Grid Computing Saves Cancer Researchers Decades 149
Stony Stevenson writes "Canadian researchers have promised to squeeze "decades" of cancer research into just two years by harnessing the power of a global PC grid. The scientists are the first from Canada to use IBM's World Community Grid network of PCs and laptops with the power equivalent to one of the globe's top five fastest supercomputers. The team will use the grid to analyze the results of experiments on proteins using data collected by scientists at the Hauptman-Woodward Medical Research Institute in Buffalo, New York. The researchers estimate that this analysis would take conventional computer systems 162 years to complete."
Oh great ... (Score:5, Funny)
Wanna bet they discover that maple syrup or Canadian back bacon cures cancer?
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I used to run Folding@... (Score:5, Insightful)
Re:I used to run Folding@... (Score:5, Informative)
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Personally, around our 3 PCs in a smoke-laden environment, I've only seen a {mobo-measured} temp increase of at most 4-5 degrees C {and usually only 2-3 degrees, on systems ranging from a PIII with XP Pro to a Athlon XP 2000+ dual-booting Ubuntu/XP Pro...}
BOINC seems to run a wee bit hotter on Ubuntu, but I've not benchmarked the two clients yet. I'm just guessing more efficient code allows for more ops per cycle meaning more CPU use and thermal waste, but that's all it is: a guess. Anyone else have any in
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It just feels too much like an economic scheme based in pseudo-science and half truths. "The world is doomed, here's how you as a consumer can spend your way to salvation! Buy a new car and light bulbs filled with mercury!"
It's poster child, Al Gore, uses the word "if" too much. It's an old debating trick, to say "if X, then Y", and focus on the terrible consequence Y, and completely avoid the debate - which is over the validity/scope/level/definition
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I don't see it as a trick, but rather as being honest. Many of the "X" items aren't certain; it would be a lie to present them as such. But we can estimate the probability of X (based on the current state of knowledge), and explore the consequences if X *does* occur. Gore's argument is
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In fact, you can even reduce your carbon emissions to zero. [google.com]
Al Gore
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Yeah, but if we did that, we'd really fuck the CO2 levels of the Earth, you know, about 2 days to a week later, anyway.
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Every vehicle he owns or uses should be converted to electric. He
should use his "clout" to make this happen and serve as a POC for
alternate fuel vehicles in general.
He should lead the way rather than being just another spoiled wealthy American.
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Are you saying the the quote is false? As, the [Citation Needed] is linked in the post.
Are you saying that when you exhale, you don't release carbon into the atmosphere? If so, you need to take a biology class.
Or, are you saying that you can survive for hours without breathing? If so, I would be very impressed by seeing a demonstration.
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Don't buy a Prius, it may get better mileage - though if you convert to gallons per mile - a true meter of energy cost, it doesn't look so good. Never mind the fact it runs on laptop batteries, which makes it a disposable vehicle at the end of the day.
Or go to a "super efficient" diesel engine. Well, there's reasons we restrict the numbers of diesels that can be put on the road, and that
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This calls into question the rest of your statements which are probably false and certainly histrionic.
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[...] Buy a new car and light bulbs filled with mercury!"
To be fair, the saved electricity means less mercury emission from coal plants, so the mercury, at least, is of little concern.
Or, you could look into LED.
non sequitur (Score:2)
This is what I hate about this climate change hype. Nowadays if you say that you want to do something for the environment, you're automatically assumed to mean that you want to prevent "global warming" or whatever. Personally I don't give a crap about climate change, I want mankind to pollute less and to use natural resources more efficiently because this results in an improvement in the environment. Sure, if mankind really is causing the climate to chang
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Re:I used to run Folding@... (Score:4, Informative)
Linux's CPU frequency scaler has this option. For example the 'conservative' governor has the file /sys/devices/system/cpu/cpu0/cpufreq/conservative/ignore_nice_load. So a program running with lower than default priority will not increase CPU frequency.
I use a script [iki.fi] to handle CPU frequency changes. When I'm at home with my laptop, I use the "ignore nice" option which in practice will turn the fan off. YMMV. When I go somewhere, I can set the CPU to full steam.
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--
Warning: Semen may contain traces of nuts.
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Definitely a better idea to use the internet for communication and to use electricity for things that benefit the household/office directly. I wouldn't be surprised if the cost in reduced years of life from increasing the pollution from running these distributed tasks outweigh the years of life extended by treating cancers.
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It's easy to feel that way until someone in your family is diagnosed with cancer. Also, treating cancer does not just "extend life". There are a lot of younger people (20 to 40 years old) who get different forms of cancer. For them, it's not "will I live to 76 or will i live to 80?" but "will I live to see 30?". Don't even get me started on the kids who are afflicted with these diseases.
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Re:I used to run Folding@... (Score:4, Insightful)
In most places, electrical energy costs a HELL of a lot more per watt-hour than other sources like natural gas, oil, propane, and so on.
So unless you heat your home with electricity, which practically no one north of Florida does unless they have VERY cheap electrical power, you'll still be paying more by running computers.
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I don't think anyone would disagree with you. The point that the parent post was trying to make is that a nice side benefit of running a distributed computing client like F@H is that the heat from your computers will help heat your home. Would anyone suggest running a bunch of quad-cores at 100% as a replacement for n
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Meanwhile, since I live in Canada and by this time of year I do need heating, I have my boinc client running at 100%, I'm doing some good, and (since the peak capacity of the machine is justified in other ways) it's not costing a penny. The heating here is electric anyway; it may as well do some computation on its way into my home!
Doing whatever@home in the winter is just good sense.
Now what's needed is a distributed computing client that is controlled by a room thermostat. No, really, I'm totally serious
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Yeah, but... (Score:1)
Me next! (Score:2)
Oh wait.
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cluster of animated Angelina Jolie-lizards?
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Storm Botnet (Score:5, Funny)
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I think you are thinking of the Folding@home project at Stanford:
http://folding.stanford.edu/English/FAQ-PS3 [stanford.edu]
How good are the programs (Score:5, Insightful)
(1) although from their point of view, it's just slow code.
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Seeing as how the lead researcher [toronto.edu] holds M.Sc. and Ph.D. degees in Computer Science, is cross-appointed to the Departments of Computer Science and Medical Biophysics at the University of Toronto, and is a Visiting Scientist with IBM's Center for Advanced Studies in Toronto...
Where on Earth does this idea come from that multi
harnessing the power.... (Score:2)
162 years? (Score:5, Insightful)
Which reminds me of how towards the end of my grad school career I did hours long simulations that would have taken weeks at the beginning of grad school. I was in grad school a long time
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- RG>
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If you want to live longer with a good quality of life, eat a healthy balanced diet, make sure you don't let your body fat percentage get too high, and find a low-impact aerobic exercise that you enjoy and can continue to do as you
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We're computer scientists. We can calculate these kinds of things. Protein folding calculations take a ridiculous amount of time and processing power. That's a reflection of how complex your dna is, not a reflection of how much processing power we have at our disposal. If we could borrow from the computing power of the future, then you might be right. But the fact remains, we only have what's at our disposal now. At the current state of computing technology, the calculations would take 162 years.
Tha
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But it's not important, it was just a one-liner from
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Better title: saves time (Score:2)
That said, just as 'cancer research' is a way to get easy funding, 'grid computing' is not much more. The theory is very nice, work on a machine anywhere in the world from your own desktop without ha
Done before (Score:1)
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The Folding@home project at Stanford has been around that long as well.
http://folding.stanford.edu/ [stanford.edu]
162 years (Score:1)
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Moore's law doesn't help us right NOW. If I promise you ten bazillion dollars in 2025, that doesn't help you buy even a stick of gum today.
Unless, of course, you'd like to stick to the realm of theoretics, in which case I postulate that cancer doesn't exist and neither do you, and by a solid application of Finagle's law I'm about to take a hatchet to my left hand. Do you see my point?
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This is great and all but... (Score:5, Interesting)
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Re:This is great and all but... (Score:4, Informative)
The research is being done by scientists at Princess Margaret Hospital in Toronto, a government run hospital. If you knew anything about health care in Ontario you'd know that profit is the last thing on their mind.
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Desktops are not supercomputers (Score:4, Informative)
Every time these "connect desktops to become the fastest computer in the world" articles come up, I have to dust off my Cluster Urban Legends [clustermonkey.net] article to clear up the mis-conceptions that abound. I also did a piece [linux-mag.com] on the Linux Magazine site as well that debunks much of the spam-bot supercomputer legend (need to register for that one)
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Re:Desktops are not supercomputers (Score:4, Insightful)
I'm not talking about spare cycles. I'm talking about the naive notion that gets repeated in the press "the combined power of all these computers equals one of the fastest supercomputers in the world" For trivial parallel applications this might be true, but just once I would like to see these "supercomputers" run a simple parallel benchmark like High Performance Linpack (used for the Top500 list). My guess is the number of real FLOPS would be much less than expected -- if it even finished. Don't get me wrong, using computers like this is great idea, it is not one of the most power computers in the world, however.
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You and Tom from Tom's Hardware should get together and chew the fat about your benchmarks.
Nobody else gives a shit if the data set is done.
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If you application needs to communicate to other versions of itself alot, then you don't want a cluster.
If your program doesn't then a cluster is fine.
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If you know so much about the topic, why aren't you at Stanford telling Dr. Pande and his group that they are wasting their time with all those desktops and PS3's? I'm sure Dr. Pande would love for you to point out how his research would be much better off if he'd just go buy some time on aupercomputer.
ht [stanford.edu]
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But the thing is, these clusters are not made for running benchmarks, but for real (and specialized) calculations. My home server processes data for the World Community Grid and I see that the client is silently numbercrunching for a few hours and then communicates for a few seconds (at the amazing speed of about 50 kB/s). And for this, actual usage the grid shows a performance that could only be replicated by a powerful supercomputer
MOD PARENT DOWN (Score:2)
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Too bad you're wrong in this case, since protein folding is embarrassingly parallel. How do you think Folding@home works?
PS3 Supercomputer (Score:4, Informative)
I run their PC sw on my systems I keep on. They are getting results, and publishing papers based on the research.
Patents? (Score:3, Interesting)
Because that would make me feel a little less charitable with my computing power. (Only a little, though.)
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The alternative is "don't help the distributed computing project" and those drugs will never be 'discovered'. Then, instead of being poor and alive, the patients will be wealthy and at room temperature.
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It it makes you feel better, the bioinformatics team is being led by a Canadian researcher out of a Candian institution (the Ontario Cancer Institute at Princess Margaret Hospital, jointly with the University of Toronto). In Canada, chemotherapy drugs are provided to patients free of charge, and pricing is cont
I don't get it... (Score:4, Informative)
They're always saying, "We've knocked decades off of our work by using the right tool for the job." That's like me saying I knocked decades off of the calculations to run an energy minimization on a hexane molecule by running it on my Core 2 Duo instead of my Atari 800.
I mean, let's face it. They weren't going to let the friggin' program run for 162 years. The problem became solveable when the hardware became available. Hell, within 5 years, that "conventional computer system" will be able to solve it in a fraction of that 162 years and 5 years later, a fraction of that. So what do you do? You wait until the hardware meets up with ability to solve the problem. They haven't saved decades. They probably haven't even saved a decade. Within a decade they'd probably be able to run it in a few days on a conventional computer.
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So, if I'm following you correctly, you want the medical researchers to stockpile all the research projects that have "heavy computing demands" until Intel comes out with their 128-core CPU? What do we do in the meantime? Just sit around say "Oh jeez, sorry we don't have a treatment for your leukemia. But in ten years, we are going to launch a computer program that will have an answer for us after running for just thirty days!"?
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No, you're not following me correctly. My point is, nobody is going to run a program that's going to take decades to run. Instead, they're going to run some scaled down version that approximates a solution or there going to find some other method to solve the problem. When the computing power is available to run it in a
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http://www.medicalnewstoday.com/articles/37480.php [medicalnewstoday.com] Apparently there's about 550,000 people die
Open Source Software Cures Cancer (Score:3, Insightful)
World Community Grid [worldcommunitygrid.org] is making [this] technology available only to public and not-for-profit organizations to use in humanitarian research that might otherwise not be completed due to the high cost of the computer infrastructure required in the absence of a public grid. As part of our commitment to advancing human welfare, all results will be in the public domain and made public to the global research community.
WCG uses the Berkeley Open Infrastructure for Network Computing (BOINC) client, an open source software project that runs on Linux, Mac and Windows. Headline should read Open Source Software Cures Cancer
BoincStats [boincstats.com] shows you who is contributing to World Community Grid projects. Check it out...and ask yourself why you aren't contributing.
How could this be? (Score:2, Funny)
I can see it now (Score:3, Interesting)
SETI (Score:1)
I OBJECT!! (Score:5, Interesting)
Let me back up and explain what the project is doing. To simplify a little bit, the vast majority of "work" in the cell is done by proteins. While DNA can be thought of as something like a simple "string", proteins have complex three-dimensional shapes. Knowing those 3D shapes is of great interest to biologists. There are several reasons for that. One is that it can allow easier design of drugs targeted at a specific part of the protein. Another is that by seeing the shape, we can understand how all the mutations that occur in disease might be affecting its function.
The primary way to determine the shape of the protein is to take the protein and to grow it into an ordered crystal. You can then shine an x-ray beam through the crystal, and the diffraction pattern that emerges can be, through some very complex math, reverse-engineered into a 3D structure. Typically the most difficult part of this process is finding the specific chemical conditions that will allow a crystal to grow. These conditions differ from protein to protein.
This project is not "solving cancer", by any means. Rather, the people in Buffalo have generated a high-throughput way of screening different chemical conditions to determine which ones might allow a protein to grow. They use robotics to screen about 1000 conditions, and take pictures of each condition. The question then becomes: can you automatically process the pictures to find crystals. That's the goal of this project, to help automatically identify crystals in this screen.
So why do I object so strongly to this work? There are three reasons.
First, the project has nothing to do with cancer. In fact, the proteins being analyzed are not in any way "cancer-specific proteins" -- many of them are not even human!! This "cancer" pitch is a sales job, and nothing but a sales job. As a cancer researcher, it offends me that people try to use the disease to justify research that is this unrelated.
Second, the project is ill-conceived, technically. In no way did the group in question (Igor Jurisica's lab, in Toronto) carefully select a machine-learning approach to identify good ways of analyzing images. Instead, they have just selected something like 1000 different techniques, and are running *all* of them on every image they have. It's a fishing expedition, with the hope that one of those thousand metrics they return will be a useful predictor.
Third, the techniques selected are basically arbitrary. Most egregiously, there appear to be NO Fourier transforms included in the analysis!! Further, the images generated by the software appear to be transforms of something called "gray level cooccurrence matrices", and the computation of those can be estimated in no more than five minutes. So why are they taking 5 hours per unit? It appears that they have chosen to implement an exhaustive GLCM search that is an order of magnitude slower, rather than using existing estimation procedures that are ~98.5% accurate. Is that an excuse to use more computer time? Is there any scientific merit to that? Why aren't Fouriers included, since they are a standard technique for image analysis?
I have a number of computers that I run various BOINC projects on, but this will NEVER be one. It's a fishing expedition, being sold as cancer research, and that is a sad way to deceive the public.
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Or, as a lot of molbio automation companies are offering, actually shine an X-ray beam through the putative crystal onto a detector and see if it diffracts.
Fully automated high-throughput crystal growing strikes me as a bit of a boondoggle; the sophisticated robots r
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In no way did the group in question (Igor Jurisica's lab, in Toronto) carefully select a machine-learning approach to identify good ways of analyzing images. Instead, they have just selected something like 1000 different techniques, and are running *all* of them on every image they have. It's a fishing expedition, with the hope that one of those thousand metrics they return will be a useful predictor.
Not quite. The machine learning bit comes second. You have to spend the CPU cycles to extract features from the images first. Only then can your favourite ML technique tell you if the features are predictive. The first ~1000 features (already computed, locally) show some promise, and that's why this project will explore the image feature space a bit more (~12000 features). Once we get Grid results back from our human-scored image set, any features that are a clear waste of time will be dropped.
Third, the techniques selected are basically arbitrary. Most egregiously, there appear to be NO Fourier transforms included in the analysis!!
Aga
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The extra hours are not busy work.
Christ
Question to people running distributed apps (Score:2)
(Of course I assume some would be tempted to reverse engineer the distributed app, because of pure curiosity).
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Cure for cancer, only decades away! (Score:2)
50 years before eternity is still eternity (Score:2)
(Yes, I know my statement is false when it comes to rats, we can cure rat cancer with astonishing effectiveness.)
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Hmmmm....using video card GPUs for scientific number crunching. I wonder why no one has thought of that one...
http://folding.stanford.edu/English/FAQ-ATI [stanford.edu]
The millions of watts of wasted energy for distiributed computing non-sense is pushing the earth to global warming.
[citation needed]
That wasted watts also mean wasted money, go give your money to a fund or university, so they could buy dedicated har
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I noticed that you omitted using linebreaks in an effort to save energy.
Seriously, I asked you to provide a source that links distributed computing to global warming and you threw a bunch of numbers together. Please provide a credible source which documents the link between PCs and global warming. Thanks.