Question: multicore Vignette or HowTo??
8.2 years ago by
Edwin Groot • 230
Edwin Groot • 230 wrote:
Hello all, I have difficulty getting the multicore package doing what it promises. Does anybody have a benchmark that demonstrates something intensive with and without multicore assistance? I have a dual dual-core Xeon, and $ top tells me all R can squeeze from my Linux system is 25% us. Here is my example: > library(Starr) #Read in a set of ChIP-chip arrays > read("array.rda") # $ top reports 25% us for the following: > array_norm <- normalize.Probes(array, method = "loess") #Try the same with multicore > library(multicore) > multicore:::detectCores()  4 #No benefit from multicore. $ top reports 25% us for the following: > array_norm <- normalize.Probes(array, method = "loess") #lattice masks out parallel from multicore. Use mcparallel instead. > pnorm <- mcparallel(normalize.Probes(array, method = "loess")) > Normalizing probes with method: loess Done with 1 vs 2 in iteration 1 #Function continues for some time and displays more messages. No benefit from multicore. $ top reports 25% us during the run... > array_norm <- collect(pnorm) #Oh dear, where did my normalized data go? > array_norm $`4037` NULL > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale:  LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C  LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8  LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8  LC_PAPER=en_GB.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages:  tools grid stats graphics grDevices utils datasets  methods base other attached packages:  geneplotter_1.26.0 annotate_1.26.1 AnnotationDbi_1.10.2  Starr_1.4.4 affxparser_1.20.0 affy_1.26.1  Ringo_1.12.0 Matrix_0.999375-39 lattice_0.18-8  limma_3.4.4 RColorBrewer_1.0-2 Biobase_2.8.0  multicore_0.1-3 loaded via a namespace (and not attached):  affyio_1.16.0 DBI_0.2-5 genefilter_1.30.0  MASS_7.3-6 preprocessCore_1.10.0 pspline_1.0-14  RSQLite_0.9-2 splines_2.11.1 survival_2.35-8  tcltk_2.11.1 xtable_1.5-6 RTFMing only gives me the syntax of some functions in the multicore package. How do I apply successfully this thing to my code? Regards, Edwin -- Dr. Edwin Groot, postdoctoral associate AG Laux Institut fuer Biologie III Schaenzlestr. 1 79104 Freiburg, Deutschland +49 761-2032945
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