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Folding@home GPU2 Beta Released, Examined

Posted by Zonk on Wed Apr 16, 2008 03:35 PM
from the nice-to-give-my-console-a-hobby dept.
Software Biotech PlayStation (Games)
ThinSkin writes "Stanford has recently released an update to their Folding@home GPU-accelerated client, which includes notable upgrades such as support for more current Radeon graphics cards and even a visualizer to see what's going on. ExtremeTech takes a good look at the new Folding@home GPU2 client and interviews Director Dr. Vijay Pande about the project. To the uninitiated, Folding@home is a distributed computing project in which hundreds of thousands of PCs and PS3s devote a portion of their computing power to crunch chunks of biological data. The goal is 'to understand protein folding, misfolding, and related diseases.'"
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Submission: Folding@home GPU2 Beta Released, Examined by ThinSkin (851769)
[+] Games: Folding@Home 2.0 - An Online Protein Folding Game 129 comments
a boy named woo writes "Tired of justifying your gaming addiction? Now you can really help accomplish something while you play... thanks to Howard Hughes Medical Institute researcher David Baker at the University of Washington." In collaboration with others, Baker has designed a game, called "Foldit," with a practical outcome: players manipulate on-screen images of protein chains and attempt to predict their folding patterns. From the article: "'Our main goal was to make sure that anyone could do it, even if they didn't know what biochemistry or protein folding was,' says [co-creator Zoran] Popovic. At the moment, the game only uses proteins whose three-dimensional structures have been solved by researchers. But, says Popovic, 'soon we'll be introducing puzzles for which we don't know the solution.'"
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  • Global Warming! (Score:5, Funny)

    by dreamchaser (49529) on Wednesday April 16 2008, @03:39PM (#23095408) Homepage Journal
    Just think of all the global warming caused by all those CPU's and GPU's cranking away day and night! And all that electricity used! The horror! They are making Al Gore cry!

    (I am joking, for those of you who are humor impaired)

    • Re:Global Warming! (Score:5, Funny)

      by JeanBaptiste (537955) on Wednesday April 16 2008, @03:44PM (#23095456)
      you should start a StopGlobalWarming@Home project, where spare CPU cycles go towards global warming research.
    • That's the price we way for trying to see God's face. We're building a modern-day Tower of Babel with our tech in our quest for the singularity.

      • That's the price we way for trying to see God's face. We're building a modern-day Tower of Babel with our tech in our quest for the singularity.

        Perhaps this machine could assist in our efforts to run through all possible permutations to discover the true name of God [lucis.net]. . .

    • Re:Global Warming! (Score:5, Informative)

      by vux984 (928602) on Wednesday April 16 2008, @04:10PM (#23095738)
      You shouldn't be joking.

      Folding @ Home on a PS3 costs the average participant around $150-200 year in electricity if they run it 24x7. Up to $400+ in places where electricity is more expensive. PCs average less, but only because so many of them are lower power, while all PS3s are high wattage.

      I think its a worthwhile project, but the electricity people are donating isn't free and F@H uses a lot more electricity than most people think. "Oh, I've got my PC on anyway", or "Oh it can't be as much as my fridge." both of which are mistaken, your fridge uses a fraction of what a PS3 running F@H does, and even if your PC is on, running at idle or going to sleep uses a LOT less power than maxxing out the cpu and/or gpu 24x7.

      A PS3 running @ 280W 24x7 for a year:

      280W x 24h/d x 365d/y = 2452800 Watt-hours/year or 2452 kWh/y

      at $@.12/kWh that'll cost you: $294.00 / year

      Then multiply that by the number of PC's running it... it adds up fast.

      Like I said, its a good program and a good cause, BUT its not free. A kid/teen shouldn't be running it without a parents permission and understanding of the cost.

      I don't like the F@H 'propaganda' because I think its somewhat deceptive about the costs. Its relying on peoples attitude that their free cpu time is truly free to prevent them thinking about the real costs. If you probe they don't lie about the costs, but ethically they really should be more upfront about them.

      And now that there is money involved, I should choose the best use of it. When I'm faced with a decision of choosing the best place to donate $300 I think their are other causes more worthy of my money than F@H. But that's a personal choice. If you want to donate to F@H, by all means do so.

      One final issue - generally when you donate more than $10-20 to charity you get a tax receipt. $150-500 quite a bit more than $10.

      • Re: (Score:2, Insightful)

        by boombaard (1001577)
        hm.. this way you're directly investing in 'new' science, and you know what the goal is.. if you invest in amnesty/OxFam/whatever you know at least 20% is lost due to "overhead", another 10% at least is lost due to corruption, and even then (in the case of oxfam and related charities), there is a chance you're funding an organization that has more than a few members (statistically speaking, based on the amount of cases that have come out over the past 5 years or so) that indulge in sex-for-food programmes w

        • Re:Global Warming! (Score:4, Insightful)

          by vux984 (928602) on Wednesday April 16 2008, @07:27PM (#23098172)
          hm.. this way you're directly investing in 'new' science, and you know what the goal is..

          Fair enough. But its a little dishonest if you don't REALIZE how much you are invested. That's my biggest issue. Once people know what it costs I have no issue if they're still willing to contribute. But it bugs me, especially since I beleive the a very significant proportion of the people contributing to F@H are not the one's paying the bills.

          The other part is how much do F@H results actually cost, in aggregate? Is it good value for the science produced? They've consumed between $50 and 100 million in electricity. Could they have made better progress towards their goals if they were given the money directly? At the very least if they built their own super computer and managed the costs directly the waste would be far far less.

          Not only would they be paying industrial rates for electricity instead of residential rates, they'd also be using far less of it because they'd have racks of CPUs not all powering hard drives, and what not needlessly.

          Hell, just take a look at the from their site: (For the purposes of this I've assumed that it costs 'volunteers' on average $10 to run a cpu per month in electricty.)

          190,000 PCs generating 182 TFLOPs. 191k cpus. Total Cost ~1.9M/month. ~$10,494/TFLOP/month
            41,000 PS3 generating 1257 TFLOPs. 41k cpus. Total Cost ~0.4M/month. ~$326/TFLOP/month

          What moron would keep the PCs running?

          A final note about overhead. You lose 10-20% efficiency right off the top with F@H due to the lack a tax receipt. I can donate $250 to a registered charity at the same cost to me as buying $200 worth of electricty due to the taxes. Or conversely when you donate $200 to F@H -you- pay an extra 20-50 in taxes vs had you given the same $200 to a registered charity.

          but if i had to choose, and if i had a choice, i'd rather invest in an @home project.. i find it a lot more intrinsically motivating than knowing i'm keeping a statistic alive that in 10-20 years might start earning their country some money through taxation because he's had his K-6 education.

          Between those two I'm inclined to agree. I tend to mostly donate to small local organizations myself.

      • Re: (Score:3, Interesting)

        by dreamchaser (49529)
        My tongue was only half in my cheek. I stopped running any and all distributed clients a couple of years ago precisely because of the resultant power/CPU utilization. I didn't do it for the environment though as I alluded to in my joke. I did it to save money on my electrical bill.

      • Re:Global Warming! (Score:4, Informative)

        by SecondHand (883047) on Wednesday April 16 2008, @04:55PM (#23096180)
        It seems that the PS3 40 GB consumes only half of what you said (135 Watts, see http://www.engadget.com/2007/10/30/40gb-ps3-features-65nm-chips-lower-power-consumption/ [engadget.com]).

        So you can go and buy a second PS3.

        • Re:Global Warming! (Score:4, Informative)

          by vux984 (928602) on Wednesday April 16 2008, @05:34PM (#23096734)
          Thanks! You are right.

          There was information when the PS3/F@H launched that consumption was 280-300W, but apparently that was actually around 200-220W so my post above was out by ~$70, and now with the newer lower wattage PS3s the price comes down even more.

          But even at 135W, assuming the same .12c kWh I used in my original post that's ~$150/year. Maybe not a big deal to some, but how many would still sign up if they had to pay $150 to f@h directly instead of having it nickle and dime them daily on their power bill? I suspect the user count would be orders of magnitude lower.

      • Re: (Score:2, Interesting)

        by dstates (629350)
        Of course there are also all of those Flash ads that continue to run even when the browser tab that they are on is not visible. They continue to consume CPU and electricity so they are also adding to your power bill. You think I am joking, but if you are like me, you may have a dozen tabs open at any given time and each of those pages may have several active graphics items on them. Adds up.

        Good reason to run FireFox and AdBlock or FlashBlock. Even better, turn your PC off when you are not using it.

        • Re: (Score:3, Informative)

          by i.of.the.storm (907783)
          Not really, it does more FLOPS but it generates less usable scientific data which is reflected in the PPD it gets, the SMP client (multiprocessor) is the client that gives them the most research value and thus is worth the most currently. Also, the GPU clients blow the PS3 out of the water in terms of FLOPS, and that was just when the x1900xtx was the top ATI folding compatible card. The R600 series GPUs have 320 stream processors and a ridiculous amount of floating point horsepower. So, you either haven't

        • Re: (Score:3, Informative)

          by vux984 (928602)
          Accounting for the electricity cost is your problem, but they should provide the details of who you donated it to that is needed for tax purposes.

          They would need to be registered charity though, for taxes. You can't just say you donated money to X and call it a day.

          • Re: (Score:3, Insightful)

            by evanbd (210358)
            They're a university. I'm sure they have that taken care of.

            • Re: (Score:3, Interesting)

              by vux984 (928602)
              They're a university. I'm sure they have that taken care of.

              Good point.

              Be interesting to see someone try and claim it though. I wonder if the IRS would agree to its validity.

              Probably help if they provided you with a proper receipt of some sort, which they don't.
              And I don't think it'll help non-americans even if they did, unless they were registered as a chairty in other countries as well.

        • Re: (Score:3, Informative)

          by vux984 (928602)
          Using a power meter connected between my desktop and the wall I only use $24 per year 24/7 (well, add 50% more for air con) on my FX55 gaming computer.

          Please show your work:

          W : Wattage of your PC running full tilt?
          P : Price of electricity in $/kwh in your area? P
          8760 : hours / year

          W x 8760 = Wh (Watt-Hours)
          Wh / 1000 = kWh (convert from Wh to kWh)
          kWh * P = Total

          I'd like to see how you get to $24. Because that would require either telling me that your "FX-55 gaming rig" is averaging ~16Watts at full load, tha

        • Re: (Score:3, Informative)

          by vux984 (928602)
          Your right I was off on the original data, by about $70 bucks, because I grabbed the wrong number. Early reports on ps3 f@h rated it at 280-300W, but this was corrected down to 190-220W thereafter. My mistake there and I've posted that I was wrong already elsewhere in this thread.

          As for the price of electricity, and your assertion that its 10c? vs 12c? Now were just playing statistics. I could justify mine by noting that prices are generally higher in Europe and Japan for electricity. (Its the equivalent of

  • I do the laundry once a week (Score:5, Funny)

    by Anonymous Coward on Wednesday April 16 2008, @03:41PM (#23095414)
    I've been doing Folding @ Home for most of my adult life. I fold shirts, pants, underwear, etc. etc.

    • Re: (Score:2, Interesting)

      by cpricejones (950353)
      You can also visualize protein folding at home by going to www.pdb.org. The Protein Data Bank website has lots of cool structures to download, from small proteins up to large RNA-protein complexes like the ribosome (http://www.pdb.org/pdb/explore.do?structureId=2J00), which is one of the more remarkable achievements in structural biology. (Note that you may need a stronger graphics card to actually look at and rotate the whole ribosome as it is 64,000 atoms.) To actually look at these structures, you can us

  • Support for NVIDIA GPUs coming? (Score:4, Insightful)

    by Grokmoo (1180039) on Wednesday April 16 2008, @03:46PM (#23095484)
    From the article:

    ET: Whenever someone hears about GPU-accelerated FAH, their first question is why there is no client with support for Nvidia cards. In the past it was said that it had more to do with Nvidia's drivers. Now that the core doesn't use DirectX, couldn't a GPU client use Nvidia's CUDA? Is there any work going on there, and if not, why not? Dr. Pande: We are interested in CUDA and are investigating how well FAH on CUDA would work.
    I am awaiting this with some serious excitement. Getting Folding@home working on Nvidia GPUs would definitely add a lot of computing power into the mix. This is especially true now, as it seems that the current crop of high end GPUs seems to favor Nvidia.

    From the benchmarks I have seen, it seems that there are currently no games that can effectively utilize, for example, 2 9800 GX2s. If Folding@home releases an Nvidia client, those people who have plunked $1000 into graphics cards may finally be able to put them to use!

  • Ati Only (Score:4, Informative)

    by Fross (83754) on Wednesday April 16 2008, @03:48PM (#23095502) Homepage
    From TFA, interestingly this bypasses DirectX and interfaces with the card directly (I guess you'd want to, to throw maths at it instead of vertices)

    However it only runs on R600-based Ati cards right now. It also requires .Net framework. They do say they're "investigating" an nVidia version, but that sounds a while away.

    Interestingly also, it claims to parallelize processing the atoms, so it must use the individual stream processors on the graphics card directly.
  • So let me get this straight, you keep your computer running for long periods of time. The goal is "to understand protein...misfolding"

    Sounds like Pornography@home to me...

  • Translation of "protein folding related diseases." (Score:3, Informative)

    by denis-The-menace (471988) on Wednesday April 16 2008, @04:17PM (#23095798)
    "to understand protein folding, misfolding, and related diseases."

    FYI: This means Prions related diseases => Mad cow disease

    • Re: (Score:2, Offtopic)

      by bradbury (33372)
      Actually this is a grossly incomplete statement. Due to the fact that the process of Non-homologous End Joining (NHEJ) repair of DNA double strand breaks involves the exonuclease (DNA end-eating) proteins WRN and DCLRE1C (Artemis), the repair of double strand breaks corrupts the genome via microdeletions. Microdeletions can result in frameshift mutations which can of course result in protein mis-folding. The accumulation of these frameshift mutations and misfolded proteins over the lifespan of cells has

  • Idea: F@H to help filter spam? (Score:4, Interesting)

    by Viking Coder (102287) on Wednesday April 16 2008, @04:27PM (#23095902)
    So, here's my thought - before someone sends an email, they contact Folding@Home, identify themselves, say who they want to send an email to, and the contents of the email. F@H gives them a work unit. When they complete it, F@H signs their email. Your email client can filter emails based on how many work units the sender did to send it to you. If someone really wants your attention, they'll process for a day or two. If it's a casual email, one work unit will do. Maybe even a fraction of a work unit.

    That way, if you read spam, at least you know that you contributed to F@H. If you want less spam, you turn up your threshold for how many work units the sender has to do.
    • Uh. I think I'd rather use the phone. And that's really saying something. Usually when someone needs my attention, they need it very soon.. talking about work situations here of course, for personal email your method would be crap to middling.
    • Yeah, because Lord knows the spammers don't have spare CPU capacity at hand on all the hijacked machines they control.

      It's worth a shot at thinking outside the box, but they have the CPU cycles and can likely hack past any kind of attempt to node lock the work units.

      I suppose a minor benefit would be that some kind of work gets done before a spam message was sent out, but there's got to be a way to get past that requirement -- F@H is based on a measure of trust (and some cross-validation) that parti

      • Re: (Score:3, Informative)

        by Viking Coder (102287)
        The stupid part about hashcash is that no useful work is done. I'm proposing an idea that would at the very least get something useful accomplished.

        There are all sorts of third parties involved in sending email. I'm not proposing a solution for everyone - I'm suggesting one possibility.

      • Actually, a very similar system was tried; I don't know if it's still in any sort of wide-spread use (or as wide-spread as it ever got) or not.

        Hashcash [wikipedia.org] involved calculating a hash, taking up CPU time, and sticking it in the email header. The recipient could easily verify that you'd spent CPU to send this message, hence, in theory, proving that you're not a spammer.

  • How about we just use this huge processing network to emulate actual neurons and link them together as close to a brain as we can. Then we can see what happens..

    i know it takes billions of neurons to do anything, but with all this extra power laying around we might just have enough to do it.

    • Re:Doing this at work? (Score:5, Insightful)

      by Gewalt (1200451) on Wednesday April 16 2008, @03:59PM (#23095642)
      Better check up on power consumption there, factor in 124 hours a week at 240 watts (conservative) x150 machines. Take a look at how much money your company is "donating" in raw power consumption, then triple it, cause for every watt of heat dissipated, it takes 2 watts of AC to remove it. See if your CEO approves of that donation to FAH that he can't even write off for tax purposes. (no receipt)

        • Re:Doing this at work? (Score:4, Insightful)

          by Gewalt (1200451) on Wednesday April 16 2008, @04:20PM (#23095834)
          There's a HUGE difference between an idle computers power consumption and ones whose CPU and RAM throughput are being taxed to the limit by a process like folding. The 240 watts I mentioned is just the CPU, northbridge, RAM, and internal heat evacuation. Drives and monitor are completely irrelevant.

          You execs are right to dismiss the notion of shutting down a computer thats idle. It's NOT consuming much. However, when that same computer is crunching foldings numbers for it.... THAT is a huge cost.
    • At my high school all computers had folding@home installed. Usually there is little strife from layer-8 types because the machines aren't doing anything during that time anyways, and a decent marketing department can spin it as some awesome PR. At the very least if you have install rights on your machine you can run the client on your workstation.
    • I used it to test out a new server once just to make sure it was stable, after having crashing/network card issues during installation of Windows. Being the IT manager (okay, so the only IT staffer, hehe) I didn't really need to get the go ahead to do that though :P I agree that for that many computers, the power consumption costs really would be too many. For your own workstation it would probably be fine. I've noticed one engineer at work had his screensaver set to do climate change calculations or someth
    • Do I see several Amiga fans' eyes glowing in the murky gloom? :)

      I guess they will still be using drivers for the cards though, even if they are not using DirectX? But this is closer to bashing right on the hardware =p if cards were all made to conform to a certain set of intructions (presumably along the lines of how all x86 processors have the same basic instructions?), we'd be able to eliminate the need for drivers there :p Old systems could use the new cards by having a driver for the new instruction

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