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PC Cluster Setup on Linux Fedora Core 5

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. Contents. Install Linux OS Set up Network Information System (NIS)

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PC Cluster Setup on Linux Fedora Core 5

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  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. 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) HPC Lab., CSIE@Tunghai University

  3. 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) HPC Lab., CSIE@Tunghai University

  4. 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) HPC Lab., CSIE@Tunghai University

  5. 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 client private ip and hostname HPC Lab., CSIE@Tunghai University

  6. 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 HPC Lab., CSIE@Tunghai University

  7. 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” HPC Lab., CSIE@Tunghai University

  8. 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 HPC Lab., CSIE@Tunghai University

  9. 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 HPC Lab., CSIE@Tunghai University

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

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

  12. 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 HPC Lab., CSIE@Tunghai University

  13. 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 HPC Lab., CSIE@Tunghai University

  14. 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] HPC Lab., CSIE@Tunghai University

  15. 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/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 • #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 HPC Lab., CSIE@Tunghai University

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

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