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Example: module load R/4.0.3 > library(plyr) > library(doParallel) Loading required package: foreach Loading required package: iterators Loading required package: parallel >cores > cores <- detectCores() > cores>cores [1] 72 > registerDoParallel(cores=12) > fake_func <- function(x) { + Sys.sleep(0.1) + return(x) + } > > library(microbenchmark) > microbenchmark( + serial = llply(1:24, fake_func), + parallel = llply(1:24, fake_func, .parallel = TRUE), + times = 1 + ) Unit: milliseconds expr min lq mean median uq max neval serial 2424.3580 2424.3580 2424.3580 2424.3580 2424.3580 2424.3580 1 parallel 226.2199 226.2199 226.2199 226.2199 226.2199 226.2199 1 > |
Sample interactive pbs run
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qsub -I -l select=1:ncpus=8:mem=12gb,walltime=1:11:00 -q small
Once you are on the compute node:
module load R/4.0.3
R
library(plyr)
library(doParallel)
cores <- detectCores()
cores
[1] 12
registerDoParallel(cores=8)
fake_func <- function(x) {
Sys.sleep(0.1)
return(x)
}
library(microbenchmark)
microbenchmark(
serial = llply(1:24, fake_func),
parallel = llply(1:24, fake_func, .parallel = TRUE),
times = 1
)
Unit: milliseconds
expr min lq mean median uq max neval
serial 2402.7702 2402.7702 2402.7702 2402.7702 2402.7702 2402.7702 1
parallel 320.0491 320.0491 320.0491 320.0491 320.0491 320.0491 1
>
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Reference
1. http://yusung.blogspot.com.au/2009/01/install-jags-and-rjags-in-fedora.html
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