R/MakeCluster.R

In jakeyeung/TissueCiradianAnalysis: Analysis of oscillatory RNASeq data

MakeCluster <- function(ncores, rscript_args){
  library(doParallel)
  # Make cluster pass no args or else it will take FOREVER for cl to be made.
  # Ref: http://stackoverflow.com/questions/23540129/what-affects-the-time-to-create-a-cluster-using-the-parallel-package
  if (missing(ncores)){
    ncores <- detectCores()
    print(paste("Cores:", ncores))
  }
  if (missing(rscript_args)){
    rscript_args = c("--no-init-file", "--no-site-file", "--no-environ")
  }
  cl <- makeCluster(ncores, rscript_args=rscript_args)
  registerDoParallel(cl)
}

unregister <- function() {
  # http://stackoverflow.com/questions/25097729/un-register-a-doparallel-cluster
  env <- foreach:::.foreachGlobals
  rm(list=ls(name=env), pos=env)
}