/usr/lib/R/site-library/BiocParallel/unitTests/test_bpiterate.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 | quiet <- suppressWarnings
.lazyCount <- function(count) {
count <- count
i <- 0L
function() {
if (i >= count)
return(NULL)
else
i <<- i + 1L
i
}
}
test_bpiterate_Params <- function()
{
message("test_bpiterate_Params")
## chunks greater than number of workers
message(" chunks greater than number of workers")
x <- 1:5
expected <- lapply(x, sqrt)
FUN <- function(count, ...) sqrt(count)
params <- list(serial=SerialParam(),
snow=SnowParam(2))
if (.Platform$OS.type != "windows")
params$mc <- MulticoreParam(2)
for (p in params) {
message(" ith param")
ITER <- .lazyCount(length(x))
quiet(res <- bpiterate(ITER, FUN, BPPARAM=p))
checkIdentical(expected, res)
}
## chunks less than number of workers
message(" chunks less than number of workers [1]")
x <- 1:2
expected <- lapply(x, sqrt)
FUN <- function(count, ...) sqrt(count)
params <- list(serial=SerialParam(),
snow=SnowParam(3))
if (.Platform$OS.type != "windows")
params$mc <- MulticoreParam(3)
for (p in params) {
message(" ith param")
ITER <- .lazyCount(length(x))
quiet(res <- bpiterate(ITER, FUN, BPPARAM=p))
checkIdentical(expected, res)
}
message(" chunks less than number of workers [2]")
doParallel::registerDoParallel(2)
params <- list(dopar=DoparParam(),
batchjobs=BatchJobsParam(2, progressbar=FALSE))
for (p in params) {
message(" ith param")
ITER <- .lazyCount(length(x))
checkException(bpiterate(ITER, FUN, BPPARAM=p), silent=TRUE)
}
## clean up
message(" cleanup")
env <- foreach:::.foreachGlobals
rm(list=ls(name=env), pos=env)
closeAllConnections()
TRUE
message("test_bpiterate_Params DONE")
}
test_bpiterate_REDUCE <- function() {
message("test_bpiterate_REDUCE")
message(" setup")
ncount <- 3L
params <- list(snow=SnowParam(ncount))
## On Windows MulticoreParam dispatches to SerialParam where
## 'reduce.in.order' does not apply (always TRUE)
if (.Platform$OS.type != "windows")
params <- c(params, multi=MulticoreParam(ncount))
for (p in params) {
message(" ith param")
## no REDUCE
message(" no REDUCE")
FUN <- function(count, ...) rep(count, 10)
ITER <- .lazyCount(ncount)
res <- bpiterate(ITER, FUN, BPPARAM=p)
checkTrue(length(res) == ncount)
expected <- list(rep(1L, 10), rep(2L, 10), rep(3L, 10))
checkIdentical(expected, res)
## REDUCE
message(" REDUCE")
FUN <- function(count, ...) rep(count, 10)
ITER <- .lazyCount(ncount)
res <- bpiterate(ITER, FUN, BPPARAM=p, REDUCE=`+`)
checkIdentical(rep(6L, 10), res)
FUN <- function(count, ...) {
Sys.sleep(3 - count)
count
}
## 'reduce.in.order' FALSE
message(" 'reduce.in.order' FALSE [1]")
ITER <- .lazyCount(ncount)
res <- bpiterate(ITER, FUN, BPPARAM=p, REDUCE=paste0,
reduce.in.order=FALSE)
checkIdentical("321", res)
message(" 'reduce.in.order' FALSE [2]")
ITER <- .lazyCount(ncount)
res <- quiet(bpiterate(ITER, FUN, BPPARAM=p, REDUCE=paste0, init=0,
reduce.in.order=FALSE))
checkIdentical("0321", res)
## 'reduce.in.order' TRUE
message(" 'reduce.in.order' TRUE [1]")
ITER <- .lazyCount(ncount)
res <- bpiterate(ITER, FUN, BPPARAM=p, REDUCE=paste0,
reduce.in.order=TRUE)
checkIdentical("123", res)
message(" 'reduce.in.order' TRUE [2]")
ITER <- .lazyCount(ncount)
res <- bpiterate(ITER, FUN, BPPARAM=p, REDUCE=paste0,
init=0, reduce.in.order=TRUE)
checkIdentical("0123", res)
}
## clean up
message(" cleanup")
closeAllConnections()
TRUE
message("test_bpiterate_REDUCE DONE")
}
|