Ubuntu Cluster - Master node

This time I want to show how to build a HPC (High Performance Computing) cluster using Ubuntu Linux.


Before to begin


My Institute (Cinvestav - www.ira.cinvestav.mx) ask me to build a small cluster to general works and it'll be a learning system for bioinformatic. The cluster name is Beagle, they put the hardware and my friend LuisD and I the hard job. The design includes a master node to access, to check status and to send jobs, and 10 slaves nodes with /home exported with NFS, a job queque created with Sun Grid Engine, Ganglia is user to monitor the systems and also include MPI support.


Hardware


  • Master Node: AMD Athlon 64 X2 4200+, 2 Gb RAM, 1 hard disk IDE 80 Gb (hda), 1 hd SATA 320 Gb (sda), 1 external USB hd 1 Tb (sdb), network card nForce 10/100/1000 (eth1), network card PCI Realtek 10/100 (eth2).
  • Slave Nodes X10: AMD Athlon 64 X2 4200+, 2 Gb RAM, 1 hard disk IDE 80 Gb, network card nForce 10/100/1000 (eth0).
  • Network Switch: 24 ports 10/100/1000.
  • Many meters of network cable.


    Install the Master Node


    We have an arch amd64, so we use the Ubuntu Desktop for amd64, we download the ISO file, burn into a CD and install:
  • File System: ext3.
  • Partitions (partition:size:mount_point):

     hda1 : 180 Mb : /boot
     hda2 : 2.0 Gb : swap
     hda4 : 24  Gb : /
     hda5 : 4.6 Gb : /tftpboot
     hda6 : 22  Gb : /var
     hda7 : 22  Gb : /usr
     sda1 : 2.0 Gb : swap
     sda2 : 292 Gb : /home

  • A general user named beagle.
  • Network has the configuration: eth1 197.1.1.1 (to send/receive with the slaves nodes), eth2 10.0.0.114 (to send/receive with out-world across our local intranet).
    Finish the installation, reboot, login and access a terminal to become root and create a password:

    sudo su -
    passwd

    DHCP server


    A DHCP server is build to talk with the slaves nodes:
    apt-get install dhcp3-server

    Now we edit /etc/dhcp3/dhcpd.conf to include the net 197.1.1.0/24 and add the MACs of each machine, include the hostname and use a netboot loader (PXE). Our file looks:

    # dhcp.conf
    # Network for the Beagle Cluster
    # Juan Caballero @ Cinvestav 2008
    ddns-update-style none;
    subnet 197.0.0.0 netmask 255.0.0.0 {
         default-lease-time 1200;
         max-lease-time 1200;
         option routers 197.1.1.1;
         option subnet-mask 255.0.0.0;
         option domain-name "local";
         option domain-name-servers 197.1.1.1;
         option nis-domain "beagle";
         option broadcast-address 197.255.255.255;
         deny unknown-clients;
         allow booting;
         allow bootp;
         if (substring (option vendor-class-identifier, 0, 20)
                         = "PXEClient:Arch:00002") {
                 # ia64
                 filename "elilo.efi";
                 next-server 197.1.1.1;
         } elsif ((substring (option vendor-class-identifier, 0, 9)
                         = "PXEClient") or
                 (substring (option vendor-class-identifier, 0, 9)
                         = "Etherboot")) {
                 # i386 and x86_64
                 filename "pxelinux.0";
                 next-server 197.1.1.1;
         } else {
                 filename "/install/sbin/kickstart.cgi";
                 next-server 197.1.1.1;
         }

         host beagle.local {
                 hardware ethernet 00:e0:7d:b4:e1:13;
                 option host-name "beagle.local";
                 fixed-address 197.1.1.1;
         }
         host node00.local {
                 hardware ethernet 00:1b:b9:e2:0d:18;
                 option host-name "node00.local";
                 fixed-address 197.1.1.100;
         }
         host node01.local {
                 hardware ethernet 00:1b:b9:e1:cf:6a;
                 option host-name "node01.local";
                 fixed-address 197.1.1.101;
         }
         host node02.local {
                 hardware ethernet 00:1b:b9:e1:be:6e;
                 option host-name "node02.local";
                 fixed-address 197.1.1.102;
         }
         host node03.local {
                 hardware ethernet 00:1b:b9:cf:f3:55;
                 option host-name "node03.local";
                 fixed-address 197.1.1.103;
         }
         host node04.local {
                 hardware ethernet 00:1b:b9:e2:14:06;
                 option host-name "node04.local";
                 fixed-address 197.1.1.104;
         }
         host node05.local {
                 hardware ethernet 00:1b:b9:ce:85:9a;
                 option host-name "node05.local";
                 fixed-address 197.1.1.105;
         }
         host node06.local {
                 hardware ethernet 00:1b:b9:e2:0c:5f;
                 option host-name "node06.local";
                 fixed-address 197.1.1.106;
         }
         host node07.local {
                 hardware ethernet 00:1b:b9:cf:f7:29;
                 option host-name "node07.local";
                 fixed-address 197.1.1.107;
         }
         host node08.local {
                 hardware ethernet 00:1b:b9:cf:f3:25;
                 option host-name "node08.local";
                 fixed-address 197.1.1.108;
         }
         host node09.local {
                 hardware ethernet 00:1b:b9:e2:14:9f;
                 option host-name "node09.local";
                 fixed-address 197.1.1.109;
         }
    }

    In the file /etc/defaults/dhcp3-server we wrote the network card to activate DHCP:
    Interfaces="eth1"

    Now we can restart the service:
    /etc/init.d/dhcp3-server restart


    More Network details


    Edit /etc/hosts to include all the nodes, our file looks:

    127.0.0.1       localhost
    197.1.1.1       beagle.local    beagle
    197.1.1.100     node00.local    node00
    197.1.1.101     node01.local    node01
    197.1.1.102     node02.local    node02
    197.1.1.103     node03.local    node03
    197.1.1.104     node04.local    node04
    197.1.1.105     node05.local    node05
    197.1.1.106     node06.local    node06
    197.1.1.107     node07.local    node07
    197.1.1.108     node08.local    node08
    197.1.1.109     node09.local    node09

    Also we create a text file in /etc/machines with the names of all slaves nodes, this will be used in scripting.

    node00
    node01
    node02
    node03
    node04
    node05
    node06
    node07
    node08
    node09


    NFS server


    Install the packages:
    apt-get nfs-common nfs-kernel-server

    Edit /etc/exports to export /home and /tftpboot:

    /home 197.1.1.0/24(rw,no_root_squash,sync,no_subtree_check)
    /tftpboot 197.1.1.0/24(rw,no_root_squash,sync,no_subtree_check)

    Start the file exportation with:
    exportfs -av


    PXE boot server


    Install tftpd-hpa:
    apt-get install tfptd-hpa

    Edit /etc/defaults/tfptd-hpa to include:

    #Defaults for tftpd-hpa
    RUN_DAEMON="yes"
    OPTIONS="-l -s /tftpboot"

    Now we download the netboot file for Ubuntu amd64:

    cd /tftpboot
    wget http://tezcatl.fciencias.unam.mx/ubuntu/dists/gutsy/main/installer-amd64/current/images/netboot/netboot.tar.gz
    tar zxvf netboot.tar.gz

    Restart the service:
    /etc/init.d/tftpd-hpa restart


    SGE server


    For the Sun Grid Engine we add an user named sgeadmin, and run the installation script, many options are defaults:

    adduser sgemaster
    wget http://gridengine.sunsource.net/download/SGE61/ge-6.1u3-common.tar.gz
    wget http://gridengine.sunsource.net/download/SGE61/ge-6.1u3-bin-lx24-amd64.tar.gz
    tar zxvf ge-6.1u3-common.tar.gz
    tar zxvf ge-6.1u3-bin-lx24-amd64.tar.gz
    ./install-qmaster


    Web server


    Install Apache:
    apt-get install apache2


    Ganglia monitor


    First we install dependencies, download the source and compile ganglia:

    apt-get install rrdtool librrds-perl librrd2-dev php5-gd
    wget http://downloads.sourceforge.net/ganglia/ganglia-3.0.7.tar.gz?modtime=1204128965&big_mirror=0
    tar zxvf ganglia*
    cd ganglia*
    ./configure --enable-gexec --with-gmetad
    make
    mkdir /var/www/ganglia
    cp web/* /var/www/ganglia

    Edit Apache configuration to access ganglia in the file /etc/apache2/sites-enabled/000-default
    Also install the packages:
    apt-get install ganglia-monitor gmetad

    You can modify the default configuration if you edit /etc/gmond.conf and /etc/gmetad.conf.


    Others programs


    Use apt-get or manually compilated packages, for example we add a SSH server, the basic compilers and MPI support:
    apt-get install openssh-server gcc g++ g77 mpich-bin openmpi-bin lam-runtime


    In the next part we'll install the slaves nodes.


    Links:


    Ubuntu http://www.ubuntu.com/
    Debian Clusters http://debianclusters.cs.uni.edu/index.php/Main_Page
    SGE http://gridengine.sunsource.net/
    Ganglia http://ganglia.info/
    NFS http://nfs.sourceforge.net/
    TFTP-HPA http://freshmeat.net/projects/tftp-hpa/
    DHCP http://www.dhcp.org/
    MPICH http://www-unix.mcs.anl.gov/mpi/mpich1/
    OpenMPI http://www.open-mpi.org/
    LAM/MPI http://www.lam-mpi.org/

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