mirror of
https://github.com/andre-wojtowicz/r-distributed-computing
synced 2024-12-21 17:40:28 +01:00
Added core files
This commit is contained in:
parent
9e72fcf957
commit
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4
.gitignore
vendored
4
.gitignore
vendored
@ -31,3 +31,7 @@ vignettes/*.pdf
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# Temporary files created by R markdown
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*.utf8.md
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*.knit.md
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.Rproj.user
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logs/*
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.R.user
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54
config-parallel.R
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54
config-parallel.R
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@ -0,0 +1,54 @@
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# ---- config-parallel ----
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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.NO.JOBS.PER.CHUNK = 30 # no. jobs per worker in step 6-2
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PARALLEL.NO.JOBS.MULTIPLIER = 2 # no. jobs multiplier per job sequence
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# to minimize worker time of waitiing for
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# remaining workers in step 6-2
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# local
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PARALLEL.LOCAL.METHOD = "PSOCK"
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PARALLEL.LOCAL.NODES = parallel::detectCores(logical = FALSE)
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PARALLEL.LOCAL.CONNECTION.TIMEOUT = 5
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PARALLEL.LOCAL.SLAVE.OUT.FILE =
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lazy(file.path(LOGGER.OUTPUT.DIR,
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paste0("worker-local-", worker.name, "-", worker.id, ".log")))
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# remote
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PARALLEL.REMOTE.METHOD = "PSOCK"
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PARALLEL.REMOTE.MASTER.IP = "192.168.0.1" # ip accessible from slaves
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PARALLEL.REMOTE.MASTER.PORT = 11000
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PARALLEL.REMOTE.MASTER.CONNECTION.TIMEOUT = 10
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PARALLEL.REMOTE.MASTER.SSH.PROGRAM = "ssh" # ssh, ssh.exe, etc.
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PARALLEL.REMOTE.MASTER.SSH.PRIV.KEY = file.path("ssh", "rsa-priv.key")
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PARALLEL.REMOTE.MASTER.SSH.NULL.DEV = "/dev/null"
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PARALLEL.REMOTE.MASTER.SSH.STRICT.HOST.KEY.CHECKING = "no"
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PARALLEL.REMOTE.MASTER.SSH.SERVER.ALIVE.INTERVAL = 30
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PARALLEL.REMOTE.MASTER.SHELL.CMD =
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paste0(
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PARALLEL.REMOTE.MASTER.SSH.PROGRAM,
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" -q",
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" -o ConnectTimeout=", PARALLEL.REMOTE.MASTER.CONNECTION.TIMEOUT,
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" -o UserKnownHostsFile=", PARALLEL.REMOTE.MASTER.SSH.NULL.DEV,
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" -o StrictHostKeyChecking=", PARALLEL.REMOTE.MASTER.SSH.STRICT.HOST.KEY.CHECKING,
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" -o ServerAliveInterval=", PARALLEL.REMOTE.MASTER.SSH.SERVER.ALIVE.INTERVAL,
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" -i ", PARALLEL.REMOTE.MASTER.SSH.PRIV.KEY)
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PARALLEL.REMOTE.MASTER.SLAVES.FILE.PATH = "remote-connection-list.txt"
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PARALLEL.REMOTE.SLAVE.OUT.FILE = lazy(paste0("worker-remote-", worker.name,
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"-", worker.id, ".log"))
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PARALLEL.REMOTE.SLAVE.SSH.USER = "root"
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PARALLEL.REMOTE.SLAVE.RSCRIPT.PATH = "/usr/bin/Rscript"
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PARALLEL.REMOTE.SLAVE.HOMOGENEOUS = TRUE
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PARALLEL.REMOTE.SLAVE.METHODS = TRUE
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PARALLEL.REMOTE.SLAVE.USEXDR = TRUE
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# perform additional custom config
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if (file.exists("config-parallel.R.user"))
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source("config-parallel.R.user")
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31
config.R
Normal file
31
config.R
Normal file
@ -0,0 +1,31 @@
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# ---- config ----
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# randomization and output files
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SEED = 1337
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OVERWRITE.OUTPUT.FILES = TRUE # overwrite created datasets and classifiers
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# extra user configuration and init
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USER.CONFIG.FILE = "config.R.user"
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USER.INIT.FILE = "init.R.user"
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# checkpoint library
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CHECKPOINT.QUICK.LOAD = FALSE # if TRUE then skip testing https and checking url
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CHECKPOINT.MRAN.URL = "http://mran.microsoft.com/"
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CHECKPOINT.SNAPSHOT.DATE = "2016-07-01"
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# logging system
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LOGGER.OUTPUT.DIR = "logs"
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LOGGER.OUTPUT.TEST.FILE = "output-test.log"
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LOGGER.LEVEL = 6 # futile.logger::INFO
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LOGGER.OVERWRITE.EXISTING.FILES = TRUE
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# load custom config
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if (file.exists(USER.CONFIG.FILE))
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{
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source(USER.CONFIG.FILE)
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}
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115
init-parallel.R
Normal file
115
init-parallel.R
Normal file
@ -0,0 +1,115 @@
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# ---- init-parallel ----
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# load setup variables
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source("config-parallel.R")
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source("utils-parallel.R")
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# create cluster
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cl = if (PARALLEL.USED.METHOD == "LOCAL")
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{
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if (PARALLEL.LOCAL.METHOD == "PSOCK")
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{
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flog.info("Creating local PSOCK cluster")
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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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} else if (PARALLEL.LOCAL.METHOD == "FORK")
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{
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flog.info("Creating local FORK cluster")
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makeForkCluster(PARALLEL.LOCAL.NODES)
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} else {
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stop.script(paste("Unknown local parallel cluster method:",
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PARALLEL.USED.METHOD))
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}
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} else if (PARALLEL.USED.METHOD == "REMOTE")
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{
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if (PARALLEL.REMOTE.METHOD == "PSOCK")
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{
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flog.info("Creating remote PSOCK cluster")
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if (!file.exists(PARALLEL.REMOTE.MASTER.SLAVES.FILE.PATH))
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{
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stop.script(paste("Unable to read list of remote hosts from",
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PARALLEL.REMOTE.MASTER.SLAVES.FILE.PATH))
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}
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slaves.list = readLines(PARALLEL.REMOTE.MASTER.SLAVES.FILE.PATH)
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make.psock.cluster(
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names = slaves.list,
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connection.timeout = PARALLEL.REMOTE.MASTER.CONNECTION.TIMEOUT,
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master = PARALLEL.REMOTE.MASTER.IP,
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port = PARALLEL.REMOTE.MASTER.PORT,
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rshcmd = PARALLEL.REMOTE.MASTER.SHELL.CMD,
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outfile = PARALLEL.REMOTE.SLAVE.OUT.FILE,
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user = PARALLEL.REMOTE.SLAVE.SSH.USER,
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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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}
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else {
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stop.script(paste("Unknown remote parallel cluster method:",
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PARALLEL.REMOTE.METHOD))
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}
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} else {
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stop.script(paste("Unknown used parallel method:", PARALLEL.USED.METHOD))
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}
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flog.info("Exporting checkpoint constants")
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clusterExport(cl, c("CHECKPOINT.QUICK.LOAD", "CHECKPOINT.MRAN.URL",
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"CHECKPOINT.SNAPSHOT.DATE", "LOGGER.LEVEL"))
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clusterEvalQ(cl, {
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library(checkpoint)
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if (CHECKPOINT.QUICK.LOAD) # approx. x10 faster checkpoint library loading
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{
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# assume https
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options(checkpoint.mranUrl = CHECKPOINT.MRAN.URL)
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# disable url checking
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assignInNamespace("is.404", function(mran, warn = TRUE) { FALSE },
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"checkpoint")
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}
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checkpoint(CHECKPOINT.SNAPSHOT.DATE, verbose = TRUE, scanForPackages = TRUE)
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library(futile.logger)
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flog.threshold(LOGGER.LEVEL)
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flog.info("Logging configured")
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})
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if (PARALLEL.DISABLE.MKL.THREADS)
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{
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clusterEvalQ(cl, {
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tryCatch({setMKLthreads(1);
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flog.info("Set MKL threads to 1 on slave")},
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error = function(e) e)
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})
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}
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flog.info("Setting cluster RNG kind")
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clusterEvalQ(cl, {
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RNGkind("L'Ecuyer-CMRG")
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})
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flog.info("Registering cluster")
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registerDoParallel(cl)
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foreach::foreach(i = 1:foreach::getDoParWorkers()) %dopar%
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{
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flog.info("Foreach startup test")
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}
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flog.info(paste(rep("*", 25), collapse = ""))
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# perform additional custom init
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if (file.exists("init-parallel.R.user"))
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source("init-parallel.R.user")
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79
init.R
Normal file
79
init.R
Normal file
@ -0,0 +1,79 @@
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# ---- init ----
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# stop cluster if it is already registered
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if ("cl" %in% ls() && !is.null(foreach::getDoParName()))
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{
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if (foreach::getDoParName() != "doSEQ")
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{
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flog.info("Stopping already registered cluster")
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stop.cluster()
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}
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}
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# clear envirionment
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rm(list = ls())
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# load setup variables
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source("config.R")
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# load library management system
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suppressPackageStartupMessages(
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library(checkpoint)
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)
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if (CHECKPOINT.QUICK.LOAD) # approx. x10 faster checkpoint library loading
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{
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# assume https
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options(checkpoint.mranUrl = CHECKPOINT.MRAN.URL)
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# disable url checking
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assignInNamespace("is.404", function(mran, warn = TRUE) { FALSE },
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"checkpoint")
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}
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checkpoint(CHECKPOINT.SNAPSHOT.DATE, verbose = TRUE, scanForPackages = TRUE)
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# load logging system
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suppressPackageStartupMessages(
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library(futile.logger)
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)
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invisible(flog.threshold(LOGGER.LEVEL))
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if (!dir.exists(LOGGER.OUTPUT.DIR))
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{
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dir.create(LOGGER.OUTPUT.DIR, recursive = TRUE)
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}
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# load libraries
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suppressPackageStartupMessages({
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library(plyr)
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library(dplyr)
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library(ttutils)
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library(lazyeval)
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library(R.utils)
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library(RCurl)
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# caret - core
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library(caret)
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library(e1071)
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# caret - classifiers
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library(kernlab) # SVM
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# parallel computation
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library(doParallel)
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})
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# load helper functions
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source("utils.R")
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# perform additional custom init
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if (file.exists(USER.INIT.FILE))
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{
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source(USER.INIT.FILE)
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}
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16
r-distributed-computing.Rproj
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16
r-distributed-computing.Rproj
Normal file
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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 4
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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520
remote-commands.sh
Normal file
520
remote-commands.sh
Normal file
@ -0,0 +1,520 @@
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#!/bin/bash
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# working with WMI Rescue - small Linux image based on
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# Debian distribution; see http://rescue.wmi.amu.edu.pl
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# config
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MRO_VERSION="3.3.1"
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SSH_OPTIONS="-o ConnectTimeout=5 -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -q"
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SSH_USER="root"
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SSHPASS_PWD="wmi"
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SSH_KEYS_DIR="ssh"
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SSH_KEY_PRIV="rsa-priv.key"
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SSH_KEY_PUB="rsa-pub.key"
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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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REMOTE_DETECT_LOGICAL_CPUS="FALSE"
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MIN_HOSTS=100
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SHELL_SCRIPT=$(basename $0)
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LOG_STEPS="logs/${SHELL_SCRIPT%.*}".log
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HOSTS_ARRAY=()
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# messaging
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report_error()
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{
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echo $1 > /tmp/command_error.$$
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}
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[[ -w /tmp ]] && report_error 0
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# https://stackoverflow.com/a/5196220
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# modified for Debian
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# Use step(), try(), and next() to perform a series of commands and print
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# [ OK ] or [FAILED] at the end. The step as a whole fails if any individual
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# command fails.
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#
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# Example:
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# step "Remounting / and /boot as read-write:"
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# try mount -o remount,rw /
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# try mount -o remount,rw /boot
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# next
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step()
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{
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echo -n "* $@ "
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STEP_OK=0
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[[ -w /tmp ]] && echo $STEP_OK > /tmp/step.$$
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}
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try()
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{
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# skip if previous command in step failed
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[[ -f /tmp/step.$$ ]] && { PREV_STEP=$(< /tmp/step.$$); }
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[[ $PREV_STEP -ne 0 ]] && return 1
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# Check for `-b' argument to run command in the background.
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local BG=
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[[ $1 == -b ]] && { BG=1; shift; }
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[[ $1 == -- ]] && { shift; }
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# Run the command.
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if [[ -z $BG ]]; then
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"$@"
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else
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"$@" &
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fi
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# Check if command failed and update $STEP_OK if so.
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local EXIT_CODE=$?
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if [[ $EXIT_CODE -ne 0 ]]; then
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STEP_OK=$EXIT_CODE
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[[ -w /tmp ]] && echo $STEP_OK > /tmp/step.$$
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if [[ -n $LOG_STEPS ]]; then
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local FILE=$(readlink -m "${BASH_SOURCE[1]}")
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local LINE=${BASH_LINENO[0]}
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mkdir -p $( dirname $LOG_STEPS )
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echo "$FILE: line $LINE: Command \`$*' failed with exit code $EXIT_CODE." >> "$LOG_STEPS"
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fi
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fi
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return $EXIT_CODE
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}
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test -t 1 && CONSOLE_STDOUT=1 || CONSOLE_STDOUT=0
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[[ $TERM != "dumb" ]] && [[ $CONSOLE_STDOUT -eq 1 ]] && CONSOLE_COLORS=1 || CONSOLE_COLORS=0
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[ $CONSOLE_COLORS -eq 1 ] && CONSOLE_RED=$(tput setaf 1)
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[ $CONSOLE_COLORS -eq 1 ] && CONSOLE_GREEN=$(tput setaf 2)
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[ $CONSOLE_COLORS -eq 1 ] && CONSOLE_YELLOW=$(tput setaf 3)
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[ $CONSOLE_COLORS -eq 1 ] && CONSOLE_NORMAL=$(tput sgr0)
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[ $CONSOLE_COLORS -eq 1 ] && CONSOLE_RESULT_POS=$[$(tput cols)-10] || CONSOLE_RESULT_POS=0
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next()
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{
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# https://stackoverflow.com/a/5506264
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[ $CONSOLE_COLORS -eq 1 ] && tput hpa ${CONSOLE_RESULT_POS}
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[[ -f /tmp/step.$$ ]] && { STEP_OK=$(< /tmp/step.$$); rm -f /tmp/step.$$; }
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[[ $STEP_OK -eq 0 ]] && printf '%s%s' "$CONSOLE_GREEN" "[ OK ]" "$CONSOLE_NORMAL" || printf '%s%s' "$CONSOLE_RED" "[FAIL]" "$CONSOLE_NORMAL"
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echo
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[[ $STEP_OK -ne 0 ]] && report_error 1
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return $STEP_OK
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}
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info()
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{
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echo -n "* $@ "
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[ $CONSOLE_COLORS -eq 1 ] && tput hpa ${CONSOLE_RESULT_POS}
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printf '%s' "[INFO]"
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echo
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}
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fail()
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{
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echo -n "* $@ "
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[ $CONSOLE_COLORS -eq 1 ] && tput hpa ${CONSOLE_RESULT_POS}
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printf '%s%s' "$CONSOLE_RED" "[FAIL]" "$CONSOLE_NORMAL"
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echo
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}
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success()
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{
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echo -n "* $@ "
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[ $CONSOLE_COLORS -eq 1 ] && tput hpa ${CONSOLE_RESULT_POS}
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printf '%s%s' "$CONSOLE_GREEN" "[ OK ]" "$CONSOLE_NORMAL"
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echo
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}
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warn()
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{
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echo -n "* $@ "
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[ $CONSOLE_COLORS -eq 1 ] && tput hpa ${CONSOLE_RESULT_POS}
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printf '%s%s' "$CONSOLE_YELLOW" "[WARN]" "$CONSOLE_NORMAL"
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echo
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}
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# functions
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||||
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generate_ssh_keys()
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{
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step "Generating SSH keys"
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||||
try mkdir -p ssh
|
||||
try ssh-keygen -q -t rsa -b 4096 -f ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} -P "" -C "rscript@remote"
|
||||
try mv ${SSH_KEYS_DIR}/${SSH_KEY_PRIV}.pub ${SSH_KEYS_DIR}/${SSH_KEY_PUB}
|
||||
next
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
install_env()
|
||||
{
|
||||
step "Installing environment"
|
||||
echo
|
||||
try apt-get update
|
||||
local DEBIAN_FRONTEND=noninteractive
|
||||
try apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew" upgrade
|
||||
try apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew" install ${DEBIAN_PACKAGES_TO_INSTALL}
|
||||
try apt-get clean
|
||||
next
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
install_mro()
|
||||
{
|
||||
step "Installing Microsoft R Open"
|
||||
echo
|
||||
|
||||
Rscript -e "invisible(TRUE)" &> /dev/null
|
||||
|
||||
if [[ $? -ne 0 ]]; then
|
||||
try wget ${MRO_INSTALL_URL}/mro/${MRO_VERSION}/microsoft-r-open-${MRO_VERSION}.tar.gz
|
||||
try tar -xvf microsoft-r-open-${MRO_VERSION}.tar.gz
|
||||
try gdebi -n microsoft-r-open/deb/microsoft-r-open-mro-${MRO_VERSION:0:3}.deb
|
||||
try gdebi -n microsoft-r-open/deb/microsoft-r-open-foreachiterators-${MRO_VERSION:0:3}.deb
|
||||
try gdebi -n microsoft-r-open/deb/microsoft-r-open-mkl-${MRO_VERSION:0:3}.deb
|
||||
try R CMD javareconf
|
||||
rm -rf microsoft-r-open*
|
||||
else
|
||||
echo "Microsoft R Open already installed"
|
||||
fi
|
||||
|
||||
try Rscript -e "install.packages('knitr')"
|
||||
|
||||
|
||||
try apt-get clean
|
||||
next
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
install_r_libraries()
|
||||
{
|
||||
step "Installing R libraries"
|
||||
echo
|
||||
try mkdir -p ~/.checkpoint
|
||||
try Rscript init.R # run checkpoint
|
||||
next
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
dump_project_r_files()
|
||||
{
|
||||
step "Making project R files dump"
|
||||
try tar -czf project-r-files.tar.gz *.R*
|
||||
next
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
dump_r_libraries()
|
||||
{
|
||||
step "Making R libraries dump"
|
||||
wd=`pwd`
|
||||
cd ~/
|
||||
try tar -czf $wd/checkpoint.tar.gz .checkpoint/*
|
||||
cd $wd
|
||||
next
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
hosts_push_ssh_key()
|
||||
{
|
||||
info "Pushing SSH keys to hosts"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
step "-- ${host}"
|
||||
try sshpass -p ${SSHPASS_PWD} ssh ${SSH_OPTIONS} ${SSH_USER}@${host} 'mkdir -p ~/.ssh'
|
||||
try sshpass -p ${SSHPASS_PWD} scp ${SSH_OPTIONS} ${SSH_KEYS_DIR}/${SSH_KEY_PUB} ${SSH_USER}@${host}:~/.ssh
|
||||
try sshpass -p ${SSHPASS_PWD} ssh ${SSH_OPTIONS} ${SSH_USER}@${host} "cat ~/.ssh/${SSH_KEY_PUB} >> ~/.ssh/authorized_keys"
|
||||
try sshpass -p ${SSHPASS_PWD} ssh ${SSH_OPTIONS} ${SSH_USER}@${host} "sed -i -e 's/#PasswordAuthentication yes/PasswordAuthentication no/ig' /etc/ssh/sshd_config; service ssh restart"
|
||||
next
|
||||
done
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
hosts_scan_available()
|
||||
{
|
||||
HOSTS_SCANNED_ARRAY=()
|
||||
|
||||
info "Scanning available hosts"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
ssh -o ConnectTimeout=2 -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o PreferredAuthentications=publickey -q -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "true"
|
||||
EXIT_CODE=$?
|
||||
if [[ $EXIT_CODE -ne 0 ]]; then
|
||||
fail "-- ${host}"
|
||||
else
|
||||
success "-- ${host}"
|
||||
HOSTS_SCANNED_ARRAY+=("$host")
|
||||
fi
|
||||
done
|
||||
|
||||
HOSTS_ARRAY=("${HOSTS_SCANNED_ARRAY[@]}")
|
||||
|
||||
if [[ ${#HOSTS_ARRAY[@]} -eq 0 ]]; then
|
||||
fail "No available hosts"
|
||||
exit 1
|
||||
else
|
||||
info "Available ${#HOSTS_ARRAY[@]} hosts"
|
||||
fi
|
||||
|
||||
if [[ ${#HOSTS_ARRAY[@]} -lt $MIN_HOSTS ]]; then
|
||||
fail "Too few hosts: ${#HOSTS_ARRAY[@]} ; min.: $MIN_HOSTS"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if [ -f ${HOSTS_SCANNED_FILE} ] ; then rm ${HOSTS_SCANNED_FILE}; fi
|
||||
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
echo ${host} >> ${HOSTS_SCANNED_FILE}
|
||||
done
|
||||
}
|
||||
|
||||
hosts_push_r_libraries_dump()
|
||||
{
|
||||
info "Pushing R libraries dump to hosts"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
step "-- ${host}"
|
||||
try scp ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} checkpoint.tar.gz ${SSH_USER}@${host}:~/
|
||||
try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "tar -xzf checkpoint.tar.gz -C ~/; rm checkpoint.tar.gz"
|
||||
next
|
||||
done
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
hosts_push_project_r_files()
|
||||
{
|
||||
info "Pushing project R files to hosts"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
step "-- ${host}"
|
||||
try scp ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} project-r-files.tar.gz ${SSH_USER}@${host}:~/
|
||||
try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "tar -xzf project-r-files.tar.gz -C ~/; rm project-r-files.tar.gz"
|
||||
next
|
||||
done
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
hosts_push_shell_script()
|
||||
{
|
||||
info "Pushing shell script to hosts"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
step "-- ${host}"
|
||||
try scp ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SHELL_SCRIPT} ${SSH_USER}@${host}:~/
|
||||
next
|
||||
done
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
hosts_install()
|
||||
{
|
||||
case "$1" in
|
||||
"env") info "Installing environment on hosts" ;;
|
||||
"mro") info "Installing Microsoft R Open on hosts" ;;
|
||||
"r_libraries") info "Installing R libraries on hosts" ;;
|
||||
*) fail "Unknown remote install command"; report_error 1; check_if_command_error
|
||||
esac
|
||||
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
info "-- Invoking ${host}"
|
||||
|
||||
{ ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "bash ${SHELL_SCRIPT} install_$1 &> install_$1.log" ;
|
||||
endcode=$?
|
||||
if [ $endcode -eq 0 ] ; then
|
||||
success "-- ${host} finished"
|
||||
else
|
||||
fail "-- ${host} finished"
|
||||
report_error 1
|
||||
fi
|
||||
} &
|
||||
|
||||
done
|
||||
|
||||
last_workers=-1
|
||||
while true; do
|
||||
current_workers=$(jobs -rp | wc -l)
|
||||
if [ $current_workers -eq 0 ] ; then break; fi
|
||||
if (( $current_workers % 5 == 0)) && [ "$current_workers" -ne "$last_workers" ] ; then
|
||||
info "- Waiting for $current_workers hosts"
|
||||
last_workers=$current_workers
|
||||
fi
|
||||
sleep 1
|
||||
done
|
||||
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
hosts_install_env() { hosts_install env; }
|
||||
hosts_install_mro() { hosts_install mro; }
|
||||
hosts_install_r_libraries() { hosts_install r_libraries; }
|
||||
|
||||
hosts_power_off()
|
||||
{
|
||||
info "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} "poweroff"
|
||||
next
|
||||
done
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
make_remote_connection_list()
|
||||
{
|
||||
info "Making remote connection list:"
|
||||
if [ -f ${CONNECTION_LIST_FILE} ] ; then rm ${CONNECTION_LIST_FILE}; fi
|
||||
case "$1" in
|
||||
"single")
|
||||
step "one connection per host"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
try echo ${host} >> ${CONNECTION_LIST_FILE}
|
||||
done
|
||||
next
|
||||
;;
|
||||
"nproc")
|
||||
info "'number of cores' per host"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
step "-- ${host}"
|
||||
cornum=`try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} '/usr/bin/Rscript -e "cat(parallel::detectCores(logical = ${REMOTE_DETECT_LOGICAL_CPUS}))"'`
|
||||
|
||||
regex='^[0-9]+$'
|
||||
if ! [[ $cornum =~ $regex ]] ; then
|
||||
try false
|
||||
else
|
||||
for ((i=1; i<=$cornum; i++)); do try echo ${host} >> ${CONNECTION_LIST_FILE}; done
|
||||
echo -n "($cornum cores) "
|
||||
fi
|
||||
next
|
||||
done
|
||||
;;
|
||||
*)
|
||||
fail "unknown type"
|
||||
report_error 1
|
||||
esac
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
make_remote_connection_list_single() { make_remote_connection_list single; }
|
||||
make_remote_connection_list_nproc() { make_remote_connection_list nproc; }
|
||||
|
||||
hosts_check_install_log()
|
||||
{
|
||||
info "Checking install log on hosts"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
step "-- ${host}"
|
||||
echo
|
||||
try ssh ${SSH_OPTIONS/-q/} -o LogLevel=error -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "cat install_$1.log"
|
||||
next
|
||||
done
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
hosts_check_install_log_env() { hosts_check_install_log env; }
|
||||
hosts_check_install_log_mro() { hosts_check_install_log mro; }
|
||||
hosts_check_install_log_r_libraries() { hosts_check_install_log r_libraries; }
|
||||
|
||||
hosts_check_worker_log()
|
||||
{
|
||||
info "Checking worker log on hosts"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
step "-- ${host}"
|
||||
echo
|
||||
try ssh ${SSH_OPTIONS/-q/} -o LogLevel=error -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "for f in worker-remote-*.log; do echo \$f; cat -n \$f; done"
|
||||
next
|
||||
done
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
hosts_clean_worker_log()
|
||||
{
|
||||
info "Cleaning workers logs"
|
||||
for host in "${HOSTS_ARRAY[@]}"; do
|
||||
step "-- ${host}"
|
||||
try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "rm -f worker-remote-*.log"
|
||||
next
|
||||
done
|
||||
check_if_command_error
|
||||
}
|
||||
|
||||
check_if_command_error()
|
||||
{
|
||||
errcode=$(< /tmp/command_error.$$)
|
||||
[[ $errcode -ne 0 ]] && { warn "Stopping script execution"; rm -f /tmp/command_error.$$; exit $errcode; }
|
||||
}
|
||||
|
||||
my_configure_hosts()
|
||||
{
|
||||
#generate_ssh_keys
|
||||
#hosts_push_ssh_key
|
||||
hosts_scan_available
|
||||
hosts_push_shell_script
|
||||
dump_project_r_files
|
||||
hosts_push_project_r_files
|
||||
hosts_install_env
|
||||
hosts_install_mro
|
||||
#hosts_install_r_libraries
|
||||
hosts_push_r_libraries_dump
|
||||
make_remote_connection_list_nproc
|
||||
#make_remote_connection_list_single
|
||||
}
|
||||
|
||||
configure_hosts()
|
||||
{
|
||||
generate_ssh_keys
|
||||
hosts_push_ssh_key
|
||||
hosts_push_shell_script
|
||||
dump_project_r_files
|
||||
hosts_push_project_r_files
|
||||
hosts_install_env
|
||||
hosts_install_mro
|
||||
hosts_install_r_libraries
|
||||
#hosts_push_r_libraries_dump
|
||||
make_remote_connection_list_nproc
|
||||
#make_remote_connection_list_single
|
||||
}
|
||||
|
||||
# read hosts from file or stdin
|
||||
|
||||
if [ -t 0 ]; then
|
||||
if [ ! -f "$HOSTS_FILE" ]
|
||||
then
|
||||
info "No hosts file, working with localhost"
|
||||
HOSTS_ARRAY+=("127.0.0.1")
|
||||
else
|
||||
readarray -t HOSTS_ARRAY < $HOSTS_FILE
|
||||
fi
|
||||
else
|
||||
while read -r host ; do
|
||||
HOSTS_ARRAY+=("$host")
|
||||
done
|
||||
fi
|
||||
|
||||
info "Working with ${#HOSTS_ARRAY[@]} hosts"
|
||||
|
||||
# read arguments as commands
|
||||
|
||||
for i in "$@"
|
||||
do
|
||||
case "$i" in
|
||||
"hosts_install"|"hosts_check_install_log"|"make_remote_connection_list"|"info"|"fail"|"success"|"warn"|"next"|"try"|"step") ;;
|
||||
*)
|
||||
if [ "$(type -t $i)" = "function" ]; then
|
||||
$i
|
||||
else
|
||||
fail "Command $i not found"
|
||||
report_error 127
|
||||
fi
|
||||
esac
|
||||
|
||||
check_if_command_error
|
||||
done
|
||||
|
||||
rm -f /tmp/command_error.$$
|
||||
41
test.R
Normal file
41
test.R
Normal file
@ -0,0 +1,41 @@
|
||||
# ---- init ----
|
||||
|
||||
source("init.R")
|
||||
|
||||
setup.logger(file.path(LOGGER.OUTPUT.DIR, LOGGER.OUTPUT.TEST.FILE),
|
||||
LOGGER.OVERWRITE.EXISTING.FILES)
|
||||
|
||||
source("init-parallel.R")
|
||||
|
||||
# ---- foreach-test ----
|
||||
|
||||
flog.info("Test foreach")
|
||||
|
||||
fdata = foreach::foreach(i = 1:foreach::getDoParWorkers(),
|
||||
.combine = c) %dopar%
|
||||
{
|
||||
Sys.sleep(1)
|
||||
return(i)
|
||||
}
|
||||
|
||||
print(fdata)
|
||||
|
||||
# ---- caret-test ----
|
||||
|
||||
flog.info("Test caret")
|
||||
|
||||
tr.control = caret::trainControl(method = "repeatedcv",
|
||||
number = 10,
|
||||
repeats = 10,
|
||||
allowParallel = TRUE)
|
||||
|
||||
model = caret::train(form = mpg ~ .,
|
||||
data = mtcars,
|
||||
method = "svmLinear",
|
||||
trControl = tr.control)
|
||||
|
||||
print(model)
|
||||
|
||||
# ---- shutdown ----
|
||||
|
||||
stop.cluster()
|
||||
88
utils-parallel.R
Normal file
88
utils-parallel.R
Normal file
@ -0,0 +1,88 @@
|
||||
make.psock.cluster = function(names, connection.timeout, ...)
|
||||
{
|
||||
if (is.numeric(names))
|
||||
{
|
||||
names = as.integer(names[1])
|
||||
if (is.na(names) || names < 1)
|
||||
{
|
||||
stop.script("Numeric 'names' must be >= 1")
|
||||
}
|
||||
names = rep("localhost", names)
|
||||
}
|
||||
|
||||
parallel:::.check_ncores(length(names))
|
||||
options = parallel:::addClusterOptions(parallel:::defaultClusterOptions,
|
||||
list(...))
|
||||
cl = vector("list", length(names))
|
||||
|
||||
for (i in seq_along(cl))
|
||||
{
|
||||
|
||||
flog.info(paste0("[", i, "/", length(cl), "] Connecting to ",
|
||||
names[[i]], " ... "))
|
||||
|
||||
options.copy = parallel:::addClusterOptions(options, NULL)
|
||||
options.out.file = parallel:::getClusterOption("outfile", options)
|
||||
if (class(options.out.file) == "lazy")
|
||||
{
|
||||
options.copy = parallel:::addClusterOptions(options,
|
||||
list("outfile" = lazy_eval(options.out.file,
|
||||
list(worker.id = i,
|
||||
worker.name = names[i]))))
|
||||
}
|
||||
|
||||
tryCatch({
|
||||
cl.node =
|
||||
evalWithTimeout(parallel:::newPSOCKnode(names[[i]],
|
||||
options = options.copy,
|
||||
rank = i),
|
||||
timeout = connection.timeout,
|
||||
onTimeout = "error")
|
||||
cl[[i]] = cl.node
|
||||
flog.info("OK")},
|
||||
error = function(e) {
|
||||
if ("TimeoutException" %in% class(e))
|
||||
{
|
||||
flog.warn("Timeout")
|
||||
} else {
|
||||
stop.script(e)
|
||||
}
|
||||
}
|
||||
)
|
||||
}
|
||||
|
||||
cl.filtered = list()
|
||||
i = 1
|
||||
for (j in seq_along(cl))
|
||||
{
|
||||
if (!is.null(cl[[j]]))
|
||||
{
|
||||
cl.filtered[[i]] = cl[[j]]
|
||||
i = i + 1
|
||||
}
|
||||
}
|
||||
|
||||
if (length(cl) != length(cl.filtered))
|
||||
{
|
||||
flog.warn(paste("Unable to connect to", length(cl) - length(cl.filtered),
|
||||
"nodes"))
|
||||
}
|
||||
|
||||
if (length(cl.filtered) == 0)
|
||||
{
|
||||
stop.script("No remote workers")
|
||||
} else {
|
||||
flog.info(paste("Working on", length(cl.filtered), "nodes"))
|
||||
}
|
||||
|
||||
class(cl.filtered) = c("SOCKcluster", "cluster")
|
||||
cl.filtered
|
||||
}
|
||||
|
||||
stop.cluster = function(cl.to.stop = cl)
|
||||
{
|
||||
flog.info("Workers shut down")
|
||||
|
||||
foreach::registerDoSEQ()
|
||||
parallel::stopCluster(cl.to.stop)
|
||||
}
|
||||
26
utils.R
Normal file
26
utils.R
Normal file
@ -0,0 +1,26 @@
|
||||
|
||||
# additional functions
|
||||
|
||||
setup.logger = function(output.file, overwrite.existing.files)
|
||||
{
|
||||
if (overwrite.existing.files & file.exists(output.file))
|
||||
{
|
||||
file.remove(output.file)
|
||||
}
|
||||
|
||||
invisible(flog.appender(appender.tee(output.file)))
|
||||
}
|
||||
|
||||
|
||||
stop.script = function(error)
|
||||
{
|
||||
if (is.character(error))
|
||||
{
|
||||
flog.error(error)
|
||||
} else {
|
||||
flog.error(getMessage(error))
|
||||
}
|
||||
|
||||
throw(error)
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user