[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
>
> _______________________________________________
> R-sig-hpc mailing list
> R-sig-hpc at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793



More information about the R-sig-hpc mailing list