[clug] workstation for processing MRI data

Paul Wayper 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
> head.
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
the time.

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
http://biojanus.anu.edu.au/~paulway/Nicholas_Cherbuin_system.pdf.  I'm
not affiliated with AusPC Market, I just buy stuff from them.


> Thanks
> Nic
>    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
>    linux?
>    Any comments would be appreciated

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