Re: cpu-gpu vs cpu

From: Axel Kohlmeyer (
Date: Tue Nov 29 2011 - 10:19:50 CST

On Tue, Nov 29, 2011 at 10:28 AM, Nicholas M Glykos <> wrote:
> I hate disagreeing with Axel, it is a dangerous proposition to disagree
> with Axel, and I will not disagree with Axel. Having said that, I believe
> that I can hear a small voice saying the following : the people that are
> determined to solve their research problems in their own way will do so no
> matter what the current 'funding-recognition' situation is. As I see it,
> you can not stop creative people from being creative. You just can't. They
> will do their thing no matter how difficult you made it for them. I do not
> imply that it should be made difficult for creative people to be creative.
> I only say that there may be something deeper than funding and recognition
> in what is being discussed.

you are not at all disagreeing with me. it is *exactly* for the reasons
that you outline that you *still* have people doing programming of their
own and developing software on their own (or with others) and regardless
of how many times they get told that they are re-inventing the wheel.
however, there would be *more* people doing this, if there was a better
attitude towards funding and supporting these efforts and particularly
those that are made available free of charge.

what i am arguing is that it is not enough to just cite the NAMD
paper, if you desire to have a feature implemented, or want/need
help getting your work done, and i also want to raise awareness
that there are more contributions to any large software package
than just the basic code framework. NAMD is a bit of a bad example,
since it is not as easy to add to NAMD than with other packages,
but VMD was also mentioned and VMD comes with a lot of add-ons
that were developed and contributed by many people from many groups.

and what i am also trying to raise awareness for is that freely
available and community supported software needs community
support and while people easily recognize that they need to
purchase computer hardware to run their simulations, they seem
to expect that their software just happens to be available and
up-to-date and with the latest greatest features without them
having to do a thing about it.

i've been having this discussion on-and-off again with different
people and am constantly surprised by how little folks know
how much effort it is to develop and maintain (scientific)
software, something that you are in a perfect position assess. ;-)
and it appears that the people that are the most offended by
my - deliberately polarizing - statements are the ones that
are and have been contributing the least and benefiting a lot.


> My twocents,

> Nicholas
> --
>            Nicholas M. Glykos, Department of Molecular Biology
>     and Genetics, Democritus University of Thrace, University Campus,
>  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
>    Ext.77620, Tel (lab) +302551030615,

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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