## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::latex() ## ----setup, echo=FALSE----------------------------------------------------- suppressPackageStartupMessages({ library(BiocParallel) }) ## ----intro----------------------------------------------------------------- library(BiocParallel) ## Pi approximation piApprox <- function(n) { nums <- matrix(runif(2 * n), ncol = 2) d <- sqrt(nums[, 1]^2 + nums[, 2]^2) 4 * mean(d <= 1) } piApprox(1000) ## Apply piApprox over param <- BatchtoolsParam() result <- bplapply(rep(10e5, 10), piApprox, BPPARAM=param) mean(unlist(result)) ## -------------------------------------------------------------------------- registryargs <- batchtoolsRegistryargs( file.dir = "mytempreg", work.dir = getwd(), packages = character(0L), namespaces = character(0L), source = character(0L), load = character(0L) ) param <- BatchtoolsParam(registryargs = registryargs) param ## -------------------------------------------------------------------------- fname <- batchtoolsTemplate("slurm") cat(readLines(fname), sep="\n") ## ----simple_sge_example, eval=FALSE---------------------------------------- # library(BiocParallel) # # ## Pi approximation # piApprox <- function(n) { # nums <- matrix(runif(2 * n), ncol = 2) # d <- sqrt(nums[, 1]^2 + nums[, 2]^2) # 4 * mean(d <= 1) # } # # template <- system.file( # package = "BiocParallel", # "unitTests", "test_script", "test-sge-template.tmpl" # ) # param <- BatchtoolsParam(workers=5, cluster="sge", template=template) # # ## Run parallel job # result <- bplapply(rep(10e5, 100), piApprox, BPPARAM=param) ## ----demo_sge, eval=FALSE-------------------------------------------------- # library(BiocParallel) # # ## Pi approximation # piApprox <- function(n) { # nums <- matrix(runif(2 * n), ncol = 2) # d <- sqrt(nums[, 1]^2 + nums[, 2]^2) # 4 * mean(d <= 1) # } # # template <- system.file( # package = "BiocParallel", # "unitTests", "test_script", "test-sge-template.tmpl" # ) # param <- BatchtoolsParam(workers=5, cluster="sge", template=template) # # ## start param # bpstart(param) # # ## Display param # param # # ## To show the registered backend # bpbackend(param) # # ## Register the param # register(param) # # ## Check the registered param # registered() # # ## Run parallel job # result <- bplapply(rep(10e5, 100), piApprox) # # bpstop(param) ## ----sessionInfo, results="asis"------------------------------------------- toLatex(sessionInfo())