Neuroimaging Centre chooses Apple technology

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Neuroimaging Centre chooses Apple technology

The University of York's Neuroimaging Centre has made a £300,000 investment in Apple technology, including the OSX operating system. Jobs which once took days now take minutes, improving productivity and lowering costs. A review by the university's computer science department found the operating system to be faster and cheaper than Windows and Linux for the scientific imagining applications.

Brain imaging is a memory-intensive task and the new system needed to be able to cope with 2GB of data per hour generated by magnetic resonance imaging (MRI) and magnetoencephalography (MEG) equipment, which runs practically 24 hours a day.

The Centre opened in May 2005 and forms part of the Department of Psychology at the University of York. It uses non-invasive imaging methods to study the structure of the human brain.

The Centre undertakes clinical and commercial work, under the trading name YNiC, as well as conducting research in the evenings. "The scanners are never turned off," said professor Gary Green, director of the Centre. "It cost £5.2 million to set up the centre and it costs around £250,000 a year to run it. To justify that, we run the scanners day and night.

"We wanted a high-performance computing system that could cope with many potential users and fast turnarounds," Green said. "In the past, processing jobs could take weeks, and yet much of the analysis is fine grained and very repetitive, so we were looking for a system that could handle large data sets in parallel."

Green wanted to deploy the system on a grid system, which could allow it to scale and evolve when necessary. He also wanted off-the-shelf software at a good price.

Having decided on the specification, an independent survey was conducted by a team of computer scientists. Windows, Linux, Mac OS X and Sun technology were all assessed with a fixed set of criteria.

A long list of standard brain-imaging software was tested on them, including Matlab, Atlas, Maple, Brainstorm, Neurolens, Brainvoyager and MPI. More general software programs were tested such as those for firewalls, databases and e-mail. Technology was also assessed for security, back-up and support, future-proofing and upgrade paths, contingency planning and cost.

"Apple won hands down," said Green. "It was the fastest and easily the cheapest option in storage, back-up and computing.

"Contingency worked well - if it turned out we didn't like Mac OS X, we could use Linux. It also ran every single one of the software packages we required. The support we received was good and there was a clear path in what Apple was doing with software," Green said.

The Centre's overall investment in Apple technology amounts to around £300,000. This includes 52 Dual Processor Xserve G5 cluster nodes, 8 Xserve G5 servers, 10 Power Mac G5s, 2 5TB and 2 3TB Xserve RAIDs (mirrored in another building for 32TB of total storage), 34 iMac G5s, 2 Opteron Linux Firewalls, 2 HP 128-port Ethernet switches, a 32-port Fibre channel switch, a HP tape library and various printers, faxes, photocopiers and digital cameras.

Green is particularly pleased with the performance of the Xserve cluster. He said: "We've already adapted software to the cluster so that it can perform proper parallel computing. Jobs that previously took days now take minutes, even seconds. This obviously makes a huge difference in terms of workflow and productivity."

The Centre also integrated the system with a Sun grid engine so the Xserve cluster could support lots of jobs. "Because Apple provided us with an off-the-shelf solution, we were able to have the Sun software up and running in four days," Green said. Similarly, integrating the HP Jukebox was literally a matter of "plug and go".

In order to increase reliability and resilience, the Apple RAID array has now been augmented by a storage area network (SAN), mainly for archiving purposes. "We identified certain bottlenecks and, to solve them, we introduced the SAN".

Because the scanners run around the clock, reliability was essential. Since the system went live in October last year, only two broken fans on the iMacs and one RAID disc that went down have caused any problems. Most of the servers have been up and running for 280 consecutive days without any problems.

Green expected demand from users to increase. "In the future we'll expand even further," said Green. "We're looking to support a wider group of users including a Europe-wide database - we also want to introduce support for external users and to create links to external grids. Apple has been a good choice for us and won't compromise our future development."

Box:

Hardware:

Xserve

Xserve RAID

Power Mac G5

iMac

Software:

Mac OS X

Mac OS X Server

Sun Grid Engine

BrainStorm

BrainVoyager

Maple

MATLAB

Neurolens





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This was first published in May 2008

 

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