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## ----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())
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