:

"Alternatively, EXPOKIT may be used under the terms of the GPL."

By so doing, it would mean that you have chosen to branch on the
GPL-alternative, while allowing others to do what they want on the
other alternatives (and it is understood that, per GPL, if someone
ever gets the GPL alternative or its derivatives, they will abide by
GPL).

In particular, possible future versions of Expokit not derived from
your copy will remain free to be licensed any way (which is an option
that commercial packages want -- even though they use EXPOKIT without
royalties).

Thanks
---
RBS

On Thu, Nov 8, 2012 at 5:44 AM, Alex Leach <albl500@york.ac.uk> wrote:
> Dear Professor Sidje,
>
> I hope this email finds you well.
>
> As way of introduction, I am a PhD student studying Computational Biology at
> the University of York. I have recently used Expokit for modelling
> polymerisation in a specific chemical reaction, and had some good
> experiences with it.
>
> I thought I'd share my joy with the SciPy community, who have implemented
> similar algorithms for computing matrix exponentials, but in Python. After
> writing a small wrapper function (and making some very minor changes to the
> Expokit source code), Expokit's dgpadm worked as a drop-in replacement for
> their `expm` implementation, but was about twice as fast.
>
> The exact changes I made can be seen in expokit.udiff, which I sent as an
> attachment with this email to the SciPy list. (The SciPy mailing system made
> the nasty file name: attachment-0001.bin.)
>
> Impressed with the speed improvements, the SciPy community would be
> interested in using Expokit in precedence of their original implementation.
>
> However, there is an issue with licensing... Python is GPL source code, and
> SciPy uses a BSD license. I'm sure you know more about these licenses than I
> do, but from what I gather, the Expokit Copyright is restrictive for
> corporations who would wish to use the software for commercial purposes,
> whereas the BSD license is non-restrictive in this sense.
>
> So, as you've probably guessed, I'm writing to ask your kind permission, on
> behalf of the SciPy community, to include and distribute the Expokit source
> code, as a part of the SciPy source code distribution.
>
> With your permission, expokit.f would be included in future SciPy releases
> and built as a Python shared module, which is compiled from intermediate C
> code that includes the relevant Python headers, etc. The first link in this
> message, above, shows the performance improvements I achieved, build
> instructions and python test module, detailing how I did this.
>
> If you have any questions or requirements with regard to the usage of
> expokit, please don't hesitate to ask.
>
> There would be some work to merge Expokit into SciPy, but there seems to be
> a lot of interest in doing this, so if you give the green light, the
> community would get this done in no time, I reckon. It's impossible to tell
> how many tools would benefit from this change downstream, but I know that
> some popular protein visualisation tools use SciPy internally, so I think
> this would benefit a massive user-base.
>
> I look forward to hearing back from you.
> Kind regards,
> Alex
>
>
> --
> Alex Leach BSc. MRes.
> Department of Biology
> University of York
> York YO10 5DD
> United Kingdom
> www: http://bioltfws1.york.ac.uk/~albl500
> EMAIL DISCLAIMER: http://www.york.ac.uk/docs/disclaimer/email.htm
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