Department of Computing Science
CMPUT 399: Computational Science and Clusters
January 2008
Lecture
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Instructor
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B2 - T,Th 9:30 to 10:50 AM, Room GSB 711
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Paul
Lu, Associate Professor, Athabasca Hall 3-40, 492-7760
E-mail: paullu
<at> cs.ualberta.ca
Except for emergencies, please use email instead of phone calls.
Office Contact Times: Tuesday, Thursday 4 to 4:30 PM
Instructor's Home Page: http://www.cs.ualberta.ca/~paullu
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Instructor's Home Page:
http://www.cs.ualberta.ca/~paullu
Course's Home Page (i.e., this document):
http://www.cs.ualberta.ca/~paullu/C399
Announcement:
Class on Thursday, March 27 is in Athabasca Hall 3-32, **10** AM to 11 AM.
Last class is Thursday, April 3. No class on April 8 and 10.
Podcasts
Papers, notes, other downloads
Contact professor for password.
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Purpose
This course is an applied systems course on the configuration and
use of clusters (i.e., networked collections of compute servers)
for computational science. As a platform, clusters are becoming
more important in computing science, computational science, and
industry. For example, clusters are used to handle the large amounts
of data in bioinformatics, to simulate ocean currents and climate,
and to calculate risks associated with complicated financial
transactions.
The course will cover the hardware, software, and conceptual
principles of cluster computing.
Prerequisites
Any 200-level CMPUT course, or permission of the instructor.
Course Outline
Some of the topics to be covered (not necessarily in the following order)
include:
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Basics of parallelism and Amdahl's Law
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Cluster hardware architecture
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commodity processors, multi-core
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interconnection networks
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Basics of systems administration for clusters
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distributions: OSCAR, NPACI ROCKS, etc.
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batch schedulers
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file system issues
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power issues
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Performance metrics
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speed-up
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response time
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throughput
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Benchmarks
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HPCC
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Scientific computation
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chemistry: GAMESS
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EAS: POP
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simulation
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data processing
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visualization
Marking Scheme
Assignment 1
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12.5% |
Due Tuesday, January 29, in class.
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Assignment 2
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12.5% |
Due Tuesday, February 26, in class.
Added Jan. 31/08:
Now on-line!!
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Midterm exam
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25% |
Tuesday, February 12, in class.
Short answers. Based on research papers and class discussion.
Added Jan. 31/08:
3 to 4 questions. 50 minutes. 100 marks.
Open book.
Here is
an example midterm question.
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Project with report
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50% |
Extended to Friday, April 11.
Due Tuesday, April 1, in class.
Student's choice, with guidance of instructor.
Added Feb. 1/08:
Now on-line!!
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Readings and Textbooks
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Various research papers and resources,
provided by the instructor (THE ONLY REQUIRED READINGS).
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B. Wilkinson and M. Allen,
Parallel Programming: Techniques and Applications Using Networked Workstations and Parallel Computers, 2/e,
Prentice Hall, 2005.
(OPTIONAL).
Web site for textbook.
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W.R. Stevens and S.A. Rago,
Advanced Programming in the Unix Environment, 2nd Edition
Addison
Wesley, 2005. (OPTIONAL). Alternatively any equivalent
book
Useful Resources
- Conferences:
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ACM SIGPLAN Principles and Practice of Parallel Programming (PPOPP)
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International Parallel and Distributed Processing Symposium (IPDPS)
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Supercomputing (SC)
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International Conference on Parallel and Distributed Processing
Techniques and Applications (PDPTA)
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International Conference on High Performance Computing (HiPC)
- Journals:
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U of Alberta Library's Electronic Journals in Computing Science
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IEEE Transactions on Parallel and Distributed Computing
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Journal of Parallel and Distributed Computing
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Concurrency: Practice and Experience
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Parallel Computing