Euro-Par 2011: Parallel Processing Workshops: CCPI, CGWS, HeteroPar, HiBB, HPCVirt, HPPC, HPSS, MDGS, ProPer, Resilience, UCHPC, VHPC, Bordeaux, France, August 29 -- September 2, 2011, Revised Selected Papers, Part II

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Overview

Lecture Notes in Computer Science

The LNCS series reports state-of-the-art results in computer science research, development, and education, at a high level and in both printed and electronic form. Enjoying tight cooperation with the R&D community, with numerous individuals, as well as with prestigious organizations and societies, LNCS has grown into the most comprehensive computer science research forum available.

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Table of Contents

HiBB 2011: 2nd Workshop on High-Performance Bioinformatics and Biomedicine

Introduction Mario Cannataro 1

On Parallelizing On-Line Statistics for Stochastic Biological Simulations Marco Aldinucci Mario Coppo Ferruccio Damiani Maurizio Drocco Eva Sciacca Salvatore Spinella Massimo Torquati Angelo Troina 3

Scalable Sequence Similarity Search and Join in Main Memory on Multi-cores Astrid Rheinländer Ulf Leser 13

Enabling Data and Compute Intensive Workflows in Bioinformatics Gaurang Mehta Ewa Deelman James A. Knowles Ting Chen Ying Wang Jens Vöckler Steven Buyske Tara Matise 23

Homogenizing Access to Highly Time-Consuming Biomedical Applications through a Web-Based Interface Luigi Grasso Nuria Medina-Medina Rosana Montes-Soldado María M. Abad-Grau 33

Distributed Management and Analysis of Omics Data Mario Cannataro Pietro Hiram Guzzi 43

Managing and Delivering Grid Services (MDGS)

Introduction Thomas Schaaf Adam S.Z. Belloum Owen Appleton Joan Serrat-Fernández Tomasz Szepieniec 53

Resource Allocation for the French National Grid Initiative Gilles Mathieu Hélène Cordier 55

On Importance of Service Level Management in Grids Tomasz Szepieniec Joanna Kocot Thomas Schaaf Owen Appleton Matti Heikkurinen Adam S.Z. Belloum Joan Serrat-Fernández Martin Metzker 64

On-Line Monitoring of Service-Level Agreements in the Grid Bartosz Balis Renata Slota Jacek Kitowski Marian Bubak 76

Challenges of Future e-Infrastructure Governance Dana Petcu 86

Influences between Performance Based Scheduling and Service Level Agreements Antonella Galizia Alfonso Quarati Michael Schiffers Mark Yampolskiy 96

User Centric Service Level Management in mOSAIC Applications Massimiliano Rak Rocco Aversa Salvatore Venticinque Beniamino Di Martino 106

Service Level Management for Executable Papers Reginald Cushing Spiros Koulouzis Rudolf Strijkers Adam S.Z. Belloum Marian Bubak 116

Change Management in e-Infrastructures to Support Service Level Agreements Silvia Knittl Thomas Schaaf Ilya Saverchenko 124

PROPER 2011: Fourth Workshop on Productivity and Performance: Tools for HPC Application Development

Introduction Michael Gerndt 135

Scout: A Source-to-Source Transformator for SIMD-Optimizations Olaf Krzikalla Kim Feldhoff Ralph Müller-Pfefferkorn Wolfgang E. Nagel 137

Scalable Automatic Performance Analysis on IBM BlueGene/P Systems Yury Oleynik Michael Gerndt 146

An Approach to Creating Performance Visualizations in a Parallel Profile Analysis Tool Wyatt Spear Allen D. Malony Chee Wai Lee Scott Biersdorff Sameer Shende 156

INAM - A Scalable InfiniBand Network Analysis and Monitoring Tool N. Dandapanthula H. Subramoni J. Vienne K. Kandalla S. Sur Dhabaleswar K. Panda Ron Brightwell 166

Auto-tuning for Energy Usage in Scientific Applications Ananta Tiwari Michael A. Laurenzano Laura Carrington Allan Snavely 178

Automatic Source Code Transformation for GPUs Based on Program Comprehension Pasquale Cantiello Beniamino Di Martino 188

Enhancing Brainware Productivity through a Performance Tuning Workflow Christian Iwainsky Ralph Altenfeld Dieter an Mey Christian Bischof 198

Workshop on Resiliency in High-Performance Computing (Resilience) in Clusters, Clouds, and Grids

Introduction Stephen L. Scott Chokchai (Box) Leangsuksun 209

The Malthusian Catastrophe Is Upon Us! Are the Largest HPC Machines Ever Up? Patricia Kovatch Matthew Ezell Ryan Braby 211

Simulating Application Resilience at Exascale Rolf Riesen Kurt B. Ferreira Maria Ruiz Varela Michela Taufer Aran Rodrigues 221

Framework for Enabling System Understanding J. Brandt F. Chen A. Gentile Chokchai (Box) Leangsuksun J. Mayo P. Pebay D. Roe N. Taerat D. Thompson M. Wong 231

Cooperative Application/OS DRAM Fault Recovery Patrick G. Bridges Mark Hoemmen Kurt B. Ferreira Michael A. Heroux Philip Soltero Ron Brightwell 241

A Tunable, Software-Based DRAM Error Detection and Correction Library for HPC David Fiala Kurt B. Ferreira Frank Mueller Christian Engelmann 251

Reducing the Impact of Soft Errors on Fabric-Based Collective Communications José Carlos Sancho Ana Jokanovic Jesus Labarta 262

Evaluating Application Vulnerability to Soft Errors in Multi-level Cache Hierarchy Zhe Ma Trevor Carlson Wim Heirman Lieven Eeckhout 272

Experimental Framework for Injecting Logic Errors in a Virtual Machine to Profile Applications for Soft Error Resilience Nathan DeBardeleben Sean Blanchard Qiang Guan Ziming Zhang Song Fu 282

High Availability on Cloud with HA-OSCAR Thanadech Thanakornworakij Rajan Sharma Blaine Scroggs Chokchai (Box) Leangsuksun Zeno Dixon Greenwood Pierre Riteau Christine Morin 292

On the Viability of Checkpoint Compression for Extreme Scale Fault Tolerance Dewan Ibtesham Dorian Arnold Kurt B. Ferreira Patrick G. Bridges 302

Can Checkpoint/Restart Mechanisms Benefit from Hierarchical Data Staging? Raghunath Rajachandrasekar Xiangyong Ouyang Xavier Besseron Vilobh Meshram Dhabaleswar K. Panda 312

Impact of Over-Decomposition on Coordinated Checkpoint/Rollback Protocol Xavier Besseron Thierry Gautier 322

UCHPC 2011: Fourth Workshop on UnConventional High-Performance Computing

Introduction Anders Hast Josef Weidendorfer Jan-Philipp Weiss 333

PACUE: Processor Allocator Considering User Experience Tetsuro Horikawa Michio Honda Jin Nakazawa Kazunori Takashio Hideyuki Tokuda 335

Workload Balancing on Heterogeneous Systems: A Case Study of Sparse Grid Interpolation Alin Murarasu Josef Weidendorfer Arndt Bode 345

Performance Evaluation of a Multi-GPU Enabled Finite Element Method for Computational Electromagnetics Tristan Cabel Joseph Charles Stéphane Lanteri 355

Study of Hierarchical N-Body Methods for Network-on-Chip Architectures Thomas Canhao Xu Pasi Liljeberg Hannu Tenhunen 365

Extending a Highly Parallel Data Mining Algorithm to the Intel® Many Integrated Core Architecture Alexander Heinecke Michael Klemm Dirk Pflüger Arndt Bode Hans-Joachim Bungartz 375

VHPC 2011: 6th Workshop on Virtualization in High-Performance Cloud Computing

Introduction Michael Alexander Gianluigi Zanetti 385

Group-Based Memory Deduplication for Virtualized Clouds Sangwook Kim Hwanju Kim Joonwon Lee 387

A Smart HPC Interconnect for Clusters of Virtual Machines Anastassios Nanos Nikos Nikoleris Stratos Psomadakis Elisavet Kozyri Nectarios Koziris 398

Coexisting Scheduling Policies Boosting I/O Virtual Machines Dimitris Aragiorgis Anastassios Nanos Nectarios Koziris 407

PIGA-Virt: An Advanced Distributed MAC Protection of Virtual Systems J. Briffaut E. Lefebvre J. Rouzaud-Cornabas C. Toinard 416

An Economic Approach for Application QoS Management in Clouds Stefania Costache Nikos Parlavantzas Christine Morin Samuel Kortas 426

Evaluation of the HPC Challenge Benchmarks in Virtualized Environments Piotr Luszczek Eric Meek Shirley Moore Dan Terpstra Vincent M. Weaver Jack Dongarra 436

DISCOVERY, Beyond the Clouds: Distributed and Cooperative Framework to Manage Virtual EnviRonments autonomicallY: A Prospective Study Adrien Lèbre Paolo Anedda Massimo Gaggero Flavien Quesnel 446

Cooperative Dynamic Scheduling of Virtual Machines in Distributed Systems Flavien Quesnel Adrien Lèbre 457

Large-Scale DNA Sequence Analysis in the Cloud: A Stream-Based Approach Romeo Kienzler Rémy Bruggmann Anand Ranganathan Nesime Tatbul 467

Author Index 477

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