1. Parallel Programming: Techniques and Applications Using Networked Workstations and Parallel Computers Chapter 2: Message-Passing Computing LAM/MPI at the University of Akron (c) Prentice-Hall Inc., 2002. All rights reserved. Based on the 1998 Notre Dame MPI Tutorial Sessions and the Fall 2002 OSC “Introduction to Cluster Ohio” Workshop at Kent State. Modified 1/10/09 by T. O’Neil for 3460:4/577, Spring 2009, Univ. of Akron. Previous revisions: 1/16/03, 1/18/03, 3/16/05, 10/7/05, 1/16/07. Barry Wilkinson and Michael Allen

2. Wilkinson & Allen, Parallel Programming: Techniques & Applications Using Networked Workstations & Parallel Computers, 1999. 2 University of Akron Cluster Configurations C.S. Cluster 22 nodes 48 processors, mostly 3.0 GHz Pentium 4 4 Gb memory/node (88 Gb total memory) Dual gigabit Ethernet interconnects Separate overhead and MPI subnets Diskless; no swap space Further details can be found in the /root/CLUSTER.HARDWARE file FAQs can be found in the /root/cluster.notes file

3. Wilkinson & Allen, Parallel Programming: Techniques & Applications Using Networked Workstations & Parallel Computers, 1999. 3 Accessing the Clusters The only way is to remotely access the front end node of the cluster: ssh your_id @cluster.cs.uakron.edu ssh sends your commands over an encrypted stream so your passwords and so forth can’t be sniffed over the network Batch nodes are not connected to the external network

4. Wilkinson & Allen, Parallel Programming: Techniques & Applications Using Networked Workstations & Parallel Computers, 1999. 4 Setting Up LAM/MPI on the Cluster The first time you access the cluster establish your identity before attempting to use other nodes. Enter the command ssh-keygen and hit return until no longer prompted Then issue the commands cat ~/.ssh/*.pub >> ~/.ssh/authorized_keys cat /root/.ssh/known_hosts >> ~/.ssh/known_hosts Now issue the command cp /root/lamboot.full. to copy the full boot file to your home directory. Assuming you don’t need all nodes for your programs, edit this file for your job size and save as hostfile.

5. Wilkinson & Allen, Parallel Programming: Techniques & Applications Using Networked Workstations & Parallel Computers, 1999. 5 Using LAM/MPI To begin using MPI ssh into the cluster and issue the command lamboot –v hostfile Now : To compile C code: mpicc –o file file.c To compile C++ code: mpiCC –o file file.cpp To execute compiled program: mpirun –v –np no_procs file To terminate processes for reboot: lamclean –v To terminate LAM: lamhalt

6. Wilkinson & Allen, Parallel Programming: Techniques & Applications Using Networked Workstations & Parallel Computers, 1999. 6 Other Points of Note If you have to change your password, change it just prior to logging out. Otherwise may have problems with the password script. Use nice values of 15-18 Acceptable values 1-20 with lower number corresponding to a higher priority Keeping this low shouldn’t impact anyone else In your code #include “unistd.h” then as soon as you can in main() nice( x );