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Category: List of Bases 2008 2008 ICTP activities in Trieste ICTP activities in Trieste
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lecture

Cosponsor(s):

Co-sponsored by : Central European Initiative (CEI), Democritos INFM, eLab, E4 Computer Engineering S.p.A., EuroTech S.p.A., IBM Italia S.p.A., Spring Firm S.r.l.

Start Time:

3 November 2008 at 09:00

Ends On:

14 November 2008

Location:

Trieste - Italy

Venue:

AGH (Kastler and Lundqvist Lecture Halls)

Organizer(s):

Directors: S. Cozzini, A. Kohlmeyer

Description:

Sponsors:




















Material:

DAY 1: Introduction to Linux and HPC

Description: Introductory day:

goals:
-introduction of the HPC concepts
-setup of the Linux workstation devoted to HPC
-get acquainted with Linux command line interface and bash scripting

Chairperson: Stefano Cozzini

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

3 November 2008
08:30
09:30
Registration
01h00'
09:30
09:40
Introduction to the School
10'
Stefano Cozzini / Axel Kohlmeyer
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy / University of Penn., Philadelphia, U.S.A
09:40
10:30
Introduction to HPC and Cluster computing
50'
Stefano Cozzini
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy
10:30
11:00
Coffee Break
30'
11:00
11:45
Introduction to Linux
45'
Axel Kohlmeyer
University of Pennsylvania, Philadelphia, U.S.A
11:45
12:30
Tools for Linux Workstations
45'
Riccardo di Meo
ICTP EU-IndiaGrid project, Trieste, Italy
-Compression and packaging utilities: tar/gzip

-ssh basic

-packages management: yum/rpm etc..

-wget

-gnuplot and/or other tool for plotting
12:30
14:00
Lunch Break
01h30'
14:00
16:00
Crash Course on Linux: Intermediate Lab (part 1)
02h00'
Piero Calucci/ Moreno Baricevic/ Riccardo di Meo
Sissa/eLab and ICTP/EundiaGrid, Trieste, Italy
Room: Adriatico Guest House Informatics Lab.
A small crash course on bash scripting etc.etc.

Materials are available starting from here:

http://www.democritos.it/hpc-wiki/index.php/Main/MasteringLinux
14:00
16:00
Crash Course on Linux: Beginner's Lab (part 1)
02h00'
Iztok Gregori & Stefano Cozzini
Sissa/eLab, Trieste, Italy
Room: Adriatico Guest House - Eklund Informatics Lab (Lower Level 1)
A small crash course on bash scripting etc.etc.

Materials are available starting from here:

http://www.democritos.it/hpc-wiki/index.php/Main/MasteringLinux
16:00
16:30
Coffee Break
30'
16:30
18:30
Crash Course on Linux: Intermediate Lab (part 2)
02h00'
Piero Calucci/ Moreno Baricevic/ Riccardo di Meo
Sissa/eLab and ICTP/EundiaGrid, Trieste, Italy
Room: Adriatico Guest House Informatics Lab.
A small crash course on bash scripting etc.etc.

Materials are available starting from here:

http://www.democritos.it/hpc-wiki/index.php/Main/MasteringLinux


16:30
18:30
Crash Course on Linux: Beginners Lab (part 2)
02h00'
Iztok Gregori & Stefano Cozzini
Sissa/eLab, Trieste, Italy
Room: Adriatico Guest House - Eklund Informatics Lab (Lower Level 1)
A small crash course on bash scripting etc.etc.

Materials are available starting from here:

http://www.democritos.it/hpc-wiki/index.php/Main/MasteringLinux
18:30
19:15
Homework: blog about the day
45'
DAY 2: Scientific Computing

Description: Goals:
-present Floating Point numbers and tricks
-discuss the full path from source code to executable
-present important tool (makefile) to easily handle compilation of scientific code

Chairperson: Axel Kohlmeyer

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

4 November 2008
09:00
09:45
Floating Points Numbers: How to work with them correctly and efficiently
45'
Stefano Cozzini
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy
09:45
10:30
From Source Code to Executable: Preprocessing/Compiling/Linking/Makefiles (part I)
45'
Axel Kohlmeyer
University of Pennsylvania, Philadelphia, U.S.A.
10:30
11:00
Coffee Break
30'
11:00
11:45
From Source Code to Executable: Preprocessing/Compiling/Linking/ Makefiles (part II)
45'
Axel Kohlmeyer
University of Pennsylvania, Philadelphia, U.S.A.
11:45
12:10
From Source Code to Executable: Preprocessing/Compiling/Linking/ Makefiles (part III)
25'
Axel Kohlmeyer
University of Pennsylvania, Philadelphia, U.S.A.
12:10
12:30
Working with svn
20'
Antonio Messina
ICTP, Trieste, Italy
A short introduction how to use svn (http://subversion.tigris.org/)
12:30
14:00
Lunch Break
01h30'
14:00
16:00
Laboratory: Install compilers and programming tools on your workstation
02h00'
Exercise Instruction available here:

http://www.democritos.it/hpc-wiki/index.php/Main/InstallingTheGNUPGIAndIntelCompilerPackages
16:00
16:30
Coffee Break
30'
16:30
18:30
Laboratory Part 2: Test Compilers on IEEE floating point arithmetic
02h00'
Exercise Instructions available here:

http://www.democritos.it/hpc-wiki/index.php/Main/TestTheCompilersAndPlayWithFPNumbers
18:30
19:15
Homework: blog about the day
45'
DAY 3: Modern architecture for HPC and how to use them efficiently

Description: Present the modern architecture and discuss how to get performances out of them.

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

5 November 2008
09:00
09:45
Modern architectures for HPC computation
45'
Stefano Cozzini
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy
Review of modern architecture: details about memory hierarchy etc..etc.
09:45
10:30
Using Compilers and Profilers to Optimize your Code for Performance
45'
Stefano Cozzini
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy
10:30
11:00
Coffee Break
30'
11:00
11:45
Mathematical Libraries part I
45'
Axel Kohlmeyer
University of Pennsylvania, Philadelphia, U.S.A.
review the main libraries for linear algebra and fftw
11:45
12:30
Mathematical Libraries Part II
45'
Luca Heltai
S.I.S.S.A. - International School for Advanced Studies, Trieste, Italy
Petcs and other toolkits..
12:30
14:00
Lunch Break
01h30'
14:00
14:20
The EuroAfrica-ICT project
20'
Peter McGrath
TWAS, Trieste, Italy
14:20
16:00
Laboratory part 1: Optimize simple codes provided by Lab; Measure memory hierarchy speed
01h40'
Exercise Instructions available here:

http://www.democritos.it/hpc-wiki/index.php/Main/OptimizeSimpleCodesProvidedByLab

http://www.democritos.it/hpc-wiki/index.php/Main/MeasureMemoryHierarchySpeed
16:00
16:30
Coffee Break
30'
16:30
18:30
Laboratory Part 2: Play with mathematical libraries
02h00'
Exercise Instructions are here:

http://www.democritos.it/hpc-wiki/index.php/Main/ComparePerformancesOfDifferentOptimizedLibrariesOnMatrixMultiplication
18:30
18:45
Homework: blog about the day
15'
DAY 4: Parallel Computation

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

6 November 2008
09:00
09:45
Parallel Computing with Linux: the cluster approach..
45'
Stefano Cozzini
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy
09:45
10:30
Introduction to Grid computing
45'
Giuliano Taffoni
INAF, Trieste, Italy
10:30
11:00
Coffee Break
30'
11:00
12:00
Introduction to MPI
01h00'
Luca Heltai
SISSA, Trieste, Italy
12:00
12:30
General instructions on compiling MPI codes on clusters
30'
Ershaad A. Basheer
JNCASR, Bangalore, India
12:30
14:00
Lunch Break
01h30'
14:00
16:00
Laboratory part 1: install MPI libraries and run parallel codes on your workstation
02h00'
Exercise Instructions are here:

http://www.democritos.it/hpc-wiki/index.php/Main/TestSimpleMPIProgramsOnASingleProcessor
16:00
16:30
Coffee Break
30'
16:30
18:30
Laboratory Part 2: Set up Mini Clusters to Test MPI
02h00'
Exercise Instructions are here:

http://www.democritos.it/hpc-wiki/index.php/Main/SetUpMiniClustersToTestMPIOnTrueParallelMachines
18:30
19:15
Homework: blog about the day
45'
DAY 5: Tools and methods for HPC

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

7 November 2008
09:00
09:30
How to benchmark your application
30'
Stefano Cozzini
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy
09:30
10:15
How to find the best resources for your Application
45'
Shawn T. Brown
Carnegie Mellon University, Pittsburgh Supercomputing Center, U.S.A.
10:15
11:00
Introduction to OpenMP ( first part)
45'
Shawn T. Brown
Carnegie Mellon University, Pittsburgh Supercomputing Center, U.S.A.
11:00
11:30
Coffee Break
30'
11:30
12:30
Error Messages and Debugging
01h00'
Axel Kohlmeyer
University of Pennsylvania, Philadelphia, U.S.A.
12:30
14:00
Lunch Break
01h30'
14:00
16:00
Question&Answer open session
02h00'
Axel Kohlmeyer/Stefano Cozzini
University of Pennsylvania, Philadelphia, U.S.A. / CNR-INFM Democritos
16:00
16:30
Coffee Break
30'
16:30
18:30
Laboratory Session second session: OpenMP examples Use of OpenMP threaded libraries
02h00'


http://www.democritos.it/hpc-wiki/index.php/Main/OpenMPExamples

http://www.democritos.it/hpc-wiki/index.php/Main/UseOfOpenMPThreadedLibraries
18:30
19:15
Homework: blog about the day
45'
DAY6: MPI tutorial (Saturday)
8 November 2008
09:00
10:30
MPI tutorial: first part
01h30'
Axel Kohlmeyer / Shawn T. Brown
University of Penn., Philadelphia, U.S.A. / CMU, PSC, Pittsburgh, U.S.A.
10:30
11:00
Coffee Break
30'
11:00
12:30
MPI tutorial: part 2
01h30'
Axel Kohlmeyer / Shawn T. Brown
Un. of Pennsylvania, Philadelphia, U.S.A. / CMU, PSC, Pittsburgh, U.S.A.
12:00
17:00
Lunch and free time
05h00'
DAY 7: FREE TIME (Sunday)
Advanced Topic session:

Description: Advanced HCP Topic

Room: Adriatico Guest House Kastler Lecture Hall

10 November 2008
09:00
09:10
Presentation of the second week activities
10'
Stefano Cozzini/Axel Kohlmeyer
CNR-INFM Democritos, Trieste, Italy/University of Penn., Philadelphia, U.S.A.
09:10
09:45
Introduction to GPU programming in the nvidia CUDA environment
35'
Ershaad A. Basheer
JNCASR, Bangalore, India
09:45
10:30
Introduction to GPU programming in the nvidia CUDA environment (second part)
45'
Ershaad A. Basheer
JNCASR, Bangalore, India
10:30
11:00
Coffee Break
30'
11 November 2008
09:00
09:45
Queue systems for HPC platform
45'
Piero Calucci
S.I.S.S.A. - International School for Advanced Studies, Trieste, Italy
09:45
10:05
High Bandwidth Data Transfer
20'
Carlos Jaime Barrios Hernadez
Laboratoire Informatique de Grenoble, France
10:05
10:30
Modeling and Evaluation of Performance of Scalable Architectures (Grid/Cluster Monitoring tools and procedures)
25'
Carlos Jaime Barrios Hernadez
Laboratoire Informatique de Grenoble, France
10:30
11:00
Coffee Break
30'
12 November 2008
09:00
09:45
An Introduction to the Lustre Parallel File System
45'
Piero Calucci
S.I.S.S.A. - International School for Advanced Studies, Trieste, Italy
09:45
10:30
Rocks: what is and how to install it
45'
Jorge Zuluaga
CRESCA- Universidad de Antioquia, Medellin, Colombia
10:30
11:00
Coffee Break
30'
Application Optimization and Parallel Programming

Description: Detail program of the laboratory will be announced later

Chairperson: Axel Kohlmeyer and Shawn T. Brown

Room: Adriatico Guest House Lundqvist Lecture Hall

Cluster Installation and management lab: how to setup HPC facilities

Chairperson: Piero Calucci and Moreno Baricevic

Location: Sissa Main Building

10 November 2008
11:00
12:00
Installation procedures for clusters
01h00'
Moreno Baricevic
CNR/INFM Democritos, Trieste, Italy
Room: Adriatico Guest House Kastler Lecture Hall
12:00
14:00
Lunch Break and transfer to SISSA lab
02h00'
14:00
18:00
LAB Session: Installation Procedure for a Cluster Master Node
04h00'
Room: SISSA MediaLab
http://www.democritos.it/hpc-wiki/index.php/Main/InstallationProcedureForAClusterMasterHeadNode
11 November 2008
11:00
12:00
How to set-up a Queue system on your cluster
01h00'
Piero Calucci
SISSA, Trieste, Italy
Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
14:00
18:00
Installing and configuring PBS and monitoring services
04h00'
12 November 2008
11:00
12:00
DEMO on I/O procedures by PANASAS
01h00'
Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
14:00
18:00
Lab: I/O configuration and Infiniband installation
04h00'
13 November 2008
14:00
18:00
Final Lab: completing all the exercises proposed
04h00'
GRID computing Lab

Description: The lab dedicated to GRID COMPUTING

Chairperson: Stefano Cozzini and Antun Balaz

Room: Adriatico Guest House Informatics Lab.

10 November 2008
11:00
12:30
Grid tutorial part 1: introduction to gLite and Gridseed
01h30'
Antun Balaz / Stefano Cozzini
Institute of Physics, Belgrade, Rep. of Serbia /CNR/INFM Democritos and Sissa/eLab, Trieste, Italy


Introduction to gLite middleware  40'
lecture_notes

Antun Balaz
Introduction to GRIDSEED  20'
lecture_notes

Stefano Cozzini
12:30
14:00
Lunch Break
01h30'
14:00
16:00
Grid tutorial 2: Security and basic Job Submission
02h00'
Riccardo Murri / Antun Balaz
Swiss Centre for Scientific Computing, Manno, Switzerland/Institute of Physics, Belgrade, Republic o


GRID authentication/authorization mechanism  35'
lecture_notes

Riccardo Murri
Basic Job Submission   35'
lecture_notes

Antun Balaz
16:00
16:30
Coffee Break
30'
16:30
18:30
Grid tutorial part 3: data management
02h00'
Giuliano Taffoni
INAF/OATS, Trieste, Italy
11 November 2008
11:00
12:30
Grid Tutorial part 4: advanced job submission
01h30'
Antun Balaz
Institute of Physics, Belgrade, Republic of Serbia
12:30
14:00
Lunch Break
01h30'
14:00
16:00
Grid tutorial hands-on session on data management and advanced job submission
02h00'
Giuliano Taffoni
INAF/OATS, Trieste, Italy
16:00
16:30
Coffee Break
30'
16:30
18:30
Grid Tutorial part 5: how to port application on the grid and parallel computing on the GRID
02h00'
Stefano Cozzini / Riccardo di Meo
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy/S.I.S.S.A. - International School for Advanced St
We will present a general overview how to port application on the grid and then we will focus on:

-MPI approach on the GRID
-SMP calculation on the GRID
-client/server mechanisms
12 November 2008
11:00
12:30
Grid Tutorial 7: problem assignments to participants
01h30'
12:30
14:00
Lunch Break
01h30'
14:00
16:00
Grid LAB: personal/group work on assigned problems
02h00'
16:00
16:30
Coffee Break
30'
16:30
18:30
GRID LAB: personal/group work on assigned problems
02h00'
13 November 2008
14:00
16:00
GRID Lab: personal/group work on assigned problems
02h00'
16:00
16:30
Coffee Break
30'
16:30
18:30
GRID LAB: personal/group work on assigned problems
02h00'
Vendors&Sponsors Session

Description: Sponsors and Vendors will present their own HPC solutions

Chairperson: Stefano Cozzini

13 November 2008
09:00
09:30
Panasas presentation
30'
09:30
09:50
E4 presentation
20'
09:50
10:10
Eurotech presentation
20'
10:10
10:30
IBM presentation
20'
10:30
11:00
Coffee Break
30'
11:00
12:20
Special Topic: How to organize a similar school in your country/institute
01h20'
Stefano Cozzini/Axel Kohlmeyer
CNR-INFM Democritos, Trieste, Italy/University of Penn., Philadelphia, U.S.A.
Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)
We will discuss with interested people how to setup a similar event in other places with or without the help of ICTP.

Logistic details (how/where to submit a proposal ) and technical ones as well will be discussed.


12:20
14:00
Lunch Break
01h40'
14:00
15:30
CEI Round Table
01h30'
Location: United Nations Room
Participants coming from CEI countries will discuss future regional initiatives in the area of HPC/GRID
Closing Session

Room: Adriatico Guest House - Kastler Lecture Hall Area (Lower Level 1)

14 November 2008
09:00
09:45
Future Perspectives in GRID and HPC
45'
Stefano Cozzini/Axel Kohlmeyer
CNR-INFM Democritos, Trieste, Italy/University of Penn., Philadelphia, U.S.A.
09:45
10:30
Presentations from Participants
45'
15 minutes each


The SEE-GRID project   15'
presentation

Antun Balaz
Benchmarking WRF on different clusters  15'
Irene Gallai
10:30
11:00
Coffee Break
30'
11:00
12:00
Presentations from Participants
01h00'


Public Cluster: An open cluster approach  20'
presentation

Zaenal Akbar  (Research Center for Physics, Indonesian Institute of Science)
APPLICATION OF GRID COMPUTING IN MODELING TSUNAMI AND DENGUE   20'
presentation

Teh Su Yean, Kew Lee Ming and Koh Hock Lye
MPICH-G2 Communication Model on the Grid  20'
presentation

Mehdi Sheikhalishahi
12:00
12:30
Wrap-up and conclusions
30'
Stefano Cozzini / Axel Kohlmeyer
CNR/INFM Democritos and Sissa/eLab, Trieste, Italy / University of Penn., Philadelphia, U.S.A
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