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makeClusterPSOCK.R
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makeClusterPSOCK.R
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#' Create a PSOCK cluster of \R workers for parallel processing
#'
#' The \code{makeClusterPSOCK()} function creates a cluster of \R workers
#' for parallel processing. These \R workers may be background \R sessions
#' on the current machine, \R sessions on external machines (local or remote),
#' or a mix of such. For external workers, the default is to use SSH to connect
#' to those external machines. This function works similarly to
#' \code{\link[parallel:makePSOCKcluster]{makePSOCKcluster}()} of the
#' \pkg{parallel} package, but provides additional and more flexibility options
#' for controlling the setup of the system calls that launch the background
#' \R workers, and how to connect to external machines.
#'
#' @param workers The hostnames of workers (as a character vector) or the number
#' of localhost workers (as a positive integer).
#'
#' @param makeNode A function that creates a \code{"SOCKnode"} or
#' \code{"SOCK0node"} object, which represents a connection to a worker.
#'
#' @param \dots Optional arguments passed to
#' \code{makeNode(workers[i], ..., rank = i)} where
#' \code{i = seq_along(workers)}.
#'
#' @param autoStop If TRUE, the cluster will be automatically stopped
# (using \code{\link[parallel:stopCluster]{stopCluster}()}) when it is
# garbage collected, unless already stopped.
#'
#' @param verbose If TRUE, informative messages are outputted.
#'
#' @return An object of class \code{c("SOCKcluster", "cluster")} consisting
#' of a list of \code{"SOCKnode"} or \code{"SOCK0node"} workers.
#'
#' @example incl/makeClusterPSOCK.R
#'
#' @export
makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto", "random"), ..., autoStop = FALSE, verbose = getOption("future.debug", FALSE)) {
if (is.numeric(workers)) {
if (length(workers) != 1L) {
stop("When numeric, argument 'workers' must be a single value: ", length(workers))
}
workers <- as.integer(workers)
if (is.na(workers) || workers < 1L) {
stop("Number of 'workers' must be one or greater: ", workers)
}
workers <- rep("localhost", times = workers)
}
verbose_prefix <- "[local output] "
if (verbose) {
message(sprintf("%sWorkers: [n = %d] %s", verbose_prefix,
length(workers), hpaste(sQuote(workers))))
}
if (is.character(port)) {
port <- match.arg(port, choices = c("auto", "random"))
if (identical(port, "auto")) {
port0 <- Sys.getenv("R_PARALLEL_PORT", "random")
if (identical(port0, "random")) {
port <- 11000:11999
} else {
port <- suppressWarnings(as.integer(port0))
if (is.na(port)) {
warning("Non-numeric value of environment variable 'R_PARALLEL_PORT' coerced to NA_integer_: ", sQuote(port0))
port <- 11000:11999
}
}
} else if (identical(port, "random")) {
port <- 11000:11999
}
} else {
port <- as.integer(port)
}
if (length(port) == 0L) {
stop("Argument 'post' must be of length one or more: 0")
}
if (length(port) > 1L) {
port <- local({
oseed <- .GlobalEnv$.Random.seed
on.exit(.GlobalEnv$.Random.seed <- oseed)
sample(port, size = 1L)
})
}
if (is.na(port) || port < 0L || port > 65535L) {
stop("Invalid port: ", port)
}
if (verbose) message(sprintf("%sBase port: %d", verbose_prefix, port))
n <- length(workers)
cl <- vector("list", length = n)
class(cl) <- c("SOCKcluster", "cluster")
for (ii in seq_along(cl)) {
if (verbose) {
message(sprintf("%sCreating node %d of %d ...", verbose_prefix, ii, n))
message(sprintf("%s- setting up node", verbose_prefix))
}
cl[[ii]] <- makeNode(workers[[ii]], port = port, ..., rank = ii,
verbose = verbose)
## Attaching session information for each worker. This is done to assert
## that we have a working cluster already here. It will also collect
## useful information otherwise not available, e.g. the PID.
if (verbose) {
message(sprintf("%s- collecting session information", verbose_prefix))
}
cl[ii] <- add_cluster_session_info(cl[ii])
if (verbose) {
message(sprintf("%sCreating node %d of %d ... done", verbose_prefix, ii, n))
}
}
if (autoStop) cl <- autoStopCluster(cl)
cl
} ## makeClusterPSOCK()
#' @param worker The hostname or IP number of the machine where the worker
#' should run.
#'
#' @param master The hostname or IP number of the master / calling machine, as
#' known to the workers. If NULL (default), then the default is
#' \code{Sys.info()[["nodename"]]} unless \code{worker} is \emph{localhost} or
#' \code{revtunnel = TRUE} in case it is \code{"localhost"}.
#'
#' @param port The port number of the master used for communicating with all
#' the workers (via socket connections). If an integer vector of ports, then a
#' random one among those is chosen. If \code{"random"}, then a random port in
#' \code{11000:11999} is chosen. If \code{"auto"} (default), then the default
#' is taken from environment variable \env{R_PARALLEL_PORT}, otherwise
#' \code{"random"} is used.
#' \emph{Note, do not use this argument to specify the port number used by
#' \code{rshcmd}, which typically is an SSH client. Instead, if the SSH daemon
#' runs on a different port than the default 22, specify the SSH port by
#' appending it to the hostname, e.g. `"remote.server.org:2200"` or via SSH
#' options \code{-p}, e.g. `rshopts = c("-p", "2200")`.}
#'
#' @param connectTimeout The maximum time (in seconds) allowed for each socket
#' connection between the master and a worker to be established (defaults to
#' 2 minutes). \emph{See note below on current lack of support on Linux and
#' macOS systems.}
#'
#' @param timeout The maximum time (in seconds) allowed to pass without the
#' master and a worker communicate with each other (defaults to 30 days).
#'
#' @param rscript,homogeneous The system command for launching \command{Rscript}
#' on the worker and whether it is installed in the same path as the calling
#' machine or not. For more details, see below.
#'
#' @param rscript_args Additional arguments to \command{Rscript} (as a character
#' vector).
#'
#' @param methods If TRUE, then the \pkg{methods} package is also loaded.
#'
#' @param useXDR If TRUE, the communication between master and workers, which is
#' binary, will use big-endian (XDR).
#'
#' @param outfile Where to direct the \link[base:stdout]{stdout} and
#' \link[base:stderr]{stderr} connection output from the workers.
#' If 'NULL', then no redirection of output is done, which means that the
#' output is relayed in the terminal on the local computer. On Windows, the
#' output is only relayed when running R from a terminal but not from a GUI.
#'
#' @param renice A numerical 'niceness' (priority) to set for the worker
#' processes.
#'
#' @param rank A unique one-based index for each worker (automatically set).
#'
#' @param rshcmd,rshopts The command (character vector) to be run on the master
#' to launch a process on another host and any additional arguments (character
#' vector). These arguments are only applied if \code{machine} is not
#' \emph{localhost}. For more details, see below.
#'
#' @param logfile (optional) If a filename, the output produced by the
#' \code{rshcmd} call is logged to this file, of if TRUE, then it is logged
#' to a temporary file. The log file name is available as an attribute
#' as part of the return node object.
#' \emph{Warning: This only works with SSH clients that support option
#' \code{-E out.log}.}
#'
#' @param user (optional) The user name to be used when communicating with
#' another host.
#'
#' @param revtunnel If TRUE, a reverse SSH tunnel is set up for each worker such
#' that the worker \R process sets up a socket connection to its local port
#' \code{(port - rank + 1)} which then reaches the master on port \code{port}.
#' If FALSE, then the worker will try to connect directly to port \code{port} on
#' \code{master}. For more details, see below.
#'
#' @param manual If TRUE the workers will need to be run manually. The command
#' to run will be displayed.
#'
#' @param dryrun If TRUE, nothing is set up, but a message suggesting how to
#' launch the worker from the terminal is outputted. This is useful for
#' troubleshooting.
#'
#' @return \code{makeNodePSOCK()} returns a \code{"SOCKnode"} or
#' \code{"SOCK0node"} object representing an established connection to a worker.
#'
#' @section Definition of \emph{localhost}:
#' A hostname is considered to be \emph{localhost} if it equals:
#' \itemize{
#' \item \code{"localhost"},
#' \item \code{"127.0.0.1"}, or
#' \item \code{Sys.info()[["nodename"]]}.
#' }
#' It is also considered \emph{localhost} if it appears on the same line
#' as the value of \code{Sys.info()[["nodename"]]} in file \file{/etc/hosts}.
#'
#' @section Default SSH client and options (arguments \code{rshcmd} and \code{rshopts}):
#' Arguments \code{rshcmd} and \code{rshopts} are only used when connecting
#' to an external host.
#'
#' The default method for connecting to an external host is via SSH and the
#' system executable for this is given by argument \code{rshcmd}. The default
#' is given by option \code{future.makeNodePSOCK.rshcmd}. If that is not
#' set, then the default is to use \command{ssh}.
#' Most Unix-like systems, including macOS, have \command{ssh} preinstalled
#' on the \code{PATH}. This is also true for recent Windows 10
#' (since version 1803; April 2018) (*).
#'
#' For \emph{Windows systems prior to Windows 10}, it is less common to find
#' \command{ssh} on the \code{PATH}. Instead it is more likely that such
#' systems have the \command{PuTTY} software and its SSH client
#' \command{plink} installed. Note, to manually set specify PuTTY as the
#' SSH client, specify the absolute pathname of \file{plink.exe} in the first
#' element and option \command{-ssh} in the second as in
#' \code{rshcmd = c("C:/Path/PuTTY/plink.exe", "-ssh")}.
#' This is because all elements of \code{rshcmd} are individually "shell"
#' quoted and element \code{rshcmd[1]} must be on the system \code{PATH}.
#'
#' Furthermore, when running \R from RStudio on Windows, the \command{ssh}
#' client that is distributed with RStudio will be also be considered.
#' This client, which is from \href{http://www.mingw.org/wiki/msys}{MinGW MSYS},
#' is search for in the folder given by the \code{RSTUDIO_MSYS_SSH} environment
#' variable - a variable that is (only) set when running RStudio.
#'
#' You can override the default set of SSH clients that are searched for
#' by specifying them in \code{rshcmd} using the format \code{<...>}, e.g.
#' \code{rshcmd = c("<rstudio-ssh>", "<putty-plink>", "<ssh>")}. See
#' below for examples.
#'
#' If no SSH-client is found, an informative error message is produced.
#'
#' (*) \emph{Known issue with the Windows 10 SSH client: There is a bug in the
#' SSH client of Windows 10 that prevents it to work with reverse SSH tunneling
#' (\url{https://github.com/PowerShell/Win32-OpenSSH/issues/1265}; Oct 2018).
#' Because of this, it is recommended to use the PuTTY SSH client or the
#' RStudio SSH client until this bug has been resolved in Windows 10.}
#'
#' Additional SSH options may be specified via argument \code{rshopts}, which
#' defaults to option \code{future.makeNodePSOCK.rshopts}. For instance, a
#' private SSH key can be provided as
#' \code{rshopts = c("-i", "~/.ssh/my_private_key")}. PuTTY users should
#' specify a PuTTY PPK file, e.g.
#' \code{rshopts = c("-i", "C:/Users/joe/.ssh/my_keys.ppk")}.
#' Contrary to \code{rshcmd}, elements of \code{rshopts} are not quoted.
#'
#' @section Accessing external machines that prompts for a password:
#' \emph{IMPORTANT: It is not possible to for these functions to log in
#' and launch R workers on external machines that requires a password to
#' be entered manually for authentication.}
#'
#' Note, depending on whether you run R in a terminal or via a GUI, you might
#' not even see the password prompt. It is also likely that you cannot enter
#' a password, because the connection is set up via a background system call.
#'
#' The poor man's workaround for setup that requires a password is to manually
#' log into the each of the external machines and launch the R workers by hand.
#' For this approach, use \code{manual = TRUE} and follow the instructions
#' which include cut'n'pasteable commands on how to launch the worker from the
#' external machine.
#'
#' However, a much more convenient and less tedious method is to set up
#' key-based SSH authentication between your local machine and the external
#' machine(s), as explain below.
#'
#' @section Accessing external machines via key-based SSH authentication:
#' The best approach to automatically launch R workers on external machines
#' over SSH is to set up key-based SSH authentication. This will allow you
#' to log into the external machine without have to enter a password.
#'
#' Key-based SSH authentication is taken care of by the SSH client and not \R.
#' To configure this, see the manuals of your SSH client or search the web
#' for "ssh key authentication".
#'
#' @section Reverse SSH tunneling:
#' The default is to use reverse SSH tunneling (\code{revtunnel = TRUE}) for
#' workers running on other machines. This avoids the complication of
#' otherwise having to configure port forwarding in firewalls, which often
#' requires static IP address as well as privileges to edit the firewall,
#' something most users don't have.
#' It also has the advantage of not having to know the internal and / or the
#' public IP address / hostname of the master.
#' Yet another advantage is that there will be no need for a DNS lookup by the
#' worker machines to the master, which may not be configured or is disabled
#' on some systems, e.g. compute clusters.
#'
#' @section Default value of argument \code{rscript}:
#' If \code{homogeneous} is FALSE, the \code{rscript} defaults to
#' \code{"Rscript"}, i.e. it is assumed that the \command{Rscript} executable
#' is available on the \code{PATH} of the worker.
#' If \code{homogeneous} is TRUE, the \code{rscript} defaults to
#' \code{file.path(R.home("bin"), "Rscript")}, i.e. it is basically assumed
#' that the worker and the caller share the same file system and \R installation.
#'
#' @section Default value of argument \code{homogeneous}:
#' The default value of \code{homogeneous} is TRUE if and only if either
#' of the following is fulfilled:
#' \itemize{
#' \item \code{worker} is \emph{localhost}
#' \item \code{revtunnel} is FALSE and \code{master} is \emph{localhost}
#' \item \code{worker} is neither an IP number nor a fully qualified domain
#' name (FQDN). A hostname is considered to be a FQDN if it contains
#' one or more periods
#' }
#' In all other cases, \code{homogeneous} defaults to FALSE.
#'
#' @section Connection time out:
#' Argument \code{connectTimeout} does \emph{not} work properly on Unix and
#' macOS due to limitation in \R itself. For more details on this, please see
#' R-devel thread 'BUG?: On Linux setTimeLimit() fails to propagate timeout
#' error when it occurs (works on Windows)' on 2016-10-26
#' (\url{https://stat.ethz.ch/pipermail/r-devel/2016-October/073309.html}).
#' When used, the timeout will eventually trigger an error, but it won't happen
#' until the socket connection timeout \code{timeout} itself happens.
#'
#' @section Communication time out:
#' If there is no communication between the master and a worker within the
#' \code{timeout} limit, then the corresponding socket connection will be
#' closed automatically. This will eventually result in an error in code
#' trying to access the connection.
#'
#' @rdname makeClusterPSOCK
#' @export
makeNodePSOCK <- function(worker = "localhost", master = NULL, port, connectTimeout = getOption("future.makeNodePSOCK.connectTimeout", 2 * 60), timeout = getOption("future.makeNodePSOCK.timeout", 30 * 24 * 60 * 60), rscript = NULL, homogeneous = NULL, rscript_args = NULL, methods = TRUE, useXDR = TRUE, outfile = "/dev/null", renice = NA_integer_, rshcmd = getOption("future.makeNodePSOCK.rshcmd", NULL), user = NULL, revtunnel = TRUE, logfile = NULL, rshopts = getOption("future.makeNodePSOCK.rshopts", NULL), rank = 1L, manual = FALSE, dryrun = FALSE, verbose = FALSE) {
localMachine <- is.element(worker, c("localhost", "127.0.0.1"))
## Could it be that the worker specifies the name of the localhost?
## Note, this approach preserves worker == "127.0.0.1" if that is given.
if (!localMachine) {
localMachine <- is_localhost(worker)
if (localMachine) worker <- "localhost"
}
attr(worker, "localhost") <- localMachine
manual <- as.logical(manual)
stop_if_not(length(manual) == 1L, !is.na(manual))
dryrun <- as.logical(dryrun)
stop_if_not(length(dryrun) == 1L, !is.na(dryrun))
## Locate a default SSH client?
if (!is.null(rshcmd)) {
rshcmd <- as.character(rshcmd)
stop_if_not(length(rshcmd) >= 1L)
}
rshopts <- as.character(rshopts)
user <- as.character(user)
stop_if_not(length(user) <= 1L)
port <- as.integer(port)
if (is.na(port) || port < 0L || port > 65535L) {
stop("Invalid port: ", port)
}
revtunnel <- as.logical(revtunnel)
stop_if_not(length(revtunnel) == 1L, !is.na(revtunnel))
if (!is.null(logfile)) {
if (is.logical(logfile)) {
stop_if_not(!is.na(logfile))
if (logfile) {
logfile <- tempfile(pattern = "future_makeClusterPSOCK_", fileext = ".log")
} else {
logfile <- NULL
}
} else {
logfile <- as.character(logfile)
logfile <- normalizePath(logfile, mustWork = FALSE)
}
}
if (is.null(master)) {
if (localMachine || revtunnel) {
master <- "localhost"
} else {
master <- Sys.info()[["nodename"]]
}
}
stop_if_not(!is.null(master))
timeout <- as.numeric(timeout)
stop_if_not(length(timeout) == 1L, !is.na(timeout), is.finite(timeout), timeout >= 0)
methods <- as.logical(methods)
stop_if_not(length(methods) == 1L, !is.na(methods))
if (is.null(homogeneous)) {
homogeneous <- {
localMachine ||
(!revtunnel && is_localhost(master)) ||
(!is_ip_number(worker) && !is_fqdn(worker))
}
}
homogeneous <- as.logical(homogeneous)
stop_if_not(length(homogeneous) == 1L, !is.na(homogeneous))
if (is.null(rscript)) {
rscript <- "Rscript"
if (homogeneous) rscript <- file.path(R.home("bin"), rscript)
} else {
rscript <- as.character(rscript)
stop_if_not(length(rscript) >= 1L)
bin <- Sys.which(rscript[1])
if (bin == "") bin <- normalizePath(rscript[1], mustWork = FALSE)
rscript[1] <- bin
}
rscript_args <- as.character(rscript_args)
useXDR <- as.logical(useXDR)
stop_if_not(length(useXDR) == 1L, !is.na(useXDR))
stop_if_not(is.null(outfile) || is.character(outfile))
renice <- as.integer(renice)
stop_if_not(length(renice) == 1L)
rank <- as.integer(rank)
stop_if_not(length(rank) == 1L, !is.na(rank))
verbose <- as.logical(verbose)
stop_if_not(length(verbose) == 1L, !is.na(verbose))
verbose_prefix <- "[local output] "
## .slaveRSOCK() command already specified?
if (!any(grepl("parallel:::.slaveRSOCK()", rscript_args, fixed = TRUE))) {
rscript_args <- c(rscript_args, "-e", shQuote("parallel:::.slaveRSOCK()"))
}
if (methods) {
rscript_args <- c("--default-packages=datasets,utils,grDevices,graphics,stats,methods", rscript_args)
}
## Port that the Rscript should use to connect back to the master
if (!localMachine && revtunnel) {
rscript_port <- port + (rank - 1L)
} else {
rscript_port <- port
}
rscript <- paste(shQuote(rscript), collapse = " ")
rscript_args <- paste(rscript_args, collapse = " ")
envvars <- paste0("MASTER=", master, " PORT=", rscript_port, " OUT=", outfile, " TIMEOUT=", timeout, " XDR=", useXDR)
cmd <- paste(rscript, rscript_args, envvars)
## Renice?
if (!is.na(renice) && renice > 0L) {
cmd <- sprintf("nice --adjustment=%d %s", renice, cmd)
}
if (!localMachine) {
## Find default SSH client
find <- is.null(rshcmd)
if (find) {
which <- NULL
if (verbose) {
message(sprintf("%sWill search for all 'rshcmd' available\n",
verbose_prefix))
}
} else if (all(grepl("^<[a-zA-Z-]+>$", rshcmd))) {
find <- TRUE
if (verbose) {
message(sprintf("%sWill search for specified 'rshcmd' types: %s\n",
verbose_prefix, paste(sQuote(rshcmd), collapse = ", ")))
}
which <- gsub("^<([a-zA-Z-]+)>$", "\\1", rshcmd)
}
if (find) {
rshcmd <- find_rshcmd(which = which,
must_work = !localMachine && !manual && !dryrun)
if (verbose) {
s <- unlist(lapply(rshcmd, FUN = function(r) {
sprintf("%s [type=%s, version=%s]", paste(sQuote(r), collapse = ", "), sQuote(attr(r, "type")), sQuote(attr(r, "version")))
}))
s <- paste(sprintf("%s %d. %s", verbose_prefix, seq_along(s), s), collapse = "\n")
message(sprintf("%sFound the following available 'rshcmd':\n%s", verbose_prefix, s))
}
rshcmd <- rshcmd[[1]]
} else {
if (is.null(attr(rshcmd, "type"))) attr(rshcmd, "type") <- "<unknown>"
if (is.null(attr(rshcmd, "version"))) attr(rshcmd, "version") <- "<unknown>"
}
s <- sprintf("type=%s, version=%s", sQuote(attr(rshcmd, "type")), sQuote(attr(rshcmd, "version")))
rshcmd_label <- sprintf("%s [%s]", paste(sQuote(rshcmd), collapse = ", "), s)
if (verbose) message(sprintf("%sUsing 'rshcmd': %s", verbose_prefix, rshcmd_label))
## User?
if (length(user) == 1L) rshopts <- c("-l", user, rshopts)
## Reverse tunneling?
if (revtunnel) {
rshopts <- c(sprintf("-R %d:%s:%d", rscript_port, master, port), rshopts)
## AD HOC: Warn about Windows 10 ssh bug with rev tunneling
if (isTRUE(attr(rshcmd, "OpenSSH_for_Windows"))) {
msg <- sprintf("WARNING: This 'rshcmd' (%s) may not support reverse tunneling (revtunnel = TRUE)", paste(sQuote(rshcmd), collapse = ", "), rshcmd_label)
if (verbose) message(c(verbose_prefix, msg))
}
}
## SSH log file?
if (is.character(logfile)) {
rshopts <- c(sprintf("-E %s", shQuote(logfile)), rshopts)
}
rshopts <- paste(rshopts, collapse = " ")
## Local commands
rsh_call <- paste(paste(shQuote(rshcmd), collapse = " "), rshopts, worker)
local_cmd <- paste(rsh_call, shQuote(cmd))
} else {
local_cmd <- cmd
}
stop_if_not(length(local_cmd) == 1L)
is_worker_output_visible <- is.null(outfile)
if (manual || dryrun) {
msg <- c("----------------------------------------------------------------------")
if (localMachine) {
msg <- c(msg, sprintf("Manually, start worker #%s on local machine %s with:", rank, sQuote(worker)), sprintf("\n %s\n", cmd))
} else {
msg <- c(msg, sprintf("Manually, (i) login into external machine %s:", sQuote(worker)),
sprintf("\n %s\n", rsh_call))
msg <- c(msg, sprintf("and (ii) start worker #%s from there:", rank),
sprintf("\n %s\n", cmd))
msg <- c(msg, sprintf("Alternatively, start worker #%s from the local machine by combining both step in a single call:", rank),
sprintf("\n %s\n", local_cmd))
}
msg <- paste(c(msg, ""), collapse = "\n")
cat(msg)
utils::flush.console()
if (dryrun) return(NULL)
} else {
if (verbose) {
message(sprintf("%sStarting worker #%s on %s: %s", verbose_prefix, rank, sQuote(worker), local_cmd))
}
input <- if (.Platform$OS.type == "windows") "" else NULL
res <- system(local_cmd, wait = FALSE, input = input)
if (verbose) {
message(sprintf("%s- Exit code of system() call: %s", verbose_prefix, res))
}
if (res != 0) {
warning(sprintf("system(%s) had a non-zero exit code: %d", local_cmd, res))
}
}
if (verbose) {
message(sprintf("%sWaiting for worker #%s on %s to connect back", verbose_prefix, rank, sQuote(worker)))
if (is_worker_output_visible) {
if (.Platform$OS.type == "windows") {
message(sprintf("%s- Detected 'outfile=NULL' on Windows: this will make the output from the background worker visible when running R from a terminal, but it will most likely not be visible when using a GUI.", verbose_prefix))
} else {
message(sprintf("%s- Detected 'outfile=NULL': this will make the output from the background worker visible", verbose_prefix))
}
}
}
con <- local({
## Apply connection time limit "only to the rest of the current computation".
## NOTE: Regardless of transient = TRUE / FALSE, it still seems we need to
## undo it manually :/ /HB 2016-11-05
setTimeLimit(elapsed = connectTimeout)
on.exit(setTimeLimit(elapsed = Inf))
warnings <- list()
tryCatch({
withCallingHandlers({
socketConnection("localhost", port = port, server = TRUE,
blocking = TRUE, open = "a+b", timeout = timeout)
}, warning = function(w) {
if (verbose) {
message(sprintf("%sDetected a warning from socketConnection(): %s", verbose_prefix, sQuote(conditionMessage(w))))
}
warnings <<- c(warnings, list(w))
})
}, error = function(ex) {
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## Post-mortem analysis
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
machineType <- if (localMachine) "local" else "remote"
msg <- sprintf("Failed to launch and connect to R worker on %s machine %s from local machine %s.\n", machineType, sQuote(worker), sQuote(Sys.info()[["nodename"]]))
## Inspect and report on the error message
cmsg <- conditionMessage(ex)
if (grepl(gettext("reached elapsed time limit"), cmsg)) {
msg <- c(msg, sprintf(" * The error produced by socketConnection() was: %s (which suggests that the connection timeout of %.0f seconds (argument 'connectTimeout') kicked in)\n", sQuote(cmsg), connectTimeout))
} else {
msg <- c(msg, sprintf(" * The error produced by socketConnection() was: %s\n", sQuote(cmsg)))
}
## Inspect and report on any warnings
if (length(warnings) > 0) {
msg <- c(msg, sprintf(" * In addition, socketConnection() produced %d warning(s):\n", length(warnings)))
for (kk in seq_along(warnings)) {
cmsg <- conditionMessage(warnings[[kk]])
if (grepl("port [0-9]+ cannot be opened", cmsg)) {
msg <- c(msg, sprintf(" - Warning #%d: %s (which suggests that this port is either already occupied by another process or blocked by the firewall on your local machine)\n", kk, sQuote(cmsg)))
} else {
msg <- c(msg, sprintf(" - Warning #%d: %s\n", kk, sQuote(cmsg)))
}
}
}
## Report on how the local socket connect was setup
msg <- c(msg, sprintf(" * The localhost socket connection that failed to connect to the R worker used port %d using a communication timeout of %.0f seconds and a connection timeout of %.0f seconds.\n", port, timeout, connectTimeout))
## Report on how the worker was launched
msg <- c(msg, sprintf(" * Worker launch call: %s.\n", local_cmd))
## Propose further troubleshooting methods
suggestions <- NULL
## Enable verbose=TRUE?
if (!verbose) {
suggestions <- c(suggestions, "Set 'verbose=TRUE' to see more details.")
}
## outfile=NULL?
if (.Platform$OS.type == "windows") {
if (is_worker_output_visible) {
suggestions <- c(suggestions, "On Windows, to see output from worker, set 'outfile=NULL' and run R from a terminal (not a GUI).")
} else {
suggestions <- c(suggestions, "On Windows, output from worker when using 'outfile=NULL' is only visible when running R from a terminal (not a GUI).")
}
} else {
if (!is_worker_output_visible) {
suggestions <- c(suggestions, "Set 'outfile=NULL' to see output from worker.")
}
}
## Log file?
if (is.character(logfile)) {
smsg <- sprintf("Inspect the content of log file %s for %s.", sQuote(logfile), sQuote(rshcmd))
lmsg <- tryCatch(readLines(logfile, n = 15L, warn = FALSE), error = function(ex) NULL)
if (length(lmsg) > 0) {
lmsg <- sprintf(" %2d: %s", seq_along(lmsg), lmsg)
smsg <- sprintf("%s The first %d lines are:\n%s", smsg, length(lmsg), paste(lmsg, collapse = "\n"))
}
suggestions <- c(suggestions, smsg)
} else {
suggestions <- c(suggestions, sprintf("Set 'logfile=TRUE' to enable logging for %s.", sQuote(rshcmd)))
}
## Special: Windows 10 ssh client may not support reverse tunneling. /2018-11-10
## https://github.com/PowerShell/Win32-OpenSSH/issues/1265
if (!localMachine && revtunnel && isTRUE(attr(rshcmd, "OpenSSH_for_Windows"))) {
suggestions <- c(suggestions, sprintf("The 'rshcmd' (%s) used may not support reverse tunneling (revtunnel = TRUE). See ?future::makeClusterPSOCK for alternatives.\n", rshcmd_label))
}
if (length(suggestions) > 0) {
suggestions <- sprintf(" - Suggestion #%d: %s\n", seq_along(suggestions), suggestions)
msg <- c(msg, " * Troubleshooting suggestions:\n", suggestions)
}
msg <- paste(msg, collapse = "")
ex$message <- msg
## Relay error and temporarily avoid truncating the error message in case it is too long
local({
oopts <- options(warning.length = 2000L)
on.exit(options(oopts))
stop(ex)
})
})
})
if (verbose) {
message(sprintf("%sConnection with worker #%s on %s established", verbose_prefix, rank, sQuote(worker)))
}
structure(list(con = con, host = worker, rank = rank, logfile = logfile),
class = if (useXDR) "SOCKnode" else "SOCK0node")
} ## makeNodePSOCK()
## Checks if a given worker is the same as the localhost. It is, iff:
##
## * worker == "localhost"
## * worker == "127.0.0.1"
## * worker == hostname
## * worker and hostname appears on the same line in /etc/hosts
##
## This should cover cases such as:
## * Calling is_localhost("n3") from machine n3
## * Calling is_localhost("n3.myserver.org") from machine n3[.myserver.org]
##
## References:
## * https://en.wikipedia.org/wiki/Hostname
is_localhost <- local({
localhosts <- c("localhost", "127.0.0.1")
non_localhosts <- character(0L)
function(worker, hostname = Sys.info()[["nodename"]], pathnames = "/etc/hosts") {
## INTERNAL: Clear list of known local hosts?
if (is.null(worker) && is.null(hostname)) {
localhosts <<- c("localhost", "127.0.0.1")
non_localhosts <<- character(0L)
return(NA)
}
stop_if_not(length(worker) == 1, length(hostname) == 1)
## Already known to a localhost or not to one?
if (worker %in% localhosts) return(TRUE)
if (worker %in% non_localhosts) return(FALSE)
if (worker == hostname) {
## Add worker to the list of known local hosts.
localhosts <<- unique(c(localhosts, worker))
return(TRUE)
}
## Scan known "hosts" files
pathnames <- pathnames[file_test("-f", pathnames)]
if (length(pathnames) == 0L) return(FALSE)
## Search for (hostname, worker) and (worker, hostname)
## occuring on the same line and are separates by one or
## more whitespace symbols (but nothing else).
pattern <- sprintf("^((|.*[[:space:]])%s[[:space:]]+%s([[:space:]]+|)|(|.*[[:space:]])%s[[:space:]]+%s([[:space:]]+|))$", hostname, worker, worker, hostname)
for (pathname in pathnames) {
bfr <- readLines(pathname, warn = FALSE)
if (any(grepl(pattern, bfr, ignore.case = TRUE))) {
## Add worker to the list of known local hosts.
localhosts <<- unique(c(localhosts, worker))
return(TRUE)
}
}
## Add worker to the list of known non-local hosts.
non_localhosts <<- unique(c(non_localhosts, worker))
FALSE
}
}) ## is_localhost()
## Checks if a worker is specified by its IP number.
is_ip_number <- function(worker) {
ip <- strsplit(worker, split = ".", fixed = TRUE)[[1]]
if (length(ip) != 4) return(FALSE)
ip <- as.integer(ip)
if (anyNA(ip)) return(FALSE)
all(0 <= ip & ip <= 255)
}
## Checks if a worker is specified as a fully qualified domain name (FQDN)
is_fqdn <- function(worker) {
grepl(".", worker, fixed = TRUE)
}
#' Search for SSH clients on the current system
#'
#' @param which A character vector specifying which types of SSH clients
#' to search for. If NULL, a default set of clients supported by the
#' current platform is searched for.
#'
#' @param first If TRUE, the first client found is returned, otherwise
#' all located clients are returned.
#'
#' @param must_work If TRUE and no clients was found, then an error
#' is produced, otherwise only a warning.
#'
#' @return A named list of pathnames to all located SSH clients.
#' If \code{first = TRUE}, only the first one is returned.
#' Attribute `version` contains the output from querying the
#' executable for its version (via command-line option `-V`).
#'
#' @export
#' @keywords internal
find_rshcmd <- function(which = NULL, first = FALSE, must_work = TRUE) {
query_version <- function(bin, args = "-V") {
v <- suppressWarnings(system2(bin, args = args, stdout = TRUE, stderr = TRUE))
paste(v, collapse = "; ")
}
find_rstudio_ssh <- function() {
path <- Sys.getenv("RSTUDIO_MSYS_SSH")
if (!file_test("-d", path)) return(NULL)
path <- normalizePath(path)
path_org <- Sys.getenv("PATH")
on.exit(Sys.setenv(PATH = path_org))
## Set PATH to only look in RSTUDIO_MSYS_SSH to avoid
## picking up other clients with the same name
## Comment: In RStudio, RSTUDIO_MSYS_SSH is appended
## to the PATH, see PATH in 'Tools -> Shell ...'.
Sys.setenv(PATH = path)
bin <- Sys.which("ssh")
if (!nzchar(bin)) return(NULL)
attr(bin, "type") <- "rstudio-ssh"
attr(bin, "version") <- query_version(bin, args = "-V")
bin
}
find_putty_plink <- function() {
bin <- Sys.which("plink")
if (!nzchar(bin)) return(NULL)
res <- c(bin, "-ssh")
attr(res, "type") <- "putty-plink"
attr(res, "version") <- query_version(bin, args = "-V")
res
}
find_ssh <- function() {
bin <- Sys.which("ssh")
if (!nzchar(bin)) return(NULL)
attr(bin, "type") <- "ssh"
v <- query_version(bin, args = "-V")
attr(bin, "version") <- v
if (any(grepl("OpenSSH_for_Windows", v)))
attr(bin, "OpenSSH_for_Windows") <- TRUE
bin
}
if (!is.null(which)) stop_if_not(is.character(which), length(which) >= 1L, !anyNA(which))
stop_if_not(is.logical(first), length(first) == 1L, !is.na(first))
stop_if_not(is.logical(must_work), length(must_work) == 1L, !is.na(must_work))
if (is.null(which)) {
if (.Platform$OS.type == "windows") {
which <- c("ssh", "putty-plink", "rstudio-ssh")
} else {
which <- "ssh"
}
}
res <- list()
for (name in which) {
pathname <- switch(name,
"ssh" = find_ssh(),
"putty-plink" = find_putty_plink(),
"rstudio-ssh" = find_rstudio_ssh(),
stop("Unknown 'rshcmd' type: ", sQuote(name))
)
if (!is.null(pathname)) {
if (first) return(pathname)
res[[name]] <- pathname
}
}
if (length(res) > 0) return(res)
msg <- sprintf("Failed to locate a default SSH client (checked: %s). Please specify one via argument 'rshcmd'.", paste(sQuote(which), collapse = ", ")) #nolint
if (must_work) stop(msg)
pathname <- "ssh"
msg <- sprintf("%s Will still try with %s.", msg, sQuote(paste(pathname, collapse = " ")))
warning(msg)
pathname
}
session_info <- function() {
list(
r = c(R.version, os.type = .Platform$OS.type),
system = as.list(Sys.info()),
process = list(pid = Sys.getpid())
)
}
add_cluster_session_info <- function(cl) {
stop_if_not(inherits(cl, "cluster"))
for (ii in seq_along(cl)) {
node <- cl[[ii]]
if (is.null(node)) next ## Happens with dryrun = TRUE
## Session information already collected?
if (!is.null(node$session_info)) next
node$session_info <- clusterCall(cl[ii], fun = session_info)[[1]]
## Sanity check, iff possible
if (inherits(node, "SOCK0node") || inherits(node, "SOCKnode")) {
pid <- capture.output(print(node))
pid <- as.integer(gsub(".* ", "", pid))
stop_if_not(node$session_info$process$pid == pid)
}
cl[[ii]] <- node
}
cl
} ## add_cluster_session_info()
#' Automatically stop a cluster when garbage collected
#'
#' Registers a finalizer to a cluster such that the cluster will
#' be stopped when garbage collected
#'
#' @param cl A cluster object
#'
#' @param debug If TRUE, then debug messages are produced when
#' the cluster is garbage collected.
#'
#' @return The cluster object with attribute `gcMe` set.
#'
#' @importFrom parallel stopCluster
#' @importFrom utils capture.output
#'
#' @seealso
#' The cluster is stopped using
#' \code{\link[parallel:stopCluster]{stopCluster}(cl)}).
#'
#' @keywords internal
#' @export
autoStopCluster <- function(cl, debug = FALSE) {
stop_if_not(inherits(cl, "cluster"))
## Already got a finalizer?
if (inherits(attr(cl, "gcMe"), "environment")) return(cl)
env <- new.env()
env$cluster <- cl
attr(cl, "gcMe") <- env
if (debug) {
reg.finalizer(env, function(e) {
message("Finalizing cluster ...")
message(capture.output(print(e$cluster)))
try(stopCluster(e$cluster), silent = FALSE)
message("Finalizing cluster ... done")
})
} else {
reg.finalizer(env, function(e) {
try(stopCluster(e$cluster), silent = TRUE)
})
}
cl
}