1. PC Cluster Setup on Linux Fedora Core 5 High Performance Computing Lab Department of Computer Science and Information Engineering Tunghai University, Taichung, Taiwan 40704, ROC Presenter: Hao-Yu Tung

2. 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)

3. HPC Lab., CSIE@Tunghai University 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)

4. HPC Lab., CSIE@Tunghai University 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 disk 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)

5. HPC Lab., CSIE@Tunghai University Install Linux OS (cont.) After installation, you will use “adduser” and “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 clien t private ip and hostname

6. HPC Lab., CSIE@Tunghai University Set up NIS (Server side) Install NIS server  #wget http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/cor e/5/i386/os/Fedora/RPMS/ypserv-2.19- 0.i386.rpm http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/cor e/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

7. HPC Lab., CSIE@Tunghai University 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”

8. HPC Lab., CSIE@Tunghai University Set up NIS (Client side) Install NIS client  #wget http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/cor e/5/i386/os/Fedora/RPMS/ypbind-1.19- 0.i386.rpm http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/cor e/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 rebo ot) Add this line

9. HPC Lab., CSIE@Tunghai University 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

10. HPC Lab., CSIE@Tunghai University Set up NIS (Client side) Enabling ypbind service  #service ypbind restart  #chkconfig –level 345 ypbind on Change to this

11. HPC Lab., CSIE@Tunghai University Set up NIS (Client side) For testing NIS on client  #yptest

12. HPC Lab., CSIE@Tunghai University 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 spac e within this lin e

13. HPC Lab., CSIE@Tunghai University 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 /homenfsdefaults 0 0 server:/usr/local /usr/localnfsdefaults 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

14. HPC Lab., CSIE@Tunghai University 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]

15. HPC Lab., CSIE@Tunghai University 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 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/Fedora/RPMS /libaio-devel-0.3.106-2.2.i386.rpm http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/core/5/i386/os/Fedora/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/Fedora/RPMS /lam-7.1.1-11.i386.rpm http://ftp.isu.edu.tw/pub/Linux/Fedora/linux/core/5/i386/os/Fedora/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

16. HPC Lab., CSIE@Tunghai University Setup MPI (cont.) Complie MPI C program  $mpicc –o file file.c Execute MPI C program  $mpirun –np file