[R-SIG-Mac] Is R more heavy on memory or processor?

[Prof Brian Ripley]

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,                  ripley at 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