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.

== 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 ==

Provider:	''www.planetdomain.com/ukcheap/home.jsp''[[BR]] Login: 	nkrasnogor[[BR]] Password: 	[BBSRC GRANT NUMBER][[BR]] 

== Domains ==

ProCKSI's main domain name is __''www.procksi.net''__, which is redirected to __''procksi.cs.nott.ac.uk''__, which is an alias for __''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   ||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:

 ||admin@procksi.net	||redirected to	||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	||''www.sitemeter.org'' 

||Login:	||s18procksi[[BR]] 

||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'': ''[[BR]] ''''procksi:x:510:510:ProCKSI-Server:/home/procksi:/bin/bash''

 * Add an entry for the new user into ''/etc/shadow'' if desired: ''[[BR]] ''''procksi:[ENCRYPTED_PASSWORD]:13483:0:99999:7:::''

 * Add a new group into ''/etc/group'', and add all users who should have access:''[[BR]] ''''procksi:x:510:dxb[[BR]] ''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[[BR]] -A RH-Firewall-1-INPUT -i eth1 -j ACCEPT[[BR]] directly after[[BR]] -A RH-Firewall-1-INPUT -i lo -j ACCEPT 

 * Restart the firewall on the head node and on each compute node:[[BR]] /sbin/service iptables restart

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

== 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:[[BR]] HOSTNAME=procksi0-priv.cs.nott.ac.uk[[BR]] The compute nodes must be named and configured accordingly.

 * Add the following to ''/etc/hosts'' on the head node:[[BR]] 127.0.0.1  procksi0-priv.cs.nott.ac.uk  procksi0-priv  localhost.localdomain  localhost[[BR]] 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:[[BR]] 192.168.199.10	procksi0-priv.cs.nott.ac.uk   procksi0-priv  [[BR]] 192.168.199.11 	procksi1-priv.cs.nott.ac.uk   procksi1-priv  [[BR]] 192.168.199.12 	procksi2-priv.cs.nott.ac.uk   procksi2-priv  [[BR]] Edit ''/etc/host.conf'' so that local setting in ''/etc/hosts'' take precedence over DNS:[[BR]] 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 (''procki0''):[[BR]] /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''):[[BR]] procksi0:/home/procksi	/home/procksi	nfs	bg,hard,intr	0 0[[BR]] procksi0:/usr/local/procksi	/usr/local/procksi	nfs	bg,hard,intr	0 0

 * Make the NFS daemons start at bootup. Enter at the command line of the head node and each compute node:[[BR]] /sbin/chkconfig nfs on

 * Start the NFS daemons. Enter at the command line on the head node and on each compute node:[[BR]] /sbin/service nfsd start

 * Generate the following temp directory on the head node and each compute node, at best on a separate partition:[[BR]] /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:''[[BR]] marian.cs.nott.ac.uk

 * Modify ''/etc/ntp.conf'' (at the of the file):[[BR]] server	marian.cs.nott.ac.uk[[BR]] 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:[[BR]] /sbin/chkconfig ntpd on

 * Start the NTP daemon. Enter at the command line:[[BR]] /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).[[BR]] 	export TORQUECFG=/usr/local/torque[[BR]]  	tar -xzvf TORQUE.tar.gz[[BR]]  	cd TORQUE[[BR]] 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 	--enable-server --enable-monitor --enable-clients [[BR]] 	 	

                        --with-server-home=$TORQUECFG --with-rcp=scp --disable-filesync --with-server-name

   	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[[BR]] 	

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

 Initialise/configure the queueing system's server daemon (pbs_server):[[BR]] 	pbs_server -t create

 [[BR]] Set the PBS operator and manager (must be a valid user name). [[BR]] 	qmgr[[BR]] 	> set server_name = procksi0-priv.cs.nott.ac.uk

 	> set server scheduling = true[[BR]] 	> set server operators += “root@procksi.cs.nott.ac.uk" [[BR]] 	> set server operators += “procksi@ procksi.cs.nott.ac.uk" [[BR]] 	> set server managers  += “root@ procksi.cs.nott.ac.uk" [[BR]] 	> set server managers  += “procksi@ procksi.cs.nott.ac.uk" [[BR]] 

 Allow only procksi and root to submit jobs into the queue:[[BR]] 	> set server acl_users = “root, procksi" [[BR]] 	> set server acl_user_enable = true

 Set the default queue to batch[[BR]] 	> set server default_queue=batch

 Set email address for email that is sent by PBS:[[BR]] 	> 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[[BR]]                               procksi1-priv.cs.nott.ac.uk[[BR]]                               procksi2-priv.cs.nott.ac.uk

 Restrict nodes that can access the PBS server:

 	> set server acl_hosts = procksi0-priv.cs.nott.ac.uk[[BR]]                              procksi1-priv.cs.nott.ac.uk[[BR]]                              procksi2-priv.cs.nott.ac.uk

 	> set acl_host_enable = true[[BR]] 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'':[[BR]] 	> create queue batch queue_type=execution[[BR]] 	> set queue batch started=true[[BR]] 	> set queue batch enabled=true[[BR]] 	> set queue batch resources_default.nodes=1

 Configure queue ''test ''accordingly''.''[[BR]] 

 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:[[BR]] 	cd $TORQUE[[BR]] 	make packages[[BR]] 	scp torque-package-mom-linux-i686.sh 	procksi1|procksi2[[BR]] 	scp torque-package-clients-linux-i686.sh procksi1|procksi2[[BR]] 	[[BR]] 

=== 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[[BR]] 	psh compute torque-package-clients-linux-i686.sh -install

 Check if the nodes know the head node[[BR]] 	$TORQUECFG/server_name[[BR]] 	procksi0-priv.cs.nott.ac.uk

 [[BR]] 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

}}}

 [[BR]] 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[[BR]] 	qstat -q[[BR]] 	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 [[BR]] 	tar -xzvf MAUI.tar.gz[[BR]]  	cd TORQUE[[BR]] 

 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 --with-pbs=$TORQUECFG --with-spooldir=$MAUIDIR[[BR]]  	make[[BR]]

  	make install 

 Fine-tune MAUI in $''MAUIDIR/maui.cfg''[[BR]] 	

{{{

        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 [[BR]] 			

        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:[[BR]]  	cp /home/procksi/latest/install/pbs_head-node /etc/init.d/pbs [[BR]]  	/sbin/chkconfig --add pbs[[BR]]  	/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:[[BR]]  	cp /home/procksi/latest/install/pbs_compute-node /etc/init.d/pbs[[BR]]  	/sbin/chkconfig --add pbs[[BR]]  	/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.

== !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.

[[BR]] 

||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 www.imagemagick.org if not already installed.

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

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[[BR]] /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;[[BR]] INSERT INTO user SET host='localhost', user='procksi_user', 		password=PASSWORD('''password_procksi_user''');[[BR]] INSERT INTO user SET host='localhost', user='procksi_admin', 			password=PASSWORD('''password_procksi_admin''');[[BR]] FLUSH PRIVILEGES;

Repeat these steps analogously for ''procksi0-priv, procksi1-priv, 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 [[BR]]  		WITH GRANT OPTION;[[BR]] GRANT SELECT, UPDATE, INSERT, DELETE ON procksi_latest.* [[BR]]  		TO procksi_user@localhost;[[BR]] GRANT ALL ON procksi_latest.* TO procksi_admin@procksi0.cs.nott.ac.uk [[BR]]  		WITH GRANT OPTION;[[BR]] GRANT SELECT, UPDATE, INSERT, DELETE ON procksi_latest.* [[BR]]  		TO procksi_user@procksi0.cs.nott.ac.uk;[[BR]] GRANT SELECT, UPDATE, INSERT, DELETE ON procksi_latest.* [[BR]]  		TO procksi_user@procksi1.cs.nott.ac.uk;[[BR]] GRANT SELECT, UPDATE, INSERT, DELETE ON procksi_latest.* [[BR]]  		TO procksi_user@procksi2.cs.nott.ac.uk;[[BR]] 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/

 !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:[[BR]] 	-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[[BR]] /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[[br]]

 /sbin/chkconfig --add postfix[[BR]] 

 /sbin/chkconfig postfix on[[br]]

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[[BR]] 

{{{

 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