[R-sig-hpc] how can I
Martin Morgan
mtmorgan at fhcrc.org
Tue Aug 23 18:01:56 CEST 2011
On 08/23/2011 06:08 AM, Takatsugu Kobayashi wrote:
> Hi,
>
> Currently I am trying to see how much parallel processing
> packages like multicore and snow can improve computing
> times.
>
> Then I would like to ask if I did anything wrong as I don't see
> any significant improvement between lapply and mclapply
> while following examples shown in "parallel computing in R"
> written by Chao and Wee:
>
> library(multicore)
> system.time(out<- mclapply(pair, geneCor)
> system.time(out<- lapply(pair, geneCor)
>
> I guess the reason would be that only a single core was being
> used even with multicore package.
>
> Then, how can I see if all the cores are being used for computation?
Hi Taka --
a favorite of mine is
> library(multicore)
> system.time(mclapply(1:4, function(i) Sys.sleep(2)))
user system elapsed
0.005 0.006 2.008
> system.time(lapply(1:4, function(i) Sys.sleep(2)))
user system elapsed
0.002 0.000 8.009
the system utility 'top' is one way of seeing processors in action. If
there are issues then
> sessionInfo()
R Under development (unstable) (2011-08-13 r56726)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] multicore_0.1-5
loaded via a namespace (and not attached):
[1] tools_2.14.0
can be essential to diagnose problems.
Martin
>
> Thanks!!!
>
> Taka
>
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