I agree with Dan, memory will often be the limiting factor. I added RAM (16GB total) to my ppc and have had a much more productive environment, both for 32 bit and 64 bit applications.
Even if a single R session cannot benefit from multiple cores, if you can break your processes into parallel pieces you can use your separate CPUs with cluster software, or just run multiple R jobs manually. I'd recommend maximizing your RAM quantity over RAM speed. Also, determine the speed gain. Speed gains of 10-fold or more are noticeable, speed gains of 2 to 3 fold rarely make much of a difference. Steven McKinney, Ph.D. Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -----Original Message----- From: r-sig-mac-boun...@stat.math.ethz.ch on behalf of Dan Putler Sent: Tue 3/24/2009 12:08 PM To: Booman, M Cc: R-SIG-Mac Subject: Re: [R-SIG-Mac] Is R more heavy on memory or processor? Hi Marije, Personally, I would be more concerned with memory than processor. Running out of memory can be an unpleasant surprise. Base R uses a single core, but Simon Urbanek's multicore package (the most recent version of which, 0.1-3, is dated today) does allow you to use multiple cores at once. I haven't used this package, so can't offer any personal experience. Dan On Tue, 2009-03-24 at 19:55 +0100, 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: > > - 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? Or can R only use one core (in which case the 4-core > 2.93GHZ machine would be better)? > > - If R does not benefot from multiple cores yet, is there anything known > about whether Snow Leopard might make a difference in this? > > - To determine if my first priority should be processor speed or RAM, on > which does R rely more heavily? > > - The new chipset has 3 memory channels (forgive me if I word this wrong, as > you may have noticed I am no computer tech) so it can read 6Gb RAM faster > than it can read 8Gb of RAM; so for a program that relies more on RAM speed > than RAM quantity it is recommended to use 6Gb instead of 8 for better > performance (or any multiple of 3). Which is more important for R, RAM speed > or RAM quantity? > > (I am not sure if it helps to know, but previously I used a Powermac G5 > quadcore (sadly I forgot which processor speed but it was the standard G5 > quadcore) with 4 Gb RAM for datasets of 30-40 microarrays of 18,000 > datapoints each, and analysis was OK except for some memory errors in a > script that used permutation analysis; but it wasn't very fast.) > > Any recommendations are welcome! > > Marije Booman > > > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de > geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken > van dit bericht, het niet openbaar maken of op enige wijze verspreiden of > vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een > incomplete aankomst of vertraging van dit verzonden bericht. > > The contents of this message are confidential and only intended for the eyes > of the addressee(s). Others than the addressee(s) are not allowed to use this > message, to make it public or to distribute or multiply this message in any > way. The UMCG cannot be held responsible for incomplete reception or delay of > this transferred message. > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Dan Putler Sauder School of Business University of British Columbia _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
