Hi, recently, i installed Gentoo in addition to SuSE on my Laptop. In order to see whether it was worth the effort, i did a small benchmark for R under SuSE and Gentoo. I guess, that the benchmarks under SuSE are also approximately valid for other binary distributions.
As a consequence, depending on your Unix/Linux experience, i would recommend Gentoo for optimal performance. If you are new to Linux and want to avoid the relatively complicated Gentoo setup, i recommend that you should least compile R from source, which should be easy also for a Linux newbie. The benchmark (see below for the script) consisted of i) Generating random normals and plotting density plots. ii) Cox model iii) Inverting random 200x200 matrices. I used different versions of R, since 2.0.1 is not yet included in the Gentoo portage tree. Here are my results: A) SuSE 9.2, R 2.0.1 (from i586 rpm): benchmark cpu.user cpu.system 1 benchmark.density 222.22 6.76 11 benchmark.survival 133.69 0.27 12 benchmark.linearalgebra 365.25 3.64 B) R 1.9.0 compiled under SuSE 9.2, without additional CFLAGS (i.e. using CFLAGS from the configure script): benchmark cpu.user cpu.system 1 benchmark.density 217.31 6.12 11 benchmark.survival 101.77 0.14 12 benchmark.linearalgebra 165.49 3.34 C) R 1.9.0 compiled under SuSE 9.2, using the same CFLAGS as in Gentoo (see below for my CFLAGS): benchmark cpu.user cpu.system 1 benchmark.density 199.16 5.96 11 benchmark.survival 94.26 0.15 12 benchmark.linearalgebra 159.17 4.93 D) R 1.9.0-r1 under Gentoo, using the CFLAGS for the whole system, not just for R. benchmark cpu.user cpu.system 1 benchmark.density 176.08 6.10 11 benchmark.survival 84.20 0.14 12 benchmark.linearalgebra 134.72 6.54 My CFLAGS (for a centrino) are: CFLAGS="-pipe -O3 -march=pentium4 -mmmx -msse -msse2 -mfpmath=sse,387 -maccumulate-outgoing-args -mno-align-stringops -fomit-frame-pointer -ffast-math -fsched-spec-load -fprefetch-loop-arrays -ftracer -fmove-all-movables" Question to the Gurus: Would it be allowed, to use -funsafe-math-optimizations? Here is my benchmark script: -------------------------------------------------- require(survival) benchmark.density <- function() { for (i in 1:1000) { x <- rnorm(100000) plot(density(x), type="l", xlim=c(-10,10), main=i) } } benchmark.survival <- function() { for (i in 1:1000) { time <- c(rexp(800, 1), rexp(800, 0.8), rexp(800, 0.9), rexp(800, 0.7), rexp(800, 0.5)) time <- round(time, digits=2) # introduce ties event <- as.integer(time <= 1) time[time > 1] <- 1 group <- c(rep(0, 800), rep(1, 800), rep(2, 800), rep(3, 800), rep(4, 800)) plot(survfit(Surv(time,event) ~ group), xlim=c(0,1)) title(main=i) dummy <- coxph(Surv(time,event) ~ group) } } benchmark.linearalgebra <- function() { for (i in 1:1000) { A <- matrix(rnorm(200*200), nrow=200, ncol=200) AI <- solve(A) residual <- A %*% AI - diag(1, 200) hist(residual, main=i) } } my.benchmark <- function(func) { funcname <- (as.character(sys.call()[[2]])) cat(funcname, "\n") times <- system.time(func()) return(data.frame(benchmark=funcname, cpu.user=times[1], cpu.system=times[2])) } result <- my.benchmark(benchmark.density) result <- rbind(result, my.benchmark(benchmark.survival)) result <- rbind(result, my.benchmark(benchmark.linearalgebra)) sink("benchmark.out") cat(Sys.info(), "\n") print(result) sink() -------------------------------------------------------------- Christian > Dear List, > I have acquired a new desktop and wanted to put a free OS on it. I am > trying Fedora Core 1, but not sure what the best Linux OS is for using R > 2.0.1? > > Thank you in advance for your input, > Tom Volscho > > ************************************ > Thomas W. Volscho > Graduate Student > Dept. of Sociology U-2068 > University of Connecticut > Storrs, CT 06269 > Phone: (860) 486-3882 > http://vm.uconn.edu/~twv00001 > > ______________________________________________ > [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 > ______________________________________________ [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