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Medicine Technology

The Science of Folding@home 88

Posted by CmdrTaco
from the i-prefer-napping@home dept.
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 @08:58AM (#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 Futile Rhetoric (1105323) on Monday June 15, 2009 @09:01AM (#28334077)

      Let me Wikipedia [wikipedia.org] that for you.

      • Next time I run into the BOINC developers, I'll have to suggest using location data from users, so you can determine how clean your computing is by integrating power generation data based on location. Better to compute near hydro, nuclear, etc. then compute using coal.
    • by Amouth (879122)

      failure to comply with a buz word does not me it use useless.

      you may have an argument on that front with RC5 cracking but not with folding

      • I agree with you there. How else would we do it without consuming the same amount of electricity? I guess it would depend on one's ideology but personally I'd rather spend the extra dollar contributing to medical research than worry about shooting a couple coal puffs into the air.
        • by SlashV (1069110)

          How else would we do it without consuming the same amount of electricity?

          With a dedicated super computer ? A dedicated super computer is likely to consume a lot less energy per FLOP than your average home PC.
          Would be interesting to see how GPGPU performance per watt compared to top500 super computers...

          • Re: (Score:3, Informative)

            by Amouth (879122)

            it would be intresting but remember that cray is now selling GPGPU powered mini super computers.

          • How else would we do it without consuming the same amount of electricity?

            With a dedicated super computer ? A dedicated super computer is likely to consume a lot less energy per FLOP than your average home PC.

            Would be interesting to see how GPGPU performance per watt compared to top500 super computers...

            At least distributed computing relies on computers that would have been on anyway.

          • by kdemetter (965669)

            The difference is , that that supercomputer will only be used for the computations , whereas a home pc will be used for other things.
            Most people won't run their pc's 24/7 .

            So , you would have to calculate how much more energy the pc uses when it's running folding@home , not how much they use in total.

            • Assuming Folding@home is always running when your computer is on, then it's a matter of power supply wattage*amount of time Folding@home runs.

              If you have a 1000 watt power supply (assuming it doesn't go into a stand-by or power saver mode), you are always drawing 1000 watts from your wall when you are running your computer. Your computer may not use all 1000 watts, but it's still drawing that much into the PSU.
      • Re: (Score:2, Insightful)

        by OeLeWaPpErKe (412765)

        Heh, if you're truly worried about that, worry about treatments. If any (non-trivial) treatment consisting of specifically folding proteins is found, then there will be exactly one way to produce said drug : genetic manipulation. Only a genetically modified cell will be able to produce those custom proteins.

        So it's not "buzzword-compliant" in more than one sence. It burns heaps of co2, it relies on genetic modification, specifically on injecting live humans with substances coming from "mutants" (just like m

        • by MikeURL (890801)
          So SkyNet could own us without ever firing a shot. Just produce a very complex protein with a timed (or keyed) payload. Very tricky and not so terribly far-fetched.
        • "If any (non-trivial) treatment consisting of specifically folding proteins is found, then there will be exactly one way to produce said drug : genetic manipulation. Only a genetically modified cell will be able to produce those custom proteins."

          This is not necessarily the case. We can predict with reasonable accuracy (about 80%) what sort of secondary structure (alpha helix, beta sheet, or coil, basically) a protein will have based solely on the protein sequence. For example, if you were to put the pr
        • This is basically a computer using a (basic) kind of artificial intelligence to respond to human questions about the real world

          Only if you're willing to horribly stretch the definition of AI.

          if an intelligence were to directly (or through deception) control a ribosome, like this one does, that would enable it to self-replicate. The question it would need to answer is one that is "but" an exercise in protein folding : "how do I fold a protein so it runs my thinking algorithm ?", even if it's much harder than the current questions being asked.

          This isn't designing proteins, it's finding the 3D structures of proteins we know. And designing a protein capable of catalyzing such a complex chain of events is orders of magnitude more complex than what it's doing right now.

          Like most research worth pursuing, it's very, very not-buzzword-compliant, and conceivably unbelievably dangerous.

          For very small values of 'conceivable'.

        • Pande explains that this is "as drug design is very hard, itâ(TM)s very easy to do more harm than good, and thatâ(TM)s one thing that we never want to see".

          Eww, smart quotes! Just use the "'" symbol (conveniently quoted for you).

    • by fuzzyfuzzyfungus (1223518) on Monday June 15, 2009 @09:17AM (#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.
      • This is all fine and well but what about when some leave their PC on anyway? Savings would assume that people aren't using their PC for some other function while this is happening.

        And it's odd that you bring up bittorrent... So if I have 3 days worth of torrents lined up and my PC is just sitting their at 2-3% CPU usage leeching and seeding, how much more is it really costing me to have it folding at the same time? And lets not even consider the number of users who leave their machines idling away for 20 h
        • by compro01 (777531) on Monday June 15, 2009 @11:27AM (#28335707)

          According to my UPS's monitoring software, by machine idles (screen off with torrents running) at 180W and hits 210W with folding@home (GPU edition on my 8800GTS) running, 30W extra. Assuming it does that 24 hours a day (it's always on anyway as it also runs as my FTP/web server and for remote access), that comes to 21.6KW-hr per month, which at local electrical rate (9.6 cents/KW-hr) comes to $2.07 per month.

          • Thanks for the information. That actually puts some numbers to the question. Now, I just wonder how far 2.07 USD would go in renting some super computer time or other areas of expendature.
      • by JustinOpinion (1246824) on Monday June 15, 2009 @09:42AM (#28334445)

        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.

        Maybe or maybe not. One would have to include in the calculation the cost of building additional computers. One of the ways in which distributed computing is "green" is that it uses computers which have already been built, but would otherwise be idle. In this sense it is re-using resources that have already been committed, rather than requiring totally new equipment to be built, which consumes new resources.

        In other words, the newly-built computers would have to be sufficiently more efficient that they fully offset their own production costs, and then some.

        As long as we accept that doing the folding is a worthwhile use of resources ... the question is a matter of how to do it most efficiently

        Indeed. For many computational projects one has to take into the account the likely scaling of computer power and algorithmic power. For instance in principle for a given problem with a given deadline, it can sometimes be cheaper to wait until new computers are on the market, if they will be sufficiently faster (at a given cost) than the older ones. (That is, you may be able to "waste time" and still make your deadline.) Alternately, it may be a total waste of modern computer resources to inefficiently search a given parameter space if we have reason to believe that drastically better algorithms will become available in a few years.

        As it turns out, problems like protein folding are very difficult, and we have no reason to believe that dramatically better techniques are on the horizon. So if (as you say) we care about the problem at all, then it would seem that we can justify the energy spent doing those calculations right now on modern general-purpose machines.

      • for the bittorrent example, you could fix that with use of www.greedytorrent.com

        too many people who charge for torrent sites are anyways seeding at MBps speeds, what are your 8-10kBps going to do??

      • by Thaelon (250687) on Monday June 15, 2009 @11:03AM (#28335383)

        Folding@Home, and torrents are more like a micropayment system that actually works.

        Sure it costs you electricity and bandwidth, but in such small amounts (typically) and over time. Plus there are no additional transaction fees or middle men taking a cut. It's tax free, and there are no forms to fill out or any other bureaucracy.

        Torrents are just a distributed micropayment system.

      • by Eil (82413)

        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?".

        Setting aside for the moment the issue of energy use, the whole point to folding@home is that it utilizes the otherwise idle processor cycles, meaning the scientists don't have to deploy their own equipment. As a nice bonus, they get a distributed processing cluster that by far exceeds anything they could ever get a grant for. Even if the dis

    • Re: (Score:2, Interesting)

      by jowilkin (1453165)

      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 compu

      • 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.

        Well, when you have thousands of volunteers running it on their desktop PCs and servers either at home or at work, it becomes pretty difficult to pool the money saved from not having Folding@Home into research grants.

    • by Anonymous Coward on Monday June 15, 2009 @09:25AM (#28334289)

      If you leave the server on anyways, the power draw at 0% usage versus 100% usage is minimal.

      eg. I have an old Dual processor Dell server that uses 170 watts idle, and 180 watts running at 100%

      the largest difference I got was on my overclocked AMD FX-55 which had a difference of 30 watts. and a laptop that had a difference in 30 watts.

      I used the Kill-A-Watt device purchased from thinkgeek.com.

    • by goombah99 (560566) on Monday June 15, 2009 @10:01AM (#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.

    • Re: (Score:2, Interesting)

      by xrobertcmx (802547)
      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.
      • Re: (Score:3, Interesting)

        by fast turtle (1118037)

        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 bein

        • The current setup for this machine is an AMD 4850e w/4gig of DDR2 800 running 64bit OpenSuSE 11.1. The motherboard in use is a hand me down from my desktop and doesn't have onboard graphics, this doesn't help with the power as I ended up putting in an old ATI X1600Pro. I plan to replace the motherboard or maybe the graphics card and add a UPS to the office when money becomes available. I also have 1x1TB, 2x500GB, and 1x300GB hard drives in there. So at 113W under full load I'm happy. Right now I only hav
    • by ID000001 (753578) on Monday June 15, 2009 @12:54PM (#28336947)
      Keep a few things in mind:

      1) A good potion of the computing power for folding@home, are from PS3, which, according to study, are one of the most efficient CPU design along the top500.

      2) Computer or Console that are running Folding@home are usually power on anyway. While increasing it's CPU utilization, the actual increased electricity use are likely lower then, say, a dedicated server just for folding.

      3) It is very spread out, instead of everything running in a data center, everyone runs one at their home. Think of this as some kinda "heatsink" so less power are used to keep this system cool down, compare to, say, concentrated computing power in the same location.

      4) It operate on many electricity grids. When it is ran across the global, it put less strain on forcing certain power plant to runs at higher capacity. I don't know if this make it more or less power efficient, but it would put less strain on individual power grid.

      5) It give everyone a chance to contribute. They have a common enemies that killed many of their relative. They fight together, by themselve or in team. They keep people motivated on something. That count for something, right?
    • by TeknoHog (164938)
      If you're worried about that, try a real mindfuck with http://www.climateprediction.net/ [climateprediction.net].
  • Not a petaflop! (Score:3, Informative)

    by tomknight (190939) on Monday June 15, 2009 @09:01AM (#28334081) Homepage Journal
    It's petaflops, not petaflop. That s means something.
  • 5 petaflops, not 1 (Score:3, Informative)

    by Anonymous Coward on Monday June 15, 2009 @09:05AM (#28334109)

    "However, even Roadrunner looks decidedly weedy compared with the power of Stanfordâ(TM)s Folding@home project. Its computational power has now surpassed the five petaflops mark."

    • Re: (Score:2, Interesting)

      by wagnerrp (1305589)
      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
  • Where's BOINC? BOINC may not have as many users or processing power, but it is more diversified than Folding@home.

  • I just got an epiphany. A scantily clad moon godess came down to me on a bolt of lightning and said: A) There are people who need their cpu cycle expensive tasks computed, they are willing to pay for it. B) Then, there are people who publish content on the web and want to get money for it. C) And then, there are millions of people who want to read the B's content without paying for it. Their PC's sit idle when they finish downloading and displaying the content while people read it. Then she left. I still
  • by Anonymous Coward

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

  • If the @home-type distributed computing systems ran on energy marked and priced as 'green', nature would not take damage from using old circuitry. The lest efficient hardware could be scrapped when energy production is insufficient, and so we can the total computational power of this planet constantly maximized. I am sure Sky Net will see that symbiosis with mankind is the optimal arrangement.

  • by Dr. Manhattan (29720) <[sorceror171] [at] [gmail.com]> on Monday June 15, 2009 @10:17AM (#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.

  • That way once we find the little ETs they can fold our laundry for us. Oh...hang on a minute. THAT Folding@home!

    BOINC sucks, btw.
  • by Seth Kriticos (1227934) on Monday June 15, 2009 @10:27AM (#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.)
  • Compare the FAH systems to BlueGene/P. BlueGene is made up of System-on-Chip PowerPC computers, stuck on DIMM-like cards and then put into arrays, which go into racks, etc. Hugely power efficient, in part because each system doesn't maintain a disk and other crap.

    On the other hand, your home computer is inefficient in terms of both heat, power, and space, because it has to run all the other hardware stuff you don't have in a proper supercomputer.

    • by Chabo (880571)

      ...inefficient in terms of both heat...

      What if we run BOINC projects in the winter, when the heat would be otherwise generated by a furnace?

      This strategy worked well for me when I came home from college; my room was across the house from the furnace, so in the winter my room would be very cold (around 45F, if it was 0F outside). I'd turn on my main computer and play Counterstrike for a couple hours with the video card overclocked, and I'd turn on my server, running BOINC. It would put the room up to a much more comfortable temperature (~60F), a

  • by Prototerm (762512) on Monday June 15, 2009 @11:01AM (#28335353)

    And here I thought that folding@home had something to do with laundry. Who knew?

  • Just one question: How exactly did you get to having one petaflop of spare CPU power? Are you working at Google?
    I meant you don't exactly put some computers together in your basement, to get to that power.

    Oh, and did you already play trough Crysis Warhead on Vista, with a ray-tracing mod, running in a virtual machine implemented as an Emacs script, running on another JavaScript based VM in the browser... or are you still planning to do it?

  • Paranoid much? (Score:3, Interesting)

    by Sporkinum (655143) on Monday June 15, 2009 @01:20PM (#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.

    • I assume somebody has disassembled the binaries and looked at them (of course then we would have to trust the disassemblers=)

  • In House MD when they suggest a diagnosis that means sure death for the patient that diagnosis is ignored because if it has no practical use anyway, no matter if it is true or not. The same logic should be applied to the folding@home project. If these guys are correct and we need to brute force this problem the way they're doing it, we're basically screwed because even with moores law running for decades more we'll still not be able to computationally solve novel proteins in any meaningful time. In essence,

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