inst/doc/Introduction_To_BiocParallel.R

In BiocParallel: Bioconductor facilities for parallel evaluation

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

## ----setup, echo=FALSE-----------------------------------------------------
suppressPackageStartupMessages({
    library(BiocParallel)
    library(VariantAnnotation)
    library(GenomicAlignments)
    library(RNAseqData.HNRNPC.bam.chr14)
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
})

## ----BiocManager, eval=FALSE-----------------------------------------------
#  
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("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_BatchtoolsParam----------------------------------------------
default <- registered()
register(BatchtoolsParam(workers = 10), default = TRUE)

## ----register_BatchtoolsParam2---------------------------------------------
names(registered())
bpparam()

## ----register_restore------------------------------------------------------
for (param in rev(default))
    register(param)

## ----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) {
  suppressPackageStartupMessages({
     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()

## ----slurm-----------------------------------------------------------------
tmpl <- system.file(package="batchtools", "templates", "slurm-simple.tmpl")
noquote(readLines(tmpl))

## ----cluster-batchtools, eval=FALSE----------------------------------------
#  ## define work to be done
#  FUN <- function(i) system("hostname", intern=TRUE)
#  
#  library(BiocParallel)
#  
#  ## register SLURM cluster instructions from the template file
#  param <- BatchtoolsParam(workers=5, cluster="slurm", template=tmpl)
#  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())