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Question: About Multicore: mclapply
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gravatar for Prashantha Hebbar
6.9 years ago by
Prashantha Hebbar260 wrote:
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 [[alternative HTML version deleted]]
ADD COMMENTlink written 6.9 years ago by Prashantha Hebbar260
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