1974 lines
58 KiB
Bash
Executable File
1974 lines
58 KiB
Bash
Executable File
#!/usr/bin/env bash
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#
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# PPSS, the Parallel Processing Shell Script
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#
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# Copyright (c) 2010, Louwrentius
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# See <http://www.gnu.org/licenses/>
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# for a copy of the GNU General Public License
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#
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# "Patches or other contributions are always welcome!"
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#
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# Handling control-c for a clean shutdown.
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trap 'kill_process' SIGINT
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# Setting some vars.
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SCRIPT_NAME="Distributed Parallel Processing Shell Script"
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SCRIPT_VERSION="2.57b1"
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# The first argument to this script can be a mode.
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MODES="node start config stop pause continue deploy status erase kill ec2"
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for x in $MODES
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do
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if [ "$x" == "$1" ]
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then
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MODE="$1"
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shift
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fi
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done
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# The working directory of PPSS can be set with
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# export PPSS_DIR=/path/to/workingdir
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if [ -z "$PPSS_DIR" ]
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then
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PPSS_DIR="./ppss_dir"
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fi
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CONFIG=""
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HOSTNAME="`hostname`"
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ARCH="`uname`"
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PPSS_HOME_DIR="ppss-home"
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PID="$$"
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GLOBAL_LOCK="$PPSS_DIR/PPSS-GLOBAL-LOCK-$PID" # Global lock file used by local PPSS instance.
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PAUSE_SIGNAL="$PPSS_DIR/pause_signal" # Pause processing if this file is present.
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PAUSE_DELAY="60" # Polling every 1 minutes by default.
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STOP_SIGNAL="$PPSS_DIR/stop_signal" # Stop processing if this file is present.
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ARRAY_POINTER_FILE="$PPSS_DIR/ppss-array-pointer-$PID" # Pointer for keeping track of processed items.
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JOB_LOG_DIR="$PPSS_DIR/job_log" # Directory containing log files of processed items.
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LOGFILE="$PPSS_DIR/ppss-log-$PID.txt" # General PPSS log file. Contains lots of info.
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STOP="0" # STOP job.
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MAX_DELAY="0" # MAX DELAY between jobs.
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MAX_LOCK_DELAY="9" #
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PERCENT="0"
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LISTENER_PID=""
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IFS_BACKUP="$IFS"
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CPUINFO="/proc/cpuinfo"
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PROCESSORS=""
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STOP_KEY="$RANDOM$RANDOM$RANDOM" # This is a signal to the listener to stop.
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KILL_KEY="$RANDOM$RANDOM$RANDOM" # This is a signal to stop immediately and kill
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RECURSION="1" # all running processes.
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START_PPSS="$(date +%s)"
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STOP_PPSS=""
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SSH_SERVER="" # Remote server or 'master'.
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SSH_KEY="" # SSH key for ssh account.
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SSH_KNOWN_HOSTS=""
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SSH_SOCKET="/tmp/ppss_ssh_socket" # Multiplex multiple SSH connections over 1 master.
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SSH_OPTS="-o BatchMode=yes -o ControlPath=$SSH_SOCKET \
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-o GlobalKnownHostsFile=./known_hosts \
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-o ControlMaster=auto \
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-o Cipher=blowfish \
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-o ConnectTimeout=10 "
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SSH_OPTS_NOMP="-o BatchMode=yes -o GlobalKnownHostsFile=./known_hosts \
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-o Cipher=blowfish \
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-o ConnectTimeout=10 "
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# Blowfish is faster but still secure.
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SSH_MASTER_PID=""
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ITEM_LOCK_DIR="$PPSS_DIR/PPSS_ITEM_LOCK_DIR" # Remote directory on master used for item locking.
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PPSS_LOCAL_TMPDIR="$PPSS_DIR/PPSS_LOCAL_TMPDIR" # Local directory on slave for local processing.
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PPSS_LOCAL_OUTPUT="$PPSS_DIR/PPSS_LOCAL_OUTPUT" # Local directory on slave for local output.
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TRANSFER_TO_SLAVE="0" # Transfer item to slave via (s)cp.
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SECURE_COPY="1" # If set, use SCP, Otherwise, use cp.
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REMOTE_OUTPUT_DIR="" # Remote directory to which output must be uploaded.
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SCRIPT="" # Custom user script that is executed by ppss.
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ITEM_ESCAPED=""
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NODE_STATUS="$PPSS_DIR/status.txt"
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showusage_short () {
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echo
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echo "|P|P|S|S| $SCRIPT_NAME $SCRIPT_VERSION"
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echo
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echo "usage: $0 [ -d <sourcedir> | -f <sourcefile> ] [ -c '<command> \"\$ITEM\"' ]"
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echo " [ -C <configfile> ] [ -j ] [ -l <logfile> ] [ -p <# jobs> ]"
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echo " [ -D <delay> ] [ -h ] [ --help ] [ -r ] "
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echo
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echo "Examples:"
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echo " $0 -d /dir/with/some/files -c 'gzip '"
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echo " $0 -d /dir/with/some/files -c 'gzip \"\$ITEM\"' -D 5"
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echo " $0 -d /dir/with/some/files -c 'cp \"\$ITEM\" /tmp' -p 2"
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}
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showusage_normal () {
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echo
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echo "|P|P|S|S| $SCRIPT_NAME $SCRIPT_VERSION"
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echo
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echo "PPSS is a Bash shell script that executes commands in parallel on a set "
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echo "of items, such as files in a directory, or lines in a file."
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echo
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echo "This short summary only discusses options for stand-alone mode. for a "
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echo "complete listing of all options, run PPSS with the options --help"
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echo
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echo "Usage $0 [ options ]"
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echo
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echo -e "--command | -c Command to execute. Syntax: '<command> ' including the single quotes."
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echo -e " Example: -c 'ls -alh '. It is also possible to specify where an item "
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echo -e " must be inserted: 'cp \"\$ITEM\" /somedir'."
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echo
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echo -e "--sourcedir | -d Directory that contains files that must be processed. Individual files"
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echo -e " are fed as an argument to the command that has been specified with -c."
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echo
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echo -e "--sourcefile | -f Each single line of the supplied file will be fed as an item to the"
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echo -e " command that has been specified with -c."
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echo
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echo -e "--config | -C If the mode is config, a config file with the specified name will be"
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echo -e " generated based on all the options specified. In the other modes".
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echo -e " this option will result in PPSS reading the config file and start"
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echo -e " processing items based on the settings of this file."
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echo
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echo -e "--enable-ht | -j Enable hyperthreading. Is disabled by default."
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echo
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echo -e "--log | -l Sets the name of the log file. The default is ppss-log.txt."
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echo
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echo -e "--processes | -p Start the specified number of processes. Ignore the number of available"
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echo -e " CPUs."
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echo
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echo -e "--delay | -D Adds an initial random delay to the start of all parallel jobs to spread"
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echo -e " the load. The delay is only used at the start of all 'threads'."
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echo
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echo -e "--no-recurse | -r By default, recursion of directories is enabled when the -d option is "
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echo -e " used. If this is not prefered, this can be disabled with this option "
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echo -e " Only files within the specified directory will be processed."
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echo
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echo -e "Example: encoding some wav files to mp3 using lame:"
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echo
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echo -e "$0 -d /path/to/wavfiles -c 'lame '"
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echo
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echo -e "Extended usage: use --help"
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echo
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}
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if [ "$#" == "0" ]
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then
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showusage_short
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exit 1
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fi
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showusage_long () {
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echo
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echo "|P|P|S|S| $SCRIPT_NAME $SCRIPT_VERSION"
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echo
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echo "PPSS is a Bash shell script that executes commands in parallel on a set "
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echo "of items, such as files in a directory, or lines in a file."
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echo
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echo "Usage: $0 [ MODE ] [ options ]"
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echo
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echo "Modes are optional and mainly used for running in distributed mode. Modes are:"
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echo
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echo " config Generate a config file based on the supplied option parameters."
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echo " deploy Deploy PPSS and related files on the specified nodes."
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echo " erase Erase PPSS and related files from the specified nodes."
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echo
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echo " start Starting PPSS on nodes."
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echo " pause Pausing PPSS on all nodes."
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echo " stop Stopping PPSS on all nodes."
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echo " node Running PPSS as a node, requires additional options."
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echo
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echo "Options are:"
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echo
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echo -e "--command | -c Command to execute. Syntax: '<command> ' including the single quotes."
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echo -e " Example: -c 'ls -alh '. It is also possible to specify where an item "
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echo -e " must be inserted: 'cp \"\$ITEM\" /somedir'."
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echo
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echo -e "--sourcedir | -d Directory that contains files that must be processed. Individual files"
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echo -e " are fed as an argument to the command that has been specified with -c."
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echo
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echo -e "--sourcefile | -f Each single line of the supplied file will be fed as an item to the"
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echo -e " command that has been specified with -c."
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echo
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echo -e "--config | -C If the mode is config, a config file with the specified name will be"
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echo -e " generated based on all the options specified. In the other modes".
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echo -e " this option will result in PPSS reading the config file and start"
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echo -e " processing items based on the settings of this file."
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echo
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echo -e "--enable-ht | -j Enable hyperthreading. Is disabled by default."
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echo
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echo -e "--log | -l Sets the name of the log file. The default is ppss-log.txt."
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echo
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echo -e "--processes | -p Start the specified number of processes. Ignore the number of available"
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echo -e " CPUs."
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echo
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echo -e "--delay | -D Adds an initial random delay to the start of all parallel jobs to spread"
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echo -e " the load. The delay is only used at the start of all 'threads'."
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echo
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echo -e "--no-recurse | -r By default, recursion of directories is enabled when the -d option is "
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echo -e " used. If this is not prefered, this can be disabled with this option "
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echo -e " Only files within the specified directory will be processed."
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echo
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echo -e "The following options are used for distributed execution of PPSS."
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echo
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echo -e "--master | -m Specifies the SSH server that is used for communication between nodes."
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echo -e " Using SSH, file locks are created, informing other nodes that an item "
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echo -e " is locked. Also, often items, such as files, reside on this host. SCP "
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echo -e " is used to transfer files from this host to nodes for local procesing."
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echo
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echo -e "--node | -n File containig a list of nodes that act as PPSS clients. One IP / DNS "
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echo -e " name per line."
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echo
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echo -e "--key | -k The SSH key that a node uses to connect to the master."
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echo
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echo -e "--known-hosts | -K The file that contains the server public key. Can often be found on "
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echo -e " hosts that already once connected to the server. See the file "
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echo -e " ~/.ssh/known_hosts or else, manualy connect once and check this file."
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echo
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echo -e "--user | -u The SSH user name that is used when logging in into the master SSH"
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echo -e " server."
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echo
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echo -e "--script | -S Specifies the script/program that must be copied to the nodes for "
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echo -e " execution through PPSS. Only used in the deploy mode."
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echo -e " This option should be specified if necessary when generating a config."
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echo
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echo -e "--transfer | -t This option specifies that an item will be downloaded by the node "
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echo -e " from the server or share to the local node for processing."
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echo
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echo -e "--no-scp | -b Do not use scp for downloading items. Use cp instead. Assumes that a"
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echo -e " network file system (NFS/SMB) is mounted under a local mountpoint."
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echo
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echo -e "--outputdir | -o Directory on server where processed files are put. If the result of "
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echo -e " encoding a wav file is an mp3 file, the mp3 file is put in the "
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echo -e " directory specified with this option."
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echo
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echo -e "--homedir | -H Directory in which directory PPSS is installed on the node."
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echo -e " Default is 'ppss'."
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echo
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echo -e "Example: encoding some wav files to mp3 using lame:"
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echo
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echo -e "$0 -c 'lame ' -d /path/to/wavfiles -j "
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echo
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echo -e "Running PPSS based on a configuration file."
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echo
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echo -e "$0 -C config.cfg"
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echo
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echo -e "Running PPSS on a client as part of a cluster."
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echo
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echo -e "$0 -d /somedir -c 'cp "$ITEM" /some/destination' -s 10.0.0.50 -u ppss -t -k ppss-key.key"
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echo
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}
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kill_process () {
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echo "$KILL_KEY" >> "$FIFO"
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}
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exec_cmd () {
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STATUS="0"
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CMD="$1"
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NOMP="$2" # Disable multiplexing.
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if [ ! -z "$SSH_SERVER" ]
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then
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if [ -z "$NOMP" ]
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then
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log DEBUG "REMOTE EXEC"
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ssh $SSH_OPTS $SSH_KEY $USER@$SSH_SERVER $CMD
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STATUS=$?
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elif [ "$NOMP" == "1" ]
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then
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log DEBUG "REMOTE EXEC NO MP"
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ssh $SSH_OPTS_NOMP $SSH_KEY $USER@$SSH_SERVER $CMD
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STATUS=$?
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fi
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else
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log DEBUG "LOCAL EXEC"
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eval "$CMD"
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STATUS=$?
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fi
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return $STATUS
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}
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# this function makes remote or local checking of existence of items transparent.
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does_file_exist () {
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FILE="$1"
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`exec_cmd "ls -1 $FILE" >> /dev/null 2>&1`
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if [ "$?" == "0" ]
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then
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return 0
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else
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return 1
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fi
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}
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check_for_interrupt () {
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does_file_exist "$STOP_SIGNAL"
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if [ "$?" == "0" ]
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then
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set_status "STOPPED"
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log INFO "STOPPING job. Stop signal found."
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STOP="1"
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return 1
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fi
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does_file_exist "$PAUSE_SIGNAL"
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if [ "$?" == "0" ]
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then
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set_status "PAUZED"
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log INFO "PAUSE: sleeping for $PAUSE_DELAY SECONDS."
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sleep 0.$PAUSE_DELAY
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check_for_interrupt
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else
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set_status "RUNNING"
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fi
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}
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cleanup () {
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#log DEBUG "$FUNCNAME - Cleaning up all temp files and processes."
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if [ -e "$FIFO" ]
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then
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rm "$FIFO"
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fi
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if [ -e "$ARRAY_POINTER_FILE" ]
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then
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rm "$ARRAY_POINTER_FILE"
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fi
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if [ -e "$GLOBAL_LOCK" ]
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then
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rm -rf "$GLOBAL_LOCK"
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fi
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if [ -e "$SSH_SOCKET" ]
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then
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rm -rf "$SSH_SOCKET"
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fi
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}
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add_var_to_config () {
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if [ "$MODE" == "config" ]
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then
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VAR="$1"
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VALUE="$2"
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echo -e "$VAR=$VALUE" >> $CONFIG
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fi
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}
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# Process any command-line options that are specified."
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while [ $# -gt 0 ]
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do
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case $1 in
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--config|-C )
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CONFIG="$2"
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if [ "$MODE" == "config" ]
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then
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if [ -e "$CONFIG" ]
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then
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echo "Do want to overwrite existing config file? [y/n]"
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read yn
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if [ "$yn" == "y" ] || [ "$yn" == "yes" ]
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then
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rm "$CONFIG"
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else
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echo "Aborting..."
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cleanup
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exit
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fi
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fi
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fi
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if [ ! "$MODE" == "config" ]
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then
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source $CONFIG
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fi
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if [ ! -z "$SSH_KEY" ]
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then
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SSH_KEY="-i $SSH_KEY"
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fi
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if [ ! -e "./known_hosts" ]
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then
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if [ -e $SSH_KNOWN_HOSTS ]
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then
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if [ ! "$SSH_KNOWN_HOSTS" == "known_hosts" ]
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then
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cat $SSH_KNOWN_HOSTS > ./known_hosts
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fi
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else
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echo "File $SSH_KNOWN_HOSTS does not exist."
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exit
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fi
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fi
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shift 2
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;;
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--working-dir|-w )
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PPSS_DIR="$2"
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add_var_to_config PPSS_DIR "$PPSS_DIR"
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shift 2
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;;
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--node|-n )
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NODES_FILE="$2"
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add_var_to_config NODES_FILE "$NODES_FILE"
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shift 2
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;;
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--sourcefile|-f )
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INPUT_FILE="$2"
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add_var_to_config INPUT_FILE "$INPUT_FILE"
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shift 2
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;;
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--sourcedir|-d )
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SRC_DIR="$2"
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add_var_to_config SRC_DIR "$SRC_DIR"
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shift 2
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;;
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--delay|-D)
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MAX_DELAY="$2"
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add_var_to_config MAX_DELAY "$MAX_DELAY"
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shift 2
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;;
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--awskeypair|-P)
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AWS_KEYPAIR="$2"
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add_var_to_config AWS_KEYPAIR "$AWS_KEYPAIR"
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shift 2
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;;
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--AMI|-A)
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AMI_ID="$2"
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add_var_to_config AMI_ID "$AMI_ID"
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shift 2
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;;
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--type|-T)
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INSTANCE_TYPE="$2"
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add_var_to_config INSTANCE_TYPE "$INSTANCE_TYPE"
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shift 2
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;;
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--security|-G)
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SECURITY_GROUP="$2"
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add_var_to_config SECURITY_GROUP "$SECURITY_GROUP"
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shift 2
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;;
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--instances|-I)
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NUM_NODES="$2"
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add_var_to_config NUM_NODES "$NUM_NODES"
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shift 2
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;;
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--command|-c )
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COMMAND="$2"
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if [ "$MODE" == "config" ]
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then
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COMMAND=\'$COMMAND\'
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add_var_to_config COMMAND "$COMMAND"
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fi
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shift 2
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;;
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-h )
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showusage_normal
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exit 1;;
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--help)
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showusage_long
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exit 1;;
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--homedir|-H )
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if [ ! -z "$2" ]
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then
|
|
PPSS_HOME_DIR="$2"
|
|
add_var_to_config PPSS_DIR $PPSS_HOME_DIR
|
|
shift 2
|
|
fi
|
|
;;
|
|
|
|
--disable-ht|-j )
|
|
HYPERTHREADING=no
|
|
add_var_to_config HYPERTHREADING $HYPERTHREADING
|
|
shift 1
|
|
;;
|
|
--log|-l )
|
|
LOGFILE="$2"
|
|
add_var_to_config LOGFILE "$LOGFILE"
|
|
shift 2
|
|
;;
|
|
--no-recurse|-r )
|
|
RECURSION="0"
|
|
add_var_to_config LOGFILE "$RECURSION"
|
|
shift 1
|
|
;;
|
|
--workingdir|-w )
|
|
WORKINGDIR="$2"
|
|
add_var_to_config WORKINGDIR "$WORKINGDIR"
|
|
shift 2
|
|
;;
|
|
--key|-k )
|
|
SSH_KEY="$2"
|
|
add_var_to_config SSH_KEY "$SSH_KEY"
|
|
if [ ! -z "$SSH_KEY" ]
|
|
then
|
|
SSH_KEY="-i $SSH_KEY"
|
|
fi
|
|
shift 2
|
|
;;
|
|
--known-hosts | -K )
|
|
SSH_KNOWN_HOSTS="$2"
|
|
add_var_to_config SSH_KNOWN_HOSTS "$SSH_KNOWN_HOSTS"
|
|
shift 2
|
|
;;
|
|
|
|
--no-scp |-b )
|
|
SECURE_COPY=0
|
|
add_var_to_config SECURE_COPY "$SECURE_COPY"
|
|
shift 1
|
|
;;
|
|
--outputdir|-o )
|
|
REMOTE_OUTPUT_DIR="$2"
|
|
add_var_to_config REMOTE_OUTPUT_DIR "$REMOTE_OUTPUT_DIR"
|
|
shift 2
|
|
;;
|
|
--processes|-p )
|
|
TMP="$2"
|
|
if [ ! -z "$TMP" ]
|
|
then
|
|
MAX_NO_OF_RUNNING_JOBS="$TMP"
|
|
add_var_to_config MAX_NO_OF_RUNNING_JOBS "$MAX_NO_OF_RUNNING_JOBS"
|
|
shift 2
|
|
fi
|
|
;;
|
|
--master|-m )
|
|
SSH_SERVER="$2"
|
|
add_var_to_config SSH_SERVER "$SSH_SERVER"
|
|
shift 2
|
|
;;
|
|
--script|-S )
|
|
SCRIPT="$2"
|
|
add_var_to_config SCRIPT "$SCRIPT"
|
|
shift 2
|
|
;;
|
|
--transfer|-t )
|
|
TRANSFER_TO_SLAVE="1"
|
|
add_var_to_config TRANSFER_TO_SLAVE "$TRANSFER_TO_SLAVE"
|
|
shift 1
|
|
;;
|
|
--user|-u )
|
|
USER="$2"
|
|
add_var_to_config USER "$USER"
|
|
shift 2
|
|
;;
|
|
|
|
--version|-v )
|
|
echo ""
|
|
echo "$SCRIPT_NAME version $SCRIPT_VERSION"
|
|
echo ""
|
|
exit 0
|
|
;;
|
|
* )
|
|
|
|
showusage_short
|
|
echo
|
|
echo "Unknown option $1 "
|
|
echo
|
|
exit 1;;
|
|
esac
|
|
done
|
|
|
|
|
|
display_header () {
|
|
|
|
log DSPLY ""
|
|
log DSPLY "========================================================="
|
|
log DSPLY " |P|P|S|S| "
|
|
log DSPLY "$SCRIPT_NAME vers. $SCRIPT_VERSION"
|
|
log DSPLY "========================================================="
|
|
log DSPLY "Hostname:\t\t$HOSTNAME"
|
|
log DSPLY "---------------------------------------------------------"
|
|
}
|
|
|
|
create_working_directory () {
|
|
|
|
if [ ! -e "$PPSS_DIR" ]
|
|
then
|
|
mkdir -p "$PPSS_DIR"
|
|
fi
|
|
}
|
|
|
|
# Init all vars
|
|
init_vars () {
|
|
|
|
create_working_directory
|
|
|
|
if [ "$ARCH" == "Darwin" ]
|
|
then
|
|
MIN_JOBS=4
|
|
elif [ "$ARCH" == "Linux" ]
|
|
then
|
|
MIN_JOBS=3
|
|
fi
|
|
|
|
if [ -e "$LOGFILE" ]
|
|
then
|
|
rm $LOGFILE
|
|
fi
|
|
|
|
display_header
|
|
|
|
if [ -z "$COMMAND" ]
|
|
then
|
|
echo
|
|
log ERROR "No command specified."
|
|
echo
|
|
showusage_normal
|
|
cleanup
|
|
exit 1
|
|
fi
|
|
|
|
echo 0 > $ARRAY_POINTER_FILE
|
|
|
|
FIFO=/tmp/ppss-fifo-$RANDOM-$RANDOM
|
|
|
|
if [ ! -e "$FIFO" ]
|
|
then
|
|
mkfifo -m 600 $FIFO
|
|
fi
|
|
|
|
exec 42<> $FIFO
|
|
|
|
set_status "RUNNING"
|
|
|
|
if [ -e "$CPUINFO" ]
|
|
then
|
|
CPU=`cat /proc/cpuinfo | grep 'model name' | cut -d ":" -f 2 | sed -e s/^\ //g | sort | uniq`
|
|
log DSPLY "CPU: $CPU"
|
|
elif [ "$ARCH" == "Darwin" ]
|
|
then
|
|
MODEL=`system_profiler SPHardwareDataType | grep "Processor Name" | cut -d ":" -f 2`
|
|
SPEED=`system_profiler SPHardwareDataType | grep "Processor Speed" | cut -d ":" -f 2`
|
|
log DSPLY "CPU: $MODEL $SPEED"
|
|
elif [ "$ARCH" == "SunOS" ]
|
|
then
|
|
CPU=`psrinfo -v | grep MHz | cut -d " " -f 4,8 | awk '{ printf ("Processor architecture: %s @ %s MHz.\n", $1,$2) }' | head -n 1`
|
|
|
|
log DSPLY "$CPU"
|
|
else
|
|
log DSPLY "CPU: Cannot determine. Provide a patch for your arch!"
|
|
log DSPLY "Arch is $ARCH"
|
|
fi
|
|
|
|
if [ -z "$MAX_NO_OF_RUNNING_JOBS" ]
|
|
then
|
|
get_no_of_cpus $HYPERTHREADING
|
|
fi
|
|
|
|
does_file_exist "$JOB_LOG_DIR"
|
|
if [ ! "$?" == "0" ]
|
|
then
|
|
log DEBUG "Job log directory $JOB_lOG_DIR does not exist. Creating."
|
|
exec_cmd "mkdir -p $JOB_LOG_DIR"
|
|
else
|
|
log DEBUG "Job log directory $JOB_LOG_DIR exists."
|
|
fi
|
|
|
|
does_file_exist "$ITEM_LOCK_DIR"
|
|
if [ ! "$?" == "0" ] && [ ! -z "$SSH_SERVER" ]
|
|
then
|
|
log DEBUG "Creating remote item lock dir."
|
|
exec_cmd "mkdir $ITEM_LOCK_DIR"
|
|
fi
|
|
|
|
if [ ! -e "$JOB_LOG_DIR" ]
|
|
then
|
|
mkdir -p "$JOB_LOG_DIR"
|
|
fi
|
|
|
|
does_file_exist "$REMOTE_OUTPUT_DIR"
|
|
if [ ! "$?" == "0" ]
|
|
then
|
|
log DEBUG "Remote output dir $REMOTE_OUTPUT_DIR does not exist."
|
|
exec_cmd "mkdir $REMOTE_OUTPUT_DIR"
|
|
fi
|
|
|
|
if [ ! -e "$PPSS_LOCAL_TMPDIR" ]
|
|
then
|
|
mkdir "$PPSS_LOCAL_TMPDIR"
|
|
fi
|
|
|
|
if [ ! -e "$PPSS_LOCAL_OUTPUT" ]
|
|
then
|
|
mkdir "$PPSS_LOCAL_OUTPUT"
|
|
fi
|
|
}
|
|
|
|
get_status () {
|
|
|
|
STATUS=`cat "$NODE_SATUS"`
|
|
echo "$STATUS"
|
|
}
|
|
|
|
set_status () {
|
|
|
|
STATUS="$1"
|
|
echo "$HOSTNAME $STATUS" > "$NODE_STATUS"
|
|
}
|
|
|
|
|
|
expand_str () {
|
|
|
|
STR=$1
|
|
LENGTH=$TYPE_LENGTH
|
|
SPACE=" "
|
|
|
|
while [ "${#STR}" -lt "$LENGTH" ]
|
|
do
|
|
STR=$STR$SPACE
|
|
done
|
|
|
|
echo "$STR"
|
|
}
|
|
|
|
log () {
|
|
|
|
# Type 'INFO' is logged to the screen
|
|
# Any other log-type is only logged to the logfile.
|
|
|
|
TYPE="$1"
|
|
MESG="$2"
|
|
TYPE_LENGTH=5
|
|
|
|
TYPE_EXP=`expand_str "$TYPE"`
|
|
|
|
DATE=`date +%b\ %d\ %H:%M:%S`
|
|
PREFIX="$DATE: ${TYPE_EXP:0:$TYPE_LENGTH}"
|
|
PREFIX_SMALL="$DATE: "
|
|
|
|
LOG_MSG="$PREFIX $MESG"
|
|
ECHO_MSG="$PREFIX_SMALL $MESG"
|
|
|
|
if [ ! -z "$PPSSDEBUG" ] && [ ! "$PPSSDEBUG" == "0" ]
|
|
then
|
|
echo -e "$LOG_MSG" >> "$LOGFILE"
|
|
|
|
elif [ "$TYPE" == "INFO" ] || [ "$TYPE" == "ERROR" ] || [ "$TYPE" == "WARN" ] || [ "$TYPE" == "DSPLY" ]
|
|
then
|
|
echo -e "$LOG_MSG" >> "$LOGFILE"
|
|
fi
|
|
|
|
if [ "$TYPE" == "DSPLY" ] || [ "$TYPE" == "ERROR" ] || [ "$TYPE" == "WARN" ]
|
|
then
|
|
echo -e "$ECHO_MSG"
|
|
fi
|
|
|
|
}
|
|
|
|
check_status () {
|
|
|
|
ERROR="$1"
|
|
FUNCTION="$2"
|
|
MESSAGE="$3"
|
|
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
log INFO "$FUNCTION - $MESSAGE"
|
|
set_status STOPPED
|
|
cleanup
|
|
exit 1
|
|
fi
|
|
|
|
}
|
|
|
|
erase_ppss () {
|
|
|
|
|
|
echo "Are you realy sure you want to erase PPSS from all nodes!? (YES/NO)"
|
|
read YN
|
|
|
|
if [ "$YN" == "yes" ] || [ "$YN" == "YES" ]
|
|
then
|
|
for NODE in `cat $NODES_FILE`
|
|
do
|
|
log INFO "Erasing PPSS homedir $PPSS_DIR from node $NODE."
|
|
ssh -q $SSH_KEY $SSH_OPTS $USER@$NODE "rm -rf $PPSS_HOME_DIR"
|
|
done
|
|
else
|
|
log DSPLY "Aborting.."
|
|
fi
|
|
sleep 1
|
|
}
|
|
|
|
ec2_get_pending_nodes() {
|
|
|
|
RES="$(ec2-describe-instances | grep 'INSTANCE' | awk '{print $4}'| grep pending)"
|
|
echo "$RES"
|
|
}
|
|
|
|
ec2_launch_nodes() {
|
|
|
|
ec2run $AMI_ID -n $NUM_NODES -t $INSTANCE_TYPE -k $AWS_KEYPAIR -g $SECURITY_GROUP
|
|
|
|
#
|
|
# Loop until all nodes are started
|
|
#
|
|
STARTING="`ec2_get_pending_nodes`"
|
|
while [ ! -z "$STARTING" ]
|
|
do
|
|
sleep 10
|
|
STARTING="`ec2_get_pending_nodes`"
|
|
log DSPLY "$STARTING"
|
|
done
|
|
#
|
|
# Write all instances / nodes to the nodes file.
|
|
#
|
|
ec2-describe-instances | grep 'INSTANCE' | awk '{print $4}' | sed '/terminated/d' | sed '/pending/d' >> $NODES_FILE
|
|
NO_OF_NODES="`wc -l $NODES_FILE`"
|
|
log DSPLY "Number of nodes / instances: $NO_OF_NODES"
|
|
}
|
|
|
|
deploy () {
|
|
|
|
NODE="$1"
|
|
|
|
SSH_OPTS_NODE="-o BatchMode=yes -o ControlPath=socket-%h \
|
|
-o GlobalKnownHostsFile=./known_hosts \
|
|
-o ControlMaster=auto \
|
|
-o Cipher=blowfish \
|
|
-o ConnectTimeout=5 "
|
|
|
|
ERROR=0
|
|
set_error () {
|
|
|
|
if [ ! "$1" == "0" ]
|
|
then
|
|
ERROR=1
|
|
fi
|
|
}
|
|
|
|
ssh -q -o ConnectTimeout=5 $SSH_KEY $USER@$NODE exit 0
|
|
set_error "$?"
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
log ERROR "Cannot connect to node $NODE."
|
|
return
|
|
fi
|
|
|
|
ssh -N -M $SSH_OPTS_NODE $SSH_KEY $USER@$NODE &
|
|
SSH_PID=$!
|
|
|
|
KEY=`echo $SSH_KEY | cut -d " " -f 2`
|
|
|
|
sleep 1
|
|
|
|
ssh -q $SSH_OPTS_NODE $SSH_KEY $USER@$NODE "cd ~ && mkdir $PPSS_HOME_DIR >> /dev/null 2>&1"
|
|
scp -q $SSH_OPTS_NODE $SSH_KEY $0 $USER@$NODE:~/$PPSS_HOME_DIR
|
|
set_error $?
|
|
scp -q $SSH_OPTS_NODE $SSH_KEY $KEY $USER@$NODE:~/$PPSS_HOME_DIR
|
|
set_error $?
|
|
scp -q $SSH_OPTS_NODE $SSH_KEY $CONFIG $USER@$NODE:~/$PPSS_HOME_DIR
|
|
set_error $?
|
|
scp -q $SSH_OPTS_NODE $SSH_KEY known_hosts $USER@$NODE:~/$PPSS_HOME_DIR
|
|
set_error $?
|
|
if [ ! -z "$SCRIPT" ]
|
|
then
|
|
scp -q $SSH_OPTS_NODE $SSH_KEY $SCRIPT $USER@$NODE:~/$PPSS_HOME_DIR
|
|
set_error $?
|
|
fi
|
|
|
|
if [ ! -z "$INPUT_FILE" ]
|
|
then
|
|
scp -q $SSH_OPTS_NODE $SSH_KEY $INPUT_FILE $USER@$NODE:~/$PPSS_HOME_DIR
|
|
set_error $?
|
|
fi
|
|
|
|
if [ "$ERROR" == "0" ]
|
|
then
|
|
log DSPLY "PPSS installed on node $NODE."
|
|
else
|
|
log DSPLY "PPSS failed to install on $NODE."
|
|
fi
|
|
|
|
kill $SSH_PID
|
|
}
|
|
|
|
deploy_ppss () {
|
|
|
|
|
|
if [ -z "$NODES_FILE" ]
|
|
then
|
|
log ERROR "ERROR - are you using the right option? -C ?"
|
|
set_status ERROR
|
|
cleanup
|
|
exit 1
|
|
fi
|
|
|
|
KEY=`echo $SSH_KEY | cut -d " " -f 2`
|
|
if [ -z "$KEY" ] || [ ! -e "$KEY" ]
|
|
then
|
|
log ERROR "Nodes require a key file."
|
|
cleanup
|
|
set_status "ERROR"
|
|
exit 1
|
|
fi
|
|
|
|
if [ ! -e "$SCRIPT" ] && [ ! -z "$SCRIPT" ]
|
|
then
|
|
log ERROR "Script $SCRIPT not found."
|
|
set_status "ERROR"
|
|
cleanup
|
|
exit 1
|
|
fi
|
|
|
|
INSTALLED_ON_SSH_SERVER=0
|
|
if [ ! -e "$NODES_FILE" ]
|
|
then
|
|
log ERROR "File $NODES with list of nodes does not exist."
|
|
set_status ERROR
|
|
cleanup
|
|
exit 1
|
|
else
|
|
if [ -z "$EC2" ]
|
|
then
|
|
ec2_launch_nodes
|
|
fi
|
|
for NODE in `cat $NODES_FILE`
|
|
do
|
|
deploy "$NODE" &
|
|
sleep 0.1
|
|
if [ "$NODE" == "$SSH_SERVER" ]
|
|
then
|
|
log DEBUG "SSH SERVER $SSH_SERVER is also a node."
|
|
INSTALLED_ON_SSH_SERVER=1
|
|
exec_cmd "mkdir -p $PPSS_HOME_DIR/$JOB_LOG_DIR"
|
|
exec_cmd "mkdir -p $ITEM_LOCK_DIR"
|
|
fi
|
|
done
|
|
if [ "$INSTALLED_ON_SSH_SERVER" == "0" ]
|
|
then
|
|
log DEBUG "SSH SERVER $SSH_SERVER is not a node."
|
|
deploy "$SSH_SERVER"
|
|
exec_cmd "mkdir -p $PPSS_HOME_DIR/$JOB_LOG_DIR"
|
|
exec_cmd "mkdir -p $ITEM_LOCK_DIR"
|
|
fi
|
|
fi
|
|
}
|
|
|
|
start_ppss_on_node () {
|
|
|
|
NODE="$1"
|
|
log DSPLY "Starting PPSS on node $NODE."
|
|
ssh $SSH_KEY $USER@$NODE -o ConnectTimeout=5 "cd $PPSS_HOME_DIR ; screen -d -m -S PPSS ~/$PPSS_HOME_DIR/$0 node --config ~/$PPSS_HOME_DIR/$CONFIG"
|
|
}
|
|
|
|
test_server () {
|
|
|
|
# Testing if the remote server works as expected.
|
|
if [ ! -z "$SSH_SERVER" ]
|
|
then
|
|
exec_cmd "date >> /dev/null"
|
|
check_status "$?" "$FUNCNAME" "Server $SSH_SERVER could not be reached"
|
|
|
|
ssh -N -M $SSH_OPTS $SSH_KEY $USER@$SSH_SERVER &
|
|
SSH_MASTER_PID="$!"
|
|
log DEBUG "SSH Master pid is $SSH_MASTER_PID"
|
|
else
|
|
log DEBUG "No remote server specified, assuming stand-alone mode."
|
|
fi
|
|
}
|
|
|
|
get_no_of_cpus () {
|
|
|
|
# Use hyperthreading or not?
|
|
HPT=$1
|
|
NUMBER=""
|
|
|
|
if [ -z "$HPT" ]
|
|
then
|
|
HPT=yes
|
|
fi
|
|
|
|
got_cpu_info () {
|
|
|
|
ERROR="$1"
|
|
check_status "$ERROR" "$FUNCNAME" "cannot determine number of cpu cores. Specify with -p."
|
|
|
|
}
|
|
|
|
if [ "$HPT" == "yes" ]
|
|
then
|
|
if [ "$ARCH" == "Linux" ]
|
|
then
|
|
NUMBER=`grep ^processor $CPUINFO | wc -l`
|
|
got_cpu_info "$?"
|
|
|
|
elif [ "$ARCH" == "Darwin" ]
|
|
then
|
|
NUMBER=`sysctl -a hw | grep -w logicalcpu | awk '{ print $2 }'`
|
|
got_cpu_info "$?"
|
|
|
|
elif [ "$ARCH" == "FreeBSD" ]
|
|
then
|
|
NUMBER=`sysctl hw.ncpu | awk '{ print $2 }'`
|
|
got_cpu_info "$?"
|
|
|
|
elif [ "$ARCH" == "SunOS" ]
|
|
then
|
|
NUMBER=`psrinfo | grep on-line | wc -l`
|
|
got_cpu_info "$?"
|
|
else
|
|
if [ -e "$CPUINFO" ]
|
|
then
|
|
NUMBER=`grep ^processor $CPUINFO | wc -l`
|
|
got_cpu_info "$?"
|
|
fi
|
|
fi
|
|
|
|
if [ ! -z "$NUMBER" ]
|
|
then
|
|
log DSPLY "Found $NUMBER logic processors."
|
|
fi
|
|
|
|
elif [ "$HPT" == "no" ]
|
|
then
|
|
log DSPLY "Hyperthreading is disabled."
|
|
|
|
if [ "$ARCH" == "Linux" ]
|
|
then
|
|
PHYSICAL=`grep 'physical id' $CPUINFO`
|
|
if [ "$?" == "0" ]
|
|
then
|
|
PHYSICAL=`grep 'physical id' $CPUINFO | sort | uniq | wc -l`
|
|
if [ "$PHYSICAL" == "1" ]
|
|
then
|
|
log DSPLY "Found $PHYSICAL physical CPU."
|
|
else
|
|
log DSPLY "Found $PHYSICAL physical CPUs."
|
|
fi
|
|
|
|
TMP=`grep 'core id' $CPUINFO`
|
|
if [ "$?" == "0" ]
|
|
then
|
|
log DEBUG "Starting job only for each physical core on all physical CPU(s)."
|
|
NUMBER=`grep 'core id' $CPUINFO | sort | uniq | wc -l`
|
|
log DSPLY "Found $NUMBER physical cores."
|
|
else
|
|
log DSPLY "Single core processor(s) detected."
|
|
log DSPLY "Starting job for each physical CPU."
|
|
NUMBER=$PHYSICAL
|
|
fi
|
|
else
|
|
log INFO "No 'physical id' section found in $CPUINFO, typical for older cpus."
|
|
NUMBER=`grep ^processor $CPUINFO | wc -l`
|
|
got_cpu_info "$?"
|
|
fi
|
|
elif [ "$ARCH" == "Darwin" ]
|
|
then
|
|
NUMBER=`sysctl -a hw | grep -w physicalcpu | awk '{ print $2 }'`
|
|
got_cpu_info "$?"
|
|
elif [ "$ARCH" == "FreeBSD" ]
|
|
then
|
|
NUMBER=`sysctl hw.ncpu | awk '{ print $2 }'`
|
|
got_cpu_info "$?"
|
|
else
|
|
NUMBER=`cat $CPUINFO | grep "cpu cores" | cut -d ":" -f 2 | uniq | sed -e s/\ //g`
|
|
got_cpu_info "$?"
|
|
fi
|
|
|
|
fi
|
|
|
|
if [ ! -z "$NUMBER" ]
|
|
then
|
|
MAX_NO_OF_RUNNING_JOBS=$NUMBER
|
|
else
|
|
log ERROR "Number of CPUs not obtained."
|
|
log ERROR "Please specify manually with -p."
|
|
set_status "ERROR"
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
random_delay () {
|
|
|
|
ARGS="$1"
|
|
|
|
if [ -z "$ARGS" ]
|
|
then
|
|
log ERROR "$FUNCNAME Function random delay, no argument specified."
|
|
set_status ERROR
|
|
exit 1
|
|
fi
|
|
|
|
NUMBER=$RANDOM
|
|
let "NUMBER %= $ARGS"
|
|
sleep "0.$NUMBER"
|
|
}
|
|
|
|
|
|
global_lock () {
|
|
|
|
mkdir $GLOBAL_LOCK > /dev/null 2>&1
|
|
ERROR="$?"
|
|
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
return 1
|
|
else
|
|
return 0
|
|
fi
|
|
}
|
|
|
|
get_global_lock () {
|
|
|
|
while true
|
|
do
|
|
global_lock
|
|
ERROR="$?"
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
random_delay $MAX_LOCK_DELAY
|
|
continue
|
|
else
|
|
break
|
|
fi
|
|
done
|
|
}
|
|
|
|
release_global_lock () {
|
|
|
|
rm -rf "$GLOBAL_LOCK"
|
|
}
|
|
|
|
are_jobs_running () {
|
|
|
|
NUMBER_OF_PROCS=`jobs | wc -l`
|
|
if [ "$NUMBER_OF_PROCS" -gt "1" ]
|
|
then
|
|
return 0
|
|
else
|
|
return 1
|
|
fi
|
|
}
|
|
|
|
escape_item () {
|
|
|
|
TMP="$1"
|
|
|
|
ITEM_ESCAPED=`echo "$TMP" | \
|
|
sed s/\\ /\\\\\\\\\\\\\\ /g | \
|
|
sed s/\\'/\\\\\\\\\\\\\\'/g | \
|
|
sed s/\\\`/\\\\\\\\\\\\\\\`/g | \
|
|
sed s/\\|/\\\\\\\\\\\\\\|/g | \
|
|
sed s/\&/\\\\\\\\\\\\\\&/g | \
|
|
sed s/\;/\\\\\\\\\\\\\\;/g | \
|
|
sed s/\\\//\\\\\\\\\\\\\\ /g | \
|
|
sed s/\(/\\\\\\\\\\(/g | \
|
|
sed s/\)/\\\\\\\\\\)/g `
|
|
}
|
|
|
|
download_item () {
|
|
|
|
ITEM="$1"
|
|
if [ -e "$ITEM" ]
|
|
then
|
|
ITEM_NO_PATH=`basename "$ITEM"`
|
|
else
|
|
escape_item "$ITEM"
|
|
ITEM_NO_PATH="$ITEM_ESCAPED"
|
|
fi
|
|
|
|
if [ "$TRANSFER_TO_SLAVE" == "1" ]
|
|
then
|
|
log DEBUG "Transfering item $ITEM_NO_PATH from source to local disk."
|
|
if [ "$SECURE_COPY" == "1" ] && [ ! -z "$SSH_SERVER" ]
|
|
then
|
|
if [ ! -z "$SRC_DIR" ]
|
|
then
|
|
ITEM_PATH="$SRC_DIR/$ITEM"
|
|
else
|
|
ITEM_PATH="$ITEM"
|
|
fi
|
|
|
|
escape_item "$ITEM_PATH"
|
|
|
|
scp -q $SSH_OPTS $SSH_KEY $USER@$SSH_SERVER:"$ITEM_ESCAPED" ./$PPSS_LOCAL_TMPDIR
|
|
log DEBUG "Exit code of remote transfer is $?"
|
|
else
|
|
cp "$ITEM" ./$PPSS_LOCAL_TMPDIR
|
|
log DEBUG "Exit code of local transfer is $?"
|
|
fi
|
|
else
|
|
log DEBUG "No transfer of item $ITEM_NO_PATH to local workpath."
|
|
fi
|
|
}
|
|
|
|
upload_item () {
|
|
|
|
|
|
ITEM="$1"
|
|
ITEMDIR="$2"
|
|
|
|
|
|
log DEBUG "Uploading item $ITEM."
|
|
if [ "$SECURE_COPY" == "1" ]
|
|
then
|
|
escape_item "$REMOTE_OUTPUT_DIR$ITEMDIR"
|
|
DIR_ESCAPED="$ITEM_ESCAPED"
|
|
|
|
scp -q $SSH_OPTS $SSH_KEY "$ITEM"/* $USER@$SSH_SERVER:"$DIR_ESCAPED"
|
|
ERROR="$?"
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
log ERROR "Uploading of $ITEM via SCP failed."
|
|
else
|
|
log DEBUG "Upload of item $ITEM success"
|
|
rm -rf ./"$ITEM"
|
|
fi
|
|
else
|
|
cp "$ITEM" "$REMOTE_OUTPUT_DIR"
|
|
ERROR="$?"
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
log DEBUG "ERROR - uploading of $ITEM vi CP failed."
|
|
fi
|
|
fi
|
|
}
|
|
|
|
lock_item () {
|
|
|
|
if [ ! -z "$SSH_SERVER" ]
|
|
then
|
|
ITEM="$1"
|
|
|
|
LOCK_FILE_NAME=`echo "$ITEM" | \
|
|
sed s/^\\\.//g | \
|
|
sed s/^\\\.\\\.//g | \
|
|
sed s/^\\\///g | \
|
|
sed s/\\\//\\\\\\ /g | \
|
|
sed s/\\ /\\\\\\\\\\\\\\ /g | \
|
|
sed s/\\'/\\\\\\\\\\\\\\'/g | \
|
|
sed s/\\\//\\\\\\\\\\\\\\ /g | \
|
|
sed s/\&/\\\\\\\\\\\\\\&/g | \
|
|
sed s/\;/\\\\\\\\\\\\\\;/g | \
|
|
sed s/\(/\\\\\\\\\\(/g | \
|
|
sed s/\)/\\\\\\\\\\)/g `
|
|
|
|
ITEM_LOCK_FILE="$ITEM_LOCK_DIR/$LOCK_FILE_NAME"
|
|
log DEBUG "Trying to lock item $ITEM - $ITEM_LOCK_FILE."
|
|
exec_cmd "mkdir $ITEM_LOCK_FILE >> /dev/null 2>&1"
|
|
ERROR="$?"
|
|
|
|
if [ "$ERROR" == "$?" ]
|
|
then
|
|
exec_cmd "touch $ITEM_LOCK_FILE/$HOSTNAME" # Record that item is claimed by node x.
|
|
fi
|
|
|
|
return "$ERROR"
|
|
fi
|
|
}
|
|
|
|
get_all_items () {
|
|
|
|
count=0
|
|
|
|
if [ -z "$INPUT_FILE" ]
|
|
then
|
|
if [ ! -z "$SSH_SERVER" ] # Are we running stand-alone or as a slave?"
|
|
then
|
|
if [ "$RECURSION" == "1" ]
|
|
then
|
|
ITEMS=`exec_cmd "find $SRC_DIR ! -type d"`
|
|
check_status "$?" "$FUNCNAME" "Could not list files within remote source directory."
|
|
else
|
|
log DEBUG "Recursion is disabled."
|
|
ITEMS=`exec_cmd "ls -1 $SRC_DIR"`
|
|
check_status "$?" "$FUNCNAME" "Could not list files within remote source directory."
|
|
fi
|
|
else
|
|
if [ -e "$SRC_DIR" ]
|
|
then
|
|
if [ "$RECURSION" == "1" ]
|
|
then
|
|
ITEMS=`find "$SRC_DIR" ! -type d`
|
|
else
|
|
log DEBUG "Recursion is disabled."
|
|
ITEMS=`ls -1 "$SRC_DIR"`
|
|
fi
|
|
else
|
|
ITEMS=""
|
|
fi
|
|
fi
|
|
IFS=$'\n'
|
|
|
|
for x in $ITEMS
|
|
do
|
|
ARRAY[$count]="$x"
|
|
((count++))
|
|
done
|
|
IFS=$IFS_BACKUP
|
|
else
|
|
if [ ! -z "$SSH_SERVER" ] # Are we running stand-alone or as a slave?"
|
|
then
|
|
log DEBUG "Running as slave, input file has been pushed (hopefully)."
|
|
fi
|
|
if [ ! -e "$INPUT_FILE" ]
|
|
then
|
|
log ERROR "Input file $INPUT_FILE does not exist."
|
|
set_status "ERROR"
|
|
cleanup
|
|
exit 1
|
|
fi
|
|
|
|
exec 10<"$INPUT_FILE"
|
|
|
|
while read LINE <&10
|
|
do
|
|
ARRAY[$count]=$LINE
|
|
((count++))
|
|
done
|
|
|
|
exec 10>&-
|
|
|
|
fi
|
|
|
|
SIZE_OF_ARRAY="${#ARRAY[@]}"
|
|
if [ "$SIZE_OF_ARRAY" -le "0" ]
|
|
then
|
|
log ERROR "Source file/dir seems to be empty."
|
|
set_status STOPPED
|
|
cleanup
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
get_item () {
|
|
|
|
check_for_interrupt
|
|
|
|
if [ "$STOP" == "1" ]
|
|
then
|
|
return 1
|
|
fi
|
|
|
|
get_global_lock
|
|
|
|
SIZE_OF_ARRAY="${#ARRAY[@]}"
|
|
|
|
# Return error if the array is empty.
|
|
if [ "$SIZE_OF_ARRAY" -le "0" ]
|
|
then
|
|
release_global_lock
|
|
return 1
|
|
fi
|
|
|
|
# This variable is used to walk thtough all array items.
|
|
ARRAY_POINTER=`cat $ARRAY_POINTER_FILE`
|
|
|
|
# Check if all items have been processed.
|
|
if [ "$ARRAY_POINTER" -ge "$SIZE_OF_ARRAY" ]
|
|
then
|
|
release_global_lock
|
|
#echo -en "\033[1A"
|
|
return 1
|
|
fi
|
|
|
|
# Select an item.
|
|
ITEM="${ARRAY[$ARRAY_POINTER]}"
|
|
if [ -z "$ITEM" ]
|
|
then
|
|
((ARRAY_POINTER++))
|
|
echo $ARRAY_POINTER > $ARRAY_POINTER_FILE
|
|
release_global_lock
|
|
get_item
|
|
else
|
|
((ARRAY_POINTER++))
|
|
echo $ARRAY_POINTER > $ARRAY_POINTER_FILE
|
|
lock_item "$ITEM"
|
|
if [ ! "$?" == "0" ]
|
|
then
|
|
log DEBUG "Item $ITEM is locked."
|
|
release_global_lock
|
|
get_item
|
|
else
|
|
log DEBUG "Got lock on $ITEM, processing."
|
|
release_global_lock
|
|
download_item "$ITEM"
|
|
return 0
|
|
fi
|
|
fi
|
|
}
|
|
|
|
start_single_worker () {
|
|
|
|
#
|
|
# This function sends an item to the fifo. This signals
|
|
# the listener process to execute a 'worker' on this
|
|
# item, using the 'commando' function.
|
|
#
|
|
|
|
get_item
|
|
ERROR=$?
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
#
|
|
# If no more items are available, the listener should be
|
|
# informed that a worker just finished / died.
|
|
# This allows the listener to determine if all processes
|
|
# are finished and it is time to stop.
|
|
#
|
|
echo "$STOP_KEY" > $FIFO
|
|
return 1
|
|
else
|
|
get_global_lock
|
|
echo "$ITEM" > $FIFO
|
|
release_global_lock
|
|
return 0
|
|
fi
|
|
}
|
|
|
|
stop-ppss () {
|
|
|
|
STOP_PPSS="$(date +%s)"
|
|
elapsed "$START_PPSS" "$STOP_PPSS"
|
|
}
|
|
|
|
|
|
elapsed () {
|
|
|
|
BEFORE="$1"
|
|
AFTER="$2"
|
|
|
|
ELAPSED="$(expr $AFTER - $BEFORE)"
|
|
|
|
REMAINDER="$(expr $ELAPSED % 3600)"
|
|
HOURS="$(expr $(expr $ELAPSED - $REMAINDER) / 3600)"
|
|
|
|
SECS="$(expr $REMAINDER % 60)"
|
|
MINS="$(expr $(expr $REMAINDER - $SECS) / 60)"
|
|
|
|
RES=`printf 'Total processing time: %02d:%02d:%02d' $HOURS $MINS $SECS`
|
|
log DSPLY "$RES"
|
|
}
|
|
|
|
commando () {
|
|
|
|
#
|
|
# This function will start a chain reaction of events.
|
|
#
|
|
# The commando executes a command on an item and, when finished,
|
|
# executes the start_single_worker. This function selects a new
|
|
# item and sends it to the fifo. The listener process receives
|
|
# the item and excutes this commando function on the item.
|
|
# So in essence, the commando function keeps calling itself
|
|
# indirectly until no items are left. This will form a single
|
|
# working queue. By executing multiple start_single_worker
|
|
# functions based on the CPU cores available, parallel processing
|
|
# is achieved, with a queue for each core.
|
|
#
|
|
|
|
ITEM="$1"
|
|
|
|
if [ -e "$ITEM" ]
|
|
then
|
|
DIRNAME=`dirname "$ITEM"`
|
|
ITEM_NO_PATH=`basename "$ITEM"`
|
|
escape_item "$ITEM_NO_PATH"
|
|
OUTPUT_DIR=$PPSS_LOCAL_OUTPUT/"$ITEM_ESCAPED"
|
|
# ^
|
|
# | This VAR can be used in scripts or command lines.
|
|
#
|
|
OUTPUT_FILE="$ITEM_ESCAPED"
|
|
else
|
|
DIRNAME=""
|
|
escape_item "$ITEM"
|
|
ITEM_NO_PATH="$ITEM_ESCAPED"
|
|
OUTPUT_DIR=$PPSS_LOCAL_OUTPUT/"$ITEM_NO_PATH"
|
|
fi
|
|
|
|
log DEBUG "Processing item: $ITEM"
|
|
#
|
|
# Decide if an item must be transfered from server to the node.
|
|
# or be processed in-place (NFS / SMB mount?)
|
|
#
|
|
if [ "$TRANSFER_TO_SLAVE" == "0" ]
|
|
then
|
|
if [ -z "$SRC_DIR" ] && [ ! -z "$INPUT_FILE" ]
|
|
then
|
|
log DEBUG "Using item straight from the server, no copy."
|
|
else
|
|
ITEM="$ITEM"
|
|
fi
|
|
else
|
|
ITEM="./$PPSS_LOCAL_TMPDIR/$ITEM_NO_PATH"
|
|
fi
|
|
|
|
LOG_FILE_NAME=`echo "$ITEM" | sed s/^\\\.//g | sed s/^\\\.\\\.//g | sed s/\\\///g | sed s/\\ /_/g`
|
|
ITEM_LOG_FILE="$JOB_LOG_DIR/$LOG_FILE_NAME"
|
|
|
|
OUTPUT_DIR=$PPSS_LOCAL_OUTPUT/"$LOG_FILE_NAME"
|
|
|
|
mkdir -p "$OUTPUT_DIR"
|
|
|
|
does_file_exist "$ITEM_LOG_FILE"
|
|
if [ "$?" == "0" ]
|
|
then
|
|
log DEBUG "Skipping item $ITEM - already processed."
|
|
else
|
|
ERROR=""
|
|
#
|
|
# Some formatting of item log files.
|
|
#
|
|
DATE=`date +%b\ %d\ %H:%M:%S`
|
|
echo "===== PPSS Item Log File =====" > "$ITEM_LOG_FILE"
|
|
echo -e "Host:\t\t$HOSTNAME" >> "$ITEM_LOG_FILE"
|
|
echo -e "Process:\t$PID" >> "$ITEM_LOG_FILE"
|
|
echo -e "Item:\t\t$ITEM" >> "$ITEM_LOG_FILE"
|
|
echo -e "Start date:\t$DATE" >> "$ITEM_LOG_FILE"
|
|
echo -e "" >> "$ITEM_LOG_FILE"
|
|
|
|
#
|
|
# The actual execution of the command as specified by
|
|
# the -c option.
|
|
#
|
|
BEFORE="$(date +%s)"
|
|
TMP=`echo $COMMAND | grep -i '$ITEM'`
|
|
if [ "$?" == "0" ]
|
|
then
|
|
eval "$COMMAND" >> "$ITEM_LOG_FILE" 2>&1
|
|
ERROR="$?"
|
|
MYPID="$!"
|
|
else
|
|
eval '$COMMAND"$ITEM" >> "$ITEM_LOG_FILE" 2>&1'
|
|
ERROR="$?"
|
|
MYPID="$!"
|
|
fi
|
|
AFTER="$(date +%s)"
|
|
|
|
echo -e "" >> "$ITEM_LOG_FILE"
|
|
|
|
# Some error logging. Success or fail.
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
echo -e "Status:\t\tFAILURE" >> "$ITEM_LOG_FILE"
|
|
else
|
|
echo -e "Status:\t\tSUCCESS" >> "$ITEM_LOG_FILE"
|
|
fi
|
|
|
|
#
|
|
# If part of a cluster, remove the downloaded item after
|
|
# it has been processed and uploaded as not to fill up disk space.
|
|
#
|
|
if [ "$TRANSFER_TO_SLAVE" == "1" ]
|
|
then
|
|
if [ -e "$ITEM" ]
|
|
then
|
|
rm "$ITEM"
|
|
else
|
|
log DEBUG "ERROR Something went wrong removing item $ITEM from local work dir."
|
|
fi
|
|
|
|
fi
|
|
|
|
escape_item "$DIRNAME"
|
|
ITEM_OUTPUT_DIR="$REMOTE_OUTPUT_DIR/$ITEM_ESCAPED"
|
|
|
|
if [ "$TRANSFER_TO_SLAVE" == "0" ]
|
|
then
|
|
log DEBUG "File transfer is disabled."
|
|
else
|
|
exec_cmd "mkdir -p $ITEM_OUTPUT_DIR"
|
|
if [ "$DIRNAME" == "." ]
|
|
then
|
|
DIRNAME=""
|
|
fi
|
|
upload_item "$PPSS_LOCAL_OUTPUT/$ITEM_NO_PATH" "$DIRNAME"
|
|
fi
|
|
|
|
|
|
elapsed "$BEFORE" "$AFTER" >> "$ITEM_LOG_FILE"
|
|
echo -e "" >> "$ITEM_LOG_FILE"
|
|
|
|
if [ ! -z "$SSH_SERVER" ]
|
|
then
|
|
log DEBUG "Uploading item log file $ITEM_LOG_FILE to master ~/$PPSS_HOME_DIR/$JOB_LOG_DIR"
|
|
scp -q $SSH_OPTS $SSH_KEY "$ITEM_LOG_FILE" $USER@$SSH_SERVER:~/$PPSS_HOME_DIR/$JOB_LOG_DIR
|
|
if [ ! "$?" == "0" ]
|
|
then
|
|
log DEBUG "Uploading of item log file failed."
|
|
fi
|
|
fi
|
|
fi
|
|
|
|
start_single_worker
|
|
return $?
|
|
}
|
|
|
|
#
|
|
# This is the listener service. It listens on the pipe for events.
|
|
# A job is executed for every event received.
|
|
# This listener enables fully asynchronous processing.
|
|
#
|
|
listen_for_job () {
|
|
FINISHED=0
|
|
DIED=0
|
|
PIDS=""
|
|
log DEBUG "Listener started."
|
|
while read event <& 42
|
|
do
|
|
if [ "$event" == "$STOP_KEY" ]
|
|
then
|
|
#
|
|
# The start_single_worker method sends a special signal to
|
|
# inform the listener that a worker is finished.
|
|
# If all workers are finished, it is time to stop.
|
|
# This mechanism makes PPSS asynchronous.
|
|
#
|
|
((DIED++))
|
|
if [ "$DIED" -ge "$MAX_NO_OF_RUNNING_JOBS" ]
|
|
then
|
|
#kill_process
|
|
break
|
|
else
|
|
RES=$((MAX_NO_OF_RUNNING_JOBS-DIED))
|
|
if [ "$RES" == "1" ]
|
|
then
|
|
log DSPLY "$((MAX_NO_OF_RUNNING_JOBS-DIED)) job is remaining. "
|
|
else
|
|
log DSPLY "$((MAX_NO_OF_RUNNING_JOBS-DIED)) jobs are remaining."
|
|
echo -en "\033[1A"
|
|
fi
|
|
fi
|
|
elif [ "$event" == "$KILL_KEY" ]
|
|
then
|
|
#
|
|
# If all workers are finished, it is time to kill all remaining
|
|
# processes, terminate ssh processes and the listener itself.
|
|
#
|
|
# This command kills all processes that are related to the master
|
|
# process as defined by $PID. All processes that have ever been
|
|
# spawned, although disowned or backgrounded will be killed...
|
|
#
|
|
PROCLIST=`ps a -o pid,pgid,ppid,command | grep [0-9] | grep $PID | grep -v -i grep`
|
|
#echo "$PROCLIST" > proclist.txt
|
|
oldIFS=$IFS # save the field separator
|
|
IFS=$'\n' # new field separator, the end of line
|
|
for x in `echo "$PROCLIST"`
|
|
do
|
|
MYPPID=`echo $x | awk '{ print $3 }'`
|
|
MYPID=`echo $x | awk '{ print $1 }'`
|
|
if [ ! "$MYPPID" == "$PID" ] && [ ! "$MYPPID" == "1" ]
|
|
then
|
|
if [ ! "$MYPID" == "$PID" ]
|
|
then
|
|
log DEBUG "Killing process $MYPID"
|
|
kill $MYPID >> /dev/null 2>&1
|
|
else
|
|
log DEBUG "Not killing master process..$MYPID.."
|
|
fi
|
|
else
|
|
log DEBUG "Not killing listener process. $MYPID.."
|
|
fi
|
|
done
|
|
IFS=$oldIFS
|
|
|
|
if [ ! -z "$SSH_MASTER_PID" ]
|
|
then
|
|
kill "$SSH_MASTER_PID"
|
|
fi
|
|
break
|
|
else
|
|
commando "$event" &
|
|
MYPID="$!"
|
|
disown
|
|
PIDS="$PIDS $MYPID"
|
|
#log DEBUG "Event $event has pid $MYPID"
|
|
fi
|
|
|
|
get_global_lock
|
|
SIZE_OF_ARRAY="${#ARRAY[@]}"
|
|
ARRAY_POINTER=`cat $ARRAY_POINTER_FILE`
|
|
release_global_lock
|
|
PERCENT=$((100 * $ARRAY_POINTER / $SIZE_OF_ARRAY ))
|
|
if [ "$DIED" == "0" ] && [ "$FINISHED" == "0" ]
|
|
then
|
|
log DSPLY "Currently $PERCENT percent complete. Processed $ARRAY_POINTER of $SIZE_OF_ARRAY items."
|
|
if [ "$PERCENT" == "100" ]
|
|
then
|
|
FINISHED=1
|
|
else
|
|
echo -en "\033[1A"
|
|
fi
|
|
fi
|
|
done
|
|
|
|
set_status STOPPED
|
|
log DEBUG "Listener stopped."
|
|
if [ ! "$PERCENT" == "100" ]
|
|
then
|
|
echo
|
|
stop-ppss
|
|
log DSPLY "Finished. Consult $JOB_LOG_DIR for job output."
|
|
log DSPLY "Press ENTER to continue."
|
|
else
|
|
stop-ppss
|
|
log DSPLY "Finished. Consult $JOB_LOG_DIR for job output."
|
|
fi
|
|
cleanup
|
|
}
|
|
|
|
# This starts an number of parallel workers based on the # of parallel jobs allowed.
|
|
start_all_workers () {
|
|
|
|
if [ "$MAX_NO_OF_RUNNING_JOBS" == "1" ]
|
|
then
|
|
log DSPLY "Starting $MAX_NO_OF_RUNNING_JOBS single worker."
|
|
else
|
|
log DSPLY "Starting $MAX_NO_OF_RUNNING_JOBS parallel workers."
|
|
fi
|
|
log DSPLY "---------------------------------------------------------"
|
|
|
|
i=0
|
|
while [ "$i" -lt "$MAX_NO_OF_RUNNING_JOBS" ]
|
|
do
|
|
start_single_worker
|
|
((i++))
|
|
|
|
if [ ! "$MAX_DELAY" == "0" ]
|
|
then
|
|
random_delay "$MAX_DELAY"
|
|
fi
|
|
done
|
|
}
|
|
|
|
get_status_of_node () {
|
|
|
|
NODE="$1"
|
|
STATUS=`ssh -o ConnectTimeout=10 $SSH_KEY $USER@$NODE cat "$PPSS_HOME_DIR/$NODE_STATUS" 2>/dev/null`
|
|
ERROR="$?"
|
|
if [ ! "$ERROR" == "0" ]
|
|
then
|
|
STATUS="UNKNOWN"
|
|
fi
|
|
echo "$STATUS"
|
|
}
|
|
|
|
show_status () {
|
|
|
|
source $CONFIG
|
|
if [ ! -z "$SSH_KEY" ]
|
|
then
|
|
SSH_KEY="-i $SSH_KEY"
|
|
fi
|
|
if [ -z "$INPUT_FILE" ]
|
|
then
|
|
ITEMS=`exec_cmd "ls -1 $SRC_DIR 2>/dev/null | wc -l" 1`
|
|
else
|
|
ITEMS=`exec_cmd "cat $PPSS_HOME_DIR/$INPUT_FILE 2>/dev/null | wc -l" 1`
|
|
fi
|
|
|
|
ITEMS=`echo $ITEMS | sed s/\ //g`
|
|
|
|
if [ ! -z "$ITEMS" ] && [ ! "$ITEMS" == "0" ]
|
|
then
|
|
PROCESSED=`exec_cmd "ls -1 $ITEM_LOCK_DIR 2>/dev/null | wc -l" 1` 2>&1 >> /dev/null
|
|
TMP_STATUS=$((100 * $PROCESSED / $ITEMS))
|
|
log DSPLY "Status:\t\t$TMP_STATUS percent complete."
|
|
else
|
|
log DSPLY "Status: UNKNOWN - is PPSS deployed on nodes?"
|
|
fi
|
|
|
|
if [ ! -z $NODES_FILE ]
|
|
then
|
|
TMP_NO=`cat $NODES_FILE | wc -l`
|
|
log DSPLY "Nodes:\t $TMP_NO"
|
|
fi
|
|
log DSPLY "Items:\t\t$ITEMS"
|
|
|
|
|
|
log DSPLY "---------------------------------------------------------"
|
|
HEADER=`echo IP-address Hostname Processed Status | awk '{ printf ("%-16s %-18s % 10s %10s\n",$1,$2,$3,$4) }'`
|
|
log DSPLY "$HEADER"
|
|
log DSPLY "---------------------------------------------------------"
|
|
PROCESSED=0
|
|
for x in `cat $NODES_FILE`
|
|
do
|
|
RES=0
|
|
NODE=`get_status_of_node "$x" | awk '{ print $1 }'`
|
|
if [ ! "$NODE" == "UNKNOWN" ]
|
|
then
|
|
STATUS=`get_status_of_node "$x" | awk '{ print $2 }'`
|
|
RES=`exec_cmd "grep -i $NODE ~/$PPSS_HOME_DIR/$JOB_LOG_DIR/* 2>/dev/null | wc -l " 1`
|
|
if [ ! "$?" == "0" ] || [ -z "$RES" ]
|
|
then
|
|
RES=0
|
|
fi
|
|
else
|
|
STATUS="UNKNOWN"
|
|
RES=0
|
|
fi
|
|
let PROCESSED="$PROCESSED+$RES"
|
|
LINE=`echo "$x $NODE $RES $STATUS" | awk '{ printf ("%-16s %-18s % 10s %10s\n",$1,$2,$3,$4) }'`
|
|
log DSPLY "$LINE"
|
|
done
|
|
log DSPLY "---------------------------------------------------------"
|
|
LINE=`echo $PROCESSED | awk '{ printf ("Total processed: % 29s\n",$1) }'`
|
|
log DSPLY "$LINE"
|
|
}
|
|
|
|
|
|
# If this is called, the whole framework will execute.
|
|
main () {
|
|
|
|
case $MODE in
|
|
node )
|
|
init_vars
|
|
test_server
|
|
get_all_items
|
|
listen_for_job "$MAX_NO_OF_RUNNING_JOBS" & 2>&1 >> /dev/null
|
|
LISTENER_PID=$!
|
|
start_all_workers
|
|
;;
|
|
start )
|
|
# This option only starts all nodes.
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
if [ ! -e "$NODES_FILE" ]
|
|
then
|
|
log ERROR "File $NODES with list of nodes does not exist."
|
|
set_status STOPPED
|
|
cleanup
|
|
exit 1
|
|
else
|
|
for NODE in `cat $NODES_FILE`
|
|
do
|
|
start_ppss_on_node "$NODE"
|
|
done
|
|
fi
|
|
cleanup
|
|
exit 0
|
|
;;
|
|
config )
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
log DSPLY "Generating configuration file $CONFIG"
|
|
add_var_to_config PPSS_LOCAL_TMPDIR "$PPSS_LOCAL_TMPDIR"
|
|
add_var_to_config PPSS_LOCAL_OUTPUT "$PPSS_LOCAL_OUTPUT"
|
|
cleanup
|
|
exit 0
|
|
;;
|
|
|
|
stop )
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
log DSPLY "Stopping PPSS on all nodes."
|
|
exec_cmd "touch $STOP_SIGNAL"
|
|
cleanup
|
|
exit
|
|
;;
|
|
pause )
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
log DSPLY "Pausing PPSS on all nodes."
|
|
exec_cmd "touch $PAUSE_SIGNAL"
|
|
cleanup
|
|
exit
|
|
;;
|
|
continue )
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
if does_file_exist "$STOP_SIGNAL"
|
|
then
|
|
log DSPLY "Continuing processing, please use $0 start to start PPSS on al nodes."
|
|
exec_cmd "rm -f $STOP_SIGNAL"
|
|
fi
|
|
if does_file_exist "$PAUSE_SIGNAL"
|
|
then
|
|
log DSPLY "Continuing PPSS on all nodes."
|
|
exec_cmd "rm -f $PAUSE_SIGNAL"
|
|
fi
|
|
cleanup
|
|
exit 0
|
|
;;
|
|
deploy )
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
log DSPLY "Deploying PPSS on nodes."
|
|
deploy_ppss
|
|
wait
|
|
cleanup
|
|
exit 0
|
|
;;
|
|
ec2)
|
|
EC2=true
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
log INFO "Deploying PPSS on EC2 nodes."
|
|
ec2_launch_nodes
|
|
deploy_ppss
|
|
wait
|
|
cleanup
|
|
exit 0
|
|
;;
|
|
status )
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
show_status
|
|
exit 0
|
|
;;
|
|
erase )
|
|
LOGFILE=/dev/null
|
|
display_header
|
|
log DSPLY "Erasing PPSS from all nodes."
|
|
erase_ppss
|
|
cleanup
|
|
exit 0
|
|
;;
|
|
kill )
|
|
LOGFILE=/dev/null
|
|
for x in `ps ux | grep ppss | grep -v grep | grep bash | awk '{ print $2 }'`
|
|
do
|
|
kill "$x"
|
|
done
|
|
cleanup
|
|
exit 0
|
|
;;
|
|
|
|
* )
|
|
init_vars
|
|
get_all_items
|
|
listen_for_job "$MAX_NO_OF_RUNNING_JOBS" & 2>&1 >> /dev/null
|
|
LISTENER_PID=$!
|
|
start_all_workers
|
|
;;
|
|
esac
|
|
}
|
|
#
|
|
# This command starts the that sets the whole framework in motion.
|
|
#
|
|
main
|
|
|
|
#
|
|
# Exit after all processes have finished.
|
|
#
|
|
wait
|