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Thread: $4,829-per-hour supercomputer built on Amazon cloud

  1. #1
    fuck entrox Donor Jason Marshall's Avatar
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    $4,829-per-hour supercomputer built on Amazon cloud

    Just wow.

    http://arstechnica.com/business/news...r-research.ars

      Spoiler:
    Cancer research is one of the last areas of human endeavor in which anyone would want to "cut corners." Yet, that’s exactly what scientists must often do when the computational resources available to them aren’t sufficient to handle all the components of experiments they want to run.

    That is the problem described by Ramy Farid, president of a New York firm called Schrödinger that makes simulation software for use in pharmaceutical and biotechnology research. The company operates a 1,500-core cluster to perform research, but it’s often not enough.

    "We cut all kinds of corners. We use less accurate scoring functions. We do less sampling of the conformations of a compound. We are always having to make decisions like that," Farid, who earned a PH.D. in chemistry from Caltech in 1991, told Ars.


    Schrödinger President Ramy Farid
    Farid and his team recently decided they wanted to stop cutting corners, specifically for a joint cancer research project conducted with Nimbus Discovery, which does computer-based drug discovery. The key was that instead of using Schrödinger’s internal cluster, they opted to build a 50,000-core supercomputer on the Amazon Elastic Compute Cloud.

    It ran for three hours on the night of March 30, at a cost of $4,828.85 per hour. Getting up to 51,132 cores required spinning up 6,742 Amazon EC2 instances running CentOS Linux. This virtual supercomputer spanned the globe, tapping data centers in four continents and every available Amazon region, from Tokyo, Singapore, and Sao Paolo, to Ireland, Virginia, Oregon, and California. As impressive as it sounds, such a cluster can be spun up by anyone with the proper expertise, without talking to a single employee of Amazon.

    Data turns up potential leads for cancer treatment

    Schrödinger’s cluster was deployed by Cycle Computing, which builds software designed to take the raw computing power offered by Amazon and turn it into what Cycle CEO Jason Stowe likes to call a "utility supercomputer." Cycle takes care of things like data routing, error handling, and various types of automation to take Amazon’s virtual servers and turn them into a "functioning computing environment that doesn’t require you to rewrite your applications because it looks like an internal high-performance computing system," Stowe said.

    The cluster proved to be a success, turning up leads for future research that Schrödinger would have missed had it been forced to cut corners by using its more limited in-house resources.


    The 50,000-core cluster scaled up steadily over three hours. The grey portions are cores that finished their most recent jobs and are about to pick up new ones.
    Cycle Computing
    Schrödinger tested 21 million synthetic compounds developed by chemistry labs that can potentially be used in drugs. While the full test was run on Amazon, Farid and his team decided to run the same tests, with corners cut, internally, to see how the results would compare.

    "When we do a virtual screen on our in-house cluster, we have to cut some corners because we can’t wait a year for the screen to finish," Farid said.

    Farid explained that his team was looking at "pharmaceutical drug targets, proteins in this case, with a drug or drug candidate, often referred to as a 'ligand,' bound to the protein. What we did on the Amazon cluster was to search, using 'virtual screening,' for ligands that are predicted to bind to a particular target that has been implicated in several different cancers." You can click here for some cool images of the compounds studied.

    As it turned out, there were false negatives produced by the internal cluster, which were correctly identified as potential drug targets by the Amazon cluster. Cutting corners can also result in false positives. With the results from the Amazon cluster, Farid said Schrödinger is going to purchase compounds for further testing that it otherwise would have missed.

    This is just the first step in an iterative process that can take many years. There’s no guarantee that any cancer medication will be developed as a result, but at least there’s a chance.

    Using a sports analogy, Farid said tapping the huge resources of Amazon is like being able to take many more shots on goal. By Stowe’s way of thinking, the utility supercomputer lets researchers ask the right questions without fear that they won’t have the computational wits to answer them.

    Scaling up to 50,000 cores

    This isn’t the first cluster Cycle Computing has built on Amazon, but it is the largest. We reported last September that Cycle built a 30,000-core cluster for $1,279 per hour for an unnamed pharmaceutical customer.

    The 51,132-core cluster didn’t start that large—it scaled up steadily, hitting its peak somewhere in the third hour. The cluster used 58.78TB of RAM, and was secured with HTTPS, SSH, and 256-bit AES encryption. Amazon is a bit secretive of what’s running on its infrastructure, but Stowe said the cluster likely accessed servers based on Intel’s Nehalem and Sandy Bridge processors.

    The cluster used a mix of 10 Gigabit Ethernet and 1 Gigabit Ethernet interconnects. However, the workload was what’s often known as "embarrassingly parallel," meaning that the calculations are independent of each other. As such, the speed of the interconnect didn’t really matter.


    Cycle Computing CEO Jason Stowe
    The $4,800 per hour cost is what was paid to Amazon. In addition, Schrödinger pays Cycle for a subscription service. But building the kind of data center that could house a 50,000-core cluster could cost $20 million to $25 million, Stowe said.

    Certainly, Amazon isn’t the only company to offer HPC services on demand. Supercomputing centers sell time to researchers, but there can often be a significant wait before resources may be accessed, Stowe said.

    With Amazon, "we can provision this environment dynamically without having to interact with people or do any form of manual labor," Stowe said.

    In future supercomputing runs, Cycle may take advantage of Amazon’s "spot instances," which let customers bid on unused capacity and can lower the price. But for the 50,000-core run, the challenge was ensuring that Cycle’s customer could get all the capacity it needed. That’s why it was run across multiple continents.

    Stowe is always trying to one-up Cycle’s past achievements, but topping 50,000 cores will take some careful planning.

    "We knew that we could hit something in this range," Stowe said. "But in order to acquire this, we had to be ready to grab infrastructure wherever we may find it."

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  2. #2
    Varcaus's Avatar
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    Super Ponerator Global Moderator Evelgrivion's Avatar
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    Quote Originally Posted by Varcaus View Post
    ? Seems like a clever application of commodity computing power to me.

  4. #4
    Varcaus's Avatar
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    Quote Originally Posted by Evelgrivion View Post
    Quote Originally Posted by Varcaus View Post
    ? Seems like a clever application of commodity computing power to me.
    Exactly

  5. #5
    Donor erichkknaar's Avatar
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    That's awesome, and it will work great until they need to use EBS for something, then it will fall over hard.
    meh

  6. #6
    THE PUNISHED
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    but can it play crysis on max settings?

  7. #7
    Destoration's Avatar
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    Quote Originally Posted by Ralara View Post
    but can it play crysis on max settings?
    You mean can it play crysis on max settings on a screen projected onto the moon.

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    THE PUNISHED
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    Quote Originally Posted by Destoration View Post
    Quote Originally Posted by Ralara View Post
    but can it play crysis on max settings?
    You mean can it play crysis on max settings on a screen projected onto the moon.
    No, it can't do that.

  9. #9
    balistic void's Avatar
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    Quote Originally Posted by Ralara View Post
    but can it play crysis on max settings?
    This is how you troll a graphics programmer.

  10. #10
    Izo Azlion's Avatar
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    Wow.

    Its cancer research, it should have the time for it when it wants it. Or maybe a 3-5 hour session a month available... Something, surely?

  11. #11
    Destoration's Avatar
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    Why? All the money that goes the cancer related charities they should get free time to use hardware? They could easily build a huge supercomputer dedicated to this if they wanted to.

  12. #12
    Joshua Foiritain's Avatar
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    Impressive



  13. #13
    Izo Azlion's Avatar
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    Quote Originally Posted by Destoration View Post
    Why? All the money that goes the cancer related charities they should get free time to use hardware? They could easily build a huge supercomputer dedicated to this if they wanted to.
    I would have thought one of the most horrible diseases that attacks anyone at any point in their life, yes, this is a good use of hardware. Considering it costs 1/16th of the cost of a guided missile to run for an hour, I think we could cut some cash out of the war chest and put it into this.


    Also doesn't it say in that article that a super computer in its own building would be a 20-25 million dollar job?


    But building the kind of data center that could house a 50,000-core cluster could cost $20 million to $25 million, Stowe said.

  14. #14
    balistic void's Avatar
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    Also Amazon constantly maintain and upgrade their nodes, this is another cost that would have to be paid to run your own.

  15. #15
    kzig's Avatar
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    I wonder how the economics of this compare to the likes of folding@home?

  16. #16
    Destoration's Avatar
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    Sure that would be great. The largest supercomputer ever should be built to solely help cure diseases and it should be done on donations received from everyone around the world. Probably won't happen though. I like that they took initiative instead of limiting themselves with their in house system.

  17. #17
    indeterminacy's Avatar
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    Quote Originally Posted by kzig View Post
    I wonder how the economics of this compare to the likes of folding@home?
    The economics of Amazon's computing service are terrible Granted, a node-hour may seem cheap but they nickle and dime users on I/O charges and network charges both coming and going.

    We run HPC services like this for far, far cheaper rates. But, we're not amazon so we're less hip and I'd guess hundreds of thousands of research dollars are wasted every year (perhaps more) by researchers here on those nickle and dime charges due to sheer ignorance / a need to be edgy. Besides, "big computing" is pretty dead in the HPC world. The real problem in the last couple of years and going forward is data. The growth in the volume of data being generated by every type of sensor you can imagine, transmitted, and stored is outstripping current technology.

  18. #18
    HEY LOOK AT ME I HAVE A TITAN LordsServant's Avatar
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    Quote Originally Posted by Izo Azlion View Post
    Quote Originally Posted by Destoration View Post
    Why? All the money that goes the cancer related charities they should get free time to use hardware? They could easily build a huge supercomputer dedicated to this if they wanted to.
    I would have thought one of the most horrible diseases that attacks anyone at any point in their life, yes, this is a good use of hardware. Considering it costs 1/16th of the cost of a guided missile to run for an hour, I think we could cut some cash out of the war chest and put it into this.


    Also doesn't it say in that article that a super computer in its own building would be a 20-25 million dollar job?


    But building the kind of data center that could house a 50,000-core cluster could cost $20 million to $25 million, Stowe said.
    Fairly certain that getting shot in the head because your country got invaded due to lack of military funding will kill you much quicker and surer than cancer will.

    Without derailing the thread too much - how's about we just cut off the scumbags on welfare and use THAT money to fund it? You want money - get a fucking job. (Actually disabled/people trying as hard as they can to make ends meet and have a job are still fine in my book, just fuck the d-bags with no job just collecting it and living off it their entire lives)
    It's 2019. Get a grip.

  19. #19
    Lowa [NSN]'s Avatar
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    This is why I love doing what I'm doing. Very clever way of thinking outside the box.
    Also kinda shows why Amazon is considered one of the most stable platforms in the world.
    Quote Originally Posted by Tarminic View Post
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  20. #20
    Steph's Avatar
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    Quote Originally Posted by LordsServant View Post
    Quote Originally Posted by Izo Azlion View Post
    Quote Originally Posted by Destoration View Post
    Why? All the money that goes the cancer related charities they should get free time to use hardware? They could easily build a huge supercomputer dedicated to this if they wanted to.
    I would have thought one of the most horrible diseases that attacks anyone at any point in their life, yes, this is a good use of hardware. Considering it costs 1/16th of the cost of a guided missile to run for an hour, I think we could cut some cash out of the war chest and put it into this.


    Also doesn't it say in that article that a super computer in its own building would be a 20-25 million dollar job?


    But building the kind of data center that could house a 50,000-core cluster could cost $20 million to $25 million, Stowe said.
    Fairly certain that getting shot in the head because your country got invaded due to lack of military funding will kill you much quicker and surer than cancer will.
    Because America isn't the single largest military spender in the world by a significant margin and is surrounded by hostile neighbours waiting to invade any moment with equal if not superior weapons technology, RITE?

    Come on, your government earmarked 707.5 billion this year for the DOD budget. That's 707,500 million. It's not as though a hypothetical 25 million spent instead on a cancer supercomputer would allow the North Korea to invade unchecked.
    Last edited by Steph; April 20 2012 at 08:19:06 PM.
    Quote Originally Posted by QuackBot View Post
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