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Folding@home GPU2 Beta Released, Examined
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.'"
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)
I've been doing Folding @ Home for most of my adult life. I fold shirts, pants, underwear, etc. etc.
Why visualize it? It's boring, and doesn't it use precious CPU/GPU power?
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!
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)
.Net framework. They do say they're "investigating" an nVidia version, but that sounds a while away.
However it only runs on R600-based Ati cards right now. It also requires
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...
What about folding@work? I have access to 150 computers, most of which stay on 24/5, and do nothing 16/5 (okay, maybe 20/5).
I, of course, would have to get the okay to do this, but I am not even sure I would want to...
Has anyone done this? How did you go about it? What concerns are there (security, reliability)?
No comprende? Let me type that a little slower for you...
http://www.extremetech.com/print_article2/0,1217,a=226537,00.asp
"to understand protein folding, misfolding, and related diseases."
FYI: This means Prions related diseases => Mad cow disease
Obama's legacy: (N)othing (S)ecure (A)nywhere and (T)error (S)imulation (A)dministration
http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userpage&teamnum=11108&username=DRAGONWEEZEL
How much is your data worth? Back it up now.
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.
Education is the silver bullet.
bypasses directX? at last! no more needing to install an old component of DX that is no longer distributed in DX9 or 10. great news...and without DX its almost ready for Linux/BSD too! :-)
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 downstream consequences including less efficient or improper cell function (cancer or aging) as well as the induction of apoptosis (managed cell death) -- more aging.
Thus the fundamental processes which will terminate most of our lives are related to mis-folded proteins. It is not limited to the less common "mad cow disease" (which few humans need to worry about) or even Alzheimer's (which more humans should be worried about as research funding is failing to keep pace with either inflation or the growth rate in people afflicted with the disease) [1].
(If any of these concepts are unfamiliar, the wikipedia discussions of the topics are not too bad.)
1. One could get into a long discussion as to whether or not to consider Alzheimer's a protein folding disease. I happen to be of the opinion that any disease involving the accumulation of molecules that are not present in "normal" cells is leaning in that direction.
/. now warns of redirects/links!? Awesome. Someone needs to combine goatse with rickrolling.. mmmmm...
which is totally what she said
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.
---- Booth was a patriot ----
http://en.wikipedia.org/wiki/List_of_causes_of_death_by_rate
Protein folding is the process of turning chains of amino acids into a molecular machine that does some sort of work. The thing is, we don't really have the foggiest of ideas how that works. Oh, we know that these chains are made up of twenty different types of amino acids, but the reliability with which these chains fold is astounding and just unbelievable.
Imagine that you have a very long rope. Tied to the rope at regular intervals are large lego pieces. Let's imagine there are 1000 lego pieces tied to this rope. Each one of these lego pieces can interact with the other in (being *far* on the low side) and say 10 different ways. That's 10^1000 different interactions these legos could have. In just a few seconds, these 1000 lego pieces will spontaneously assemble into a shape. The same shape. Every time. It is mathematically absurd and our understanding of it is quite limited.
While we do have some understanding of chaperone molecules in the process, the whole thing is just a mystery.
It doesn't count as "examined" until we can see the source.
Support SETI@home
FYI:
Old PS3s (90nm):
Folding@Home with visuals: 215 watts.
Folding@Home screen saver: 185 watts.
New PS3s (65nm):
Running Folding @ home 157
Considering the GPU is still 90nm, that 157 figure should drop to ~127 watts when the screen saver kicks in.
Typical energy costs are also more like $.10/kWh.
127W x 24h/d x 365d/y = 1112520 Watt-hours/y or 1113 kWh/y
at $.10/kWh that actually costs moar like: $111/y.
Or if for some reason you're paying $12/kWh, that's still only $134, less than half of your estimate.
Please stop spreading FUD about F@H and inflating the costs by more than a factor of two. It's important science that benefits everyone and the PS3 is actually very power efficient -- drawing less energy with F@H than your desktop 3D card does idle doing nothing.
If you don't want to participate in F@H and help science and humanity, that's your choice, but at least post the correct data to support your argument.
I really hope no one got dissuaded by the bad data in your argument into not running F@H when they might've contributed a key bit of research important for understanding drug candidates for P53 cancer suppression or Alzheimer's disease treatments. Perhaps I'm being melodramatic, but arguing against F@H makes me a sad panda.
Unless of course you're a highly developed tumor who figured out how to post on Slashdot and fear F@H as a matter of self-preservation, which I could hardly blame you for.
KEEP FOLDING!
String theory has the exact same problems. They need to look at these chains as if they were quantum strings. DNA,RNA and proteins are a three part system much like the three quark system in protons . The climb to the quantum computer is only a few shoulders away. The folding problem and string are important steping stones in this climb.
Not necessarily. While it's true that prion diseases are caused by proteins with unusual folding capabilities (prions cause other, similar proteins to fold up like themselves, which cause more proteins to fold like themselves...), many common diseases are cause by protein misfolding. Proteopothies (the link is quite technical in parts, sorry) include diseases such as cystic fibrosis, type II diabetes, and Alzheimer's. I guess what I'm trying to say here, is that a greater understanding of protein folding has the potential to benefit research into diseases much more widespread than only prion-related diseases.
You would also be filtering your email based on how much processing power they have available? (My gaming rig can knock off about 8 work units in the time it takes my older rig to do 1, and my work PC would take twice as long again).
And heaven forbid that someone who actually USES thier computer try and send you an important/urgent email. After all, the more processing cycles they use on anything other than F@H means less cycles sitting around for F@H to use, which means slower processing of work units. If someone really wants your attention, they'll process for a day or two "Hmm, I have this really important document that I need you to read and sign off on, and I need it done asap. I'll just sit here processing F@H for couple of days then..."
I could probably think of a few more reasons why this is stupid, but if you don't get the drift by now...
Regarding heart disease... If one leaves out those aspects of the disease which may be caused by specific genetic mutations the answer is no. Most heart disease is caused by poor diet, lack of exercise and an immune system which evolved under prehistoric conditions where food was not as abundant (or as fatty) and exercise was a requirement for survival.
Heart disease is one area you can generally attribute to a genetic program not designed for the era we live in rather than specific defects (or accumulated defects) which result in protein misfolding.