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## ----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())
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