588 lines
16 KiB
Bash
588 lines
16 KiB
Bash
#!/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 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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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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generate_ssh_keys()
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{
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step "Generating SSH keys"
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try mkdir -p ssh
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try ssh-keygen -q -t rsa -b 4096 -f ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} -P "" -C "rscript@remote"
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try mv ${SSH_KEYS_DIR}/${SSH_KEY_PRIV}.pub ${SSH_KEYS_DIR}/${SSH_KEY_PUB}
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next
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check_if_command_error
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}
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install_env()
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{
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step "Installing environment"
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echo
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try apt-get update
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local DEBIAN_FRONTEND=noninteractive
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try apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew" upgrade
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try apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew" install ${DEBIAN_PACKAGES_TO_INSTALL}
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try apt-get clean
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next
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check_if_command_error
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}
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install_mro()
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{
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step "Installing Microsoft R Open"
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echo
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Rscript -e "invisible(TRUE)" &> /dev/null
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if [[ $? -ne 0 ]]; then
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try wget ${MRO_INSTALL_URL}/mro/${MRO_VERSION}/microsoft-r-open-${MRO_VERSION}.tar.gz
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try tar -xvf microsoft-r-open-${MRO_VERSION}.tar.gz
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try gdebi -n microsoft-r-open/deb/microsoft-r-open-mro-${MRO_VERSION:0:3}.deb
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try gdebi -n microsoft-r-open/deb/microsoft-r-open-foreachiterators-${MRO_VERSION:0:3}.deb
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try gdebi -n microsoft-r-open/deb/microsoft-r-open-mkl-${MRO_VERSION:0:3}.deb
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try R CMD javareconf
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rm -rf microsoft-r-open*
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else
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echo "Microsoft R Open already installed"
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fi
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try Rscript -e "install.packages('knitr')"
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try apt-get clean
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next
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check_if_command_error
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}
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install_r_libraries()
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{
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step "Installing R libraries"
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echo
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try mkdir -p ~/.checkpoint
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try Rscript init.R # run checkpoint
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next
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check_if_command_error
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}
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dump_project_r_files()
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{
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step "Making project R files dump"
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try tar -czf project-r-files.tar.gz *.R*
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next
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check_if_command_error
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}
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dump_r_libraries()
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{
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step "Making R libraries dump"
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wd=`pwd`
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cd ~/
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try tar -czf $wd/checkpoint.tar.gz .checkpoint/*
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cd $wd
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next
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check_if_command_error
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}
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hosts_push_ssh_key()
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{
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info "Pushing SSH keys to hosts"
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for host in "${HOSTS_ARRAY[@]}"; do
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step "-- ${host}"
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try sshpass -p ${SSHPASS_PWD} ssh ${SSH_OPTIONS} ${SSH_USER}@${host} 'mkdir -p ~/.ssh'
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try sshpass -p ${SSHPASS_PWD} scp ${SSH_OPTIONS} ${SSH_KEYS_DIR}/${SSH_KEY_PUB} ${SSH_USER}@${host}:~/.ssh
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try sshpass -p ${SSHPASS_PWD} ssh ${SSH_OPTIONS} ${SSH_USER}@${host} "cat ~/.ssh/${SSH_KEY_PUB} >> ~/.ssh/authorized_keys"
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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"
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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_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 $POWEROFF_TIME <<< poweroff &> /dev/null"
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next
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done
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check_if_command_error
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}
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hosts_scan_available()
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{
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HOSTS_SCANNED_ARRAY=()
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info "Scanning available hosts"
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for host in "${HOSTS_ARRAY[@]}"; do
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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"
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EXIT_CODE=$?
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if [[ $EXIT_CODE -ne 0 ]]; then
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fail "-- ${host}"
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else
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success "-- ${host}"
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HOSTS_SCANNED_ARRAY+=("$host")
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fi
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done
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HOSTS_ARRAY=("${HOSTS_SCANNED_ARRAY[@]}")
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if [[ ${#HOSTS_ARRAY[@]} -eq 0 ]]; then
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fail "No available hosts"
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exit 1
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else
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info "Available ${#HOSTS_ARRAY[@]} hosts"
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fi
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if [[ ${#HOSTS_ARRAY[@]} -lt $MIN_HOSTS ]]; then
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fail "Too few hosts: ${#HOSTS_ARRAY[@]} ; min.: $MIN_HOSTS"
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exit 1
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fi
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if [ -f ${HOSTS_SCANNED_FILE} ] ; then rm ${HOSTS_SCANNED_FILE}; fi
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for host in "${HOSTS_ARRAY[@]}"; do
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echo ${host} >> ${HOSTS_SCANNED_FILE}
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done
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}
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hosts_enable_swap()
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{
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info "Enabling swap on hosts"
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for host in "${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} "if [ \$(lvs | grep -P 'swap(.*)-wi--' | wc -l) -eq 1 ]; then vgchange -a y linux > /dev/null; fi ;swapon $SWAP_PART"
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next
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done
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check_if_command_error
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}
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hosts_disable_swap()
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{
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info "Disabling swap on hosts"
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for host in "${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} "swapoff -a"
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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_push_r_libraries_dump()
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{
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info "Pushing R libraries dump to hosts"
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for host in "${HOSTS_ARRAY[@]}"; do
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step "-- ${host}"
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try scp ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} checkpoint.tar.gz ${SSH_USER}@${host}:~/
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try ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "tar -xzf checkpoint.tar.gz -C ~/; rm checkpoint.tar.gz"
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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_push_project_r_files()
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{
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info "Pushing project R files to hosts"
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for host in "${HOSTS_ARRAY[@]}"; do
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step "-- ${host}"
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try scp ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} project-r-files.tar.gz ${SSH_USER}@${host}:~/
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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"
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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_push_shell_script()
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{
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info "Pushing shell script to hosts"
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for host in "${HOSTS_ARRAY[@]}"; do
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step "-- ${host}"
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try scp ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SHELL_SCRIPT} ${SSH_USER}@${host}:~/
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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_install()
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{
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case "$1" in
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"env") info "Installing environment on hosts" ;;
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"mro") info "Installing Microsoft R Open on hosts" ;;
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"r_libraries") info "Installing R libraries on hosts" ;;
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*) fail "Unknown remote install command"; report_error 1; check_if_command_error
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esac
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for host in "${HOSTS_ARRAY[@]}"; do
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info "-- Invoking ${host}"
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{ ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "bash ${SHELL_SCRIPT} install_$1 &> install_$1.log" ;
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endcode=$?
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if [ $endcode -eq 0 ] ; then
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success "-- ${host} finished"
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else
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fail "-- ${host} finished"
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report_error 1
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fi
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} &
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done
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last_workers=-1
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while true; do
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current_workers=$(jobs -rp | wc -l)
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if [ $current_workers -eq 0 ] ; then break; fi
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if (( $current_workers % 5 == 0)) && [ "$current_workers" -ne "$last_workers" ] ; then
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info "- Waiting for $current_workers hosts"
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last_workers=$current_workers
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fi
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sleep 1
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done
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check_if_command_error
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}
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hosts_install_env() { hosts_install env; }
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hosts_install_mro() { hosts_install mro; }
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hosts_install_r_libraries() { hosts_install r_libraries; }
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hosts_power_off()
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{
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info "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} "poweroff"
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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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make_remote_connection_list()
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{
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info "Making remote connection list:"
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if [ -f ${CONNECTION_LIST_FILE} ] ; then rm ${CONNECTION_LIST_FILE}; fi
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case "$1" in
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"single")
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step "one connection per host"
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for host in "${HOSTS_ARRAY[@]}"; do
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try echo ${host} >> ${CONNECTION_LIST_FILE}
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done
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next
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;;
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"nproc")
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info "'number of cores' per host"
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for host in "${HOSTS_ARRAY[@]}"; do
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step "-- ${host}"
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[[ $REMOTE_DETECT_LOGICAL_CPUS == "TRUE" ]] && cornum=`ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} 'lscpu | grep "^CPU(s):" | grep -o "[0-9]*"'` || cornum=`ssh ${SSH_OPTIONS} -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} 'A=\$(lscpu | grep "Socket(s):" | grep -o "[0-9]*"); B=\$(lscpu | grep "Core(s) per socket:" | grep -o "[0-9]*"); echo \$((A*B))'`
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regex='^[0-9]+$'
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if ! [[ $cornum =~ $regex ]] ; then
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try false
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else
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for ((i=1; i<=$cornum; i++)); do try echo ${host} >> ${CONNECTION_LIST_FILE}; done
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echo -n "($cornum cores) "
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fi
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next
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done
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;;
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*)
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fail "unknown type"
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report_error 1
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esac
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check_if_command_error
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}
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make_remote_connection_list_single() { make_remote_connection_list single; }
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make_remote_connection_list_nproc() { make_remote_connection_list nproc; }
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hosts_check_install_log()
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{
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info "Checking install log on hosts"
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for host in "${HOSTS_ARRAY[@]}"; do
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step "-- ${host}"
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echo
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try ssh ${SSH_OPTIONS/-q/} -o LogLevel=error -i ${SSH_KEYS_DIR}/${SSH_KEY_PRIV} ${SSH_USER}@${host} "cat install_$1.log"
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next
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done
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check_if_command_error
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}
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hosts_check_install_log_env() { hosts_check_install_log env; }
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hosts_check_install_log_mro() { hosts_check_install_log mro; }
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hosts_check_install_log_r_libraries() { hosts_check_install_log r_libraries; }
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hosts_check_worker_log()
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{
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info "Checking worker log on hosts"
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for host in "${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_check_worker_dmesg()
|
|
{
|
|
info "Checking dmesg 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} "dmesg -T | tail -n 20"
|
|
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 $errcode; }
|
|
}
|
|
|
|
my_configure_hosts()
|
|
{
|
|
hosts_scan_available
|
|
hosts_push_shell_script
|
|
dump_project_r_files
|
|
dump_r_libraries
|
|
hosts_push_project_r_files
|
|
hosts_install_env
|
|
hosts_install_mro
|
|
hosts_push_r_libraries_dump
|
|
make_remote_connection_list_nproc
|
|
}
|
|
|
|
configure_hosts()
|
|
{
|
|
generate_ssh_keys
|
|
hosts_push_ssh_key
|
|
hosts_change_password
|
|
hosts_push_shell_script
|
|
hosts_enable_swap
|
|
dump_project_r_files
|
|
dump_r_libraries
|
|
hosts_push_project_r_files
|
|
hosts_install_env
|
|
hosts_set_power_off
|
|
hosts_install_mro
|
|
hosts_push_r_libraries_dump
|
|
#hosts_install_r_libraries
|
|
make_remote_connection_list_nproc
|
|
#make_remote_connection_list_single
|
|
}
|
|
|
|
# check if new password is set
|
|
|
|
if [ "$NEW_PASS" == "" ]; then
|
|
warn "Empty new password"
|
|
fi
|
|
|
|
# read hosts from file or stdin
|
|
|
|
if [ -t 0 ]; then
|
|
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.$$
|