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## -----------------------------------------------------------------------------
library(BiocParallel)
## ----quick_start FUN----------------------------------------------------------
FUN <- function(x) { round(sqrt(x), 4) }
## ----quick_start registry-----------------------------------------------------
registered()
## ----configure_registry, eval=FALSE-------------------------------------------
# options(MulticoreParam=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()
## ----db_problems, eval = FALSE------------------------------------------------
# library(org.Hs.eg.db)
# FUN <- function(x, ...) {
# ...
# mapIds(org.Hs.eg.db, ...)
# ...
# }
# bplapply(X, FUN, ..., BPPARAM = 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)
## ----db_solution_2, eval = FALSE----------------------------------------------
# register(SnowParam()) # default evaluation
# bpstart() # start the cluster
# ...
# bplapply(X, FUN1, ...)
# ...
# bplapply(X, FUN2, ...) # re-use workers
# ...
# bpstop()
## ----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--------------------------------------------------------------
sessionInfo()
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