Slurm Installation on Debian

Job Scheduler Slurm

Slurm Installation

In this section we describe all the administration tasks for the Slurm Workload Manager in the frontend node (Server) and in the compute nodes (Client)

Slurm Installation on Debian from repositories

1. Make sure the clocks, users and groups (UIDs and GIDs) are synchronized across the cluster.

2. Install MUNGE

   apt-get install -y libmunge-dev libmunge2 munge

3. Generate MUNGE key. There are various ways to do this, depending on the desired level of key quality. Refer to the MUNGE installation guide for complete details.

   Wait around for some random data (recommended for the paranoid):

   dd if=/dev/random bs=1 count=1024 > /etc/munge/munge.key

   Grab some pseudorandom data (recommended for the impatient):

   dd if=/dev/urandom bs=1 count=1024 > /etc/munge/munge.key

   Permissions

   chown munge:munge /etc/munge/munge.key chmod 400 /etc/munge/munge.key

4. Edit file /etc/passwd

   vi /etc/passwd

   Modify user munge in each machine

   File: /etc/passwd

   munge:x:501:501::var/run/munge;/sbin/nologin

5. Start MUNGE

   /etc/init.d/munge start

6. Testing Munge

   The following steps can be performed to verify that the software has been properly installed and configured:

   Generate a credential on stdout:

   munge -n

   Check if a credential can be locally decoded:

   munge -n | unmunge

   Check if a credential can be remotely decoded:

   munge -n | ssh somehost unmunge

   Run a quick benchmark:

   remunge

7. Install SLURM from repositories

   apt-get install -y slurm-wlm slurm-wlm-doc

8. Create and copy slurm.conf

   Exist some ways to generate the slurm.cfg file. It have a web-based configuration tool which can be used to build a simple configuration file, which can then be manually edited for more complex configurations. The tool is located in /usr/share/doc/slurmctld/slurm-wlm-configurator.html

   Open this file in your browser

   sftp://ip-server/usr/share/doc/slurmctld/slurm-wlm-configurator.html

   NOTE: Executing the command slurmd -C on each compute node will print its physical configuration (sockets, cores, real memory size, etc.), which can be used in constructing the slurm.conf file.

   Copy the result from web-based configuration tool in /etc/slurm/slurm.conf and configure it such that it looks like the following (This is a example - build a configuration file customized for your environment) - http://slurm.schedmd.com/slurm.conf.html

   File: /etc/slurm/slurm.conf

   #
   # slurm.conf file generated by configurator.html.
   #
   # See the slurm.conf man page for more information.
   #
   ClusterName=GUANE
   ControlMachine=guane
   #
   SlurmUser=slurm
   SlurmctldPort=6817
   SlurmdPort=6818
   AuthType=auth/munge
   StateSaveLocation=/tmp
   SlurmdSpoolDir=/var/spool/slurm/slurmd
   SwitchType=switch/none
   MpiDefault=none
   SlurmctldPidFile=/var/run/slurmctld.pid
   SlurmdPidFile=/var/run/slurmd.pid
   ProctrackType=proctrack/pgid
   CacheGroups=0
   ReturnToService=1
   #
   # TIMERS
   SlurmctldTimeout=300
   SlurmdTimeout=300
   InactiveLimit=0
   MinJobAge=300
   KillWait=30
   Waittime=0
   #
   # SCHEDULING
   SchedulerType=sched/backfill
   SelectType=select/linear
   FastSchedule=1
   #
   # LOGGING
   SlurmctldDebug=3
   SlurmdDebug=3
   JobCompType=jobcomp/none
   JobCompLoc=/tmp/slurm_job_completion.txt
   #
   # ACCOUNTING
   JobAcctGatherType=jobacct_gather/linux
   JobAcctGatherFrequency=30
   #
   #AccountingStorageType=accounting_storage/slurmdbd
   #AccountingStorageHost=slurm
   #AccountingStorageLoc=/tmp/slurm_job_accounting.txt
   #AccountingStoragePass=
   #AccountingStorageUser=
   #
   # COMPUTE NODES
   # control node
   NodeName=guane NodeAddr=192.168.1.70 Port=17000 State=UNKNOWN
   
   # each logical node is on the same physical node, so we need different ports for them
   # name guane-[*] is arbitrary
   NodeName=guane-1 NodeAddr=192.168.1.71 Port=17002 State=UNKNOWN
   NodeName=guane-2 NodeAddr=192.168.1.72 Port=17003 State=UNKNOWN
   
   # PARTITIONS
   # partition name is arbitrary
   PartitionName=guane Nodes=guane-[1-2] Default=YES MaxTime=8-00:00:00 State=UP
   

9. Install munge in each node of cluster

   apt-get install -y libmunge-dev libmunge2 munge

10. Copy munge.key file from server to each node from cluster

    scp /etc/munge/munge.key root@node:/etc/munge/munge.key

11. Install SLURM compute node daemon

    apt-get install -y slurmd

12. Start slurm in the nodes and server

    /etc/init.d/slurmd start
    /etc/init.d/slurmctld start

Slurm Installation on Debian from source

CONTROLLER CONFIGURATION

http://wildflower.diablonet.net/~scaron/slurmsetup.html

1. Prerequisites

   apt-get install -y build-essential

2. Install MUNGE

   apt-get install -y libmunge-dev libmunge2 munge

3. Generate MUNGE key. There are various ways to do this, depending on the desired level of key quality. Refer to the MUNGE installation guide for complete details.

   Wait around for some random data (recommended for the paranoid):

   dd if=/dev/random bs=1 count=1024 > /etc/munge/munge.key

   Grab some pseudorandom data (recommended for the impatient):

   dd if=/dev/urandom bs=1 count=1024 > /etc/munge/munge.key

   Permissions

   chown munge:munge /etc/munge/munge.key chmod 400 /etc/munge/munge.key

4. Edit file /etc/passwd

   vi /etc/passwd

   Modify user munge in each machine

   File: /etc/passwd

   munge:x:501:501::var/run/munge;/sbin/nologin

5. Start MUNGE

   /etc/init.d/munge start

6. Testing Munge

   The following steps can be performed to verify that the software has been properly installed and configured:

   Generate a credential on stdout:

   munge -n

   Check if a credential can be locally decoded:

   munge -n | unmunge

   Check if a credential can be remotely decoded:

   munge -n | ssh somehost unmunge

   Run a quick benchmark:

   remunge

7. Install MySQL server (for SLURM accounting) and development tools (to build SLURM). We'll also install the BLCR tools so that SLURM can take advantage of that checkpoint-and-restart functionality.

   apt-get install mysql-server libmysqlclient-dev libmysqld-dev libmysqld-pic apt-get install gcc bison make flex libncurses5-dev tcsh pkg-config apt-get install blcr-util blcr-testsuite libcr-dbg libcr-dev libcr0

8. Download lastets version. (http://www.schedmd.com/#repos)

   wget http://www.schedmd.com/download/latest/slurm-14.11.6.tar.bz2

9. Unpack and build SLURM

   tar xvf slurm-14.11.6.tar.bz2

   cd slurm-14.11.6 ./configure --enable-multiple-slurmd make make install</nowiki>}}

.

10. Exist some ways to generate the slurm.cfg file. It have a web-based configuration tool which can be used to build a simple configuration file, which can then be manually edited for more complex configurations. The tool is located in doc/html/configurator.html, this file can opened in the browser if it's copy to /usr/share/ (sftp://ip-server/usr/share/doc/slurm/configurator.html)

    mkdir /usr/share/doc/slurm/ cd [slurm-src]/doc/html/ cp configurator.* /usr/share/doc/slurm/

    Other way is copy the example configuration files out to /etc/slurm.

    mkdir /etc/slurm cd [slurm-src] cp etc/slurm.conf.example /etc/slurm/slurm.conf cp etc/slurmdbd.conf.example /etc/slurm/slurmdbd.conf

    Executing the command slurmd -C on each compute node will print its physical configuration (sockets, cores, real memory size, etc.), which can be used in constructing the slurm.conf file.

11. Set things up for slurmdbd (the SLURM accounting daemon) in MySQL

    mysql -u root -p create database slurm_db; create user 'slurm'@'localhost'; set password for 'slurm'@'localhost' = password('MyPassword'); grant usage on *.* to 'slurm'@'localhost'; grant all privileges on slurm_db.* to 'slurm'@'localhost'; flush privileges; quit

12. Configure /usr/local/etc/slurmdbd.conf such that it looks like the following:

    {{File|/usr/local/etc/slurmdbd.conf|

    <nowiki>  
    #
    # Example slurmdbd.conf file.
    #
    # See the slurmdbd.conf man page for more information.
    #
    # Archive info
    #ArchiveJobs=yes
    #ArchiveDir="/tmp"
    #ArchiveSteps=yes
    #ArchiveScript=
    #JobPurge=12
    #StepPurge=1
    #
    # Authentication info
    AuthType=auth/munge
    AuthInfo=/var/run/munge/munge.socket.2
    #
    # slurmDBD info
    DbdAddr=localhost
    DbdHost=localhost
    #DbdPort=7031
    SlurmUser=slurm
    #MessageTimeout=300
    DebugLevel=4
    #DefaultQOS=normal,standby
    LogFile=/var/log/slurm/slurmdbd.log
    PidFile=/var/run/slurmdbd.pid
    #PluginDir=/usr/lib/slurm
    #PrivateData=accounts,users,usage,jobs
    #TrackWCKey=yes
    #
    # Database info
    StorageType=accounting_storage/mysql
    #StorageHost=localhost
    #StoragePort=1234
    StoragePass=MyPassword
    StorageUser=slurm
    StorageLoc=slurm_db
    

    </nowiki>

13. Configure /usr/local/etc/slurm.conf such that it looks like the following:

    {{File|//usr/local/etc/slurm.conf|

    <nowiki>  
    #
    # slurm.conf file generated by configurator.html.
    #
    # See the slurm.conf man page for more information.
    #
    ClusterName=GUANE
    ControlMachine=guane
    #ControlAddr=
    #BackupController=
    #BackupAddr=
    #
    SlurmUser=slurm
    #SlurmdUser=root
    SlurmctldPort=6817
    SlurmdPort=6818
    AuthType=auth/munge
    #JobCredentialPrivateKey=
    #JobCredentialPublicCertificate=
    StateSaveLocation=/tmp
    SlurmdSpoolDir=/var/spool/slurm/slurmd
    SwitchType=switch/none
    MpiDefault=none
    SlurmctldPidFile=/var/run/slurmctld.pid
    SlurmdPidFile=/var/run/slurmd.pid
    ProctrackType=proctrack/pgid
    #PluginDir=
    CacheGroups=0
    #FirstJobId=
    ReturnToService=1
    #MaxJobCount=
    #PlugStackConfig=
    #PropagatePrioProcess=
    #PropagateResourceLimits=
    #PropagateResourceLimitsExcept=
    #Prolog=
    #Epilog=
    #SrunProlog=
    #SrunEpilog=
    #TaskProlog=
    #TaskEpilog=
    #TaskPlugin=
    #TrackWCKey=no
    #TreeWidth=50
    #TmpFS=
    #UsePAM=
    #
    # TIMERS
    SlurmctldTimeout=300
    SlurmdTimeout=300
    InactiveLimit=0
    MinJobAge=300
    KillWait=30
    Waittime=0
    #
    # SCHEDULING
    SchedulerType=sched/backfill
    #SchedulerAuth=
    #SchedulerPort=
    #SchedulerRootFilter=
    SelectType=select/linear
    FastSchedule=1
    #PriorityType=priority/multifactor
    #PriorityDecayHalfLife=14-0
    #PriorityUsageResetPeriod=14-0
    #PriorityWeightFairshare=100000
    #PriorityWeightAge=1000
    #PriorityWeightPartition=10000
    #PriorityWeightJobSize=1000
    #PriorityMaxAge=1-0
    #
    # LOGGING
    SlurmctldDebug=3
    #SlurmctldLogFile=
    SlurmdDebug=3
    #SlurmdLogFile=
    JobCompType=jobcomp/none
    JobCompLoc=/tmp/slurm_job_completion.txt
    #
    # ACCOUNTING
    JobAcctGatherType=jobacct_gather/linux
    JobAcctGatherFrequency=30
    #
    #ccountingStorageEnforce=limits,qos
    AccountingStorageType=accounting_storage/slurmdbd
    AccountingStorageHost=slurm
    AccountingStorageLoc=/tmp/slurm_job_accounting.txt
    #AccountingStoragePass=
    #AccountingStorageUser=
    #
    
    # COMPUTE NODES
    # control node
    NodeName=guane NodeAddr=192.168.1.75 Port=17000 State=UNKNOWN
    
    # each logical node is on the same physical node, so we need different ports for them
    # name guane-[*] is arbitrary
    NodeName=guane-1 NodeAddr=192.168.1.71 Port=17002 State=UNKNOWN
    NodeName=guane-2 NodeAddr=192.168.1.72 Port=17003 State=UNKNOWN
    
    # PARTITIONS
    # partition name is arbitrary
    PartitionName=guane Nodes=guane-1 Default=YES MaxTime=8-00:00:00 State=UP
    

    </nowiki>

14. Create init scripts to /etc/init.d

    .

    touch /etc/init.d/slurmctl touch /etc/init.d/slurmdbd chmod +x /etc/init.d/slurm chmod +x /etc/init.d/slurmdbd
    File: /etc/init.d/slurmctl

    <nowiki>
    #!/bin/sh
    #
    # chkconfig: 345 90 10
    # description: SLURM is a simple resource management system which \
    #              manages exclusive access o a set of compute \
    #              resources and distributes work to those resources.
    #
    # processname: /usr/local/sbin/slurmctld
    # pidfile: /var/run/slurm/slurmctld.pid
    #
    # config: /etc/default/slurmctld
    #
    ### BEGIN INIT INFO
    # Provides:          slurmctld
    # Required-Start:    $remote_fs $syslog $network munge
    # Required-Stop:     $remote_fs $syslog $network munge
    # Should-Start:      $named
    # Should-Stop:       $named
    # Default-Start:     2 3 4 5
    # Default-Stop:      0 1 6
    # Short-Description: slurm daemon management
    # Description:       Start slurm to provide resource management
    ### END INIT INFO
    
    BINDIR="/usr/local/bin"
    CONFDIR="/usr/local/etc"
    LIBDIR="/usr/local/lib"
    SBINDIR="/usr/local/sbin"
    
    # Source slurm specific configuration
    if [ -f /etc/default/slurmctld ] ; then
        . /etc/default/slurmctld
    else
        SLURMCTLD_OPTIONS=""
    fi
    
    # Checking for slurm.conf presence
    if [ ! -f $CONFDIR/slurm.conf ] ; then
        if [ -n "$(echo $1 | grep start)" ] ; then
          echo Not starting slurmctld
        fi
          echo slurm.conf was not found in $CONFDIR
        exit 0
    fi
    
    DAEMONLIST="slurmctld"
    test -f $SBINDIR/slurmctld || exit 0
    
    #Checking for lsb init function
    if [ -f /lib/lsb/init-functions ] ; then
      . /lib/lsb/init-functions
    else
      echo Can\'t find lsb init functions
      exit 1
    fi
    # setup library paths for slurm and munge support
    export LD_LIBRARY_PATH=$LIBDIR${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}
    
    #Function to check for cert and key presence and key vulnerabilty
    checkcertkey()
    {
      MISSING=""
      keyfile=""
      certfile=""
    
      if [ "$1" = "slurmctld" ] ; then
        keyfile=$(grep JobCredentialPrivateKey $CONFDIR/slurm.conf | grep -v "^ *#")
        keyfile=${keyfile##*=}
        keyfile=${keyfile%#*}
        [ -e $keyfile ] || MISSING="$keyfile"
      fi
    
      if [ "${MISSING}" != "" ] ; then
        echo Not starting slurmctld
        echo $MISSING not found
        exit 0
      fi
    
      if [ -f "$keyfile" ] && [ "$1" = "slurmctld" ] ; then
        keycheck=$(openssl-vulnkey $keyfile | cut -d : -f 1)
        if [ "$keycheck" = "COMPROMISED" ] ; then
          echo Your slurm key stored in the file $keyfile
          echo is vulnerable because has been created with a buggy openssl.
          echo Please rebuild it with openssl version \>= 0.9.8g-9
          exit 0
        fi
      fi
    }
    
    get_daemon_description()
    {
        case $1 in
          slurmd)
            echo slurm compute node daemon
            ;;
          slurmctld)
            echo slurm central management daemon
            ;;
          *)
            echo slurm daemon
            ;;
        esac
    }
    
    start() {
      CRYPTOTYPE=$(grep CryptoType $CONFDIR/slurm.conf | grep -v "^ *#")
      CRYPTOTYPE=${CRYPTOTYPE##*=}
      CRYPTOTYPE=${CRYPTOTYPE%#*}
      if [ "$CRYPTOTYPE" = "crypto/openssl" ] ; then
        checkcertkey $1
      fi
    
      # Create run-time variable data
      mkdir -p /var/run/slurm
      chown slurm:slurm /var/run/slurm
    
      # Checking if StateSaveLocation is under run
      if [ "$1" = "slurmctld" ] ; then
        SDIRLOCATION=$(grep StateSaveLocation /usr/local/etc/slurm.conf \
                           | grep -v "^ *#")
        SDIRLOCATION=${SDIRLOCATION##*=}
        SDIRLOCATION=${SDIRLOCATION%#*}
        if [ "${SDIRLOCATION}" = "/var/run/slurm/slurmctld" ] ; then
          if ! [ -e /var/run/slurm/slurmctld ] ; then
            ln -s /var/lib/slurm/slurmctld /var/run/slurm/slurmctld
          fi
        fi
      fi
    
    desc="$(get_daemon_description $1)"
      log_daemon_msg "Starting $desc" "$1"
      unset HOME MAIL USER USERNAME
      #FIXME $STARTPROC $SBINDIR/$1 $2
      STARTERRORMSG="$(start-stop-daemon --start --oknodo \
                       --exec "$SBINDIR/$1" -- $2 2>&1)"
      STATUS=$?
      log_end_msg $STATUS
      if [ "$STARTERRORMSG" != "" ] ; then
        echo $STARTERRORMSG
      fi
      touch /var/lock/slurm
    }
    
    stop() {
        desc="$(get_daemon_description $1)"
        log_daemon_msg "Stopping $desc" "$1"
        STOPERRORMSG="$(start-stop-daemon --oknodo --stop -s TERM \
                        --exec "$SBINDIR/$1" 2>&1)"
        STATUS=$?
        log_end_msg $STATUS
        if [ "$STOPERRORMSG" != "" ] ; then
          echo $STOPERRORMSG
        fi
        rm -f /var/lock/slurm
    }
    
    getpidfile() {
        dpidfile=`grep -i ${1}pid $CONFDIR/slurm.conf | grep -v '^ *#'`
        if [ $? = 0 ]; then
            dpidfile=${dpidfile##*=}
            dpidfile=${dpidfile%#*}
        else
            dpidfile=/var/run/${1}.pid
        fi
    
        echo $dpidfile
    }
    
    #
    # status() with slight modifications to take into account
    # instantiations of job manager slurmd's, which should not be
    # counted as "running"
    #
    
    slurmstatus() {
        base=${1##*/}
    
        pidfile=$(getpidfile $base)
    
        pid=`pidof -o $$ -o $$PPID -o %PPID -x $1 || \
             pidof -o $$ -o $$PPID -o %PPID -x ${base}`
    
        if [ -f $pidfile ]; then
            read rpid < $pidfile
            if [ "$rpid" != "" -a "$pid" != "" ]; then
                for i in $pid ; do
                    if [ "$i" = "$rpid" ]; then
                        echo "${base} (pid $pid) is running..."
                        return 0
                    fi
                done
            elif [ "$rpid" != "" -a "$pid" = "" ]; then
    #           Due to change in user id, pid file may persist
    #           after slurmctld terminates
                if [ "$base" != "slurmctld" ] ; then
                   echo "${base} dead but pid file exists"
                fi
                return 1
           fi
    
        fi
    
        if [ "$base" = "slurmctld" -a "$pid" != "" ] ; then
            echo "${base} (pid $pid) is running..."
            return 0
        fi
    
        echo "${base} is stopped"
    
        return 3
    }
    
    #
    # stop slurm daemons,
    # wait for termination to complete (up to 10 seconds) before returning
    #
    
    slurmstop() {
        for prog in $DAEMONLIST ; do
           stop $prog
           for i in 1 2 3 4
           do
              sleep $i
              slurmstatus $prog
              if [ $? != 0 ]; then
                 break
              fi
           done
        done
    }
    
    #
    # The pathname substitution in daemon command assumes prefix and
    # exec_prefix are same.  This is the default, unless the user requests
    # otherwise.
    #
    # Any node can be a slurm controller and/or server.
    #
    case "$1" in
        start)
            start slurmctld "$SLURMCTLD_OPTIONS"
            ;;
        startclean)
            SLURMCTLD_OPTIONS="-c $SLURMCTLD_OPTIONS"
            start slurmctld "$SLURMCTLD_OPTIONS"
            ;;
        stop)
            slurmstop
            ;;
        status)
            for prog in $DAEMONLIST ; do
               slurmstatus $prog
            done
            ;;
        restart)
            $0 stop
            $0 start
            ;;
        force-reload)
            $0 stop
            $0 start
            ;;
        condrestart)
            if [ -f /var/lock/subsys/slurm ]; then
                for prog in $DAEMONLIST ; do
                     stop $prog
                     start $prog
                done
            fi
            ;;
        reconfig)
            for prog in $DAEMONLIST ; do
                PIDFILE=$(getpidfile $prog)
                start-stop-daemon --stop --signal HUP --pidfile \
                  "$PIDFILE" --quiet $prog
            done
            ;;
        test)
            for prog in $DAEMONLIST ; do
                echo "$prog runs here"
            done
            ;;
        *)
            echo "Usage: $0 {start|startclean|stop|status|restart|reconfig|condrestart|tes$
            exit 1
            ;;
    esac
    

    </nowiki>
    </

15. Add SLURM user:

    echo "slurm:x:2000:2000:slurm admin:/home/slurm:/bin/bash" >> /etc/passwd echo "slurm:x:2000:slurm >> /etc/group pwconv

16. Create SLURM spool and log directories and set permissions accordingly:

    mkdir /var/spool/slurm chown -R slurm:slurm /var/spool/slurm mkdir /var/log/slurm chown -R slurm:slurm /var/log/slurm

CONTROLLER CONFIGURATION

COMPUTE NODE CONFIGURATION

1. Install munge in each node of cluster

   apt-get install -y libmunge-dev libmunge2 munge

2. Copy munge.key file from server to each node from cluster

   scp /etc/munge/munge.key root@node:/etc/munge/munge.key

COMPUTE NODE CONFIGURATION

Slurm Installation on Debian from source