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Networking Supercomputing Linux

Ask Slashdot: Best Use For a New Supercomputing Cluster? 387

Supp0rtLinux writes "In about 2 weeks time I will be receiving everything necessary to build the largest x86_64-based supercomputer on the east coast of the U.S. (at least until someone takes the title away from us). It's spec'ed to start with 1200 dual-socket six-core servers. We primarily do life-science/health/biology related tasks on our existing (fairly small) HPC. We intend to continue this usage, but to also open it up for new uses (energy comes to mind). Additionally, we'd like to lease access to recoup some of our costs. So, what's the best Linux distro for something of this size and scale? Any that include a chargeback option/module? Additionally, due to cost contracts, we have to choose either InfiniBand or 10Gb Ethernet for the backend: which would Slashdot readers go with if they had to choose? Either way, all nodes will have four 1Gbps Ethernet ports. Finally, all nodes include only a basic onboard GPU. We intend to put powerful GPUs into the PCI-e slot and open up the new HPC for GPU related crunching. Any suggestions on the most powerful Linux friendly PCI-e GPU available?"
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Ask Slashdot: Best Use For a New Supercomputing Cluster?

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  • by sconeu ( 64226 ) on Tuesday September 13, 2011 @05:36PM (#37392058) Homepage Journal

    No way in hell a project that big gets approved without a rationale.

    And no way in hell the administrator of such a project would ask Slashdot what to do with it.

  • Ummm two things (Score:4, Insightful)

    by Sycraft-fu ( 314770 ) on Tuesday September 13, 2011 @05:36PM (#37392060)

    1) Something with 10gb really isn't a "supercomputer" it is a cluster. Fine, but call it what it is. I really wouldn't call a cluster with Infiniband a supercomputer either.

    2) You really should maybe get someone who knows more about your project and someone who knows more about clusters/supercomputers. The questions you are asking are not ones I would want to see form the guy making the choices on a multimillion dollar project.

  • Uh oh.. (Score:5, Insightful)

    by joib ( 70841 ) on Tuesday September 13, 2011 @05:36PM (#37392066)
    Shouldn't you have figured out answers too all these (simple) questions before ordering several million $$$worth of hardware? Sheesh.. As for you specific questions: - IB vs. 10GbE: IB hands down. Much better latency and more mature RDMA software stacks (e.g. for MPI and Lustre). Cheaper and higher BW as well. - GPU: NVidia Fermi 2090 cards. CUDA is far ahead of everything else at the moment.
  • EPIC TROLLING (Score:5, Insightful)

    by jpedlow ( 1154099 ) on Tuesday September 13, 2011 @05:44PM (#37392142)
    Wow, he just TROLLED THE CRAP out of slashdot. We mad, bros!
  • Re:SETI ! (Score:4, Insightful)

    by Jarik C-Bol ( 894741 ) on Tuesday September 13, 2011 @09:49PM (#37393920)
    screw SETI, run folding@home and find the cure for cancer. We need that a little more than we need to stare at the sky, wishing someone would call from alpha centauri or some such place.
  • What? (Score:3, Insightful)

    by sycodon ( 149926 ) on Tuesday September 13, 2011 @11:37PM (#37394498)

    Isn't this shit you should have had all figured out before you even applied to whatever company, agency, government, etc, you got the money from?

    WTF is this? I can only hope you didn't get money from the feds.

    "Hey, look! The feds gave me a shit load of money to get this cool super computer...what should I do with it?"

    Seriously...if you got any government money for this then you are first class tool for not having all of this known before you even applied.

  • by robotkid ( 681905 ) <> on Wednesday September 14, 2011 @02:00AM (#37395170)

    Ever wonder why the option at the end of every damn Government spending cycle to NOT spend the money is never an option to choose? Like we have to wonder how the hell we ended up trillions of dollars in debt.

    Sad to say, I've seen Government "last-minute" spending like this too, but not exactly to this level of magnitude. This is a shitload of money "left over". This may have come from somewhere, but "budget" obviously had nothing to do with it.

    Yeah, I used to wonder that too. Then my wife got a job in state government. And the answer became painfully obvious judging by the maximum pace at which stuff gets done even when you have people willing to work hard and important problems sitting right in front of you. If you allowed unspent money to roll over indefinitely, that would create an irresistible incentive to do the cheapest job that won't get you in trouble and then hoard, hoard that money. Heck, you could stretch that 3-year project into a 5-year one by doing it very slowly. You could build up a war chest and use it on pet projects that noone approved. Or you could wait till no-one even remembers the project existed anymore and then embezzle it.

    So as inefficient as it is, the blanket rule that all money must be spent the year in which it is allocated is a simple way to increase transparency and accountability across the board. It may even be one of the driving forces anything gets done remotely on schedule in an environment where purchasing a USB cable requires 2 requisition forms, 3 vendor quotes, the signature of your boss (who is in an all-day meeting), your boss's boss (who is talking with legislators today and can't be disturbed), and pre-approval from someone in accounting (who just went on vacation yesterday).

    Of course, it would be great if getting the job done on time and under-cost were somehow rewarded. But that's incentivizing success, that's the profit maximizing, the corporate bottom line, whereas the the Gub'ment bottom line is minimizing "embarrassment" (be it from the media, the voting public, and especially legislators on the appropriations committee). You use a Gub'ment bureaucracy for things you can't trust the for-profit world to do on their own, so the service provided has to be somewhat divorced from the revenue stream if you want to ensure more reliable results than just contracting out to a private company. (I'm sure Ron Paul would beg to differ, but then again he also probably enjoys being able drink water out of the tap without getting sick). You wouldn't pay a health inspector, for example, just based on the number of sites inspected per day because that encourages as cursory a job as possible on as many sites as possible. Instead, you set a minimum quota they have to fulfill, and then make it known you'll have their head on a platter if a restaurant shows up in the news for salmonella poisoning the week after you've signed off on it. That's the Gub'ment way. .. .

"I prefer the blunted cudgels of the followers of the Serpent God." -- Sean Doran the Younger