Hello all, I upgraded my R workstation, and to my dismay, only one core appears to be used during intensive computation of a bioconductor function. What I have now is two dual-core Xeon 5160 CPUs and 10 GB RAM. When I fully load it, top reports about 25% user, 75% idle and 0.98 short-term load. The archives gave nothing helpful besides mention of snow. I thought of posting to HPC, but this system is fairly modest WRT processing power. Any pointers of where to start? --- #Not running anything at the moment> sessionInfo()R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.11.1 --- $ uname -a Linux laux29 2.6.26-2-amd64 #1 SMP Sun Jun 20 20:16:30 UTC 2010 x86_64 GNU/Linux --- Thanks for your help, Edwin -- Dr. Edwin Groot, postdoctoral associate AG Laux Institut fuer Biologie III Schaenzlestr. 1 79104 Freiburg, Deutschland +49 761-2032945
?multicore perhaps On 09/14/2010 10:01 AM, Edwin Groot wrote:> Hello all, > I upgraded my R workstation, and to my dismay, only one core appears to > be used during intensive computation of a bioconductor function. > What I have now is two dual-core Xeon 5160 CPUs and 10 GB RAM. When I > fully load it, top reports about 25% user, 75% idle and 0.98 short-term > load. > The archives gave nothing helpful besides mention of snow. I thought of > posting to HPC, but this system is fairly modest WRT processing power. > Any pointers of where to start? > --- > #Not running anything at the moment >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > loaded via a namespace (and not attached): > [1] tools_2.11.1 > --- > $ uname -a > Linux laux29 2.6.26-2-amd64 #1 SMP Sun Jun 20 20:16:30 UTC 2010 x86_64 > GNU/Linux > --- > Thanks for your help, > Edwin
Hello Cedrick, Ah, yes, that looks like it would apply to my situation. I was previously reading on snow, which is tailored for clusters, rather than a single desktop computer. Anyone with experience adapting multicore to an R-script? I have to admit I know little about parallel processing, multiprocessing and cluster processing. Edwin On Tue, 14 Sep 2010 10:15:42 -0400 "Johnson, Cedrick W." <cedrick at cedrickjohnson.com> wrote:> ?multicore perhaps > > On 09/14/2010 10:01 AM, Edwin Groot wrote: > > Hello all, > > I upgraded my R workstation, and to my dismay, only one core > appears to > > be used during intensive computation of a bioconductor function. > > What I have now is two dual-core Xeon 5160 CPUs and 10 GB RAM. When > I > > fully load it, top reports about 25% user, 75% idle and 0.98 > short-term > > load. > > The archives gave nothing helpful besides mention of snow. I > thought of > > posting to HPC, but this system is fairly modest WRT processing > power. > > Any pointers of where to start? > > --- > > #Not running anything at the moment > >> sessionInfo() > > R version 2.11.1 (2010-05-31) > > x86_64-pc-linux-gnu > > > > locale: > > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods > base > > > > > > loaded via a namespace (and not attached): > > [1] tools_2.11.1 > > --- > > $ uname -a > > Linux laux29 2.6.26-2-amd64 #1 SMP Sun Jun 20 20:16:30 UTC 2010 > x86_64 > > GNU/Linux > > --- > > Thanks for your help, > > Edwin > > ______________________________________________ > R-help at r-project.org 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.Dr. Edwin Groot, postdoctoral associate AG Laux Institut fuer Biologie III Schaenzlestr. 1 79104 Freiburg, Deutschland +49 761-2032945