Basic installation of Debian Squeeze

Networking

Interfaces

edit /etc/networks/interfaces Note that at some point eth1 should be configured by DHCP, it is on the UCD LAN and must be registered correctly (update MAC address with services). eth0 is the internal network.

auto lo eth0 eth1 eth2 

iface lo inet loopback

iface eth0 inet static
	address 192.168.20.254
	netmask 255.255.255.0


iface eth1 inet static
	address 192.168.21.254
	netmask 255.255.255.0


iface eth2 inet dhcp

Install non-free linux firmware for network interface (eth0). This will allow Gigabit operation on eth0 with the tg3 hardware (I think). Edit /etc/apt/sources.list including the lines:

deb http://ftp.ie.debian.org/debian/ squeeze main contrib non-free
deb-src http://ftp.ie.debian.org/debian/ squeeze main contrib non-free

Install firmware-linux:

apt-get update && apt-get install firmware-linux

You probably need to reboot now.

DNS / BIND

We will run our own DNS server for the cluster. Because dhclient is running on eth2, we need to stop it breaking resolv.conf. Add to /etc/dhcp/dhclient.conf

supersede domain-name "heterogeneous.ucd.ie ucd.ie";
prepend domain-name-servers 127.0.0.1;

After running dhclient, resolv.conf should read:

domain heterogeneous.ucd.ie
search heterogeneous.ucd.ie ucd.ie
nameserver 127.0.0.1
nameserver 137.43.116.19
nameserver 137.43.116.17
nameserver 137.43.105.22

Now install bind9 (apt-get install bind9). Edit /etc/bind/named.conf.local and set the domain zones for the cluster (forwards and reverse). We have two subdomains where reverse lookups will have to be specified 192.168.20 and 192.168.21

//
// Do any local configuration here
//

// Consider adding the 1918 zones here, if they are not used in your
// organization
//include "/etc/bind/zones.rfc1918";

include "/etc/bind/rndc.key";

controls {
	inet 127.0.0.1 allow { localhost; } keys { "rndc-key"; };
};

zone "heterogeneous.ucd.ie" {
	type master;
	file "db.heterogeneous.ucd.ie";
};

zone "21.168.192.in-addr.arpa" {
	type master;
	file "db.192.168.21";
};

zone "20.168.192.in-addr.arpa" {
        type master;
        file "db.192.168.20";
};

Also edit the options file: /etc/bind/named.conf.options, note the subnet we define in the allow sections, 192.168.20/23, it will permit access from 192.168.20.* and 192.168.21.* addresses.

options {
        directory "/var/cache/bind";

        // If there is a firewall between you and nameservers you want
        // to talk to, you may need to fix the firewall to allow multiple
        // ports to talk.  See http://www.kb.cert.org/vuls/id/800113

        // If your ISP provided one or more IP addresses for stable
        // nameservers, you probably want to use them as forwarders.
        // Uncomment the following block, and insert the addresses replacing
        // the all-0's placeholder.

        forwarders {
                137.43.116.19;
                137.43.116.17;
                137.43.105.22;
        };

        recursion yes;

        version "REFUSED";

        allow-recursion {
                127.0.0.1;
                192.168.20.0/23;
        };

        allow-query {
                127.0.0.1;
                192.168.20.0/23;
        };

        auth-nxdomain no;    # conform to RFC1035
        listen-on-v6 { any; };
};

Now work on the zone files specified /var/cache/bind/db.heterogneneous.ucd.ie and the reverse maps /var/cache/bind/db.192.168.21 & /var/cache/bind/db.192.168.21 Populate them with all nodes of the cluster.

IP Tables

Set up iptables. We want to implement NAT between the internal network (eth0) and external one (eth1). Add a script to /etc/network/if-up.d directory, named 00iptables. All scripts in this directory will be executed after network interfaces are brought up, so this will persist:

#!/bin/sh

PATH=/usr/sbin:/sbin:/bin:/usr/bin

IF_INT=eth0
IF_EXT=eth1

#
# delete all existing rules.
#
iptables -F
iptables -t nat -F
iptables -t mangle -F
iptables -X

# Always accept loopback traffic
iptables -A INPUT -i lo -j ACCEPT


# Allow established connections, and those not coming from the outside
iptables -A INPUT -m state --state ESTABLISHED,RELATED -j ACCEPT
iptables -A INPUT -m state --state NEW ! -i $IF_EXT -j ACCEPT
iptables -A FORWARD -i $IF_EXT -o $IF_INT -m state --state ESTABLISHED,RELATED -j ACCEPT

# Allow outgoing connections from the LAN side.
iptables -A FORWARD -i $IF_INT -o $IF_EXT -j ACCEPT

# Masquerade.
iptables -t nat -A POSTROUTING -o $IF_EXT -j MASQUERADE

# Don't forward from the outside to the inside.
iptables -A FORWARD -i $IF_EXT -o $IF_EXT -j REJECT

# Enable routing.
echo 1 > /proc/sys/net/ipv4/ip_forward

NFS

Install:

apt-get install nfs-kernel-server nfs-common portmap

Add to /etc/exports

/home   192.168.20.0/255.255.254.0(rw,sync,no_root_squash,no_subtree_check)

Restart nfs server with

exportfs -a

Clonezilla

Firstly, Clonezilla is probably going to pollute a lot of your server configuration when it sets itself up. Be prepared to loose your IPtables configuration, NFS (if any) and DHCP settings. Maybe more.

follow the guide to installing Clonezilla here. Essentially:

add repository key

wget -q http://drbl.sourceforge.net/GPG-KEY-DRBL -O- | apt-key add -

the line add to /etc/apt/sources.list:

deb http://drbl.sourceforge.net/drbl-core drbl stable

run:

apt-get update && apt-get install drbl && /opt/drbl/sbin/drbl4imp

accept default options to drbl4imp.

After Clonezilla has installed edit /etc/dhcpd3/dhcpd.conf, adding all entries for test nodes hcl07 and hcl03. Also ensure these nodes have been removed from the inplace heterogeneous.ucd.ie server so that they are only served by one machine.

default-lease-time			300;
max-lease-time				300;
option subnet-mask			255.255.255.0;
option domain-name-servers  		137.43.116.19,137.43.116.17,137.43.105.22;
option domain-name			"ucd.ie";	
ddns-update-style                       none; # brett had ad-hoc ...?
server-name 				drbl;
filename = "pxelinux.0";


subnet 192.168.21.0 netmask 255.255.255.0 {
    option subnet-mask	255.255.255.0;
    option routers 192.168.21.1;
    next-server 192.168.21.254;

    pool {
      # allow members of "DRBL-Client";
      range 192.168.21.200 192.168.21.212;
    }

        host hcl03 {
                option host-name "hcl03.ucd.ie";
                hardware ethernet 00:14:22:0A:22:6C;
                fixed-address 192.168.21.5;
        }
	host hcl03_eth1 {
                option host-name "hcl03_eth1.ucd.ie";
                hardware ethernet 00:14:22:0A:22:6D;
                fixed-address 192.168.21.105;
        }
        host hcl07 {
                option host-name "hcl07.ucd.ie";
                hardware ethernet 00:14:22:0A:20:E2;
                fixed-address 192.168.21.9;
        }
        host hcl07_eth1 {
                option host-name "hcl07_eth1.ucd.ie";
                hardware ethernet 00:14:22:0A:20:E3;
                fixed-address 192.168.21.109;
        }

	default-lease-time 21600;	
	max-lease-time 43200;
}

NTP Daemon

Nodes in the cluster should use the Network Time Protocol to set their clocks, heterogeneous.ucd.ie should provide them that service. Install ntpd with the following command:

apt-get install ntp

Configure the daemon with the following line in /etc/ntp.conf:

restrict 192.168.20.0 mask 255.255.254.0 nomodify notrap

Install DHCP

Install the DHCP server package with apt-get install dhcp3-server. When you install Clonezilla it will probably pollute your DHCP server setup, so make ... TODO

Install NIS

Copy users from passwd, groups and shadow from /etc on hcl01.

Install nis. Set domain to

heterogeneous.ucd.ie

Edit /etc/defaultdomain so that it contains:

heterogeneous.ucd.ie

Edit /etc/default/nis so that it contains:

# Are we a NIS server and if so what kind (values: false, slave, master)
NISSERVER=master

Edit /etc/ypserv.securenets so that is contains:

# allow connects from local
255.0.0.0	127.0.0.0
# allow connections from heterogeneous subnets .20 and .21
255.255.254.0 192.168.20.0

The NIS host is also a client of itself, so do the client set up as follows:

Edit /etc/hosts end ensure the NIS Master is listed

192.168.20.254		heterogeneous.ucd.ie	heterogeneous

Edit /etc/yp.conf and ensure that it contains:

domain heterogeneous.ucd.ie server localhost

Edit /etc/passwd adding a line to the end that reads: +::::::. Edit /etc/group with a line +::: at the line.

The NIS Makefile will not pull userid and groupids that are lower than a certain value, we must set this to 500 in /var/yp/Makefile

MINUID=500
MINGID=500

Start the ypbind and yppasswd services. Then initialise the NIS database:

/usr/lib/yp/ypinit -m

Accept defaults at prompts.

Now start other NIS services

service nis start

Installing Ganglia Frontend

Install the packages gmetad and ganglia-webfrontend.

Configure the front end by appending to /etc/apache2/apache2.conf, the following:

Include /etc/ganglia-webfrontend/apache.conf

Configure gmetad by adding to the /etc/ganglia/gmetad.conf, the following line:

data_source "HCL Cluster" 192.168.20.1 192.168.20.16
data_source "HCL Service" localhost:8648

This means that the gmetad collector connect to hcl01 and hcl16 on the .20 subnet to gather data for the frontend to use.

After all packages are configured execute:

service apache2 restart
service gmetad restart

Pointing your browser to here should display the monitoring page for HCL Cluster. gmond must also be installed and configured on the cluster nodes.

Hardware Monitoring & Backup

Disk Monitoring

Install smartmontools as per here. Briefly:

apt-get install smartmontools

Edit /etc/defaults/smartmontools so that it contains:

# List of devices you want to explicitly enable S.M.A.R.T. for
# Not needed (and not recommended) if the device is monitored by smartd
enable_smart="/dev/sda"

# uncomment to start smartd on system startup
start_smartd=yes

# uncomment to pass additional options to smartd on startup
smartd_opts="--interval=1800"

Open /etc/smartd.conf and edit the first line that begins with DEVICESCAN (all lines after the first instance of DEVICESCAN are ignored). Have it read something like:

DEVICESCAN -d removable -n standby -m root -m robert_higgins@iol.ie -M exec /usr/share/smartmontools/smartd-runner

Then start the service /etc/init.d/smartmontools start Note, consider installing this on all nodes, as it would be interesting to have prior notice of any failing disks.

Torque - PBS

Torque is now in the Debian repository, but we are using the newer version and compiling from sources. But apt-get installs the libtorque2 with open-MPI, this leads to two versions of the library; in /usr/lib and /usr/local/lib. If you manually set LD_LIBRARY_PATH just make sure that /usr/local/lib is first.

Download Torque from here. Extract archive and configure:

./configure --prefix=/usr/local

Run make && make install. Torque will have installed files under /usr/local and /var/spool/torque. Edit the Torque config file /var/spool/torque/torque.cfg adding the line:

SERVERHOST=192.168.20.254

Add the compute nodes of the cluster to the file /var/spool/torque/server_priv/nodes

hcl01
hcl02
hcl03
hcl04
hcl05
hcl06
hcl07
hcl08
hcl09
hcl10
hcl11
hcl12
hcl13
hcl14
hcl15
hcl16

By default /usr/local/lib may not be in the list of directories to search for dynamic-linked libraries. If so, add that path to the end of /etc/ld.so.conf.d/local.conf, and run "ldconfig" to update.

Now return to the extracted source distribution, find the contrib/init.d folder and copy the debian.pbs_server to /etc/init.d/pbs_server. Edit the inplace file so that the header reads:

#!/bin/sh
### BEGIN INIT INFO
# Provides:          pbs_server
# Required-Start:    $local_fs $named
# Should-Start:
# Required-Stop:

This will ensure that important services are started before the PBS/Torque daemon. then run

update-rc.d pbs_server defaults
pbs_server -t create
qterm
pbs_server

Packages for nodes

make packages
scp torque-package-mom-linux-i686.sh hclxx:
scp torque-package-clients-linux-i686.sh hclxx:

Queues

We will configure 4 queues, with varying priority and preemption policies.

The first is the normal queue. This will be where most jobs, which should not be interrupted, will be placed. It has the highest priority.
The second queue is lowpri, it is for running jobs which may run for extended periods but are interruptible. Should a job A be placed on the normal queue while a lowpri job B is running, B will be sent a kill signal, so it may shut down cleanly, and then it will be requeued on the system, so it can resume running after Ab has finished.
The third queue is for running of service jobs like the homedir backup. It is named service. This will have lower priority than the above queues and jobs running on this queue will be preemptable.
The final queue is the volunteer queue. This has the lowest priority and is for executing volunteer computing jobs during otherwise idle periods. These jobs will also be preemptable.

Queue Setup

Enter the queue manager program qmgr as the root user on heterogeneous. Send it the following commands:

Allow all users to see all queued jobs:

set server query_other_jobs=TRUE'

Create the default normal queue

create queue normal
set queue normal queue_type = Execution
set queue normal Priority = 10000
set queue normal enabled = True
set queue normal started = True

Create lowpri queue

create queue lowpri
set queue lowpri queue_type = Execution
set queue lowpri Priority = 1000
set queue lowpri enabled = True
set queue lowpri started = True

Create service queue

create queue service
set queue service queue_type = Execution
set queue service Priority = 100
set queue service enabled = True
set queue service started = True

Create volunteer queue

create queue volunteer
set queue volunteer queue_type = Execution
set queue volunteer Priority = 0
set queue volunteer enabled = True
set queue volunteer started = True

Set some server settings

set server default_queue=normal
set server resources_default.nodes = 1
set server resources_default.walltime = 12:00:00

Misc

Everyone can see every job: in qmgr

set server query_other_jobs = True

Maui Scheduler

Download from here, unpack and run

./configure --with-pbs --with-spooldir=/var/spool/maui

Edit /var/spool/maui/maui.cfg

SERVERHOST            heterogeneous
ADMIN1                root
RMCFG[HETEROGENEOUS] TYPE=PBS
AMCFG[bank]  TYPE=NONE

RMPOLLINTERVAL        00:00:01
QUEUETIMEWEIGHT 0
PREEMPTIONPOLICY	REQUEUE
DEFERTIME 0
DEFERCOUNT 86400
NODEALLOCATIONPOLICY  FIRSTAVAILABLE

QOSWEIGHT 1
QOSCFG[normal]  QFLAGS=PREEMPTOR
QOSCFG[lowpri]  QFLAGS=PREEMPTEE:PREEMPTOR QTWEIGHT=0
QOSCFG[service]   QFLAGS=PREEMPTEE:PREEMPTOR QTWEIGHT=0
QOSCFG[volunteer]  QFLAGS=PREEMPTEE:PREEMPTOR QTWEIGHT=0

CREDWEIGHT	1
CLASSWEIGHT	1
CLASSCFG[normal] QDEF=normal PRIORITY=10000
CLASSCFG[lowpri] QDEF=lowpri PRIORITY=1000
CLASSCFG[service] QDEF=service PRIORITY=100
CLASSCFG[volunteer] QDEF=volunteer PRIORITY=1

edit /etc/profile

if [ "`id -u`" -eq 0 ]; then
  PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/maui/bin:/usr/local/maui/sbin"
else
  PATH="/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/local/maui/bin"
fi

HCL cluster/heterogeneous.ucd.ie install log

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