PC Cluster Setup on Linux Fedora Core 5

High Performance Computing LabDepartment of Computer Science and Infor

mation EngineeringTunghai University, Taichung, Taiwan 40704,

ROCPresenter: Hao-Yu Tung

HPC Lab., CSIE@Tunghai University

Contents Install Linux OS Set up Network Information System (NIS) Set up Network File System (NFS) Set up Secure Shell (SSH) Set up Message Passing Interface (MPI)

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Install Linux OS Install Fedora Core 5 Linux distribution

Install from CD-ROM Install from network (create a boot disk) Full install or custom if you are an expert Set separate IP for each machine (e.g. 192.168.1.1,

192.168.1.2)Com3

eth0: 192.168.1.1

eth1: 140.128.101.xxx

eth0: 192.168.1.2

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Install Linux OS (cont.) Partition

Consider you have a hard driver with 30GB in size Full installation of Fedora Core 5 will using 5GB available di

sk space Server side:

/ 10GB, holding root file system and RPM packages

Swap 256MB, as large as your physical memory /home the rest size of the disk , for NFS home usage

Client side: Swap 256MB, as large as your physical memory / the rest size of the disk

Disable the firewall and reboot #chkconfig --level 345 iptables off #chkconfig --level 345 ip6tables off (optional)

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Install Linux OS (cont.) After installation, you will use “adduser” a

nd “passwd” to add a normal user on server #adduser [test] #passwd [test]

Editing your “/etc/hosts” file # vi /etc/hosts

Here should be your server and client private ip and hostname

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Set up NIS (Server side) Install NIS server

#wget http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/core/5/i386/os/Fedora/RPMS/ypserv-2.19-0.i386.rpm

#rpm –ivh ypserv-2.19-0.i386.rpm Setting up NIS domain name on file “/etc/rc.

d/rc.local" #nisdomainname cluster #vi /etc/rc.d/rc.local

Temporary (Disappears after

reboot)

Add this line

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Set up NIS (Server side) Enabling ypserv and yppasswdd service

#service ypserv restart #service yppasswdd restart #chkconfig –level 345 ypserv on #chkconfig –level 345 yppasswdd on

Makefile #cd /var/yp #make

You’ll see this after

using the command “make”

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Set up NIS (Client side) Install NIS client

#wget http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/core/5/i386/os/Fedora/RPMS/ypbind-1.19-0.i386.rpm

#rpm –ivh ypbind-1.19-0.i386.rpm Setting up NIS domain name on file “/etc/rc.

d/rc.local" #nisdomainname cluster #vi /etc/rc.d/rc.local

Temporary (Disappears after

reboot)

Add this line

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Set up NIS (Client side) Enabling ypbind service

#service ypbind restart #chkconfig –level 345 ypbind on

Editing “/etc/nsswitch” file # vi /etc/nsswitch.conf

Original file

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Set up NIS (Client side)

Enabling ypbind service #service ypbind restart

#chkconfig –level 345 ypbind on

Change to this

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Set up NIS (Client side) For testing NIS on client

#yptest

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Set up NFS (Server side) Server Side

Create file “/etc/exports” to configure NFS in /etc directory by root privilege

/home 192.168.1.0/255.255.255.0(rw,no_root_squash) /usr/local 192.168.1.0/255.255.255.0(rw,no_root_squash)

Enable the NFS daemon #chkconfig --level 345 nfs on #service nfs restart

No blank space within

this line

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Set up NFS (Client side) Client Sides

Testing configuration (Optional) #mount –t nfs server:/home /home #mount –t nfs server:/usr/local /usr/local

Edit file “/etc/fstab” by adding the following two lines

server:/home /home nfs defaults 0 0 server:/usr/local /usr/local nfs defaults 0 0

Move original home to home2 and create a new home

#mv home home2 #mkdir home

Re-mount file system or reboot #mount –a

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Set up SSH Enable SSH server

#chkconfig --level 345 sshd on #service sshd restart

If you want to use ssh without password by the following steps in your account $ssh-keygen -t rsa

$cd /home/[user]/.ssh/ $cp id_rsa.pub authorized_keys2 $ssh [client_machine]

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Setup MPI Install MPI on server and client respectively by using root account

#wget http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/core/5/i386/os/Fedora/RPMS/libaio-0.3.106-2.2.i386.rpm

#rpm –ivh libaio-0.3.106-2.2.i386.rpm #wget http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/core/5/i386/os/Fedor

a/RPMS/libaio-devel-0.3.106-2.2.i386.rpm #rpm –ivh libaio-devel-0.3.106-2.2.i386.rpm #wget http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/core/5/i386/os/Fedor

a/RPMS/lam-7.1.1-11.i386.rpm #rpm –ivh lam-7.1.1-11.i386.rpm

Use MPI (cannot use root account) Create file “lamhost”

$recon –v lamhost $lamboot –v lamhost $wipe –v lamhost

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Setup MPI (cont.) Complie MPI C program

$mpicc –o file file.c Execute MPI C program

$mpirun –np <process number> file