[R] Issue with mcapply

[Rainer M Krug]

Please keep this on the r-help mailing list.

AROONALOK PYNE <aroonalok.pyne at gmail.com> writes:

> R version 3.0.2 (2013-09-25)
>
>
> Large value : 9999999
>
>
> I rerun the code as c(10000000) for which your machine works fine but
> my code still hangs on reaching b(). I am running it from Linux
> Terminal.

Might be memory allocation issue (hardware)? I have 1GB of memory. If I
am not mistaken, all the data is copied into different R threads when
using mclapply - so the memory requirement is much bigger.

Cheers,

Rainer


>
>
> On Thu, Jun 11, 2015 at 2:15 PM, Rainer M Krug <Rainer at krugs.de> wrote:
>
>> AROONALOK PYNE <aroonalok.pyne at gmail.com> writes:
>>
>> > Please check this code :
>> >
>> > library(parallel)
>> > workerFunc <- function(n) { return(n^2) }
>> > a <- function(){
>> >   CurrentTime <- Sys.time()
>> >   res <- lapply(values, workerFunc)
>> >   TimeTaken <- Sys.time() - CurrentTime
>> >   print(TimeTaken)
>> > }
>> > b <- function(){
>> >   CurrentTime <- Sys.time()
>> >   numWorkers <- detectCores()
>> >   res <- mclapply(values, workerFunc, mc.cores = numWorkers-2)
>> >   TimeTaken <- Sys.time() - CurrentTime
>> >   print(TimeTaken)
>> > }
>> > c <- function(n){
>> >   values <<- 1:n
>> >   print("Evaluating a : ")
>> >   a()
>> >   print("Evaluating b : ")
>> >   b()
>> > }
>> >
>> > For large values of n, the code calculates a() but the hangs indefinitely
>> > on reaching b(). How do I correct it ?
>> > I am using Ubuntu 14.04 and core i7 Processor
>>
>> Which version of R and what are "large values"?
>>
>> I just did the following successfully:
>>
>> ,----
>> | > c(100)
>> | [1] "Evaluating a : "
>> | Time difference of 0.0002059937 secs
>> | [1] "Evaluating b : "
>> | Time difference of 0.02037406 secs
>> | > c(1000)
>> | [1] "Evaluating a : "
>> | Time difference of 0.001929998 secs
>> | [1] "Evaluating b : "
>> | Time difference of 0.01943302 secs
>> | > c(1000000)
>> | [1] "Evaluating a : "
>> | Time difference of 1.822959 secs
>> | [1] "Evaluating b : "
>> | Time difference of 1.46111 secs
>> | > c(10000000)
>> | [1] "Evaluating a : "
>> | Time difference of 23.55863 secs
>> | [1] "Evaluating b : "
>> | Time difference of 15.90938 secs
>> | >
>> `----
>>
>> Cheers,
>>
>> Rainer
>> --
>> Rainer M. Krug
>> email: Rainer<at>krugs<dot>de
>> PGP: 0x0F52F982
>>

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug

PGP: 0x0F52F982
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