[R-sig-hpc] multicore performance question
Mauricio Zambrano-Bigiarini
mauricio.zambrano at jrc.ec.europa.eu
Mon Jul 9 10:49:54 CEST 2012
Dear list,
I need to evaluate a vectorial function (~30 dimensions), and I would
like to know if it is possible to take advantage of a multicore machine.
So far, I'm using the multicore package, and I'm not getting any time
saving. I guess the larger the computation time the larger the gain in
performance, and probably that is the reason why I'm not speeding up my
computations by using multicore.
However, I would like to ask you if the reason for not getting any time
saving by using 'multicore' is the short time of my computations OR the
way in which I defined the function to be run (fn and fn1):
----------- START --------------
library(multicore)
fn <- function(x) {
n <- length(x)
return(1 + (1/4000) * sum(x^2) - prod(cos(x/sqrt(seq(1:n)))))
}
fn1 <- function(i, x) fn(x[i,])
nr <- 500
X <- matrix(rnorm(1000), ncol=30, nrow=nr)
# No multicore
set.seed(100)
system.time(
unlist(lapply(1:nr, FUN=fn1, x=X))
)
# multicore
set.seed(100)
system.time(
unlist(mclapply(1:nr, FUN=fn1, x=X, mc.cores=6))
)
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] multicore_0.1-7 hydroPSO_0.1-57 hydroTSM_0.3-5-2 xts_0.8-6
[5] zoo_1.7-7 sp_0.9-99
loaded via a namespace (and not attached):
[1] automap_1.0-12 class_7.3-4 cluster_1.14.2 e1071_1.6
grid_2.15.0
[6] gstat_1.0-12 Hmisc_3.9-3 lattice_0.20-6 tools_2.15.0
----------- END --------------
any comment will be very much appreciated.
Thanks in advance,
Mauricio Zambrano-Bigiarini
--
====================================================
Water Resources Unit
Institute for Environment and Sustainability (IES)
Joint Research Centre (JRC), European Commission
webinfo : http://floods.jrc.ec.europa.eu/
====================================================
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