## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------
BiocStyle::latex()

## ----biocLite, eval=FALSE------------------------------------------------
## source("http://bioconductor.org/biocLite.R")
## biocLite("BiocParallel")

## ----BiocParallel--------------------------------------------------------
library(BiocParallel)

## ----quickstart_FUN------------------------------------------------------
FUN <- function(x) { round(sqrt(x), 4) }

## ----quickstart_registry-------------------------------------------------
registered()

## ----configure_registry, eval=FALSE--------------------------------------
## options(MulticoreParam=quote(MulticoreParam(workers=4)))

## ----quickstart_bplapply_default, eval=FALSE-----------------------------
## bplapply(1:4, FUN)

## ----quickstart_snow-----------------------------------------------------
param <- SnowParam(workers = 2, type = "SOCK")
bplapply(1:4, FUN, BPPARAM = param)

## ----BiocParallelParam_SerialParam---------------------------------------
serialParam <- SerialParam()
serialParam

## ----BiocParallelParam_MulticoreParam------------------------------------
multicoreParam <- MulticoreParam(workers = 8)
multicoreParam

## ----register_registered-------------------------------------------------
registered()

## ----register_bpparam----------------------------------------------------
bpparam()

## ----register_BatchJobsParam---------------------------------------------
register(BatchJobsParam(workers = 10), default = TRUE)

## ----register_BatchJobsParam2--------------------------------------------
names(registered())
bpparam()

## ----error-vignette, eval=FALSE------------------------------------------
## browseVignettes("BiocParallel")

## ----use_cases_data------------------------------------------------------
library(RNAseqData.HNRNPC.bam.chr14)
fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES

## ----forking_gr, message=FALSE-------------------------------------------
library(GenomicAlignments) ## for GenomicRanges and readGAlignments()
gr <- GRanges("chr14", IRanges((1000:3999)*5000, width=1000))

## ----forking_param-------------------------------------------------------
param <- ScanBamParam(which=range(gr))

## ----forking_FUN---------------------------------------------------------
FUN <- function(fl, param) {
  gal <- readGAlignments(fl, param = param)
  sum(countOverlaps(gr, gal))
}

## ----forking_default_multicore-------------------------------------------
MulticoreParam()

## ----cluster_FUN---------------------------------------------------------
FUN <- function(fl, param, gr) {
  library(GenomicAlignments)
  gal <- readGAlignments(fl, param = param)
  sum(countOverlaps(gr, gal))
}

## ----cluster_snow_param--------------------------------------------------
snow <- SnowParam(workers = 2, type = "SOCK")

## ----cluster_bplapply----------------------------------------------------
bplapply(fls[1:3], FUN, BPPARAM = snow, param = param, gr = gr)

## ----ad_hoc_sock_snow_param----------------------------------------------
hosts <- c("rhino01", "rhino01", "rhino02")
param <- SnowParam(workers = hosts, type = "SOCK")

## ----cluster-MPI-work, eval=FALSE----------------------------------------
## library(BiocParallel)
## library(Rmpi)
## FUN <- function(i) system("hostname", intern=TRUE)

## ----cluster-MPI, eval=FALSE---------------------------------------------
## param <- SnowParam(mpi.universe.size() - 1, "MPI")
## register(param)

## ----cluster-MPI-do, eval=FALSE------------------------------------------
## xx <- bplapply(1:100, FUN)
## table(unlist(xx))
## mpi.quit()

## ----cluster-MPI-bpstart, eval=FALSE-------------------------------------
## param <- bpstart(SnowParam(mpi.universe.size() - 1, "MPI"))
## register(param)
## xx <- bplapply(1:100, FUN)
## bpstop(param)
## mpi.quit()

## ----cluster-BatchJobs, eval=FALSE---------------------------------------
## ## define work to be done
## FUN <- function(i) system("hostname", intern=TRUE)
## 
## library(BiocParallel)
## library(BatchJobs)
## 
## ## register SLURM cluster instructions from the template file
## funs <- makeClusterFunctionsSLURM("slurm.tmpl")
## param <- BatchJobsParam(4, resources=list(ncpus=1),
##                         cluster.functions=funs)
## register(param)
## 
## ## do work
## xx <- bplapply(1:100, FUN)
## table(unlist(xx))

## ----devel-bplapply------------------------------------------------------
system.time(x <- bplapply(1:3, function(i) { Sys.sleep(i); i }))
unlist(x)

## ----sessionInfo, results="asis"-----------------------------------------
toLatex(sessionInfo())