Great. I will try it. Thank you. -Christos
-----Original Message----- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Wednesday, November 08, 2006 1:21 PM To: Christos Hatzis Cc: 'Stefan Grosse'; [email protected]; 'Taka Matzmoto' Subject: RE: [R] CPU or memory On Wed, 8 Nov 2006, Christos Hatzis wrote: > Prof. Ripley, > > Do you mind providing some pointers on how "coarse-grained parallelism" > could be implemented on a Windows environment? Would it be as simple > as running two R-console sessions and then (manually) combining the > results of these simulations. Or it would be better to run them as batch processes. That is what I would do in any environment (I don't do such things under Windows since all my fast machines run Linux/Unix). Suppose you want to do 10000 simulations. Set up two batch scripts that each run 5000, and save() the results as a list or matrix under different names, and set a different seed at the top. Then run each via R CMD BATCH simultaneously. When both have finished, use an interactive session to load() both sets of results and merge them. > RSiteSearch('coarse grained') did not produce any hits so this topic > might have not been discussed on this list. > > I am not really familiar with running R in any mode other than the > default (R-console in Windows) so I might be missing something really > obvious. I am interested in running Monte-Carlo cross-validation in > some sort of a parallel mode on a dual core (Pentium D) Windows XP machine. > > Thank you. > -Christos > > Christos Hatzis, Ph.D. > Nuvera Biosciences, Inc. > 400 West Cummings Park > Suite 5350 > Woburn, MA 01801 > Tel: 781-938-3830 > www.nuverabio.com > > > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Prof Brian > Ripley > Sent: Wednesday, November 08, 2006 5:29 AM > To: Stefan Grosse > Cc: [email protected]; Taka Matzmoto > Subject: Re: [R] CPU or memory > > On Wed, 8 Nov 2006, Stefan Grosse wrote: > >> 64bit does not make anything faster. It is only of use if you want to >> use more then 4 GB of RAM of if you need a higher precision of your >> variables >> >> The dual core question: dual core is faster if programs are able to >> use that. What is sure that R cannot make (until now) use of the two >> cores if you are stuck on Windows. It works excellent if you use >> Linux. So if you want dual core you should work with linux (and then >> its faster of course). > > Not necessarily. We have seen several examples in which using a > multithreaded BLAS (the only easy way to make use of multiple CPUs > under Linux for a single R process) makes things many times slower. > For tasks that are do not make heavy use of linear algebra, the > advantage of a multithreaded BLAS is small, and even from those which > do the speed-up is rarely close to double for a dual-CPU system. > > John mentioned simulations. Often by far the most effective way to > use a multi-CPU platform (and I have had one as my desktop for over a > decade) is to use coarse-grained parallelism: run two or more > processes each doing some of the simulation runs. > >> The Core 2 duo is the fastest processor at the moment however. >> >> (the E6600 has a good price/performance ration) >> >> What I already told Taka is that it is probably always a good idea to >> improve your code for which purpose you could ask in this mailing >> list... (And I am very sure that you have there a lot of potential). >> Another speeding up possibility is e.g. using the atlas library... >> (where I am not sure if you already use it) >> >> Stefan >> >> John C Frain schrieb: >>> *Can I extend Taka's question?* >>> ** >>> *Many of my programs in (mainly simulations in R which are cpu >>> bound) on a year old PC ( Intel(R) Pentium(R) M processor 1.73GHz or >>> Dell GX380 with 2.8Gh Pentium) are taking hours and perhaps days to >>> complete on a one year old PC. I am looking at an upgrade but the >>> variety of cpu's available is >>> confusing at least. Does any one know of comparisons of the Pentium >>> 9x0, Pentium(r) >>> Extreme/Core 2 Duo, AMD(r) Athlon(r) 64 , AMD(r) Athlon(r) 64 >>> FX/Dual Core AM2 and >>> similar chips when used for this kind of work. Does anyone have any >>> advice on (1) the use of a single core or dual core cpu or (2) on >>> the use of 32 bit and 64 bit cpu. This question is now much more >>> difficult as the numbers on the various chips do not necessarily >>> refer to the relative speed of the chips. >>> * >>> *John >>> >>> * On 06/11/06, Taka Matzmoto <[EMAIL PROTECTED]> wrote: >>> >>> >>>> Hi R users >>>> >>>> Having both a faster CPU and more memory will boost computing power. >>>> I was wondering if only adding more memory (1GB -> 2GB) will >>>> significantly reduce R computation time? >>>> >>>> Taka, >>>> >>>> _________________________________________________________________ >>>> Get FREE company branded e-mail accounts and business Web site from >>>> Microsoft Office Live >>>> >>>> ______________________________________________ >>>> [email protected] mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>> PLEASE do read the posting guide >>>> http://www.R-project.org/posting-guide.html >>>> and provide commented, minimal, self-contained, reproducible code. >>>> >>>> >>> >>> >>> >>> >> >> ______________________________________________ >> [email protected] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
