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message("Testing rng")
test_rng_lapply <- function()
{
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
.workerLapply <- BiocParallel:::.workerLapply
.RNGstream <- BiocParallel:::.RNGstream
.rng_next_substream <- BiocParallel:::.rng_next_substream
OPTIONS <- BiocParallel:::.workerOptions()
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
SEED <- .RNGstream(bpstart(SerialParam()))
checkIdentical(
## same sequence of random number streams
.workerLapply(1:2, function(i) rnorm(1), NULL, OPTIONS, SEED),
.workerLapply(1:2, function(i) rnorm(1), NULL, OPTIONS, SEED)
)
SEED1 <- .RNGstream(bpstart(SerialParam()))
SEED2 <- .rng_next_substream(SEED1)
target <- .workerLapply(1:2, function(i) rnorm(2), NULL, OPTIONS, SEED1)
obs <- c(
.workerLapply(1, function(i) rnorm(2), NULL, OPTIONS, SEED1),
.workerLapply(1, function(i) rnorm(2), NULL, OPTIONS, SEED2)
)
checkIdentical(target, obs)
checkTrue(identical(state, .rng_get_generator()))
}
test_rng_bplapply <- function()
{
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
p1 <- SerialParam(RNGseed = 123)
p2 <- SnowParam(3, RNGseed = 123)
p3 <- SnowParam(5, RNGseed = 123)
FUN <- function(i) rnorm(2)
## SerialParam / SnowParam same results
target <- bplapply(1:11, FUN, BPPARAM = p1)
checkIdentical(bplapply(1:11, FUN, BPPARAM = p2), target)
## SerialParam / SnowParam same results, different number of workers
checkIdentical(bplapply(1:11, FUN, BPPARAM = p3), target)
if (identical(.Platform$OS.type, "unix")) {
## SerialParam / TransientMulticoreParam same results
p4a <- MulticoreParam(5, RNGseed = 123)
checkIdentical(bplapply(1:11, FUN, BPPARAM = p4a), target)
## SerialParam / MulticoreParam same results
p4b <- bpstart(MulticoreParam(5, RNGseed = 123))
checkIdentical(bplapply(1:11, FUN, BPPARAM = p4b), target)
bpstop(p4b)
}
## single worker coerced to SerialParam
p5 <- SnowParam(1, RNGseed = 123)
checkIdentical(bplapply(1:11, FUN, BPPARAM = p5), target, "p5")
checkIdentical(state$kind, .rng_get_generator()$kind)
}
test_rng_bpiterate <- function()
{
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
FUN <- function(i) rnorm(2)
ITER_factory <- function() {
x <- 1:11
i <- 0L
function() {
i <<- i + 1L
if (i > length(x))
return(NULL)
x[[i]]
}
}
p1 <- SerialParam(RNGseed = 123)
p2 <- SnowParam(3, RNGseed = 123)
p3 <- SnowParam(5, RNGseed = 123)
target <- bplapply(1:11, FUN, BPPARAM = p1)
checkIdentical(target, bpiterate(ITER_factory(), FUN, BPPARAM = p1), "p1")
checkIdentical(target, bpiterate(ITER_factory(), FUN, BPPARAM = p2), "p2")
checkIdentical(target, bpiterate(ITER_factory(), FUN, BPPARAM = p3), "p3")
if (identical(.Platform$OS.type, "unix")) {
## SerialParam / TransientMulticoreParam same results
p4a <- MulticoreParam(5, RNGseed = 123)
checkIdentical(
target, bpiterate(ITER_factory(), FUN, BPPARAM = p4a),
"p4a"
)
## SerialParam / MulticoreParam same results
p4b <- bpstart(MulticoreParam(5, RNGseed = 123))
checkIdentical(
target, bpiterate(ITER_factory(), FUN, BPPARAM = p4b),
"p4b"
)
bpstop(p4b)
}
checkIdentical(state$kind, .rng_get_generator()$kind)
}
test_rng_bpstart <- function()
{
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
state <- .rng_get_generator()
FUN <- function(i) rnorm(2)
ITER_factory <- function() {
x <- 1:11
i <- 0L
function() {
i <<- i + 1L
if (i > length(x))
return(NULL)
x[[i]]
}
}
## bplapply
p0 <- bpstart(SerialParam()) # random seed
result1 <- unlist(bplapply(1:11, FUN, BPPARAM = p0))
result2 <- unlist(bplapply(1:11, FUN, BPPARAM = p0))
checkTrue(!any(result1 %in% result2))
bpstart(bpstop(p0)) # different random seed
result3 <- unlist(bplapply(1:11, FUN, BPPARAM = p0))
checkTrue(!any(result3 %in% result1))
p0 <- bpstart(SerialParam(RNGseed = 123)) # set seed
result1 <- unlist(bplapply(1:11, FUN, BPPARAM = p0))
result2 <- unlist(bplapply(1:11, FUN, BPPARAM = p0))
checkTrue(!any(result1 %in% result2))
bpstart(bpstop(p0)) # reset seed, same stream
result3 <- unlist(bplapply(1:11, FUN, BPPARAM = p0))
result4 <- unlist(bplapply(1:11, FUN, BPPARAM = p0))
checkIdentical(result3, result1)
checkIdentical(result4, result2)
## bpiterate
p0 <- bpstart(SerialParam()) # random seed
result1 <- unlist(bpiterate(ITER_factory(), FUN, BPPARAM = p0))
result2 <- unlist(bpiterate(ITER_factory(), FUN, BPPARAM = p0))
checkTrue(!any(result1 %in% result2))
bpstart(bpstop(p0)) # different random seed
result3 <- unlist(bpiterate(ITER_factory(), FUN, BPPARAM = p0))
checkTrue(!any(result3 %in% result1))
p0 <- bpstart(SerialParam(RNGseed = 123)) # set seed
result1 <- unlist(bpiterate(ITER_factory(), FUN, BPPARAM = p0))
result2 <- unlist(bpiterate(ITER_factory(), FUN, BPPARAM = p0))
checkTrue(!any(result1 %in% result2))
bpstart(bpstop(p0)) # reset seed, same stream
result3 <- unlist(bpiterate(ITER_factory(), FUN, BPPARAM = p0))
result4 <- unlist(bpiterate(ITER_factory(), FUN, BPPARAM = p0))
checkIdentical(result3, result1)
checkIdentical(result4, result2)
checkIdentical(state$kind, .rng_get_generator()$kind)
}
.test_rng_bpstart_does_not_iterate_rng_seed <- function(param) {
.rng_get_generator <- BiocParallel:::.rng_get_generator
state <- .rng_get_generator()
set.seed(123L)
target <- runif(1L)
## bpstart() should not increment the random number seed
set.seed(123L)
bpstart(param)
checkIdentical(target, runif(1L))
bpstop(param)
## bplapply does not increment stream
set.seed(123)
result <- bplapply(1:3, runif, BPPARAM = param)
checkIdentical(target, runif(1L))
## bplapply uses internal stream
set.seed(123)
result <- bplapply(1:3, runif, BPPARAM = param)
checkTrue(!identical(result, bplapply(1:3, runif, BPPARAM = param)))
checkIdentical(target, runif(1L))
target1 <- lapply(1:3, runif)
checkTrue(!identical(result, target1))
checkIdentical(state$kind, .rng_get_generator()$kind)
}
test_rng_bpstart_does_not_iterate_rng_seed <- function() {
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
TEST_FUN <- .test_rng_bpstart_does_not_iterate_rng_seed
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
TEST_FUN(SerialParam())
TEST_FUN(SnowParam(2))
if (identical(.Platform$OS.type, "unix"))
TEST_FUN(MulticoreParam(2))
}
.test_rng_global_and_RNGseed_indepenent <- function(param_fun) {
set.seed(123)
target <- bplapply(1:3, runif, BPPARAM = param_fun())
current <- bplapply(1:3, runif, BPPARAM = param_fun(RNGseed = 123))
checkTrue(!identical(target, current))
}
test_rng_global_and_RNGseed_independent <- function() {
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
TEST_FUN <- .test_rng_global_and_RNGseed_indepenent
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
TEST_FUN(SerialParam)
TEST_FUN(SnowParam)
if (identical(.Platform$OS.type, "unix"))
TEST_FUN(MulticoreParam)
}
.test_rng_lapply_bpredo_impl <- function(param) {
FUN <- function(i) rnorm(1)
target <- unlist(bplapply(1:11, FUN, BPPARAM = param))
FUN0 <- function(i) {
if (identical(i, 7L)) {
stop("i == 7")
} else rnorm(1)
}
result <- bptry(bplapply(1:11, FUN0, BPPARAM = param))
checkIdentical(unlist(result[-7]), target[-7])
checkTrue(inherits(result[[7]], "remote_error"))
FUN1 <- function(i) {
if (identical(i, 7L)) {
## the random number stream should be in the same state as the
## first time through the loop, and rnorm(1) should return
## same result as FUN
rnorm(1)
} else {
## if this branch is used, then we are incorrectly updating
## already calculated elements -- '0' in the output would
## indicate this error
0
}
}
result <- unlist(bplapply(1:11, FUN1, BPREDO = result, BPPARAM = param))
checkIdentical(result, target)
bpstart(param)
target1 <- unlist(bplapply(1:11, FUN, BPPARAM = param))
target2 <- unlist(bplapply(1:11, FUN, BPPARAM = param))
target3 <- unlist(bplapply(1:11, FUN, BPPARAM = param))
bpstop(param)
bpstart(param)
result1 <- bptry(bplapply(1:11, FUN0, BPPARAM = param))
result1_redo1 <- unlist(bplapply(1:11, FUN1, BPREDO = result1, BPPARAM = param))
result2 <- unlist(bplapply(1:11, FUN, BPPARAM = param))
result1_redo2 <- unlist(bplapply(1:11, FUN1, BPREDO = result1, BPPARAM = param))
result3 <- unlist(bplapply(1:11, FUN, BPPARAM = param))
checkIdentical(target1, result1_redo1)
checkIdentical(target1, result1_redo2)
checkIdentical(target2, result2)
checkIdentical(target3, result3)
}
test_rng_lapply_bpredo <- function()
{
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
param <- SerialParam(RNGseed = 123, stop.on.error = FALSE)
.test_rng_lapply_bpredo_impl(param)
if (identical(.Platform$OS.type, "unix")) {
param <- MulticoreParam(3, RNGseed = 123, stop.on.error = FALSE)
.test_rng_lapply_bpredo_impl(param)
}
}
.test_rng_iterate_bpredo_impl <- function(param) {
FUN <- function(i) rnorm(1)
target <- unlist(bplapply(1:11, FUN, BPPARAM = param))
FUN0 <- function(i) {
if (identical(i, 7L)) {
stop("i == 7")
} else rnorm(1)
}
iter_factory <- function(n){
i <- 0L
function() if(i<n) i <<- i + 1L
}
result <- bptry(bpiterate(iter_factory(11), FUN0, BPPARAM = param))
checkIdentical(unlist(result[-7]), target[-7])
checkTrue(is.null(result[[7]]))
checkTrue(inherits(attr(result,"errors")[[1]], "remote_error"))
FUN1 <- function(i) {
if (identical(i, 7L)) {
## the random number stream should be in the same state as the
## first time through the loop, and rnorm(1) should return
## same result as FUN
rnorm(1)
} else {
## if this branch is used, then we are incorrectly updating
## already calculated elements -- '0' in the output would
## indicate this error
0
}
}
result <- unlist(bpiterate(iter_factory(11), FUN1, BPREDO = result, BPPARAM = param))
checkIdentical(result, target)
bpstart(param)
target1 <- unlist(bplapply(1:11, FUN, BPPARAM = param))
target2 <- unlist(bplapply(1:11, FUN, BPPARAM = param))
target3 <- unlist(bplapply(1:11, FUN, BPPARAM = param))
bpstop(param)
bpstart(param)
result1 <- bptry(bpiterate(iter_factory(11), FUN0, BPPARAM = param))
result1_redo1 <- unlist(bpiterate(iter_factory(11), FUN1, BPREDO = result1, BPPARAM = param))
result2 <- unlist(bpiterate(iter_factory(11), FUN, BPPARAM = param))
result1_redo2 <- unlist(bpiterate(iter_factory(11), FUN1, BPREDO = result1, BPPARAM = param))
result3 <- unlist(bpiterate(iter_factory(11), FUN, BPPARAM = param))
bpstop(param)
checkIdentical(target1, result1_redo1)
checkIdentical(target1, result1_redo2)
checkIdentical(target2, result2)
checkIdentical(target3, result3)
}
test_rng_iterate_bpredo <- function()
{
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
param <- SerialParam(RNGseed = 123, stop.on.error = FALSE)
.test_rng_iterate_bpredo_impl(param)
if (identical(.Platform$OS.type, "unix")) {
param <- MulticoreParam(3, RNGseed = 123, stop.on.error = FALSE)
.test_rng_iterate_bpredo_impl(param)
}
}
test_rng_fallback_SerialParam <- function()
{
.rng_get_generator <- BiocParallel:::.rng_get_generator
.rng_reset_generator <- BiocParallel:::.rng_reset_generator
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
FUN <- function(i) rnorm(1)
param <- SerialParam(RNGseed = 123, stop.on.error = FALSE)
target <- unlist(bplapply(1:2, FUN, BPPARAM = param))
param2 <- SnowParam(RNGseed = 123, workers = 1L)
checkIdentical(unlist(bplapply(1:2, FUN, BPPARAM = param2)), target)
bpstart(param2)
checkIdentical(bplapply(1, FUN, BPPARAM = param2)[[1]], target[1])
checkIdentical(bplapply(1, FUN, BPPARAM = param2)[[1]], target[2])
bpstop(param2)
}
test_rng_reproducibility_across_versions <- function()
{
p <- SerialParam(RNGseed = 123)
bptasks(p) <- 3
## This number should NEVER change across version
res0 <- list(14L, 14L, 6L, 17L, 20L,
5L, 16L, 1L, 4L, 16L,
4L, 20L, 20L, 3L, 3L,
17L, 11L, 19L, 1L, 3L)
fun <- function(x) sample(1:20, 1)
res1 <- bplapply(1:20, fun, BPPARAM = p)
checkIdentical(res1, res0)
iter_factory <- function(n){
i <- 0L
function() if(i<n) i <<- i + 1L
}
res2 <- bpiterate(iter_factory(20), fun, BPPARAM = p)
checkIdentical(res2, res0)
}
test_rng_reset_seed <- function()
{
## the seed stream must be the same
## if the seed is set to the same value
## no matter if the BPPARAM has been started or not
p <- SerialParam()
bpstart(p)
opts <- bpoptions(RNGseed = 123)
res1 <- bplapply(1:3, function(x) runif(1),
BPPARAM = p,
BPOPTIONS = opts)
res2 <- bplapply(1:3, function(x) runif(1),
BPPARAM = p,
BPOPTIONS = opts)
checkIdentical(res1, res2)
}
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