HPC High Processing Cluster in BITS PILANI - Revision history

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2026-07-25T15:59:56Z

Flag as outdated (client review pass)

← Older revision		Revision as of 15:59, 25 July 2026
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			{{Outdated\|reason=Old Technology and Customer But Relevant for Understanding\|date=2026-07}}
	[[category:Bits pilani]]		[[category:Bits pilani]]

Navdeep: /* INSTALLATION OF MPI(MESSAGE PASSING INTERFACE) */

2013-01-22T10:08:48Z

INSTALLATION OF MPI(MESSAGE PASSING INTERFACE)

← Older revision		Revision as of 10:08, 22 January 2013
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	mkdir /home/wolf/mpich2-install		mkdir /home/wolf/mpich2-install
	cd /home/wolf/mpich2-install/mpich2-install		cd /home/wolf/mpich2-install/mpich2-install
	./configure ~~–prefix~~=/home/wolf/mpich2-install/ 2>&1 \| tee c.~~txtmake~~ 2>&1 \| tee m.txt		./configure --prefix=/home/wolf/mpich2-install/ 2>&1 \| tee c.txt
			make 2>&1 \| tee m.txt
	make check		make check
	make install 2>&1 \| tee mi.txt		make install 2>&1 \| tee mi.txt

Biswajit: /* Preparation of Master node(IBM-39) */

2012-12-29T13:45:55Z

Preparation of Master node(IBM-39)

← Older revision		Revision as of 13:45, 29 December 2012
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	* Two groups was created and a two users who will be responsible for operating cluster was added as follows.		* Two groups was created and a two users who will be responsible for operating cluster was added as follows.

	groupadd beowulf2		groupadd beowulf2
			useradd -g beowulf2 wolf2
	useradd -g beowulf2 wolf2		groupadd prolam1
			useradd –g prolam1 lam1
	groupadd prolam1

	useradd –g prolam1 lam1

	'''Note : This document is concern about wolf2 user.'''		'''Note : This document is concern about wolf2 user.'''
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	* Following line were added in /home/wolf2/.bash_profile		* Following line were added in /home/wolf2/.bash_profile

	umask 007		umask 007

	* '''Mount all home directories for these HPC2 Cluster i.e.'''		* '''Mount all home directories for these HPC2 Cluster i.e.'''
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	Mkdir /ugassignments /pgassignments		Mkdir /ugassignments /pgassignments

	mount –t nfs 172.20.4.43: /ugassignments /ugassignments		mount –t nfs 172.20.4.43: /ugassignments /ugassignments
			mount –t nfs 172.20.4.43: /pgassignments /pgassignments
	mount –t nfs 172.20.4.43: /pgassignments /pgassignments

	Then make permanent entry on fstab		Then make permanent entry on fstab
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	Uncomment the following in /etc/sshd/sshd_config		Uncomment the following in /etc/sshd/sshd_config

	<nowiki>#RSAAuthentication yes </nowiki>		<nowiki>#RSAAuthentication yes </nowiki>
			<nowiki>#AuthorizedKeysFile .ssh/authorized_keys </nowiki>
	<nowiki>#AuthorizedKeysFile .ssh/authorized_keys </nowiki>

	* Reboot and login as wolf because operation of cluster will always be done by user “wolf”		* Reboot and login as wolf because operation of cluster will always be done by user “wolf”
	* To generate your public and private SSH keys, do this:		* To generate your public and private SSH keys, do this:

	ssh-keygen –t rsa		ssh-keygen –t rsa

	This will generate the two public/private key pain in .ssh directory. Copy the id_rsa.pub file into a file called "authorized_keys" right there in the .ssh directory.This key will be used later. Modify the security of file and directory		This will generate the two public/private key pain in .ssh directory. Copy the id_rsa.pub file into a file called "authorized_keys" right there in the .ssh directory.This key will be used later. Modify the security of file and directory

	chmod 644 ~/.ssh/auth*		chmod 644 ~/.ssh/auth*
			chmod 755 ~/.ssh
	chmod 755 ~/.ssh

	* Add these entries is /home/wolf/.bash_profile		* Add these entries is /home/wolf/.bash_profile

	export LAMRSH='ssh -x'		export LAMRSH='ssh -x'
			ssh-agent sh -c 'ssh-add && bash'
	ssh-agent sh -c 'ssh-add && bash'

	* Install MPI as above HPC1 section		* Install MPI as above HPC1 section
	* Install slave nodes as above section but home directories mount as a nfs.		* Install slave nodes as above section but home directories mount as a nfs.
	* Install Ganglia as above HPC1 section		* Install Ganglia as above HPC1 section

Biswajit: /* INSTALLATION OF MPI(MESSAGE PASSING INTERFACE) */

2012-12-29T13:43:48Z

INSTALLATION OF MPI(MESSAGE PASSING INTERFACE)

← Older revision		Revision as of 13:43, 29 December 2012
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	1. Unpack the tar ﬁle.		1. Unpack the tar ﬁle.

	tar -zxvf mpich2-1.2.tar.gz		tar -zxvf mpich2-1.2.tar.gz

	2. Choose an installation directory (the default is /usr/local/bin):		2. Choose an installation directory (the default is /usr/local/bin):


	mkdir /home/wolf/mpich2-install		mkdir /home/wolf/mpich2-install
			cd /home/wolf/mpich2-install/mpich2-install
	cd /home/wolf/mpich2-install/mpich2-install		./configure –prefix=/home/wolf/mpich2-install/ 2>&1 \| tee c.txtmake 2>&1 \| tee m.txt
			make check
	./configure –prefix=/home/wolf/mpich2-install/ 2>&1 \| tee c.txtmake 2>&1 \| tee m.txt		make install 2>&1 \| tee mi.txt

	make check

	make install 2>&1 \| tee mi.txt

	Set the enviroment variable for user “wolf” in /home/wolf/.bash_profile		Set the enviroment variable for user “wolf” in /home/wolf/.bash_profile
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	Add following lines.		Add following lines.

	MPICH2=/home/wolf/mpich2-install/bin/		MPICH2=/home/wolf/mpich2-install/bin/
			PATH=$PATH:$HOME/bin:$MPICH2/bin
	PATH=$PATH:$HOME/bin:$MPICH2/bin

	2.MPICH2, uses an external process manager for scalable startup of large MPI jobs. The default process manager is called MPD, which is a ring of daemons on the machines where you will run your MPI programs.		2.MPICH2, uses an external process manager for scalable startup of large MPI jobs. The default process manager is called MPD, which is a ring of daemons on the machines where you will run your MPI programs.
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	For security reasons, mpd looks in your home directory for a ﬁle named .mpd.conf containing the line in home directory. So create this file as follows		For security reasons, mpd looks in your home directory for a ﬁle named .mpd.conf containing the line in home directory. So create this file as follows

	cd $HOME		cd $HOME
			touch .mpd.conf
	touch .mpd.conf		chmod 600 .mpd.conf

	chmod 600 .mpd.conf

	add a line		add a line

	<nowiki>secretword=<anysecretword> </nowiki>		<nowiki>secretword=<anysecretword> </nowiki>

	we used “redhat123” as secretword in our case.		we used “redhat123” as secretword in our case.
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	3.The ﬁrst sanity check consists of bringing up a ring of one mpd on the local machine, testing one mpd command, and bringing the “ring” down.		3.The ﬁrst sanity check consists of bringing up a ring of one mpd on the local machine, testing one mpd command, and bringing the “ring” down.

	mpd &		mpd &
			mpdtrace
			mpdallexit
	mpdtrace


	mpdallexit


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	4.Now we will bring up a ring of mpd’s on a set of machines. Create a ﬁle consisting of a list of machine names, one per line. Name this ﬁle .mpd.hosts in home directory of user wolf. These hostnames will be used as targets for ssh so include full domain names if necessary. Check that you can reach these machines with ssh without entering a password. You can test by doing.		4.Now we will bring up a ring of mpd’s on a set of machines. Create a ﬁle consisting of a list of machine names, one per line. Name this ﬁle .mpd.hosts in home directory of user wolf. These hostnames will be used as targets for ssh so include full domain names if necessary. Check that you can reach these machines with ssh without entering a password. You can test by doing.

	Ssh node1 –l wolf		Ssh node1 –l wolf

	# Start the daemons on (some of) the hosts in the ﬁle mpd.hosts		# Start the daemons on (some of) the hosts in the ﬁle mpd.hosts

	<nowiki>mpdboot -n <number to start> -f mpd.hosts </nowiki>		<nowiki>mpdboot -n <number to start> -f mpd.hosts </nowiki>

	The number to start can be less than 1 + number of hosts in the ﬁle,but cannot be greater than 1 + the number of hosts in the ﬁle. One mpd is always started on the machine where mpdboot is run, and is counted in the number to start, whether or not it occurs in the ﬁle. By default, mpdboot will only start one mpd per machine even if the machine name appears in the hosts ﬁle multiple times.		The number to start can be less than 1 + number of hosts in the ﬁle,but cannot be greater than 1 + the number of hosts in the ﬁle. One mpd is always started on the machine where mpdboot is run, and is counted in the number to start, whether or not it occurs in the ﬁle. By default, mpdboot will only start one mpd per machine even if the machine name appears in the hosts ﬁle multiple times.

	mpdboot -n 5 -f mpd.hosts		mpdboot -n 5 -f mpd.hosts

	This will start the cluster.		This will start the cluster.

	mpdtrace		mpdtrace

	This command will show you the nodes in the cluster like below		This command will show you the nodes in the cluster like below
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	b. Edit file /home/wolf/.bash_pofile		b. Edit file /home/wolf/.bash_pofile

	export LAMRSH='ssh -x'		export LAMRSH='ssh -x'
			ssh-agent
	ssh-agent		MPICH2=/home/wolf/mpich2-install/mpich2
			PATH=$HOME/bin:$MPICH2/bin
	MPICH2=/home/wolf/mpich2-install/mpich2

	PATH=$HOME/bin:$MPICH2/bin

	Make /linuxeda directory		Make /linuxeda directory

	mkdir /linuxeda		mkdir /linuxeda

	This file have all the binaries and need to rsync with all when changes occurred.		This file have all the binaries and need to rsync with all when changes occurred.

	chmod 770 /linuxeda		chmod 770 /linuxeda

	All home directories are in lvm mode name and location		All home directories are in lvm mode name and location
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	Following entry is made in /etc/exports file		Following entry is made in /etc/exports file

	/staff <nowiki>* (rw,no_root_squash,sync) </nowiki>		/staff <nowiki>* (rw,no_root_squash,sync) </nowiki>
			/projects <nowiki>* (rw,no_root_squash,sync) </nowiki>
	/projects <nowiki>* (rw,no_root_squash,sync) </nowiki>		/ugassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>
			/pgassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>
	/ugassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>		<nowiki># service nfs start ; chkconfig nfs on</nowiki>

	/pgassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>

	<nowiki># service nfs start ; chkconfig nfs on</nowiki>

	c. Reboot all the nodes.		c. Reboot all the nodes.
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	'''Note''': Firewall should be disabled in all nodes as MPI uses randoms ports each time it is started.		'''Note''': Firewall should be disabled in all nodes as MPI uses randoms ports each time it is started.

	“mpdboot -n 2 -f mpd.hosts” command should be executed as wolf user from master node. This will start mpd daemon in slave nodes		“mpdboot -n 2 -f mpd.hosts” command should be executed as wolf user from master node. This will start mpd daemon in slave nodes

	Now we will run an MPI job, using the mpiexec command as specified in the MPI-2 standard.		Now we will run an MPI job, using the mpiexec command as specified in the MPI-2 standard.
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	mpiexec -n 2 ./examples/cpi		mpiexec -n 2 ./examples/cpi

Biswajit: /* Preparation of Master node(IBM-39) */

2012-12-29T13:39:46Z

Preparation of Master node(IBM-39)

← Older revision		Revision as of 13:39, 29 December 2012
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	* Two groups was created and a two users who will be responsible for operating cluster was added as follows.		* Two groups was created and a two users who will be responsible for operating cluster was added as follows.

	groupadd beowulf		groupadd beowulf
			useradd -g beowulf wolf
	useradd -g beowulf wolf		groupadd prolam
			useradd –g prolam lam
	groupadd prolam

	useradd –g prolam lam

	'''Note : This document is concern about wolf user.'''		'''Note : This document is concern about wolf user.'''
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	* Following line were added in /home/wolf/.bash_profile		* Following line were added in /home/wolf/.bash_profile

	umask 007		umask 007

	* NFS server was created as follows in master node.		* NFS server was created as follows in master node.

	mkdir /linuxeda		mkdir /linuxeda

	This file have all the binaries and need to rsync with all when changes occurred.		This file have all the binaries and need to rsync with all when changes occurred.

	chmod 770 /linuxeda		chmod 770 /linuxeda

	All home directories are in lvm mode name and location		All home directories are in lvm mode name and location
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	'''Following entry is made in /etc/exports file '''		'''Following entry is made in /etc/exports file '''

	/staff <nowiki>* (rw,no_root_squash,sync) </nowiki>		/staff <nowiki>* (rw,no_root_squash,sync) </nowiki>
			/projects <nowiki>* (rw,no_root_squash,sync) </nowiki>
	/projects <nowiki>* (rw,no_root_squash,sync) </nowiki>		/ugassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>
			/pgassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>
	/ugassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>

	/pgassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>

	<nowiki># service nfs start ; chkconfig nfs on</nowiki>		<nowiki># service nfs start ; chkconfig nfs on</nowiki>


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	Uncomment the following in /etc/sshd/sshd_config		Uncomment the following in /etc/sshd/sshd_config

	<nowiki>#RSAAuthentication yes </nowiki>		<nowiki>#RSAAuthentication yes </nowiki>
			<nowiki>#AuthorizedKeysFile .ssh/authorized_keys </nowiki>
	<nowiki>#AuthorizedKeysFile .ssh/authorized_keys </nowiki>

	* Reboot and login as wolf because operation of cluster will always be done by user “wolf”		* Reboot and login as wolf because operation of cluster will always be done by user “wolf”
	* To generate your public and private SSH keys, do this:		* To generate your public and private SSH keys, do this:

	ssh-keygen –t rsa		ssh-keygen –t rsa

	This will generate the two public/private key pain in .ssh directory. Copy the id_rsa.pub file into a file called "authorized_keys" right there in the .ssh directory.This key will be used later. Modify the security of file and directory		This will generate the two public/private key pain in .ssh directory. Copy the id_rsa.pub file into a file called "authorized_keys" right there in the .ssh directory.This key will be used later. Modify the security of file and directory

	chmod 644 ~/.ssh/auth*		chmod 644 ~/.ssh/auth*
			chmod 755 ~/.ssh
	chmod 755 ~/.ssh

	* Add these entries is /home/wolf/.bash_profile		* Add these entries is /home/wolf/.bash_profile

	export LAMRSH='ssh -x'		export LAMRSH='ssh -x'

	ssh-agent sh -c 'ssh-add && bash'		ssh-agent sh -c 'ssh-add && bash'

	=<center>'''INSTALLATION OF MPI(MESSAGE PASSING INTERFACE)'''</center>=		=<center>'''INSTALLATION OF MPI(MESSAGE PASSING INTERFACE)'''</center>=

Biswajit at 10:13, 29 December 2012

2012-12-29T10:13:11Z

← Older revision		Revision as of 10:13, 29 December 2012
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	<center>[[Image:bits_p.png]]<center>		<center>[[Image:bits_p.png]]</center>


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	* Ldap user add script is located at on both servers under “/root/script/”, by default password is “user123”.		* Ldap user add script is located at on both servers under “/root/script/”, by default password is “user123”.

	'''IBM 2-Node Machines IP/HOSTNAME Details :'''		='''IBM 2-Node Machines IP/HOSTNAME Details :'''=


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	'''Sunfire 9-Node Machines IP/HOSTNAMES Details :'''		=='''Sunfire 9-Node Machines IP/HOSTNAMES Details :'''==


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	# <center>'''INTRODUCTION OF HIGH PROCESSING CLUSTER'''</center>		== <center>'''INTRODUCTION OF HIGH PROCESSING CLUSTER'''</center>==

	'''HPC cluster''' are used to run parallel programs for time-intensive computations and are of special interest to the scientific community. It commonly run simulations and other CPU-intensive programs that would take an inordinate amount of time to run on regular hardware.		'''HPC cluster''' are used to run parallel programs for time-intensive computations and are of special interest to the scientific community. It commonly run simulations and other CPU-intensive programs that would take an inordinate amount of time to run on regular hardware.
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	<center>'''The basic cluster Design'''</center>		<center>'''The basic cluster Design'''</center>

	<center>[[Image:]]</center>		<center>[[Image:bits-1.png]]</center>

	Grid computing is a broad term that typically refers to a service-oriented architecture (SOA) with collaboration among loosely coupled systems. Cluster-based HPC is a special case of grid computing in which the nodes are tightly coupled.		Grid computing is a broad term that typically refers to a service-oriented architecture (SOA) with collaboration among loosely coupled systems. Cluster-based HPC is a special case of grid computing in which the nodes are tightly coupled.


	# <center>'''REQUIREMENT OF BITS-PILANI'''</center>		==<center>'''REQUIREMENT OF BITS-PILANI'''</center>==

	BITS had a requirement of High Processing Cluster for there applications .For this one slave node server with one master node server and Eight Slave node server with one master node server were used. RHEL5 server where installed in two node cluster and CENTOS5 server installed in 9 node cluster.		BITS had a requirement of High Processing Cluster for there applications .For this one slave node server with one master node server and Eight Slave node server with one master node server were used. RHEL5 server where installed in two node cluster and CENTOS5 server installed in 9 node cluster.
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	# <center>'''INSTALLATION OF 2-Node(IBM) HIGH PROCESSING CLUSTER'''</center>		=<center>'''INSTALLATION OF 2-Node(IBM) HIGH PROCESSING CLUSTER'''</center>=

	'''Master node'''		=='''Master node'''==

	* NFS server running in High Availability.		* NFS server running in High Availability.
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	* user lam and group prolam responsible for operating for all projects members,here “projects” is an OU of ldap. All “projects” members use only lam user for HPC		* user lam and group prolam responsible for operating for all projects members,here “projects” is an OU of ldap. All “projects” members use only lam user for HPC

	'''Slave node'''		=='''Slave node'''==

	* NFS server running in High Availability		* NFS server running in High Availability
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	* First the entries where made in /etc/hosts of each cluster as follows		* First the entries where made in /etc/hosts of each cluster as follows

	~~172.20.4.39 ibm-39.bits.acibm-39~~

	#		172.20.4.39 ibm-39.bits.ac ibm-39
	##		172.20.4.40 ibm-40.bits.ac ibm-40
	~~###~~
	~~####~~ ibm-40.bits.~~acibm~~-40

	* Two groups was created and a two users who will be responsible for operating cluster was added as follows.		* Two groups was created and a two users who will be responsible for operating cluster was added as follows.
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	ssh-agent sh -c 'ssh-add && bash'		ssh-agent sh -c 'ssh-add && bash'

	# <center>'''INSTALLATION OF MPI(MESSAGE PASSING INTERFACE)'''</center>		=<center>'''INSTALLATION OF MPI(MESSAGE PASSING INTERFACE)'''</center>=

	The MPI mpich2 can be downloaded from [http://www.mpich.org/static/tarballs/1.2/mpich2-1.2.tar.gz http://www.mpich.org/static/tarballs/1.2/mpich2-1.2.tar.gz]		The MPI mpich2 can be downloaded from [http://www.mpich.org/static/tarballs/1.2/mpich2-1.2.tar.gz http://www.mpich.org/static/tarballs/1.2/mpich2-1.2.tar.gz]
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	The cpi example will tell you which hosts it is running on.		The cpi example will tell you which hosts it is running on.

	'''How to Run Cadence Application : '''		='''How to Run Cadence Application : '''=

	# Firstly copy your application into /linuxeda		# Firstly copy your application into /linuxeda
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	'''Note : lam have same configuration as wolf'''		'''Note : lam have same configuration as wolf'''

	# <center>'''INSTALLATION OF 9-Node(SUNFIRE) HIGH PROCESSING CLUSTER'''</center>		= <center>'''INSTALLATION OF 9-Node(SUNFIRE) HIGH PROCESSING CLUSTER'''</center>=

	'''Master node'''		=='''Master node'''==

	* NFS Client		* NFS Client
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	* user lam1 and group prolam1 responsible for operating for all projects members,here “ugassignments” is an OU of ldap. All “ugassignments” members use only lam user for HPC		* user lam1 and group prolam1 responsible for operating for all projects members,here “ugassignments” is an OU of ldap. All “ugassignments” members use only lam user for HPC

	'''Slave node'''		=='''Slave node'''==

	* NFS client		* NFS client

Biswajit: /* ARCHITECTURE – VLSI LAB DATA CENTER (BITS-PILANI) */

2012-12-29T10:05:24Z

ARCHITECTURE – VLSI LAB DATA CENTER (BITS-PILANI)

@@ Line 11: / Line 11: @@
-[[Image:bits_p.png]]
+<center>[[Image:bits_p.png]]<center>
-'''BETWEEN'''
+==<center>'''ARCHITECTURE DETAILS'''</center>==
 * They have two IBM servers and nine Sunfire servers.

Biswajit: /* ARCHITECTURE – VLSI LAB DATA CENTER (BITS-PILANI) */

2012-12-29T10:02:48Z

ARCHITECTURE – VLSI LAB DATA CENTER (BITS-PILANI)

← Older revision		Revision as of 10:02, 29 December 2012
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	== <center>'''ARCHITECTURE – VLSI LAB DATA CENTER (BITS-PILANI)'''</center>==		== <center>'''ARCHITECTURE – VLSI LAB DATA CENTER (BITS-PILANI)'''</center>==


			[[Image:bits_p.png]]

	<center>'''HPC-1(IBM SERVERS -2 NODE SEPARATE CLUSTERS)'''</center>		<center>'''HPC-1(IBM SERVERS -2 NODE SEPARATE CLUSTERS)'''</center>
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	* user lam and group prolam responsible for operating for all projects members,here “projects” is an OU of ldap. All “projects” members use only lam user for HPC		* user lam and group prolam responsible for operating for all projects members,here “projects” is an OU of ldap. All “projects” members use only lam user for HPC

	Note : wolf and lam are local system users in master and slave nodes.,		Note : wolf and lam are local system users in master and slave nodes.,


	== Preparation of Master node(IBM-39) ==		== Preparation of Master node(IBM-39) ==

Biswajit at 09:57, 29 December 2012

2012-12-29T09:57:57Z

← Older revision		Revision as of 09:57, 29 December 2012
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	[[category:Bits pilani]]		[[category:Bits pilani]]

	<center>'''HIGH PROCESSING CLUSTER USING MPICH2'''</center>		==<center>'''HIGH PROCESSING CLUSTER USING MPICH2'''</center>==

	~~<center>~~'''FOR 2 NODES AND 9 NODES CLUSTER'''~~</center>~~		'''FOR 2 NODES AND 9 NODES CLUSTER'''

			'''NAVDEEP MATHUR'''

	~~<center>'''NAVDEEP MATHUR'''</center>~~

			== <center>'''ARCHITECTURE – VLSI LAB DATA CENTER (BITS-PILANI)'''</center>==
	# <center>'''ARCHITECTURE – VLSI LAB DATA CENTER (BITS-PILANI)'''</center>

	<center>'''HPC-1(IBM SERVERS -2 NODE SEPARATE CLUSTERS)'''</center>		<center>'''HPC-1(IBM SERVERS -2 NODE SEPARATE CLUSTERS)'''</center>

Biswajit at 09:54, 29 December 2012

2012-12-29T09:54:41Z

← Older revision		Revision as of 09:54, 29 December 2012
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			[[category:Bits pilani]]

	<center>'''HIGH PROCESSING CLUSTER USING MPICH2'''</center>		<center>'''HIGH PROCESSING CLUSTER USING MPICH2'''</center>