[clug] workstation for processing MRI data
paul.wayper at anu.edu.au
Fri Aug 4 06:53:28 GMT 2006
Nicolas Cherbuin wrote:
> Thanks to those who have responded to my query. It does not look as if
> I will gain much with a 64 bit machine and a cluster is way above my
It depends on the software you're using. If it doesn't already support
running in some parallel framework - PVM or MPI are the two main 'open
source' ones - then clustering is a no-go. If it does support one of
these frameworks then you're in with a chance.
> I am still wondering if somebody would have a specific
> motherboard/processor combination to recommend that could accommodate
> 8 gigs of RAM and is particularly good.
I'd recommend the Tyan Opteron motherboards, myself. I'm running a
cheap one - 'cheap' here means that it's sharing the memory between all
the processors, rather than giving each processor its own RAM to use.
The Tyans range from workstation to high-end servers - you can get
four-way Opteron boards, for instance. (I prefer Opterons because Xeons
are all 64-bit, rather than allowing 64-bit and 32-bit simultaneously,
and are too expensive and run very hot.) The motherboard I'm running
has 4GB in it and is steady as a rock.
> Also, is it feasible/worthwhile to get a 64 bit machine and run it
> initially with a 32 bit OS (linux) as a way of future proofing? Drew
> gave a link for distributions that are planning a mix of 32 and 64 bit
> applications but given my knowledge of linux and time restrictions I
> cannot deal with something too new and potentially unstable.
I'm puzzled by this question. I'm running the x86_64 version of Fedora
Core 5 with no problems. It will run 32-bit apps at the same time as
64-bit ones, so the architecture doesn't really limit you to one or the
other. About the only minor problem is that you can't use the Flash
plugin for your 64-bit browser, but that's a blessing in disguse half
Again, the question really comes down to what your application
requires. A quick look at the Freesurfer site and doing a couple of
searches for things like 'Freesurfer MPI' show that it's a single-thread
application. This means that having more than one core will only buy
you a tiny amount of speedup for the application (the other CPU will be
handling all the other system work, which on a single-app system is
probably less than 1% time). If your usage is simply to process one
scan at a time, it looks like your best bet will be to buy the fastest
processor that you can. So getting a quad-way system is right out.
If you get e.g. a dual-core or dual-CPU machine, you can run two
Freesurfer processes simultaneously - processing the results of one scan
while you visualise another, for instance. Given the price/performance
ratio of high-end processors, I personally think you're better spending
your money on a dual-processor or dual-core machine: two Opteron 250s
(2.4GHz) cost less than a single Opteron 254 (2.8GHz) that is only 16%
faster. If you're efficient about using CPU time, the first run will be
16% slower but the next run will be effectively instant (for an overall
saving of 83% time...).
A quick pricing exercise (which I always enjoy) on AusPC Market says a
fast system is going to cost $4500 ex tax; $2000 of this is in 8GB of
fast RAM. I'd start off with e.g. 4GB of RAM and see how that goes,
myself. The costing can be seen at
not affiliated with AusPC Market, I just buy stuff from them.
> I am researching hardware specification for a workstation that will
> be used to process resource intensive MRI data (3D brain imaging)
> using the OSS Freesurfer running under linux. I am wondering if some
> of us have had similar requirements (particularly in image
> manipulation) and what their choices have been.
> The guys producing Freesurfer recommend greater CPU speed and RAM
> (min 2gig, 4gigs recommended) with normal specs for HD drives. Given
> that with these specs the processing of one scan can take 18 hours,
> I am keen to get more than the minimum. I have to process
> potentially hundreds of scan but at least in the tens.
> I was thinking of getting at least a dual core Athlon 4800? and 8
> gig of ram and use Fedora for simplicity (I am not a linux expert).
> Budget is around $3-5000 possibly more if it can be justified.
> I am trying to answer the following questions:
> 1. If I get a 64 bit processor will it make much difference and will
> I still be able to run 32 bit software (freesurfer is supported in
> 64bits architectures). what processor should I choose?
> 2. What sort of motherboard should I choose and do some support 2 x
> dual core chips?
> 3. The graphics card needs to support openGL but does not need to be
> especially good. Which card is going to provide least trouble under
> Any comments would be appreciated
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