r-bioc-biocparallel 1.12.0-2 / usr / lib / R / site-library / BiocParallel / doc / Introduction_To_BiocParallel.R

This file is indexed.

/usr/lib/R/site-library/BiocParallel/doc/Introduction_To_BiocParallel.R is in r-bioc-biocparallel 1.12.0-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
## ----style, eval=TRUE, echo=FALSE, results="asis"--------------------------
BiocStyle::latex()

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

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

## ----register_BatchJobsParam2----------------------------------------------
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()

## ----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())

APT Browse - Built by Thomas Orozco.