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.workerEnvironmentVariable <-
function(variable, default = NA_integer_)
{
result <- withCallingHandlers({
value <- Sys.getenv(variable, default)
as.integer(value)
}, warning = function(w) {
txt <- sprintf(
paste0(
"Trying to coercing the environment variable '%s' to an ",
"integer caused a warning. The value of the environment ",
"variable was '%s'. The warning was: %s"
),
variable, value, conditionMessage(w)
)
.warning(txt)
invokeRestart("muffleWarning")
})
if (!is.na(result) && (result <= 0L)) {
txt <- sprintf(
"The environment variable '%s' must be > 0. The value was '%d'.",
variable, result
)
.stop(txt)
}
result
}
.defaultWorkers <-
function()
{
## assign default cores
## environment variables; least to most compelling
result <- .workerEnvironmentVariable("R_PARALLELLY_AVAILABLECORES_FALLBACK")
max_number <- .workerEnvironmentVariable("BIOCPARALLEL_WORKER_MAX", result)
default_number <-
.workerEnvironmentVariable("BIOCPARALLEL_WORKER_NUMBER", result)
if (is.na(max_number)) {
result <- default_number
} else {
result <- min(max_number, default_number, na.rm = TRUE)
}
## fall back to detectCores() if necessary
if (is.na(result)) {
result <- parallel::detectCores()
if (is.na(result))
result <- 1L
result <- max(1L, result - 2L)
}
## respect 'mc.cores', overriding env. variables an detectCores()
result <- getOption("mc.cores", result)
## coerce to integer; check for valid value
tryCatch({
result <- as.integer(result)
if ( length(result) != 1L || is.na(result) || result < 1L )
stop("number of cores must be a non-negative integer")
}, error = function(e) {
msg <- paste0(
conditionMessage(e), ". ",
"Did you mis-specify R_PARALLELLY_AVAILABLECORES_FALLBACK, ",
"BIOCPARALLEL_WORKER_NUMBER, or options('mc.cores')?"
)
.stop(msg)
})
## override user settings by build-system configurations
if (identical(Sys.getenv("IS_BIOC_BUILD_MACHINE"), "true"))
result <- min(result, 4L)
## from R-ints.texi
## @item _R_CHECK_LIMIT_CORES_
## If set, check the usage of too many cores in package @pkg{parallel}. If
## set to @samp{warn} gives a warning, to @samp{false} or @samp{FALSE} the
## check is skipped, and any other non-empty value gives an error when more
## than 2 children are spawned.
## Default: unset (but @samp{TRUE} for CRAN submission checks).
check_limit_cores <- Sys.getenv("_R_CHECK_LIMIT_CORES_", NA_character_)
check_limit_cores_is_set <-
!is.na(check_limit_cores) &&
!identical(toupper(check_limit_cores), "FALSE")
if (check_limit_cores_is_set)
result <- min(result, 2L)
result
}
.enforceWorkers <-
function(workers, type = NULL)
{
## Ensure that user 'workers' does not exceed hard limits; most-
## to least stringent. Usually on build systems
## R CMD check limit (though it applies outside check, too...
check_limit_cores <- Sys.getenv("_R_CHECK_LIMIT_CORES_", NA_character_)
check_limit_cores_is_set <-
!is.na(check_limit_cores) &&
!identical(toupper(check_limit_cores), "FALSE")
if (workers > 2L && check_limit_cores_is_set) {
if (!identical(check_limit_cores, "warn")) {
.stop(
"_R_CHECK_LIMIT_CORES_' environment variable detected, ",
"BiocParallel workers must be <= 2 was (", workers, ")"
)
}
.warning(
"'_R_CHECK_LIMIT_CORES_' environment variable detected, ",
"setting BiocParallel workers to 2 (was ", workers, ")"
)
workers <- 2L
}
## Bioconductor build system
test <-
(workers > 4L) && identical(Sys.getenv("IS_BIOC_BUILD_MACHINE"), "true")
if (test) {
.warning(
"'IS_BIOC_BUILD_MACHINE' environment variable detected, ",
"setting BiocParallel workers to 4 (was ", workers, ")"
)
workers <- 4L
}
worker_max <- .workerEnvironmentVariable("BIOCPARALLEL_WORKER_MAX")
if (!is.na(worker_max) && workers > worker_max) {
.warning(
"'BIOCPARALLEL_WORKER_MAX' environment variable detected, ",
"setting BiocParallel workers to ", worker_max, " ",
"(was ", workers, ")"
)
workers <- worker_max
}
## limit on number of available sockets
if (!is.null(type) && workers > .snowCoresMax(type)) {
max <- .snowCoresMax(type)
.warning(
"worker number limited by available socket connections, ",
"setting BiocParallel workers to ", max, " (was ", workers, ")"
)
workers <- max
}
workers
}
|
