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