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Medicine Technology

The Science of Folding@home 88

mr_sifter writes "As previously discussed, computers running Folding@home now contribute over 1 petaflop of processing power to research into protein folding, making Folding@home the most successful example yet of a distributed computing app. It's also at the forefront of GPGPU computing, with both Nvidia and ATI keen to push how well their graphics chips perform when folding. So the technology is great, but what about the science? This feature looks at how the Folding project was developed, how it's helping researchers and the thorny question of how long it might be until the software running on your PC or PS3 actually produces real-world results."
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The Science of Folding@home

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  • i use folding@home (Score:5, Interesting)

    by ionix5891 ( 1228718 ) on Monday June 15, 2009 @07:58AM (#28334055)

    well its more like folding@office and making better use of the taxpayers money (research facility workstations)

    but one thing bugs me

    has anyone done the maths as to the electricity used by folding@home so far? the servers i run this on when i go home are always at 100% and by time i return in morning the office is nice and warm, since im not the one paying for the electric i dont really care

    im not really sure this project is "green" is what im trying to say

  • by fuzzyfuzzyfungus ( 1223518 ) on Monday June 15, 2009 @08:17AM (#28334195) Journal
    The (somewhat trickier) question, is not "How much energy does folding@home use?"; but "How does folding@home compare to other methods of doing the same calculations?".

    As long as we accept that doing the folding is a worthwhile use of resources(which, unless we are busy communing with the moon goddess or wearing uncured leather and killing bears with our teeth, is probably agreeable to most) the question is a matter of how to do it most efficiently; balanced by the fact that sometimes doing it inefficiently is the only way to do it.

    Unfortunately, I suspect that folding@home might fall into that category. If everybody participating were able to total up the costs they incur by doing so, and just donate that to the project, you could probably get better results by buying hardware well matched to the task. Unfortunately, because of transaction costs and psychological factors, and people who don't (directly) pay for electricity, it is much easier to get "in kind" donations of CPU time, even if they are less efficient. It's rather like bittorrent that way. Looking at the costs across the network, it'd almost certainly be cheaper to have Akamai or Amazon host the stuff, and have downloaders pay $.50 or so, rather than keeping their computers on for hours in order to pay in their (limited) upstream bandwidth. However, donations in upstream bandwidth are quite easy to collect, while handling money introduces complexity.
  • by jowilkin ( 1453165 ) on Monday June 15, 2009 @08:20AM (#28334229)

    I think it's debatable if using research facility workstations for FAH is a good use of taxpayer money. What about powering them down instead?

    I have been wondering about power consumption of these distributed computing projects for a while. How do you justify the sheer amount of energy used to run these things?

    SETI is a much more questionable use of power IMO, but Folding@home has not really shown to be enormously useful considering the amount of power it uses.

    Why not put all the money used powering computers involved in FAH into innovative research grants instead? Granted this is logistically much harder than convincing people to install a program on their computer, but it would be much more effective in furthuring cancer research.

  • by Anonymous Coward on Monday June 15, 2009 @08:47AM (#28334509)

    Anyone know how this compares to the World Community Grid [worldcommunitygrid.org]?

  • Re:BOINC? (Score:2, Interesting)

    by jedirock ( 1453977 ) on Monday June 15, 2009 @08:52AM (#28334533)

    It's more general purpose, and you can make your own UIs for it. I'm in the middle of doing one myself.

  • by goombah99 ( 560566 ) on Monday June 15, 2009 @09:01AM (#28334631)

    Rosetta at home [bakerlab.org] is another and arguably much more efficient folding project. It actually predicts protein structures at high resolution, allows docking, and design of proteins. put your cycles there. Also if you like this kind of thing then try out foldit [fold.it]. it a multiplayer game in which you race others either collaboratively or in cometition to fold proteins. The games are chosen so the answers help investigators studying the protein folding process! The idea is to separate what humans do best--large scale long range geometry-- with what computers do best--fine tuning interactions.

  • by Dr. Manhattan ( 29720 ) <sorceror171 AT gmail DOT com> on Monday June 15, 2009 @09:17AM (#28334791) Homepage
    Sometimes I need to leave my PS3 on for a while. (Recharging the controllers, big download, whatever.) I have the "automatically turn off after one hour of inactivity" setting checked, so sometimes the process wouldn't finish before it shut down.

    So, I fire up Folding@Home (technically called "Life With Playstation" [wikipedia.org] now) before I go to bed. Takes about six hours, plus or minus. Enough time for downloads or recharging, does something useful while the PS3's on, shuts off once the work unit's done, everybody's happy.

  • by xrobertcmx ( 802547 ) on Monday June 15, 2009 @09:19AM (#28334821) Journal
    One of the things I did to resolve this at my home was to build a reasonably powerful 100W server. I use this machine to serve video to my PS3, as a Samba file server, and a few other things, but since I already wanted it on 24/7 I also run the smp package for folding at home on it. Total power used is 118W per the killowatt.
  • by wagnerrp ( 1305589 ) on Monday June 15, 2009 @09:20AM (#28334829)
    The thing is that Roadrunner can run programs that are not ridiculously parallel. Folding is split into discrete units that are computed and sent back up to months later. The units have absolutely no bearing on anything else running, and there is no need for intercommunication. If you had to perform some task that could not reasonably fit within the free resources of an idle computer, you're sunk. Sure, it has a huge amount of capacity, but you cannot compare it to something like the Roadrunner because it cannot, and was never intended to, perform the same sorts of tasks.
  • by Seth Kriticos ( 1227934 ) on Monday June 15, 2009 @09:27AM (#28334921)
    I donate my idle processing power to the aqua@home project ( http://aqua.dwavesys.com/ [dwavesys.com] ). They (d-wave) are building quantum computers and that's a field I'm more familiar with than medicine. Guess both are more sensible than looking for E.T. though. (Just my personal opinion.)
  • by fast turtle ( 1118037 ) on Monday June 15, 2009 @11:13AM (#28336401) Journal

    Strange as I built my desktop two years ago with energy efficiency as the primary goal. I'm currently running a 64bit multi-lib version of Gentoo on a C2D e6300 (1.8GHz) with 8GB of memory and F@H using the 64bit SMP version set to Large (>10M) work units and my system is using a grand total of 120 watts average (that includes my LCD monitor and Linksys WiFi router) according to my APC battery backup. Hell I rarely turn my system off so it makes sense to run F@H and use the CPU while my system isn't being used for much else.

    Based on my normal usage, I could actually get by with a 700Mhz Celeron and Win95 if it weren't for flash and Folding.

  • Paranoid much? (Score:3, Interesting)

    by Sporkinum ( 655143 ) on Monday June 15, 2009 @12:20PM (#28337287)

    My paranoid mind wonders how we really know these CPU cycles are working for good and not evil? It could be decrypting keys for all I know, or working out some sort of weapon system. We just have their assurances that a "work unit" really is going toward something worthwhile, and not to the CIA or NSA.

Every nonzero finite dimensional inner product space has an orthonormal basis. It makes sense, when you don't think about it.