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Advanced School in High Performance and GRID Computing - Concepts and Applications
FIRST WEEK:
SECOND WEEK:
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| 1 |
PRELIMINARY ACTIVITIES:
- register on the Moodle portal
- update and complete your profile
- take the preliminary Linux Quiz
- fill in the questionnaire
- take lessons proposed in order to be able at least to
- use basic linux commands
- create/edit files
- create plots
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| 2 |
DAY 1: Introduction to Linux and to the concepts of HPC and GRID (Monday, November 30)
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| 08:30 - 09:30
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Registration & Administrative Formalities
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| 09:30 - 09:40
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Stefano Cozzini / Axel Kohlmeyer: Introduction to the School (slides);
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| 09:40 - 10:30
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Stefano Cozzini: Introduction to HPC and Cluster Computing (slides);
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| 10:30 - 11:00
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--- Coffee Break ---
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| 11:00 - 11:45
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Bob Johnson: Introduction to Linux Commands (part 1) (slides);
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| 11:45 - 12:15
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Moreno Baricevic: Introduction to Networking (slides: 30' version or full version);
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| 12:15 - 12:45
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Bob Johnson: Introduction to Linux Commands (part 2) (slides);
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12:45 - 14:00
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--- Lunch Break ---
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| 14.00 - 14:30
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Stefano Cozzini: Introduction to the moodle e-learning platform
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| 14:30 - 16:00
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Crash Course on Linux; Beginners Lab (part 1)
A small Crash Course on bash scripting
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Crash Course on Linux; Intermediate Lab (part 1)
A small Crash Course on bash scripting
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| 16:00 - 16:30
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--- Coffee Break ---
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| 16:30 - 18:30
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Crash Course on Linux; Beginners Lab (part 2)
A small Crash Course on bash scripting
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Crash Course on Linux: Intermediate Lab (part 2)
Bash Scripting for Scientific Computation Lesson
Bonus pack (optional) HPC BASH Scripting
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| 18:30 - 19:15
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Homework: blog about the day, take the quiz
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| 3 |
08:30 -09:00
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Review of previous day's activities (Axel & Stefano)
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| 09:00 - 10:00
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Stefano Cozzini: Floating Points Numbers (slides)
How to work with them correctly and efficiently
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10:00-
10:30
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Shawn Brown: From Source Code to Executable (Part 1) (slides)
What happens during preprocessing and compiling
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| 10:30 - 11:00
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--- Coffee Break ---
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| 11:00 - 11:45
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Shawn Brown: From Source Code to Executable (Part 2) (slides)
Compiler flags and linking.
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| 11:45 - 12:30
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Axel Kohlmeyer: From Source Code to Executable (Part 3) (slides)
Makefiles
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| 12:30 - 14:00
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--- Lunch Break ---
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14:00 - 14.30
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Alberto Campagnari / A. Messina : Introduction to the e-lab gforge portal and svn server (slides) (subversion slides)
A short introduction how to use gforge.escience-lab.org web portal ant its svn server
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| 14:30 - 16:00
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Laboratory Part 1: Installing compilers
Instructions available here:Installing compilers on your desktop Lesson
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| 16:00 - 16:30
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--- Coffee Break ---
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| 16:30 - 18:30
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Laboratory Part 2:
Test the Compilers on IEEE floating point arithmetic
and
Installing scientific packages on HPC resources: Part 1
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| 18:30 -19:00
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Homework: blog about the day and take quiz of the day
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| 5 |
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| 6 |
08:30 - 09:00
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Review of previous day's activities (Axel & Stefano)
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| 9:00 - 09:45
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Axel Kohlmeyer: Introduction to OpenMP (slides)
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| 9:45 - 10:30
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Ben Levine: Introduction to GPU Computing (part1):
(slides) GPU Hardware, Parallelization and Programming model
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| 10:30 - 11:00
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--- Coffee Break ---
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| 11:00 - 11:30
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Ben Levine: Introduction to GPU Computing (part 2):
(slides) Introduction to programming with CUDA
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| 11:30 - 12:30
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Axel Kohlmeyer: Error messages and debugging (slides)
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| 12:30 - 14:00
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--- Lunch Break ---
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| 14:00 - 16:00
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Laboratory Part 1: Debugging codes
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| 16:00 - 16:30
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--- Coffee Break ---
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| 16:30 - 18:30
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Laboratory Part 2:
Compiling and testing OpenMP programs
Use of OpenMP threaded libraries Lesson
Compiling and testing CUDA programs and libraries.
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18:30 - 19.00
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Homework: take quiz of the day and perform assignment
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8.30 - 09.00
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Review of previous day's activities (Axel & Stefano)
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| 9:00 - 09:45
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Stefano Cozzini: How to benchmark your application.
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| 9:45 - 10:30
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Axel Kohlmeyer: 40 ways to simulate liquid Argon (part 1).
A case study in optimization and parallelization. (slides)
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| 10:30 - 11:00
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--- Coffee Break ---
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| 11:00 - 12:00
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Axel Kohlmeyer: 40 ways to simulate liquid Argon (part 2).
More techniques on parallelization and optimization are discussed with a real scientific application example. (slides)
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| 12:00 - 12:30
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First week wrap up session. Questions from participants. Lab Assignments for week 2 afternoon labs.
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| 12:30 - 14:00
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--- Lunch Break ---
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| 14:00 - on
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Free time
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DAY 7: Rest (Sunday, 6 December)
A day to rest and recover |
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| 9 |
| Advanced Topic Section (Room: Adriatico Guest House Kastler Lecture Hall)
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| 09:00 - 09:45
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Introduction to Grid computing (Antun Balaz) (slides)
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| 09:45 - 10:30
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How to choose the right architecture for your computation (Shawn Brown) (slides)
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| 10:30 - 11:00
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--- Coffee Break ---
(Room: Adriatico Guest House (Lower Level 1))
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| Parallel sessions
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Application Optimization and Parallel Programming
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Cluster Installation and management lab
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GRID computing Lab (Eklund Lab)
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| 11:00 - 12:00
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Ben Levine: Introduction to GPU computing (part 3): CUDA programming and optimization examples. (slides)
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Moreno Baricevic: Installation procedures for clusters (Part 1, Part 2 and Intro to Hands-on Lab)
(Room: Lundqvist)
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Antun Balaz / Stefano Cozzini: Grid tutorial (Part 1): Introduction to gLite and Gridseed (slides)
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| 12:00 - 14:00
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--- Lunch Break ---
(Room: Adriatico Guest House Cafeteria)
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| 14:00 - 16:00
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Optimization/Parallelization of your own code (Shawn Brown).
or
CUDA Porting of your own code (Ben Levine)
or
Optimization of the Liquid
Argon simulation code.
(Axel Kohlmeyer)
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Cluster Installation Lab Part 1: Installation of a masternode and setup of the netboot environment
(Room: Lundqvist)
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Grid tutorial (Part 2): Security/ Authorization and Advanced Grid Jobs Submission
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| 16:00 - 16:30
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--- Coffee Break ---
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| 16:30 - 18:30
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Optimization/Parallelization of your own code (Shawn Brown).
or
CUDA Porting of your own code (Ben Levine)
or
Optimization of the Liquid
Argon simulation code.
(Axel Kohlmeyer)
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Cluster Installation Lab Part 1: Installation of a masternode and setup of the netboot environment
(Room: Lundqvist)
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Grid tutorial (part 3): Data management
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| 10 |
| Advanced Topic Section (Room: Adriatico Guest House Kastler Lecture Hall)
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| 09:00 - 09:45
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Christopher Dahnken: Intel tools for HPC
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| 09:45 - 10:30
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Sergio Maffioletti: Grid middleware and arc overview (slides)
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| 10:30 - 11:00
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--- Coffee Break ---
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Application Optimization and Parallel Programming
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Cluster Installation and management lab
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GRID computing Lab
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| 11:00 - 12:00
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Shawn Brown:
MPI Tutorial
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Moreno Baricevic: Cluster Installation Part 3: Management Tools
Martin Scarcia: Environment Modules
(Room: Lundqvist)
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Arc Tutorial ( part I) (slides)
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| 12:00 - 14:00
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--- Lunch Break ---
(Room: Adriatico Guest House Cafeteria)
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| 14:00 - 16:00
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Optimization/Parallelization of your own code (Shawn Brown).
or
CUDA Porting of your own code (Ben Levine)
or
MPI-parallelization of the Liquid
Argon simulation code.
(Axel Kohlmeyer)
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Cluster Installation Lab Part 2: Setup of the queue system and the parallel/cluster environment
(Room: Lundqvist)
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Arc Tutorial ( part II) (slides)
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| 16:00 - 16:30
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--- Coffee Break ---
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| 16:30 - 18:30
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Optimization/Parallelization of your own code (Shawn Brown).
or
CUDA Porting of your own code (Ben Levine)
or
MPI-parallelization of the Liquid
Argon simulation code.
(Axel Kohlmeyer)
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Cluster Installation Lab Part 2: Setup of the queue system and the parallel/cluster environment
(Room: Lundqvist)
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Arc Tutorial ( part III)
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| 11 |
| Advanced Topic Section (Room: Adriatico Guest House Kastler Lecture Hall)
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| 09:00 - 09:45
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Carlo Cavazzoni: Hybrid OpenMP/MPI programming (part 1) (slides)
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| 09:45 - 10:30
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Carlo Cavazzoni: Hybrid OpenMP/MPI programming (part 2) (slides)
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| 10:30 - 11:00
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--- Coffee Break ---
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Application Optimization and Parallel Programming
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Cluster Installation and management lab
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GRID computing Lab
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| 11:00 - 12:00
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Panel Discussion on Coordinating Software Development. Strategies, Caveats, Tools, Examples
Panelists: A. Kohlmeyer, S. Brown, C. Cavazzoni, A. Campagnari
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Piero Calucci: how to setup a queue system on your cluster
(Room: Lundqvist)
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J.Mosicki: Ganga and Diane tools (video-conference) (slides)
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| 12:00 - 14:00
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--- Lunch Break ---
(Room: Adriatico Guest House Cafeteria)
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| 14:00 - 16:00
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Optimization/Parallelization of your own code (Shawn Brown).
or
CUDA Porting of your own code (Ben Levine)
or
OpenMP-parallelization of the Liquid
Argon simulation code.
(Axel Kohlmeyer)
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Antonio Messina: RAID and LVM (slides)
Installing Ganglia
(Room: Lundqvist)
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Ganga tutorial
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| 16:00 - 16:30
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--- Coffee Break ---
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| 16:30 - 18:30
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Optimization/Parallelization of your own code (Shawn Brown).
or
CUDA Porting of your own code (Ben Levine)
or
OpenMP parallelization of the Liquid
Argon simulation code.
(Axel Kohlmeyer)
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Completing all the exercises proposed and/or optional exercises (IPMI & SNMP; DNS Configuration; Setup of the Infiniband Network; NAT and IP Forwarding; Bonding; Virtual Machines as Test/Development Platform)
(Room: Lundqvist)
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Ganga tutorial
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| 12 |
| Advanced Topic Section (Room: Adriatico Guest House Kastler Lecture Hall)
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09:00 -
10:30
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Massimiliano Fatica: Optimal GPU programming:
Presentation and discussion of implementing a spectral Poisson solver with CUDA using the cuFFT library. (slides)
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| 10:30 - 11:00
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--- Coffee Break ---
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Application Optimization and Parallel Programming
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Cluster Installation and management lab
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GRID computing Lab
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| 11:00 - 12:00
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Axel Kohlmeyer:
LJMD code revisited for participants in the software lab.
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Piero Calucci: C4 tools for cluster computing
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Individual project
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| 12:00 - 14:00
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--- Lunch Break ---
(Room: Adriatico Guest House Cafeteria)
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| 14:00 - 16:00
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Optimization/Parallelization of your own code (Shawn Brown).
or
CUDA Porting of your own code (Ben Levine)
or
Hybrid OpenMP/MPI parallelization of the Liquid Argon simulation code. (Axel Kohlmeyer)
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Final Lab: completing all the exercises proposed
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Individual project
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| 16:00 - 16:30
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--- Coffee Break ---
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| 16:30 - 18:30
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Optimization/Parallelization of your own code (Shawn Brown).
or
CUDA Porting of your own code (Ben Levine)
or
CUDA porting of the Liquid Argon simulation code. (Axel Kohlmeyer)
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Final Lab: completing all the exercises proposed
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Individual project
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| 13 |
| Wrap-up session
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| 9:00 - 10.00
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Selected presentation from participants - Riccardo Sabatini: Code profiling with TAU (slides) - Michele Paulatto: Travel-time seismic tomography in a Nuttshell (slides) - Alan Bizjak: Reprt From software lab CUDA/GPU Computing (slides)
Reports/summaries from the labs: Hardware Lab (slides)
Wrap-up of the school activities
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Workshop on GPU perspective in HPC
(Room: Adriatico Guest House Kastler Lecture Hall)
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| 10:00 - 10:15
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E4 roadmap toward CPU/GPU computing (F.Magugliani)
(slides)
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| 10:15 - 11:00
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GPU computing perspective (E.Orlotti / M.Fatica, Nvidia) (slides)
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| 11:00 - 11:30
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--- Coffee Break ---
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11.30 - 12.00
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HPC for AFRICA (Clement Onime) (slides)
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12.00 - 12.45
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Teaching GPU approach in HPC workshop: report from the GPU lab and future perspective (Axel)
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12.45 - 13.00
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Workshop Conclusion (Stefano / Axel)
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e-learning platform for eLab 
