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Prashantha Hebbar
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260
@prashantha-hebbar-3526
Last seen 5.0 years ago
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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