added renice, changing passwords, setting poweroff;

fixed displaying errors

config-parallel.R

@@ -3,6 +3,7 @@
 PARALLEL.USED.METHOD               = "REMOTE" # LOCAL or REMOTE
 PARALLEL.DISABLE.MKL.THREADS       = TRUE
 
+PARALLEL.RENICE                    = 19 # [-20; 19] or NA
 
 # local
 PARALLEL.LOCAL.METHOD              = "PSOCK"

init-parallel.R

@@ -15,7 +15,9 @@ cl = if (PARALLEL.USED.METHOD == "LOCAL")
         make.psock.cluster(
             names              = PARALLEL.LOCAL.NODES,
             connection.timeout = PARALLEL.LOCAL.CONNECTION.TIMEOUT,
-            outfile            = PARALLEL.LOCAL.SLAVE.OUT.FILE)
+            outfile            = PARALLEL.LOCAL.SLAVE.OUT.FILE,
+            renice             = PARALLEL.RENICE
+            )
     } else if (PARALLEL.LOCAL.METHOD == "FORK")
     {
         flog.info("Creating local FORK cluster")
@@ -49,7 +51,8 @@ cl = if (PARALLEL.USED.METHOD == "LOCAL")
             rscript            = PARALLEL.REMOTE.SLAVE.RSCRIPT.PATH,
             homogeneous        = PARALLEL.REMOTE.SLAVE.HOMOGENEOUS,
             methods            = PARALLEL.REMOTE.SLAVE.METHODS,
-            useXDR             = PARALLEL.REMOTE.SLAVE.USEXDR)
+            useXDR             = PARALLEL.REMOTE.SLAVE.USEXDR,
+            renice             = PARALLEL.RENICE)
     }
     else {
         stop.script(paste("Unknown remote parallel cluster method:",

remote-commands.sh

@@ -16,10 +16,12 @@ MRO_INSTALL_URL="https://mran.microsoft.com/install"
 HOSTS_FILE="remote-hosts.txt"
 CONNECTION_LIST_FILE="remote-connection-list.txt"
 HOSTS_SCANNED_FILE="remote-hosts-scanned.txt"
-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"
+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"
 REMOTE_DETECT_LOGICAL_CPUS="FALSE"
 MIN_HOSTS=1
 SWAP_PART="/dev/mapper/linux-swap"
+NEW_PASS=""
+POWEROFF_TIME="7:00"
 
 SHELL_SCRIPT=$(basename $0)
 LOG_STEPS="logs/${SHELL_SCRIPT%.*}".log
@@ -243,6 +245,28 @@ hosts_push_ssh_key()
     check_if_command_error
 }
 
+hosts_change_password()
+{
+    info "Changing user password on hosts"
+    for host in "${HOSTS_ARRAY[@]}"; do
+        step "-- ${host}"
+        try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "chpasswd <<< $SSH_USER:$NEW_PASS"
+        next
+    done
+    check_if_command_error
+}
+
+hosts_set_power_off()
+{
+    info "Setting power-off on hosts"
+    for host in "${HOSTS_ARRAY[@]}"; do
+        step "-- ${host}"
+        try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "at $POWEROFF_TIME <<< poweroff &> /dev/null"
+        next
+    done
+    check_if_command_error
+}
+
 hosts_scan_available()
 {
     HOSTS_SCANNED_ARRAY=()
@@ -480,11 +504,13 @@ my_configure_hosts()
     #generate_ssh_keys
     #hosts_push_ssh_key
     hosts_scan_available
+    hosts_change_password
     hosts_push_shell_script
     dump_project_r_files
     dump_r_libraries
     hosts_push_project_r_files
     hosts_install_env
+    hosts_set_power_off
     hosts_install_mro
     #hosts_install_r_libraries
         hosts_push_r_libraries_dump
@@ -496,12 +522,14 @@ configure_hosts()
 {
     generate_ssh_keys
     hosts_push_ssh_key
+    hosts_change_password
     hosts_push_shell_script
     hosts_enable_swap
     dump_project_r_files
     dump_r_libraries
     hosts_push_project_r_files
     hosts_install_env
+    hosts_set_power_off
     hosts_install_mro
     hosts_push_r_libraries_dump
         #hosts_install_r_libraries
@@ -509,6 +537,12 @@ configure_hosts()
         #make_remote_connection_list_single
 }
 
+# check if new password is set
+
+if [ "$NEW_PASS" == "" ]; then
+    warn "Empty new password"
+fi
+
 # read hosts from file or stdin
 
 if [ -t 0 ]; then

utils-parallel.R

@@ -33,9 +33,9 @@ make.psock.cluster = function(names, connection.timeout, ...)
 
         tryCatch({
             cl.node =
-                evalWithTimeout(parallel:::newPSOCKnode(names[[i]],
+                evalWithTimeout(new.psock.node(names[[i]],
-                                                        options = options.copy,
+                                               options = options.copy,
-                                                        rank = i),
+                                               rank = i),
                                 timeout = connection.timeout,
                                 onTimeout = "error")
             cl[[i]] = cl.node
@@ -79,6 +79,65 @@ make.psock.cluster = function(names, connection.timeout, ...)
     cl.filtered
 }
 
+new.psock.node = function(machine = "localhost", ...,
+                          options = parallel:::defaultClusterOptions, rank)
+{
+    options <- parallel:::addClusterOptions(options, list(...))
+    if (is.list(machine)) {
+        options <- parallel:::addClusterOptions(options, machine)
+        machine <- machine$host
+    }
+    outfile <- parallel:::getClusterOption("outfile", options)
+    master <- if (machine == "localhost")
+        "localhost"
+    else parallel:::getClusterOption("master", options)
+    port <- parallel:::getClusterOption("port", options)
+    manual <- parallel:::getClusterOption("manual", options)
+    timeout <- parallel:::getClusterOption("timeout", options)
+    methods <- parallel:::getClusterOption("methods", options)
+    useXDR <- parallel:::getClusterOption("useXDR", options)
+    env <- paste0("MASTER=", master, " PORT=", port, " OUT=",
+                  outfile, " TIMEOUT=", timeout, " XDR=", useXDR)
+    arg <- "parallel:::.slaveRSOCK()"
+    rscript <- if (parallel:::getClusterOption("homogeneous", options)) {
+        shQuote(parallel:::getClusterOption("rscript", options))
+    }
+    else "Rscript"
+    rscript_args <- parallel:::getClusterOption("rscript_args", options)
+    if (methods)
+        rscript_args <- c("--default-packages=datasets,utils,grDevices,graphics,stats,methods",
+                          rscript_args)
+    cmd <- if (length(rscript_args))
+        paste(rscript, paste(rscript_args, collapse = " "), "-e",
+              shQuote(arg), env)
+    else paste(rscript, "-e", shQuote(arg), env)
+    renice <- parallel:::getClusterOption("renice", options)
+    if (!is.na(renice) && renice)
+        cmd <- sprintf("nice -%d %s", as.integer(renice), cmd)
+    if (manual) {
+        cat("Manually start worker on", machine, "with\n    ",
+            cmd, "\n")
+        utils::flush.console()
+    }
+    else {
+        if (machine != "localhost") {
+            rshcmd <- parallel:::getClusterOption("rshcmd", options)
+            user <- parallel:::getClusterOption("user", options)
+            cmd <- shQuote(cmd)
+            cmd <- paste(rshcmd, "-l", user, machine, cmd)
+        }
+        if (.Platform$OS.type == "windows") {
+            system(cmd, wait = FALSE, input = "")
+        }
+        else system(cmd, wait = FALSE)
+    }
+    con <- socketConnection("localhost", port = port, server = TRUE,
+                            blocking = TRUE, open = "a+b", timeout = timeout)
+    structure(list(con = con, host = machine, rank = rank), class = if (useXDR)
+        "SOCKnode"
+        else "SOCK0node")
+}
+
 stop.cluster = function(cl.to.stop = cl)
 {
     flog.info("Workers shut down")

utils.R

@@ -17,10 +17,11 @@ stop.script = function(error)
     if (is.character(error))
     {
         flog.error(error)
+    } else if ("message" %in% attributes(x)$names) {
+        flog.error(error$message)
     } else {
-        flog.error(getMessage(error))
+        try(flog.error(getMessage(error)), silent = TRUE)
     }
 
     throw(error)
 }
-