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Cluster Environment 

Purpose: In order to provide ETLab Shared HPC Facility Users with up-to-date information about available clusters and the technologies associated with them, this boot camp is designed to cover subjects of general interest and issues associated with specific research group’s activities. A Q&A session provides the opportunity for the system administration and programmer staff to answer and try to help resolve users’ questions on a face-to-face manner.
Date: August 7, 2006
Location: Ryals 407 (Morning sessions) and Ryals 417/ Ryals 127 for afternoon hand-on sessions
Format: General subjects related to the HPC usage, followed with the parallel group-specific hand-on exercises
Attendees: ETLab Shared HPC Facility users are all eligible. RSVP is REQUIRED. Please email to
Wiki Page: HPC - High Performance Computing

**NOTE: You will need RealPlayer to view videos.

8:00-8:30 BREAKFAST and COFFEE

8:30-8:45 Welcome and Opening Remark Robert Kimberly
Bharat Soni
8:45-9:00 Cluster environment:
i. Background and Overview
ii. Policies
iii. What services are provided, and what are not.
Alan Shih
9:00-9:45 Cluster setup
i. What is a headnode,
• What a headnode is for, and
• Why you should not run jobs on the headnode, etc.
ii. Where things are (software paths, software list, software paths, etc.)
iii. How to report a problem (ETLab HPC trouble ticket system)
iv. Wiki
Tommy Foley,
John-Paul Robinson
9:45-10:15 Linux commands
i. Basic commands (ls, cd, pwd, and other)
ii. Bash/csh/tcsh….
iii. Advanced topics (scripting, how and where to get information, etc.)
Corey Shum
10:15-10:30 Break

10:30-11:00 Job Queuing Systems
i. PBS/Pro
ii. SGE 
iii. Debug
iv. Other (LSF, etc.)
Mark Dillavou
11:00-12:15 Cluster Q&A and Problem Solving
i. Questions about the subjects covered today
ii. User comments and feedbacks for improving ETLab HPC operation
iii. User’s current outstanding issues that need to be addressed
12:15-1:30 Lunch Break

1:30-3:00 Group-specific hand-on Examples (Parallel Sessions)
SSG (Meet at Ryals 417)
i. R code/SGE example
ii. Structure/STRAT/PBS example
ME (Meet at Ryals 127)
Structural Biology (Meet at Ryals 407)
Tapan Mehta,
Vinodh Srinivasasainagendra,
Mark Dillavou