mirror of
https://github.com/andre-wojtowicz/r-distributed-computing
synced 2024-12-21 17:40:28 +01:00
added renice, changing passwords, setting poweroff;
fixed displaying errors
This commit is contained in:
parent
3acc1457b7
commit
2db3c06d02
@ -3,6 +3,7 @@
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PARALLEL.USED.METHOD = "REMOTE" # LOCAL or REMOTE
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PARALLEL.DISABLE.MKL.THREADS = TRUE
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PARALLEL.RENICE = 19 # [-20; 19] or NA
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# local
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PARALLEL.LOCAL.METHOD = "PSOCK"
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@ -15,7 +15,9 @@ cl = if (PARALLEL.USED.METHOD == "LOCAL")
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make.psock.cluster(
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names = PARALLEL.LOCAL.NODES,
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connection.timeout = PARALLEL.LOCAL.CONNECTION.TIMEOUT,
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outfile = PARALLEL.LOCAL.SLAVE.OUT.FILE)
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outfile = PARALLEL.LOCAL.SLAVE.OUT.FILE,
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renice = PARALLEL.RENICE
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)
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} else if (PARALLEL.LOCAL.METHOD == "FORK")
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{
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flog.info("Creating local FORK cluster")
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@ -49,7 +51,8 @@ cl = if (PARALLEL.USED.METHOD == "LOCAL")
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rscript = PARALLEL.REMOTE.SLAVE.RSCRIPT.PATH,
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homogeneous = PARALLEL.REMOTE.SLAVE.HOMOGENEOUS,
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methods = PARALLEL.REMOTE.SLAVE.METHODS,
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useXDR = PARALLEL.REMOTE.SLAVE.USEXDR)
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useXDR = PARALLEL.REMOTE.SLAVE.USEXDR,
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renice = PARALLEL.RENICE)
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}
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else {
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stop.script(paste("Unknown remote parallel cluster method:",
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@ -16,10 +16,12 @@ MRO_INSTALL_URL="https://mran.microsoft.com/install"
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HOSTS_FILE="remote-hosts.txt"
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CONNECTION_LIST_FILE="remote-connection-list.txt"
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HOSTS_SCANNED_FILE="remote-hosts-scanned.txt"
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DEBIAN_PACKAGES_TO_INSTALL="build-essential gfortran ed htop libxml2-dev ca-certificates curl libcurl4-openssl-dev gdebi-core sshpass default-jre default-jdk libpcre3-dev zlib1g-dev liblzma-dev libbz2-dev libicu-dev"
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DEBIAN_PACKAGES_TO_INSTALL="build-essential gfortran ed htop libxml2-dev ca-certificates curl libcurl4-openssl-dev gdebi-core sshpass default-jre default-jdk libpcre3-dev zlib1g-dev liblzma-dev libbz2-dev libicu-dev at"
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REMOTE_DETECT_LOGICAL_CPUS="FALSE"
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MIN_HOSTS=1
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SWAP_PART="/dev/mapper/linux-swap"
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NEW_PASS=""
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POWEROFF_TIME="7:00"
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SHELL_SCRIPT=$(basename $0)
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LOG_STEPS="logs/${SHELL_SCRIPT%.*}".log
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@ -243,6 +245,28 @@ hosts_push_ssh_key()
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check_if_command_error
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}
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hosts_change_password()
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{
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info "Changing user password on hosts"
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for host in "${HOSTS_ARRAY[@]}"; do
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step "-- ${host}"
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try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "chpasswd <<< $SSH_USER:$NEW_PASS"
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next
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done
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check_if_command_error
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}
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hosts_set_power_off()
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{
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info "Setting power-off on hosts"
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for host in "${HOSTS_ARRAY[@]}"; do
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step "-- ${host}"
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try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "at $POWEROFF_TIME <<< poweroff &> /dev/null"
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next
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done
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check_if_command_error
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}
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hosts_scan_available()
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{
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HOSTS_SCANNED_ARRAY=()
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@ -480,11 +504,13 @@ my_configure_hosts()
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#generate_ssh_keys
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#hosts_push_ssh_key
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hosts_scan_available
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hosts_change_password
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hosts_push_shell_script
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dump_project_r_files
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dump_r_libraries
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hosts_push_project_r_files
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hosts_install_env
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hosts_set_power_off
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hosts_install_mro
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#hosts_install_r_libraries
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hosts_push_r_libraries_dump
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@ -496,12 +522,14 @@ configure_hosts()
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{
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generate_ssh_keys
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hosts_push_ssh_key
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hosts_change_password
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hosts_push_shell_script
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hosts_enable_swap
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dump_project_r_files
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dump_r_libraries
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hosts_push_project_r_files
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hosts_install_env
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hosts_set_power_off
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hosts_install_mro
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hosts_push_r_libraries_dump
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#hosts_install_r_libraries
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@ -509,6 +537,12 @@ configure_hosts()
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#make_remote_connection_list_single
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}
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# check if new password is set
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if [ "$NEW_PASS" == "" ]; then
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warn "Empty new password"
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fi
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# read hosts from file or stdin
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if [ -t 0 ]; then
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@ -33,9 +33,9 @@ make.psock.cluster = function(names, connection.timeout, ...)
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tryCatch({
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cl.node =
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evalWithTimeout(parallel:::newPSOCKnode(names[[i]],
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options = options.copy,
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rank = i),
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evalWithTimeout(new.psock.node(names[[i]],
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options = options.copy,
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rank = i),
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timeout = connection.timeout,
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onTimeout = "error")
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cl[[i]] = cl.node
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@ -79,6 +79,65 @@ make.psock.cluster = function(names, connection.timeout, ...)
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cl.filtered
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}
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new.psock.node = function(machine = "localhost", ...,
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options = parallel:::defaultClusterOptions, rank)
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{
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options <- parallel:::addClusterOptions(options, list(...))
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if (is.list(machine)) {
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options <- parallel:::addClusterOptions(options, machine)
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machine <- machine$host
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}
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outfile <- parallel:::getClusterOption("outfile", options)
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master <- if (machine == "localhost")
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"localhost"
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else parallel:::getClusterOption("master", options)
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port <- parallel:::getClusterOption("port", options)
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manual <- parallel:::getClusterOption("manual", options)
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timeout <- parallel:::getClusterOption("timeout", options)
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methods <- parallel:::getClusterOption("methods", options)
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useXDR <- parallel:::getClusterOption("useXDR", options)
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env <- paste0("MASTER=", master, " PORT=", port, " OUT=",
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outfile, " TIMEOUT=", timeout, " XDR=", useXDR)
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arg <- "parallel:::.slaveRSOCK()"
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rscript <- if (parallel:::getClusterOption("homogeneous", options)) {
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shQuote(parallel:::getClusterOption("rscript", options))
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}
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else "Rscript"
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rscript_args <- parallel:::getClusterOption("rscript_args", options)
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if (methods)
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rscript_args <- c("--default-packages=datasets,utils,grDevices,graphics,stats,methods",
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rscript_args)
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cmd <- if (length(rscript_args))
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paste(rscript, paste(rscript_args, collapse = " "), "-e",
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shQuote(arg), env)
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else paste(rscript, "-e", shQuote(arg), env)
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renice <- parallel:::getClusterOption("renice", options)
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if (!is.na(renice) && renice)
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cmd <- sprintf("nice -%d %s", as.integer(renice), cmd)
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if (manual) {
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cat("Manually start worker on", machine, "with\n ",
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cmd, "\n")
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utils::flush.console()
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}
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else {
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if (machine != "localhost") {
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rshcmd <- parallel:::getClusterOption("rshcmd", options)
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user <- parallel:::getClusterOption("user", options)
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cmd <- shQuote(cmd)
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cmd <- paste(rshcmd, "-l", user, machine, cmd)
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}
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if (.Platform$OS.type == "windows") {
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system(cmd, wait = FALSE, input = "")
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}
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else system(cmd, wait = FALSE)
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}
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con <- socketConnection("localhost", port = port, server = TRUE,
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blocking = TRUE, open = "a+b", timeout = timeout)
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structure(list(con = con, host = machine, rank = rank), class = if (useXDR)
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"SOCKnode"
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else "SOCK0node")
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}
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stop.cluster = function(cl.to.stop = cl)
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{
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flog.info("Workers shut down")
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