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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Utils
## Extract static and dynamic data from a task Return NULL if no
## static data can be extracted
.task_const <-
function(value)
{
## Supports EXEC task only
if (value$type != "EXEC")
return(NULL)
if (isTRUE(value$dynamic.only))
return(NULL)
if (value$static.fun)
fun <- value$data$fun
else
fun <- NULL
fullArgNames <- names(value$data$args)
if (all(value$static.args %in% fullArgNames)) {
args <- value$data$args[value$static.args]
if (!length(args)) args <- NULL
} else {
args <- NULL
}
if (!is.null(fun) || !is.null(args))
list(fun = fun, args = args, fullArgNames = fullArgNames)
else
NULL
}
## Extract the dynamic part from a task
.task_dynamic <-
function(value)
{
## Supports EXEC task only
if (value$type != "EXEC")
return(value)
if (value$static.fun)
value$data$fun <- TRUE
if (length(value$static.args))
value$data$args[value$static.args] <- NULL
if (value$static.fun || length(value$static.args))
value$dynamic.only <- TRUE
value
}
## Recreate the task from the dynamic and static parts of the task
## It is safe to call the function if the task is complete
## (Not extracted by `.task_dynamic`) or `static_Data` is NULL
.task_remake <-
function(value, static_data = NULL)
{
if (is.null(static_data))
return(value)
if (value$type != "EXEC")
return(value)
if (!isTRUE(value$dynamic.only))
return(value)
if (value$static.fun)
value$data$fun <- static_data$fun
if (length(value$static.args)) {
value$data$args <- c(value$data$args, static_data$args)
value$data$args <- value$data$args[static_data$fullArgNames]
}
value$dynamic.only <- NULL
value
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Worker commands
### Support for SOCK, MPI and FORK connections.
### Derived from snow version 0.3-13 by Luke Tierney
### Derived from parallel version 2.16.0 by R Core Team
.EXEC <-
function(tag, fun, args, static.fun = FALSE, static.args = NULL)
{
list(
type = "EXEC",
data = list(tag = tag, fun = fun, args = args),
static.fun = static.fun,
static.args = static.args
)
}
.VALUE <-
function(tag, value, success, time, log, sout)
{
list(
type = "VALUE",
tag = tag, value = value, success = success, time = time,
log = log, sout = sout
)
}
.DONE <-
function()
{
list(type = "DONE")
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Worker options and function to run the task
.workerOptions <-
function(
log = FALSE,
threshold = "INFO",
stop.on.error = TRUE,
as.error = TRUE,
timeout = WORKER_TIMEOUT,
exportglobals = TRUE,
force.GC = FALSE)
{
force(log)
force(threshold)
force(stop.on.error)
force(as.error)
force(timeout)
force(force.GC)
if (exportglobals) {
blocklist <- c(
"askpass", "asksecret", "buildtools.check",
"buildtools.with", "pager", "plumber.swagger.url",
"profvis.print", "restart", "reticulate.repl.hook",
"reticulate.repl.initialize", "reticulate.repl.teardown",
"shiny.launch.browser", "terminal.manager", "error",
"topLevelEnvironment", "connectionObserver"
)
globalOptions <- base::options()
globalOptions <- globalOptions[!names(globalOptions) %in% blocklist]
} else {
globalOptions <- NULL
}
list(
log = log,
threshold = threshold,
stop.on.error = stop.on.error,
as.error = as.error,
timeout = timeout,
force.GC = force.GC,
globalOptions = globalOptions
)
}
.composeTry <-
function(FUN, OPTIONS, SEED)
{
FUN <- match.fun(FUN)
ERROR_OCCURRED <- FALSE
## use `ERROR_CALL_DEPTH` to trim call stack. default: show all
ERROR_CALL_DEPTH <- -.Machine$integer.max
UNEVALUATED <- .error_unevaluated() # singleton
log <- OPTIONS$log
stop.on.error <- OPTIONS$stop.on.error
as.error <- OPTIONS$as.error
timeout <- OPTIONS$timeout
force.GC <- OPTIONS$force.GC
globalOptions <- OPTIONS$globalOptions
handle_warning <- function(w) {
.log_warn(log, "%s", w)
w # FIXME: muffleWarning; don't rely on capture.output()
}
handle_error <- function(e) {
ERROR_OCCURRED <<- TRUE
.log_error(log, "%s", e)
call <- rev(tail(sys.calls(), -ERROR_CALL_DEPTH))
.error_remote(e, call)
}
if (!is.null(SEED))
SEED <- .rng_reset_generator("L'Ecuyer-CMRG", SEED)$seed
function(...) {
if (!identical(timeout, WORKER_TIMEOUT)) {
setTimeLimit(timeout, timeout, TRUE)
on.exit(setTimeLimit(Inf, Inf, FALSE))
}
if (!is.null(globalOptions))
base::options(globalOptions)
if (stop.on.error && ERROR_OCCURRED) {
UNEVALUATED
} else {
.rng_reset_generator("L'Ecuyer-CMRG", SEED)
## capture warnings and errors. Both are initially handled
## by `withCallingHandlers()`.
##
## 'error' conditions are logged (via `handle_error()`),
## annotated, and then re-signalled via `stop()`. The
## condition needs to be handled first by
## `withCallingHandlers()` so that the full call stack to
## the error can be recovered. The annotated condition
## needs to be resignalled so that it can be returned as
## 'output'; but the condition needs to be silenced by the
## outer `tryCatch()`.
##
## 'warning' conditions are logged (via
## `handle_warning()`). The handler returns the original
## condition, and the 'muffleWarning' handler is invoked
## somewhere above this point.
output <- tryCatch({
withCallingHandlers({
## emulate call depth from 'inside' FUN, to
## account for frames from tryCatch,
## withCallingHandlers
ERROR_CALL_DEPTH <<- (\() sys.nframe() - 1L)()
FUN(...)
}, error = function(e) {
annotated_condition <- handle_error(e)
stop(annotated_condition)
}, warning = handle_warning)
}, error = identity)
## Trigger garbage collection to cut down on memory usage within
## each worker in shared memory contexts. Otherwise, each worker is
## liable to think the entire heap is available (leading to each
## worker trying to fill said heap, causing R to exhaust memory).
if (force.GC)
gc(verbose=FALSE, full=FALSE)
SEED <<- .rng_next_substream(SEED)
output
}
}
}
.workerLapply_impl <-
function(X, FUN, ARGS, OPTIONS, BPRNGSEED,
GLOBALS = NULL, PACKAGES = NULL)
{
state <- .rng_get_generator()
on.exit(.rng_reset_generator(state$kind, state$seed))
## FUN is not compiled when using MulticoreParam
FUN <- compiler::cmpfun(FUN)
if (!is.null(OPTIONS$globalOptions)) {
oldOptions <- base::options()
on.exit(base::options(oldOptions), add = TRUE)
}
## Set log
.log_load(OPTIONS$log, OPTIONS$threshold)
for (pkg in PACKAGES) {
suppressPackageStartupMessages(library(pkg, character.only = TRUE))
}
## Add variables to the global space and remove them afterward
## Recover the replaced variables at the end if necessary
replaced_variables <- new.env(parent = emptyenv())
if (length(GLOBALS)) {
for (i in names(GLOBALS)) {
if (exists(i, envir = .GlobalEnv))
replaced_variables[[i]] <- .GlobalEnv[[i]]
assign(i, GLOBALS[[i]], envir = .GlobalEnv)
}
on.exit({
remove(list = names(GLOBALS), envir = .GlobalEnv)
for (i in names(replaced_variables))
assign(i, replaced_variables[[i]], envir = .GlobalEnv)
},
add = TRUE)
}
composeFunc <- .composeTry(FUN, OPTIONS, BPRNGSEED)
args <- c(list(X = X, FUN = composeFunc), ARGS)
do.call(lapply, args)
}
## reduce the size of the serialization of .workerLapply_impl from
## 124k to 3k
.workerLapply <- eval(
parse(text = "function(...) BiocParallel:::.workerLapply_impl(...)"),
envir = getNamespace("base")
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Worker loop. Error handling is done in .composeTry.
.bpworker_EXEC <-
function(msg, sink.sout = TRUE)
{
## need local handler for worker read/send errors
if (sink.sout) {
on.exit({
sink(NULL, type="message")
sink(NULL, type="output")
close(file)
})
file <- rawConnection(raw(), "r+")
sink(file, type="message")
sink(file, type="output")
}
t1 <- proc.time()
value <- tryCatch({
do.call(msg$data$fun, msg$data$args)
}, error=function(e) {
## return as 'list()' because msg$fun has lapply semantics
list(.error_worker_comm(e, "worker evaluation failed"))
})
t2 <- proc.time()
if (sink.sout) {
sout <- rawToChar(rawConnectionValue(file))
if (!nchar(sout)) sout <- NULL
} else {
sout <- NULL
}
success <- !(inherits(value, "bperror") || !all(bpok(value)))
log <- .log_buffer_get()
## Reset the log buffer
.log_buffer_init()
value <- .VALUE(
msg$data$tag, value, success, t2 - t1, log, sout
)
}
.bpworker_impl <-
function(worker)
{
repeat {
tryCatch({
msg <- .recv(worker)
if (inherits(msg, "error"))
## FIXME: try to return error to manager
break # lost socket connection?
if (msg$type == "DONE") {
.close(worker)
break
} else if (msg$type == "EXEC") {
value <- .bpworker_EXEC(msg)
.send(worker, value)
}
}, interrupt = function(e) {
NULL
})
}
}
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