On Tue, 24 Mar 2009, Simon Urbanek wrote:
On Mar 24, 2009, at 14:55 , Booman, M wrote:
Dear all,
I am going to purchase a Power Mac (a new one, with Nehalem processor) for
my R-based microarray analyses. I use mainly Bioconductor packages, and a
typical dataset would consist of 50 microarrays with 40,000 datapoints
each. To make the right choice of processor and memory, I have a few
questions:
I don't use BioC [you may want to ask on the BioC list instead (or hopefully
some BioC users will chip in)], so my recommendations may be based on
slightly different problems.
- would the current version of R benefit from the 8 cores in the new Intel
Xeon Nehalem 8-core Mac Pro? So would an 8-core 2.26GHz machine be better
than a 4-core 2.93GHz?
Unfortunately I cannot comment on Nehalems, but in general with Xeons you do
feel quite a difference in the clock speed, so I wouldn't trade 2.93GHz for
2.26GHz regardless of the CPU generation. It is true that pre-Nehalem Mac
Pros cannot feed 8 cores, so you want go for the new Mac Pros, but I wouldn't
even think about the 2.26GHz option. Some benchmarks suggest that the 2.26
Nehalem can still compete favorably if a lot of memory/io is involved, but it
was not very convincing and I cannot tell first hand.
Simon,
We've some experience with recent Xeons on Linux serrers, and that
says that the size of the L1 cache is at least as important as clock
speed. The following figures are from memory and rounded .... A dual
quad-core 2.5GHz 12Mb cache system (we've an identical pair, one my
server, bought in January) outperforms a dual quad-core 3CHz 6Mb cache
system bought 9 months earlier. That's running R, and in particular
multiple R jobs. At least here, the extra cost of the 2.93GHz
processor is phenomenal.
Also, it looks to us like the Achilles' Heel of the Mac Pro is its
disk system. Even if you load it up with a RAID controller and extra
discs (pretty exorbitant, too) it is still on paper way down on my
server -- and the 3GHz server does considerably outperform mine on
disc I/O as it has more discs and a better RAID controller, and our
Solaris servers are better still.
Just a bit of background,
Brian
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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