ProCKSI

= Installation Guide =

This guide describes the installation procedure for ''ProCKSI''. 

 ||'''Release'''     ||procksi_8-2

 ||'''Environment''' ||Cluster with one head node and two compute nodes 

All installations must be done with ''root'' access.

= System Design and Requirements =

== Cluster Design ==

The cluster is assumed to have a ''head node'' and several ''compute nodes''. 

 * The head node runs the webserver, the file server, the central database server, the email server, and the server for the queuing system. It can be used as a compute node itself. 

 * The compute nodes run the calculations.

[[Image(ClusterDesign.png)]]

== Software Requirements ==

We are assuming the following software components to be already installed the '''head node''':

 ||'''Operating system''' ||''Centos4'' (''RHEL4'')

 ||'''Webserver''' 	  ||Apache2 

 ||'''Database'''	  ||MySQL

 ||'''Email server'''	  ||Postfix (SMTP) 

 ||'''Queuing system'''	  ||PBS torque + maui

The '''compute nodes''' only requires the following components:

 ||'''Operating system'''||	''Centos4'' (''RHEL4'')

 ||'''Queuing system  '''||	PBS torque

The configuration for these components will be described later in this installation guide.

= URL and Email Forwarding =

ProCKSI uses URL and email forwarding in order to provide a stable internet address and corresponding email addresses.

== Provider ==

These are data for the domain and email domain provider.

 ||'''Provider'''  ||	[http://www.planetdomain.com/ukcheap/home.jsp www.planetdomain.com/ukcheap/home.jsp]

 ||'''Login'''     || 	nkrasnogor

 ||'''Password'''  || 	[BBSRC GRANT NUMBER]

== Domains ==

ProCKSI's main domain name is [http://www.procksi.net www.procksi.net], which is redirected to [http://procksi.cs.nott.ac.uk procksi.cs.nott.ac.uk], which is an alias for [http://procksi0.cs.nott.ac.uk procksi0.cs.nott.ac.uk]. All other domain names are redirected to its main domain name.

 ||'''Domain Name''' ||'''Redirected to'''                                  ||'''Expires at'''

 ||www.procksi.net   ||[http://procksi.cs.nott.ac.uk procksi.cs.nott.ac.uk] ||11-01-2011 

 ||www.procksi.org   ||[http://www.procksi.net/ www.procksi.net]            ||11-01-2011 

 ||www.procksi.com   ||[http://www.procksi.net/ www.procksi.net]            ||11-01-2011 

 ||www.procksi.info  ||[http://www.procksi.net/ www.procksi.net]            ||11-01-2008 

== DNS Settings	 ==

The primary and secondary DNS servers must be set as follows:

 {{{

 Primary	ns1.iprimus.com.au

 Secondary	ns2.iprimus.com.au 

 }}}

The following changes must be made manually in ''Advanced DNS settings'':

 {{{

 CNAME    *.procksi.net	    procksi.cs.nott.ac.uk.

 CNAME    *.procksi.org	    www.procksi.net.

 CNAME    *.procksi.com	    www.procksi.net.

 CNAME    *.procksi.info    www.procksi.net.

 }}}

== Email Settings ==

The following email addresses must be created and redirected to ''procksi@cs.nott.ac.uk'', which must be available:

 ||'''Email Address'''  ||'''Redirected to'''	

 ||admin@procksi.net	||procksi@cs.nott.ac.uk

 ||develop@procksi.net	||procksi@cs.nott.ac.uk   

 ||info@procksi.net	||procksi@cs.nott.ac.uk

 ||research@procksi.net	||procksi@cs.nott.ac.uk

 ||pbs@procksi.net	||procksi@cs.nott.ac.uk

 ||webmaster@procksi.net||procksi@cs.nott.ac.uk

The following changes must be made manually in ''Advanced DNS settings:''

 {{{

 MX    @.procksi.net    mailhost.planetdomain.com    10

 }}}

== Domain Usage Monitoring ==

The usage of ProCKSI's domains is monitored. 

 ||Provider	||[http://www.sitemeter.com www.sitemeter.com] 

 ||Login:	||s18procksi

 ||Password:	||FAKUIL

All HTML documents must contain the following code in order to be tracked correctly.

 {{{

<!-- Site Meter -->

	<script type="text/javascript" src="http://s18.sitemeter.com/js/counter.js?site=s18procksi">

	</script>

	<noscript>

		<a href="http://s18.sitemeter.com/stats.asp?site=s18procksi" target="_top">

			<img	src=[http://s18.sitemeter.com/meter.asp?site=s18procksi http://s18.sitemeter.com/meter.asp?site=s18procksi]

    				alt="Site Meter" border="0"/>

		</a>

	</noscript>

<!-- Copyright (c)2006 Site Meter -->

 }}}

= Data Management and Exchange  =

The head node and all compute nodes must be able to communicate with each other and exchange data. Therefore, a common user management and shared file system is necessary.

== User Management ==

Make the following changes on the head node and each compute node:

 * Add a new user into ''/etc/passwd'': 

   {{{

   procksi:x:510:510:ProCKSI-Server:/home/procksi:/bin/bash

   }}}

 * Add an entry for the new user into ''/etc/shadow'' if desired: 

   {{{

   procksi:[ENCRYPTED_PASSWORD]:13483:0:99999:7:::

   }}}

 * Add a new group into ''/etc/group'', and add all users who should have access:

   {{{

   procksi:x:510:dxb

   }}} 

   The members for group procksi are now: ''procksi'', ''dxb''

 * Generate home directory for ''procksi''

== Firewall ==

 All network traffic using the internal (private) network is trusted and considered to be secure. So no firewall is needed on the internal network interface (''eth1'').

 * Modify ''/etc/sysconfig/iptables'' on the head node and on each compute node. [[BR]] 

   If ''eth1'' is on the private network, add

   {{{

   -A RH-Firewall-1-INPUT -i eth1 -j ACCEPT

   }}}

   directly after

   {{{

    -A RH-Firewall-1-INPUT -i lo -j ACCEPT 

   }}}

 * Restart the firewall on the head node and on each compute node:

   {{{

   /sbin/service iptables restart

   }}}

 Changes in the firewall settings regarding the external network interface (''eth0'') will be described in other sections where necessary.

== DHCP Configuration ==

All machines obtain their IP addresses, names, etc. dynamically for the internal interface.

=== DHCP Server ===

Make sure that the DHCP server only responds to queries from the internal interface (ETH1).

Modify ''/etc/sysconfig/dhcpd'':

{{{

# Command line options here

DHCPDARGS=eth1

}}}

Modifiy ''/etc/dhcpd.conf'' on the head nodde:

{{{

#Allow to send negative acknowledgements (NAK) to clients

#authoritative;

ddns-update-style    none;

default-lease-time   259200;

#Allow clients with unknown MAC address to obtain an IP

#(useful for installing new machines)

boot-unknown-cliensts = true;

use-host-decl-names   = true;

subnet 192.168.199.0 netmask 255.255.255.0 {

   #Default Gateway

   option routers       192.168.199.10;

   option subnet-mask   255.255.255.0;

   #DNS Options

   option domain-name         "procksi.local";

#  option domain-name-servers 192.168.199.10;

   #NIS Options

#  option nis-domain    "procksi.nis";

#  option nis-servers   192.168.199.10;

   #Time Options

   option ntp-servers   128.243.21.16, 128.243.21.19;

   #Fixed IP Settings

   host procksi0-priv {

      option host-name "procksi0-priv";

      hardware ethernet 00:00:5A:9D:44:54;

      fixed-address 192.168.199.10;

   }

   host procksi1-priv {

      option host-name "procksi1-priv";

      hardware ethernet 00:15:C5:5D:89:5A;

      fixed-address 192.168.199.11;

   }

   host procksi2-priv {

      option host-name "procksi2-priv";

      hardware ethernet 00:15:C5:5D:B8:AC;

      fixed-address 192.168.199.12;

   }

  host procksi3-priv {

     option host-name "procksi3-priv";

     hardware ethernet ;

     fixed-address 192.168.199.13;

  }

  host procksi4-priv {

     option host-name "procksi4-priv";

     hardware ethernet 00:E0:81:48:19:80;

     fixed-address 192.168.199.14;

  }

}}}

Enable DHCP server at boottime

{{{

chkconfig dhcpd on

}}}

Start DHCP server

{{{

/sbin/service dhcpd start

}}}

=== DHCP Client ===

Modify ''/etc/sysconfig/network-scripts/ifcfg-eth0'' (INTERNAL INTERFACE) on each slave node and the head node:

{{{

DEVICE=eth0

BOOTPROTO=dhcp

HWADDR= [add MAC address here]

ONBOOT=yes

TYPE=Ethernet

}}}

== Host Name Resolution ==

As each node consists of two network interfaces (= multihomed host), the host name resolution must be configured correctly in order to prioritize the internal, trusted network for communication between different nodes.

 * The official hostname for each node must be set to the ''internal'' name of the machine in ''/etc/sysconfig/network''. This is an example for the head node:

 {{{

 HOSTNAME=procksi0-priv.cs.nott.ac.uk

 }}}

 The compute nodes must be named and configured accordingly.

 * Add the following to ''/etc/hosts'' on the head node:

 {{{

 127.0.0.1  procksi0-priv.cs.nott.ac.uk  procksi0-privlocalhost.localdomain  localhost

 }}}

 and alter the line for each compute node (procksi1, procksi2) accordingly.

 * Add the following to ''/etc/hosts'' on the head node and each compute node:

 {{{

 192.168.199.10  procksi0-priv.cs.nott.ac.uk  procksi0-priv

 192.168.199.11  procksi1-priv.cs.nott.ac.uk  procksi1-priv

 192.168.199.12  procksi2-priv.cs.nott.ac.uk  procksi2-priv

 }}}

 Edit ''/etc/host.conf'' so that local setting in ''/etc/hosts'' take precedence over DNS:

 {{{

 order hosts,bind

 }}}

== Data Access ==

 The head node hosts a RAID system of hard disks that will store all data generated by ProCKSI on all compute nodes and the head node itself. This partition must be accessible by all nodes and is exported as a network file system (NFS) therefore. Executables used by ProCKSI must be installed locally on each compute node for better performance.

 * Add the following to the end of ''/etc/exports'' on the head node (''procksi0''):

   {{{

   /home/procksi  procksi?-priv.cs.nott.ac.uk(sync,rw,no_root_squash)

   }}}

 * Add the following to the end of ''/etc/fstab'' on each compute node (''procksi1'', ''procksi2''): 

   {{{

   procksi0:/home/procksi       /home/procksi       nfs  bg,hard,intr  0 0

   procksi0:/usr/local/procksi	/usr/local/procksi  nfs  bg,hard,intr  0 0

   }}}

 * Tune NFS by increasing the number of nfsd threads. Modify ''/etc/sysconfig/nfs'':

   {{{

   RPCNFSDCOUNT=32

   }}}

 * Make the NFS daemons start at bootup. Enter at the command line of the head node and each compute node: 

   {{{

   /sbin/chkconfig  nfs  on

   }}}

 * Start the NFS daemons. Enter at the command line on the head node and on each compute node:

   {{{

   /sbin/service  nfsd  start

   }}}

 * Generate the following temp directory on the head node and each compute node, at best on a separate partition:

   {{{ 

   mkdir /scratch

   }}}

== Time Synchronisation ==

 The system time on all nodes must be synchronized as 

 a) data is written/read on/from a common, shared file system or even expires after a certain period of time and must be deleted, and 

 b) system logs are maintained independently but entries must be able to be associated with each other.

 * Add your own time server to ''/etc/ntp/ntpservers'': 

   {{{   

   marian.cs.nott.ac.uk

   }}}

 * Modify ''/etc/ntp.conf'' (at the of the file):

   {{{

   server    marian.cs.nott.ac.uk

   restrict  marian.cs.nott.ac.uk  mask 255.255.255.255  nomodify  notrap  noquery

   }}}

 * Make the NTP daemon start at bootup. Enter at the command line:

   {{{

   /sbin/chkconfig  ntpd  on

   }}}

 * Start the NTP daemon. Enter at the command line:

   {{{

   /sbin/service ntpd start

   }}}

= Queuing System =

 The queueing system (resource manager) is the heart of the distributed computing on a cluster. It consists of three parts, the server, the scheduler, and the machine-oriented mini-server (MOM) executing the jobs.

 We are assuming the following configuration:

 ||PBS TORQUE|| version 2.1.6           ||server, basic scheduler, mom 

 ||MAUI      || version 3.2.6.p18	||scheduler

 The sources can be obtained from:

 ||PBS TORQUE ||http://www.clusterresources.com/pages/products/torque-resource-manager.php

 ||MAUI       ||http://www.clusterresources.com/pages/products/maui-cluster-scheduler.php

 The install directories for ''TORQUE'' and ''MAUI'' will be:

 ||PBS TORQUE ||''/usr/local/torque''

 ||MAUI       ||''/usr/local/maui''

== TORQUE ==

=== Register new services ===

  Edit ''/etc/services'' and add at the end:

  {{{

  # PBS/Torque services

  pbs           15001/tcp    # pbs_server

  pbs           15001/udp    # pbs_server

  pbs_mom       15002/tcp    # pbs_mom <-> pbs_server

  pbs_mom       15002/udp    # pbs_mom <-> pbs_server

  pbs_resmom    15003/tcp    # pbs_mom resource management

  pbs_resmom    15003/udp    # pbs_mom resource management

  pbs_sched     15004/tcp    # pbs scheduler (pbs_sched)

  pbs_sched     15004/udp    # pbs scheduler (pbs_sched)

  }}}

=== Setup and Configuration on the Head Node ===

Extract and build the distribution TORQUE on the head node. Configure server, monitor and clients to use secure file transfer (scp).

{{{

export TORQUECFG=/usr/local/torque

tar -xzvf TORQUE.tar.gz

cd TORQUE

}}}

Configuration for a 64bit machine with the following compiler options:

{{{

FFLAGS   = “-m64 -march=nocona -O3 -fPIC"

CFLAGS   = “-m64 -march=nocona -O3 -fPIC"

CXXFLAGS = “-m64 -march=nocona -O3 -fPIC"

LDFLAGS	 = “-L/usr/local/lib -L/usr/local/lib64"

}}}

Configure, build, and install:

{{{

./configure  --enable-server  --enable-monitor  --enable-clients

             --with-server-home=$TORQUECFG  --with-server-name

             --with-rcp=scp  --disable-filesync

make

make install 

}}}

If not configures otherwise, binaries are installed in ''/usr/local/bin'' and ''/usr/local/sbin''. You should have these directories included in your path. But you can configure TORQUE to have the binaries in the default system directory with

{{{

./configure --bindir=/usr/bin --sbindir=/usr/sbin

}}}

Initialise/configure the queueing system's server daemon (pbs_server):

{{{

pbs_server -t create

}}}

Set the PBS operator and manager (must be a valid user name). 

{{{

qmgr

> set server_name = procksi0-priv.cs.nott.ac.uk

> set server scheduling = true

> set server operators += “root@procksi.cs.nott.ac.uk"

> set server operators += “procksi@ procksi.cs.nott.ac.uk"

> set server managers  += “root@ procksi.cs.nott.ac.uk"

> set server managers  += “procksi@ procksi.cs.nott.ac.uk"

}}}

Allow only ''procksi'' and ''root'' to submit jobs into the queue:

{{{

> set server acl_users = “root, procksi" 

> set server acl_user_enable = true

}}}

Set the default queue to ''batch''

{{{

> set server default_queue=batch

}}}

Set email address for email that is sent by PBS:

{{{

> set mail_from = pbs@procksi.net	

}}}

Allow submissions from compute hosts (only):

{{{

> set server allow_node_submit = true

> set server submit_hosts = procksi0-priv.cs.nott.ac.uk

                            procksi1-priv.cs.nott.ac.uk

                            procksi2-priv.cs.nott.ac.uk

}}}

Restrict nodes that can access the PBS server:

{{{

> set server acl_hosts = procksi0-priv.cs.nott.ac.uk

                         procksi1-priv.cs.nott.ac.uk                           

                         procksi2-priv.cs.nott.ac.uk

> set acl_host_enable = true

}}}

And set in ''torque.cfg'' in order to use the internal interface:

{{{

SERVERHOST              procksi0-priv.cs.nott.ac.uk

ALLOWCOMPUTEHOSTSUBMIT  true

}}}

Configure the main queue ''batch'':

{{{

> create queue batch queue_type=execution

> set queue batch started=true

> set queue batch enabled=true

> set queue batch resources_default.nodes=1

}}}

Configure queue ''test ''accordingly''. 

Configure default node to be used (see below):

{{{

> set server default_node = slave

}}}

Specify all compute nodes to be used by creating/editing ''$TORQUECFG/server_priv/nodes.'' This may include the same machine where pbs_server will run. If the compute nodes have more than one processor, just add np=X after the name with X being the number of processors. Add node attributes so that a subset of nodes can be requested during the submission stage.

{{{

procksi0-priv.cs.nott.ac.uk  np=1  procksi  head

procksi1-priv.cs.nott.ac.uk  np=2  procksi  slave  slave1

procksi2-priv.cs.nott.ac.uk  np=2  procksi  slave  slave2

}}}

Although the head node (''procksi0'') has two processors as well, we only allow one processor to be used for the queueing system as the other processor will be used for handling all frontend communication and I/O. (Make sure that hyperthreading technology is disabled on the head node and all compute nodes!)

Build packages for the compute nodes and copy them to each compute node:

{{{

cd $TORQUE

make packages

scp torque-package-mom-linux-i686.sh     procksi1|procksi2

scp torque-package-clients-linux-i686.sh procksi1|procksi2

}}}

=== Setup and Configuration on the Compute Nodes ===

Install prepared packes. A directory similar to ''$TORQUECFG'' will be automatically created.

{{{

psh compute torque-package-mom-linux-i686.sh -install

psh compute torque-package-clients-linux-i686.sh -install

}}}

Check if the nodes know the head node

{{{

$TORQUECFG/server_name

#procksi0-priv.cs.nott.ac.uk

}}}

Configure the compute nodes by creating/editing ''$TORQUECFG/mom_priv/config''. The first line specifies the PBS server, the second line specifies hosts which can be trusted to access mom services as non-root, and the last line allows to copy data via NFS without using SCP.

{{{

$pbsserver   procksi0-priv.cs.nott.ac.uk

$loglevel    255

$restricted  procksi?-priv.cs.nott.ac.uk

$usecp       procksi0-priv.cs.nott.ac.uk:/home/procksi  /home/procksi

}}}

Start the queueing system (manually) in the correct order:

 * Start the mom:

 {{{

 /usr/local/sbin/pbs_mom

 }}}

 * Kill the server:

 {{{

 /usr/local/sbin/qterm -t quick

 }}}

 * Start the server:

 {{{ 

 /usr/local/sbin/pbs_server

 }}}	

 * Start the scheduler:		

 {{{

 /usr/local/sbin/pbs_sched

 }}} 

If you want to use MAUI as the final scheduler, keep in mind to kill ''pbs_sched'' after testing the TORQURE installation.

Check that all nodes are properly configured and correctly reporting

{{{

qstat  -q

pbsnodes -a

}}}

=== Prologue and Epilogue Scripts ===

The ''prologue'' script is executed just before the submitted job starts. Here, it generates a unique temp directory for each job in ''/scratch''. It must be installed on each node:

{{{

cp $PROCKSI/install/prologue $TORQUECFG/mom_priv

chmod 500 $TORQUECFG/mom_priv/prologue

}}}

The ''epilogue'' script is executed right after the submitted job has ended. Here, it deletes the job's temp directory from ''/scratch.'' It must be installed on each node:

{{{

cp $PROCKSI/install/epilogue $TORQUECFG/mom_priv

chmod 500 $TORQUECFG/mom_priv/epilogue

}}}

== MAUI ==

=== Register new services ===

Edit ''/etc/services'' and add at the end:

{{{ 

# PBS/MAUI services

pbs_maui  42559/tcp    # pbs scheduler (maui)

pbs_maui  42559/udp    # pbs scheduler (maui)

}}}

=== Setup and Configuration on the Head Node ===

Extract and build the distribution MAUI.

{{{

export MAUIDIR=/usr/local/maui

tar -xzvf MAUI.tar.gz

cd TORQUE

}}}

Configuration for a 64bit machine with the following compiler options:

{{{

FFLAGS   = “-m64 -march=nocona -O3 -fPIC"

CFLAGS   = “-m64 -march=nocona -O3 -fPIC"

CXXFLAGS = “-m64 -march=nocona -O3 -fPIC"

LDFLAGS	 = “-L/usr/local/lib -L/usr/local/lib64"

}}}

Configure, build, and install:

{{{

./configure --with-pbs=$TORQUECFG --with-spooldir=$MAUIDIR

make

make install 

}}}

Fine-tune MAUI in $''MAUIDIR/maui.cfg'':

{{{

SERVERHOST            procksi0-priv.cs.nott.ac.uk

# primary admin must be first in list

ADMIN1                procksi

ADMIN1                root

# Resource Manager Definition

RMCFG[PROCKSI0-PRIV.CS.NOTT.AC.UK]		

TYPE=PBS 			

HOST=PROCKSI0-PRIV.CS.NOTT.AC.UK 		

PORT=15001

EPORT=15004	[CAN BE ALTERNATIVELY: 15017 - TRY!!!]

SERVERPORT  42559

SERVERMODE  NORMAL

# Node Allocation:

NODEALLOCATIONPOLICY  PRIORITY

NODECFG[DEFAULT] PRIORITY='- JOBCOUNT'

}}}

Configure attributes of compute nodes:

{{{

qmgr

> set node procksi0.cs.nott.ac.uk properties = “procksi, head"

> set node procksi1.cs.nott.ac.uk properties = “procksi, slave"

> set node procksi0.cs.nott.ac.uk properties = “procksi, slave"

}}}

Request job to be run on specific nodes (on submission):

 * Run on any compute node: 	

 {{{

 qsub -q batch -l nodes=1:procksi

 }}}

 * Run on any slave node:	

 {{{

 qsub -q batch -l nodes=1:slave

 }}}

 * Run on head node:		

 {{{

 qsub -q batch -l nodes=1:head

 }}}

Start the MAUI scheduler manually. Make sure that pbs_sched is not running any longer.

 * Start the scheduler:

 {{{

 /usr/local/sbin/maui

 }}}

Make the entire queueing system start at bootup:

{{{

cp /home/procksi/latest/install/pbs_head-node /etc/init.d/pbs 

/sbin/chkconfig --add pbs

/sbin/chkconfig pbs on

}}}

=== Setup and Configuration on the Compute Nodes ===

__Attention:__ 	If the head node is a compute node itself, do NOT proceed with the following steps as the head node was configured in the previous step!

Make the entire queueing system start at bootup:

{{{

cp /home/procksi/latest/install/pbs_compute-node /etc/init.d/pbs

/sbin/chkconfig --add pbs

/sbin/chkconfig pbs on

}}}

= Cluster Monitoring =

== Ganglia ==

“Ganglia is a scalable distributed monitoring system for high-performance computing systems such as clusters and Grids."

See [http://ganglia.sourceforge.net/ http://ganglia.sourceforge.net] for information on requirements, configuration and installation.

Install Ganglia into ''/usr/local/ganglia'', its web frontend into ''/usr/local/ganglia/html/', and its databases into ''/usr/local/ganglia/rrds/'.

=== Further Customisation ===

In order to display more fine-grained time intervals, edit the following files in ''/usr/local/ganglia/html/'':

 * '''header.php'''

 {{{

  if (!$physical) {

   $context_ranges[]="10 minutes";

   $context_ranges[]="20 minutes";

   $context_ranges[]="30 minutes";

   $context_ranges[]="1 hour";

   $context_ranges[]="2 hours";

   $context_ranges[]="4 hours";

   $context_ranges[]="8 hours";

   $context_ranges[]="12 hours";

   $context_ranges[]="1 day";

   $context_ranges[]="2 days";

   $context_ranges[]="week";

   $context_ranges[]="month";

   $context_ranges[]="year";

 }}}

 * '''get_context.php'''

 {{{

  switch ($range) {

   case "10 minutes":   $start = -600; break;

   case "20 minutes":   $start = -1200; break;

   case "30 minutes":   $start = -1800; break;

   case "1 hour":       $start = -3600; break;

   case "2 hours":      $start = -7200; break;

   case "4 hours":      $start = -14400; break;

   case "8 hours":      $start = -28800; break;

   case "12 hours":     $start = -43200; break;

   case "1 day":        $start = -86400; break;

   case "2 days":       $start = -172800; break;

   case "week":         $start = -604800; break;

   case "month":        $start = -2419200; break;

   case "year":         $start = -31449600; break;

 }}}

== !JobMonarch ==

!JobMonarch is an add-on to Ganglia which provides PBS job monitoring through the web browser.

See [http://subtrac.rc.sara.nl/oss/jobmonarch/wiki/Documentation http://subtrac.rc.sara.nl/oss/jobmonarch/wiki/Documentation] for information on requirements, configuration and installation.

= Additional Software  =

== PERL Libraries ==

Please make sure that the following libraries are installed in the official library directory and install all depending libraries, if necessary. For ''Image::Magick'', use the corresponding libraries that come with the main installation.

||Error[[BR]]Image::Magick[[BR]] Digest::MD5[[BR]] Config::Simple[[BR]] DBI[[BR]] CGI[[BR]] CGI::Session[[BR]] Data::!FormValidator[[BR]] HTML::Template[[BR]] HTML::Template::Pro[[BR]] MIME::Lite[[BR]] !FreezeThaw[[BR]] Storable||  0.17008[[BR]]6.0.7[[BR]]2.36[[BR]]4.58[[BR]]1.53[[BR]]3.25[[BR]]4.13[[BR]]4.40[[BR]]2.8[[BR]]0.64[[BR]]3.01[[BR]]0.43[[BR]]2.12  ||Time::Format[[BR]]IMAP::Client[[BR]]File::Copy[[BR]] WWW::Mechanize[[BR]]Time::Local[[BR]]Clone[[BR]]SOAP::Lite[[BR]]||  1.02[[BR]]2.2.9[[BR]]2.08[[BR]]1.20[[BR]]1.13[[BR]]0.22[[BR]]0.69  ||

PERL modules are installed best with the CPAN shell:

{{{

perl -MCPAN -eshell

}}}

== Third Party Executables for ProCKSI ==

Generate the following directories on each compute node to contain important executables:

{{{

/usr/local/procksi/Cluster/

/usr/local/procksi/DaliLite

/usr/local/procksi/MaxCMO

/usr/local/procksi/MolScript

}}}

For the following installation of the ProCKSI server components, the following executables must be present:

{{{

/usr/local/procksi/Cluster/qclust

/usr/local/procksi/DaliLite/DaliLite

/usr/local/procksi/MaxCMO/ProtCompVNS

/usr/local/procksi/molauto

/usr/local/procksi/molscript

}}}

== Image Software ==

=== Installation ===

   * Install ''!ImageMagick'' from [http://www.imagemagick.org www.imagemagick.org] if not already installed.

   * Install ''!MolScript'' from [http://www.avatar.se/molscript www.avatar.se/molscript]. Please link the MesaGL libraries instead of the OpenGL libraries; a modified makefile can be found under [source:ProCKSI/install/Makefile.molscript]

=== Virtual Display  ===

!MolScript needs an X display in order to generate images (jpg, gif, …). Its possible to use the console X display for the OpenGL bits even if it is not logged in. Therefore, ''procksi'' must be authenticated and allowed to use this X display virtually.

On each node copy magic cookie file for x-authentication:

{{{

cp /home/procksi/latest/install/:0.Xauth /var/gdm/:0.Xauth

}}}

On each node copy scripts for automatic x-authentication:

{{{

cp /home/procksi/latest/install/procksixauth /usr/local/sbin/procksixauth

cp /home/procksi/latest/install/:0 /etc/X11/gdm/Init/:0

}}}

Restart the X display manager for the changes to take effect:

{{{

/usr/sbin/gdm-restart

}}}

The virtual X display can be used with unix socket '':0'', e.g.:

{{{

molauto protein.pdb | DISPLAY=unix:0.0 molscript -jpeg -out protein.jpeg

}}}

= ProCKSI Server Component =

== Installation and Basic Configuration ==

This section describes the installation and configuration of the ProCKSI server component. This includes the configuration of the web server and the database.

The server component will be installed into the home directory of the user ''procksi''. Therefore, make sure that it is on a separate partition / hard disk with much space. In the best case, this will be a RAID system.

Get the latest release of the server component, referred to in the following as ''RELEASE'', and extract it into ''/home/procksi/RELEASE.'' 

{{{

tar -xvzf RELEASE.tgz

}}}

Create a softlink from ''RELEASE'' to a generic directory ''/home/procksi/latest''. This will be accessed by the web server:

{{{

ln -s /home/procksi/RELEASE /home/procksi/latest

}}}

In order to test new versions, referred in the following as ''TEST'', before taking them officially online, create a softlink from ''TEST'' to a generic directory ''/home/procksi/test''. This will be accessed by the web server:

{{{

ln -s /home/procksi/TEST /home/procksi/test

}}}

In case that you want to bring the test version online, just delete the softlinks and repeat the previous steps for the new release. Please make sure that always both softlinks exist!

Change into the administrative directory and run the installation script. Change the server settings, database settings and directory settings if necessary.

{{{

cd /home/procksi/latest/admin

./configure.pl

}}}

== Database Configuration ==

Make sure that the MySQL daemon is running, and that it will start at boot time:

{{{

/sbin/service mysqld start

/sbin/chkconfig --add mysqld

/sbin/chkconfig mysqld on

}}}

Make sure that you have access to the MySQL database management as ''root'' and login as user ''root ''with the corresponding password:

{{{

mysql -u root -p

}}}

Create new mysql users ''procksi_user ''and ''procksi_admin'':

{{{

USE mysql;

INSERT INTO user SET host='localhost', user='procksi_user', password=PASSWORD('''password_procksi_user''');

INSERT INTO user SET host='localhost', user='procksi_admin', password=PASSWORD('''password_procksi_admin''');

FLUSH PRIVILEGES;

}}}

Repeat these steps analogously for ''procksi0-priv'', ''procksi1-priv'', and ''procksi2-priv.''

Create a new database:

{{{

CREATE DATABASE procksi_latest;

}}}

Give privileges to users  ''procksi_user ''and ''procksi_admin'' for all compute nodes:

{{{

GRANT ALL ON procksi_latest.* TO procksi_admin@localhost WITH GRANT OPTION;

GRANT SELECT, UPDATE, INSERT, DELETE ON procksi_latest.* TO procksi_user@localhost;

GRANT ALL ON procksi_latest.* TO procksi_admin@procksi0.cs.nott.ac.uk WITH GRANT OPTION;

GRANT SELECT, UPDATE, INSERT, DELETE ON procksi_latest.* TO procksi_user@procksi0.cs.nott.ac.uk;

GRANT SELECT, UPDATE, INSERT, DELETE ON procksi_latest.* TO procksi_user@procksi1.cs.nott.ac.uk;

GRANT SELECT, UPDATE, INSERT, DELETE ON procksi_latest.* TO procksi_user@procksi2.cs.nott.ac.uk;

FLUSH PRIVILEGES;

}}}

If you change the password for ''procksi_user'', please make sure that you also change it in ''/home/procksi/latest/config/main.ini''

Import the main database ''procksi_latest'' from the backup given in ''/home/procksi/RELEASE/admin'':

{{{

msysql -u procksi_admin -p procksi_latest < procksi_latest.sql

}}}

In order to create a database ''procksi_test'' for the test version, repeat the previous steps and set the privileges accordingly.

== Web Server Configuration ==

Make the following changes to the Apache configuration file (''/etc/httpd/conf/httpd.conf''):

{{{

User  			procksi

Group 			procksi

ServerAdmin		procksi@cs.nott.ac.uk

ServerName 		procksi.cs.nott.ac.uk

DocumentRoot /home/procksi/latest/html

<Directory /home/procksi/latest/html">

   AllowOverride AuthConfig

</Directory>

LogFormat "%t %h %l %u \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\"" combined

LogFormat "%t %h %l %u \"%r\" %>s %b" common

LogFormat "%t %{Referer}i -> %U" referer

LogFormat "%t %{User-agent}i" agent

#Exclude Logging of Ganglia Requests

SetEnvIf Request_URI "ganglia" ganglia

#

# The location and format of the access logfile (Common Logfile Format).

# If you do not define any access logfiles within a <VirtualHost>

# container, they will be logged here.  Contrariwise, if you *do*

# define per-<VirtualHost> access logfiles, transactions will be

# logged therein and *not* in this file.

#

CustomLog /home/procksi/latest/logs/access.log common env=!ganglia

#

# If you would like to have agent and referer logfiles, uncomment the

# following directives.

#

CustomLog /home/procksi/latest/logs/referer.log referer env=!ganglia

CustomLog /home/procksi/latest/logs/agent.log agent env=!ganglia

#

# For a single logfile with access, agent, and referer information

# (Combined Logfile Format), use the following directive:

#

#CustomLog logs/access_log combined env=!ganglia

ScriptAlias /cgi-bin/ /home/procksi/latest/cgi-bin/

<Directory "/home/procksi/latest/cgi-bin">

    AllowOverride None

    Options None

    Order allow,deny

    Allow from all

</Directory>

Alias  /data/ 	  /home/procksi/latest/data/

Alias  /images/   /home/procksi/latest/images/

Alias  /styles/   /home/procksi/latest/styles/

Alias  /applets/  /home/procksi/latest/applets/

Alias  /scripts/  /home/procksi/latest/scripts/

Alias  /ganglia/  /usr/local/ganglia/html/

#Redirection

Redirect /trac https://psiren.cs.nott.ac.uk/projects/procksi/

AddLanguage de .de

AddLanguage en .en

AddLanguage es .es

AddLanguage fr .fr 

LanguagePriority en es de fr

Alias /errordocs/ "/home/procksi/errordocs"

<IfModule mod_negotiation.c>

    <IfModule mod_include.c>

        <Directory /home/procksi/errordocs>

            AllowOverride none

            Options MultiViews IncludesNoExec FollowSymLinks

            AddType text/html .shtml

            <FilesMatch "\.shtml[.$]">

                SetOutputFilter INCLUDES

            </FilesMatch>

        </Directory>

        ErrorDocument 400 /errordocs/400_BAD_REQUEST

        ErrorDocument 401 /errordocs/401_UNAUTHORIZED

        ErrorDocument 403 /errordocs/403_FORBIDDEN

        ErrorDocument 404 /errordocs/404_NOT_FOUND

        ErrorDocument 405 /errordocs/405_METHOD_NOT_ALLOWED

        ErrorDocument 406 /errordocs/406_NOT_ACCEPTABLE

        ErrorDocument 408 /errordocs/408_REQUEST_TIMEOUT

        ErrorDocument 410 /errordocs/410_GONE

        ErrorDocument 411 /errordocs/411_LENGTH_REQUIRED

        ErrorDocument 412 /errordocs/412_PRECONDITION_FAILED

        ErrorDocument 413 /errordocs/413_REQUEST_ENTITY_TOO_LARGE

        ErrorDocument 414 /errordocs/414_REQUEST_URI_TOO_LARGE

        ErrorDocument 415 /errordocs/415_UNSUPPORTED_MEDIA_TYPE

        ErrorDocument 500 /errordocs/500_INTERNAL_SERVER_ERROR

        ErrorDocument 501 /errordocs/501_NOT_IMPLEMENTED

        ErrorDocument 502 /errordocs/502_BAD_GATEWAY

        ErrorDocument 503 /errordocs/503_SERVICE_UNAVAILABLE

        ErrorDocument 506 /errordocs/506_VARIANT_ALSO_VARIES

    </IfModule>

</IfModule>

<Location /server-status>

    SetHandler server-status

    Order deny,allow

    Deny from all

    Allow from .cs.nott.ac.uk

</Location>

<Location /server-info>

    SetHandler server-info

    Order deny,allow

    Deny from all

    Allow from .cs.nott.ac.uk

</Location>

}}} 

Make sure that the server accepts connections to port 80. Check the firewall settings in  ''/etc/sysconfig/iptables'' for the following entry:

{{{

-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 80 -j ACCEPT

}}}

Make sure that the apache daemon is running, and that it will start at boot time:

{{{

/sbin/service httpd start

/sbin/chkconfig --add httpd

/sbin/chkconfig httpd on

}}}

== Email Configuration ==

The ProCKSI server component send emails to the user for several occasions. In order to make sure that they are delivered correctly even when the internet is temporarily not available, a local SMTP server (''postfix'') is set up. This will accect emails from the private network only, store them temporarily (if necessary), and forward them to an email relay server.

Make sure that ''postfix'' is the default mailing software (and not ''sendmail''!).

{{{

system-switch-mail -activate postfix

}}}

Make the following changes to the ''postfix ''configuration file (''/etc/postfix/main.cf''):

{{{

myhostname = procksi0.cs.nott.ac.uk

mydomain = cs.nott.ac.uk

myorigin = $mydomai

inet_interfaces = all

mydestination = $myhostname, localhost.$mydomain, localhost

mynetworks_style = subnet

virtual_alias_maps = hash:/etc/postfix/virtual

relayhost = marian.cs.nott.ac.uk

}}}

Create or modify ''/etc/postfix/virtual'':

{{{

root        root@localhost

postmaster  postmaster@localhost

adm         root@localhost

}}}

Generate the corresponding database file (''virtual.db''):

{{{

postmap /etc/postfix/virtual

}}}

Make sure that the postfix daemon is running, and that it will start at boot time:

{{{

/sbin/service postfix start

/sbin/chkconfig --add postfix

/sbin/chkconfig postfix on

}}}

Make sure that the firewall is not open for port 25 or port 28!

Check that the STMTP server in ''/home/procksi/latest/conf/main.ini'' is set correctly set to ''procksi0.cs.nott.ac.uk''

== Garbage Cleanup Scheduling ==

After a certain period of time, given in ''/home/procksi/latest/conf/main.ini'', sessions and requests expire and must be deleted. 

Edit ''procksi's'' crontab file taking effect for the ''latest'' and ''test'' version:

{{{

crontab -e

  0-59/1 * * * * /home/procksi/latest/cron/check_sessions.sh

  1-59/1 * * * * /home/procksi/latest/cron/check_tasks.sh

  2-59/1 * * * * /home/procksi/latest/cron/check_requests.sh

}}}

Analogously for ''/home/procksi/test''.

== Linking External Software ==

Make sure that all links in ''/home/procksi/latest/bin'' point to the correct files of the operating system: 

{{{

sh, compress, bzip2, gzip, zip, ppmz, qsub

}}}

Make sure that all further executable links in ''/home/procksi/latest/bin'' point to the correct files on the file system: 

{{{

 exec_cluster, exec_!DaliLite, exec_MaxCMO, exec_molauto, exec_molscript

}}}