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Is a Linux supercomputer in your future?

By on August 26, 2003 (8:00:00 AM)

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- by Chris Gulker -
Linux admins, start checking out the HOWTOs and FAQs on Linux clusters. While they might not be as common as file and print servers, Linux-based supercomputers are increasingly showing up at medium and large-sized business to simulate everything from product designs to the company's own business processes.

Large corporations have been using supercomputers for more than a decade. Global oil companies, for instance, initially used the machines to model the geology of potential drilling sites. Some companies began to use the machines to try "what-if" scenarios about their own business processes when advanced mathematical modeling applications became available. Only supercomputers could handle the dizzying number of variables that describe a large business.

Those programs cost millions to run annually, not to mention the multi-tens-of-millions of bucks that the hardware cost. A decade later, however, Linux supercomputers that can be had for tens or hundreds of thousands of dollars are already at work doing engineering models, visualizing crash tests, and performing lots of other jobs that save corporations big money.

One area where the convergence of cheap computer power and developments in mathematical modeling applications is starting to bear fruit is business process modeling, where a company builds a complex model of its own processes. Then, if it wants to see what happens if it, say, raises prices, it can get an idea of the possibilities without taking the risk of trying it out on real live customers.

Once the province of mega-billion-dollar multi-nationals, business sims are showing up at very grounded enterprises like breweries, delivery companies, and retailers, according to reports. Why are these nuts-and-bolts businesses plunking down serious cash for a Linux cluster in these tough economic times?

Linux clusters are "a kind of parallel batch processor," says Jan Silverman, vice president of strategic initiatives at SGI. "Typically each instance of the problem runs on one node of the cluster, so you set the product price at $14 on one node, and $15 on another, and so on. So, depending on the number of nodes, you can run 100 or 1,000 sims simultaneously and look for the interesting scenarios." Each simulation can take from minutes to days to run, so the clusters are much faster than single machines for trying out lots of different what-if scenarios.

David Alexander, who heads the High Performance Computing Center at Wichita State University, is in a particularly good place to witness how processes that were developed by scientists are now being used by business. Alexander says that physicists and chemists have been using the cluster strategy to look at large classes of objects for interesting behavior. "A quantum chemist might run a sim on 1,000 molecules, looking for the few most interesting ones, on our Linux cluster. He would then move the most interesting candidates over to a conventional supercomputer to run sims at higher resolution," thus maximizing the efficient use of computing resources.

Linux clusters in the old days, while cheap, had enormous administration burdens. Early clusters usually came with a cart holding a monitor and keyboard, which admins would wheel from node to node to perform upgrades and maintenance -- which, in the case of a 4,096-node machine, could be quite time-consuming.

Modern clusters allow everything, including OS and application upgrades, to be scripted, so that the administration burdens are within the budget reach of mid-size universities and corporations. Intelligent queuing software is also starting to have an impact, because it allows jobs to be scheduled and dispatched to the right hardware at the right time without intercession by administrators. This also means that researchers and business people don't have to be computer scientists in order to figure out how to make their applications run efficiently.

Wichita's Alexander says that this trend "is one of the great advances in cluster computing in the last few years. Improved ease-of-use applies both to the system administrators who have to keep the machine and software up and running, and to the end users who just want to get their work done."

Once the realm of only the wealthiest organizations, supercomputing is becoming much less expensive, thanks to Linux. And while it may not yet be quite within the reach of the casual office worker, the power of Linux clusters is becoming steadily more accessible to power users. So, Linux admins, it may be time to start brushing up on your 'cluster literacy'...

Chris Gulker, a Silicon Valley-based freelance technology writer, has authored more than 130 articles and columns since 1998. He shares an office with 7 computers that mostly work, an Australian Shepherd, and a small gray cat with an attitude.

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on Is a Linux supercomputer in your future?

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Not only clusters but also GRID's

Posted by: gerardm on August 26, 2003 06:16 PM
Not only clusters provide for a bigger processing bang but so do GRID's. When you consider the amount of processing capacity time wasted on the average computer in a company, GRID's are to be considered.

Given that SUSE in its districution supports GRID's for some time now. Given that the Globus Toolkit 3 is now available, it is time to harnass those desktop PC's and put them to use.

Thanks,

    Gerard

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Re:Not only clusters but also GRID's

Posted by: Anonymous Coward on August 26, 2003 09:23 PM
How 'bout some links? I've been looking at moving to a Mosix-based setup here, but if there's other options, I'd like to see 'em.

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Condor

Posted by: Nick LeRoy on August 26, 2003 10:35 PM
Sorry to "spam", but your readers may also be interested in the software being developed by the Condor Project of the University of Wisconsin. Condor is a "high throughtput computing" system. The Condor project is quite active in many grid projects, and has recently been relicenced with a BSD style license. You can learn more from http://www.condorproject.org .

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old clusters & monitor/keyboard on cart

Posted by: ziggyzag on August 27, 2003 01:43 AM
A keyboard/mouse/monitor on a cart being wheeled from machine to machine is a sign of a Unix/Linux/*BSD admin who doesn't know what the heck they're doing. It wasn't necessary then either, with the correct setup.

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Ever heard of MPI or PVM or Mosix or ...

Posted by: Anonymous Coward on August 27, 2003 09:44 PM
This article presents an extremely limited view of Linux clusters. It ignores anything about networking among them, and ability for machines to work together to solve problems.

The earliest and simplest clusters used the approach described here of parceling out individual jobs to individual nodes for each one to solve independent of the others. But since NASA invented Beowulf about ten years ago, tools such as MPI and PVM have been used to run parallel jobs across an entire Linux cluster (even longer than that if one includes non-Linux clusters).

And Mosix allows transparent use of threaded code on clusters: if multiple threads or processes are running on one machine, it migrates them to others, and uses the network to create the illusion of shared memory among all threads. In other words, anything that will run on a "supercomputer" will run on a Mosix cluster, with the only differentiating factor being the relative speeds of communication between nodes. And though a handful of applications require the extremely fast communication of a "supercomputer" like the SGI Altix (e.g. density functional theory calculations for electronic structure), a great many can run at full processor utilization even with limited network bandwidth.

This ability to run parallel jobs has been the focus of Beowulf supercomputing since the beginning, and it's sad to see it being omitted from a piece like this in 2003. The author would do well to read up on the subject before writing about it publicly; I recommend the June 2003 issue of Linux Magazine, which has a variety of historical and other information about clusters.

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Re:Ever heard of MPI or PVM or Mosix or ...

Posted by: Anonymous Coward on August 27, 2003 10:22 PM
Some DFT codes, (eg. VASP), scale quite nice on a cluster. Of course, it's even better to have a decent interconnect like myrinet or quadrics.

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Re:Ever heard of MPI or PVM or Mosix or ...

Posted by: Anonymous Coward on August 28, 2003 06:26 AM
Sorry, didn't know that VASP scaled on a cluster (a friend who does DFT and uses VASP mentioned that he needed shared memory).

I'd be curious as to how it gets around the orthogonality requirement without severe communication bottlenecks -- it seems every piece of data needs to "see" every other...

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