Re: cpu-gpu vs cpu

From: Nicholas M Glykos (
Date: Tue Nov 29 2011 - 09:28:34 CST

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.

My twocents,

On Tue, 29 Nov 2011, Axel Kohlmeyer wrote:

> On Tue, 2011-11-29 at 07:44 +0100, Francesco Pietra wrote:
> [...]
> > The answer should not be that any NAMD user has to develop the
> > application he is interested in, or pay for that. Such a (recurring)
> > answer forgets how much time is required to stay aware, for example,
> > as a chemist dealing with biology. On the other hand, the inventor of
> > GNU or free-to-use-for-noncommercial-purposes software is paid back in
> > visibility (citations/year) much more than those using his software
> > are.
> please explain on which authority you can make these statements?
> i contend that the "payback" in citations is rather minimal in
> relation to the effort that is required to implement a feature.
> if at all, only the authors of the "reference publication" get
> credited, rarely the ones that provide additional features, let
> alone the ones that provide the user support that is essential
> to many projects, particularly for people that have little
> technical expertise of their own. claiming that you can pay
> pack for that by simply including a citation in your paper
> is neglecting most of the effort that goes into maintaining
> and supporting an free to use open source software package.
> with an "essential" package like NAMD, it is almost inevitable
> to no cite it, but with VMD, for example, the situation is already
> different. i have seen countless paper where VMD was used for
> visualization (or analysis) purposes, but no credit was given
> at all. ...and then how about the many, many contributed modules
> in VMD. people may cite VMD, i've very rarely seen a mention
> of any contributed feature. how does that match with your
> assessment that a citation of the software pays for it?
> i have been working on several open source or free for use software
> projects for more than 10 years now, but it would have been completely
> impossible to have done this without being "cross financed" through
> other activities, and i know that the majority of people working
> on such software are. there is _very_ little funding to be had
> for scientific software development.
> nobody says that you do have to be an expert in implementing a
> specific feature that you need, but have you ever thought about
> including an "software feature development fee" or a like in any
> of your grant applications that will allow you to (part-time) fund
> somebody to have a feature that *you* need to be implemented?
> if more people would do that, there would be a "market" so that
> folks can get paid to focus on developing scientific software
> and that people with the proper skills would want to go that
> route, since there is a chance that you can make a living off it.
> right now we are stuck in a situation, where the number of users
> has been continuously growing, but the number of developers
> (and the amount of funding) at best remained constant, but
> in many cases declined. people entering "the business"
> have in general less IT/programming skills than they used to
> have and that makes it much less likely that want to do
> software development of any kind. in fact, even the number
> of people volunteering to support "no-cost" scientific software
> is declining, since many consider this time as "lost", and
> would rather spend it on doing more research work. in the
> extremely competitive "business of research" that is an
> understandable reaction, but that doesn't help the
> software project.
> in my observation, it is particularly people with an attitude
> of "i am a researcher, i don't need to care about software
> development. that is what 'the developers' are for, they
> already get paid to do what i need" that are essentially
> pulling the rug underneath themselves. if the current trends
> continue, there will only be a small number of overworked
> enthusiasts left that have to face a huge number of inexperienced
> users that need so much "hand holding" that there will be
> no more time left to develop new features, improve the software
> or fix bugs.
> > Thanks for predicting a possible date for that transition. It is known
> what transition?
> > that software for QM calculations is being developed (for example
> > GAUSSIAN-NVIDIA). I know that these are commercial enterprises, but
> > all us help (the little anyone can) NAMD-VMD getting public funds.
> what has that to do with the price of rice in china?
> i fail to see how the gaussian folks jumping on the
> GPU bandwagon as one of the last(!) in the field is
> helping NAMD or VMD? this is just a "must do" PR move.
> there are already packages out there like TeraChem
> that, being developed from ground up to run on GPUs,
> will outrun anything that the gaussian folks will ever
> come up with (but of course nobody will be permitted
> to provide any numbers proving it).
> cheers,
> axel.
> > francesco pietra
> >

            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,

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:02 CST