Dear All,
Since upgrading to 3.6.0, I've been getting a strange error messages
from the child process when using mcparallel/mccollect. Before filing a report
in the Bugzilla, I want to figure out whether I had been doing something wrong
all this time and R 3.6.0 has exposed it, or whether something else is going on.
# Background #
Ultimately, what I want to do is to be able to set a time limit for an
expression to be evaluated that would be enforced even inside compiled
code. (R.utils::withTimeout() uses base::setTimeLimit(), which can only
enforce within R code.)
# Implementation #
The approach that my implementation, statnet.common::forkTimeout()
(source attached for convenience), uses is to call mcparallel() to
evaluate the expression in a child process, then mccollect() with
wait=FALSE and a timeout to give it a chance to finish. If it runs past
the timeout, the child process is killed and an onTimeout value is
returned. (This only works on Unix-alikes, but it's better than
nothing.)
# The problem #
Since 3.6.0---and I've tested fresh installs of 3.6.0 and 3.5.3 side-
by-side---I've been getting strange messages.
Running
source("forkTimeout.R") # attached
repeat print(forkTimeout({Sys.sleep(1);TRUE}, timeout=3))
results in
[1] TRUE
[1] TRUE
Error in mcexit(0L) : ignoring SIGPIPE signal
[1] TRUE
[1] TRUE
Error in mcexit(0L) : ignoring SIGPIPE signal
[1] TRUE
[1] TRUE
[1] TRUE
until interrupted. Running
options(error=traceback)
repeat print(forkTimeout({Sys.sleep(1);TRUE}, timeout=3))
results in sporadic messages of the form:
Error in mcexit(0L) : ignoring SIGPIPE signal
6: selectChildren(jobs, timeout)
5: parallel::mccollect(child, wait = FALSE, timeout = timeout) at
forkTimeout.R#75
4: withCallingHandlers(expr, warning = function(w)
invokeRestart("muffleWarning"))
3: suppressWarnings(parallel::mccollect(child, wait = FALSE, timeout =
timeout)) at forkTimeout.R#75
2: forkTimeout({
Sys.sleep(1)
...
1: print(forkTimeout({
Sys.sleep(1)
...
So, these messages do not appear to prevent the child process from
returning valid output, but I've never seen them before R 3.6.0, so I
wonder if I am doing something wrong. Session info is also attached.
Thanks in advance,
Pavel
--
Pavel Krivitsky
Lecturer in Statistics
National Institute of Applied Statistics Research Australia (NIASRA)
School of Mathematics and Applied Statistics | Building 39C Room 154
University of Wollongong NSW 2522 Australia
T +61 2 4221 3713
Web (NIASRA): http://niasra.uow.edu.au/index.html
Web (Personal): http://www.krivitsky.net/research
ORCID: 0000-0002-9101-3362
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R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.utf8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.utf8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0 parallel_3.6.0
#' Evaluate an \R expression with a hard time limit by forking a process
#'
#' This function uses
#' #ifndef windows
#' [parallel::mcparallel()],
#' #endif
#' #ifdef windows
#' `parallel::mcparallel()`,
#' #endif
#' so the time limit is not
#' enforced on Windows. However, unlike functions using [setTimeLimit()], the
time
#' limit is enforced even on native code.
#'
#' @param expr expression to be evaluated.
#' @param timeout number of seconds to wait for the expression to
#' evaluate.
#' @param unsupported a character vector of length 1 specifying how to
#' handle a platform that does not support
#' #ifndef windows
#' [parallel::mcparallel()],
#' #endif
#' #ifdef windows
#' `parallel::mcparallel()`,
#' #endif
#' \describe{
#'
#' \item{`"warning"` or `"message"`}{Issue a warning or a message,
#' respectively, then evaluate the expression without the time limit
#' enforced.}
#'
#' \item{`"error"`}{Stop with an error.}
#'
#' \item{`"silent"`}{Evaluate the expression without the time limit
#' enforced, without any notice.}
#'
#' } Partial matching is used.
#' @param onTimeout Value to be returned on time-out.
#'
#' @return Result of evaluating `expr` if completed, `onTimeout`
#' otherwise.
#'
#' @note `onTimeout` can itself be an expression, so it is, for
#' example, possible to stop with an error by passing
#' `onTimeout=stop()`.
#'
#' @note Note that this function is not completely transparent:
#' side-effects may behave in unexpected ways. In particular, RNG
#' state will not be updated.
#'
#' @examples
#'
#' forkTimeout({Sys.sleep(1); TRUE}, 2) # TRUE
#' forkTimeout({Sys.sleep(1); TRUE}, 0.5) # NULL (except on Windows)
#' @export
forkTimeout <- function(expr, timeout, unsupported =
c("warning","error","message","silent"), onTimeout = NULL){
loadNamespace("parallel")
loadNamespace("tools")
env <- parent.frame()
if(!exists("mcparallel", where=asNamespace("parallel"), mode="function")){ #
fork() is not available on the system.
unsupported <- match.arg(unsupported)
warnmsg <- "Your platform (probably Windows) does not have fork()
capabilities. Time limit will not be enforced."
errmsg <- "Your platform (probably Windows) does not have fork()
capabilities."
switch(unsupported,
message = message(warnmsg),
warning = warning(warnmsg),
error = stop(errmsg))
out <- eval(expr, env)
}else{ # fork() is available on the system.
## TODO: The suppressWarnings() are working around a bug in
## current parallel package. They should not be necessary after
## the next R release.
child <- parallel::mcparallel(eval(expr, env), mc.interactive=NA)
out <- suppressWarnings(parallel::mccollect(child, wait=FALSE,
timeout=timeout))
if(is.null(out)){ # Timed out with no result: kill.
tools::pskill(child$pid)
out <- onTimeout
}else{
out <- out[[1L]]
}
suppressWarnings(parallel::mccollect(child)) # Clean up.
}
out
}
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