Hello friends,
I was tryig to parallize a function using mclapply. But I find lapply() executes in lesser time than mclapply(). I have given here my system time taken for both the functions.
>library(ShortRead)
>library(multicore)> fqFiles <- list.files("./test")
> system.time(lapply(fqFiles, function(fqFiles){
  readsFq <- readFastq(dirPath="./test",pattern=fqFiles)
  }))
   user  system elapsed 
  0.399   0.021   0.419 
> system.time(mclapply(fqFiles, function(fqFiles){
   readsFq <- readFastq(dirPath="./test",pattern=fqFiles)},mc.cores=3))
   user  system elapsed 
  0.830   0.151   0.261 

Since the ./test directory contains three fastq files. I have used mc.cores = 3.

here is my mpstat output for mclapply()

04:47:55 PM  CPU   %user   %nice    %sys %iowait    %irq   %soft  %steal   %idle    intr/s
04:47:56 PM  all   13.86    0.00    1.37    0.00    0.00    0.00    0.00   84.77   1023.23
04:47:56 PM    0   21.21    0.00    2.02    0.00    0.00    0.00    0.00   76.77   1011.11
04:47:56 PM    1   33.00    0.00    2.00    0.00    0.00    0.00    0.00   65.00      9.09
04:47:56 PM    2    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00      0.00
04:47:56 PM    3    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00      3.03
04:47:56 PM    4    3.03    0.00    2.02    0.00    0.00    0.00    0.00   94.95      0.00
04:47:56 PM    5    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00      0.00
04:47:56 PM    6    0.00    0.00    0.00    0.00    0.00    0.00    0.00  100.00      0.00
04:47:56 PM    7   53.00    0.00    4.00    0.00    0.00    0.00    0.00   43.00      0.00

Hence,Can you please suggest me, why mclapply has taken more time than lapply()?

Thanking you in anticipation.
Regards,
Prashantha
Prashantha Hebbar Kiradi,

E-mail: prashantha.hebbar@dasmaninstitute.org

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