
Euro-Par 2011: Parallel Processing Workshops
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Content
- Title
- Preface
- Organization
- Table of Contents - Part II
- HiBB 2011: 2nd Workshop on High-Performance Bioinformatics and Biomedicine
- HiBB 2011: 2nd Workshop on High Performance Bioinformatics and Biomedicine
- On Parallelizing On-Line Statistics for Stochastic Biological Simulations
- Introduction
- The CWC Formalism and Its Parallel Simulator
- On Line Statistical Tools
- Typical Patterns for Biological Trajectories
- Examples
- Related Work
- Conclusions
- References
- Scalable Sequence Similarity Search and Join in Main Memory on Multi-cores
- Introduction
- Preliminaries
- Data Structure and Algorithms
- Algorithms
- Parallelization with In-memory MapReduce
- Evaluation
- Performance of Similarity-Based Operators
- Scalability of PeARL
- Related Work
- Conclusions and Future Work
- References
- Enabling Data and Compute Intensive Workflows in Bioinformatics
- Introduction
- Motivation
- Workflow Technology
- Workflows in Bioinformatics
- Proteomics: MassMatrix
- RNA Sequencing: Transcriptional Atlas of the Developing Human Brain
- RNA Sequencing: Cancer Genome Atlas Using SeqWare
- Quality Assurance and Quality Control: Population Architecture Using Genomics and Epidemiology (PAGE)
- Workflows in a Virtual Machine
- Related Works
- Future Works and Conclusion
- References
- Homogenizing Access to Highly Time-Consuming Biomedical Applications through a Web-Based Interface
- Introduction
- BioBench: A Framework to Integrate and to Transform Text-Based User Interfaces into Homogeneous Web-Based Ones
- Description
- Design
- Software Development
- BiosH: A Case Study
- Conclusions
- References
- Distributed Management and Analysis of Omics Data
- Introduction
- Management of Omics Data
- Genomics Databases
- Proteomics Databases
- Interactomics Databases
- Omics Data Analysis
- Microarray Data Analysis
- Mass Spectrometry Data Analysis
- Protein-to-Protein Interaction Data Analysis
- Tools for Distributed Management of Omics Data
- Micro-CS
- MS-Analyzer
- IMPRECO
- OntoPIN
- Conclusion and Future Work
- References
- Managing and Delivering Grid Services (MDGS)
- Managing and Delivering Grid Services (MDGS)
- Resource Allocation for the French National Grid Initiative
- Context and Definitions
- Context of Current Work
- Definition of "User Communities"
- Definition of "Resource Providers" and "Service Providers"
- Definition of "Resource Allocation"
- Identified Needs and Goals
- Improve Service Delivery to the French Community
- Measure What Is Done
- Inspiration from Existing Resource Allocation Mechanisms
- High Performance Computing (HPC) World
- Worldwide LHC Computing Grid (WLCG)
- Other National Grids
- Definition of the Strategy
- Key Principles
- Allocating Resources to New Users and French Communities
- Allocating Resources to Established International Communities
- Next Steps
- References
- On Importance of Service Level Management in Grids
- Introduction
- Background: On the Relevance of SLM
- Model of SLM for Grids
- Elements of SLM in Grid Theory
- Actors Perspective
- Customer Perspective
- Sites Perspective
- Grid Infrastructure Provider Perspective
- Application Scenarios That Require SLM
- Large Collaboration Case
- Data Challenges
- Urgent Computing
- Related Works
- Examples of Implementation of SLM Elements in Grids
- Summary
- References
- On-Line Monitoring of Service-Level Agreements in the Grid
- Introduction and Motivation
- Related Work
- On-Line SLA Monitoring Framework
- Architecture
- Design and Implementation
- Defining Composite SLA Metrics Using EPL
- Registry
- SLA Monitoring for Data-Intensive Computations
- Conclusion
- References
- Challenges of Future e-Infrastructure Governance
- Introduction
- e-IRG Recommendations
- e-Governance Management
- Future of Research Networks
- Authentication, Authorization and Accounting
- Energy and Green IT
- Exascale Computing and Related Software
- e-Infrastructure Services
- Data Infrastructures
- Service-Orientation of the Future Open e-Infrastructures
- Conclusions
- References
- Influences between Performance Based Scheduling and Service Level Agreements
- Introduction
- An SLA Aware Job Allocation Architecture
- Benchmarks Characterizing Resource Performance
- Evaluation of a Performance-Based Job Allocation
- Characterizing the Test Bed
- Simulating the Architecture
- Conclusion
- References
- User Centric Service Level Management in mOSAIC Applications
- Introduction
- Related Work
- mOSAIC API
- Vision and Approach
- General Overview of the SLA Architecture
- An Example of mOSAIC Approach
- Conclusions
- References
- Service Level Management for Executable Papers
- Introduction
- Executable Papers Lifecycle
- Exploitation of Executable Papers
- Challenges Facing the Implementation of Executable Papers
- Discussions
- Conclusion
- References
- Change Management in e-Infrastructures to Support Service Level Agreements
- IT Service Management and e-Infrastructures
- Case Study: e-Infrastructure for High Performance Computing
- Related Work
- Design of an Inter-organizational Change-Management
- Summary
- References
- PROPER 2011: Fourth Workshop on Productivity and Performance: Tools for HPC Application Development
- PROPER 2011: Fourth Workshop on Productivity and Performance Tools for HPC Application Development
- Scout: A Source-to-Source Transformator for SIMD-Optimizations
- Introduction
- Related Tools
- The Vectorizing Source-to-Source Transformator Scout
- Unroll-and-Jam
- Configuring Scout
- Partial Vectorization
- Practical Results
- Summary and Conclusion
- Future Work
- References
- Scalable Automatic Performance Analysis on IBM BlueGene/P Systems
- Introduction
- BlueGene/P Architecture
- Periscope Design
- Tool Architecture
- Current Design Shortcomings
- BlueGene/P Tailored Design Alternatives
- MPMD Approach
- Implementation Based on the HTC Mode
- I/O Nodes Agents Placement
- Comparison of Design Alternatives
- Evaluation
- Related Works
- Conclusion and Outlook
- References
- An Approach to Creating Performance Visualizations in a Parallel Profile Analysis Tool
- Introduction
- Design Approach
- Examples
- Sweep3D
- S3D Use Case
- GCRM/ZGrd Use Case: 3D Correlation Plot
- Related Work
- Conclusion
- References
- INAM - A Scalable InfiniBand Network Analysis and Monitoring Tool
- Introduction
- Background
- InfiniBand
- OFED
- Design and Implementation of INAM
- Features of INAM
- Experimental Results
- Experimental Setup
- Visualizing Port Counters
- Point to Point Visualization: Synthetic Communication Pattern
- Link Utilization of Collective Operations: Case Study with MPI_Bcast Operation
- Application Visualization: SpecMPI - LU
- Overhead of Running INAM
- Related Tools
- Conclusions and Future Work
- References
- Auto-tuning for Energy Usage in Scientific Applications
- Introduction
- Motivation
- Experiments
- Power/Energy Measurement
- Auto-tuning Feedback Metric
- Experimental Platform
- Results for Poisson's Equation Solver (PES)
- Future Work
- Related Work
- Conclusion
- References
- Automatic Source Code Transformation for GPUs Based on Program Comprehension
- Introduction
- Related Works
- Source Code Transformation
- Algorithm Recognition
- Source to Source Transformation
- Prototype Tool
- Case Study
- Conclusion
- References
- Enhancing Brainware Productivity through a Performance Tuning Workflow
- Introduction
- Brainware for Green HPC
- A Performance Tuning Workflow
- Initial Meeting
- Base-Line
- Pathology
- Tuning Cycle
- Results/Handover
- Conclusion
- References
- Workshop on Resiliency in High-Performance Computing (Resilience) in Clusters, Clouds, and Grids
- Workshop on Resiliency in High Performance Computing (Resilience) in Clusters, Clouds, and Grids
- The Malthusian Catastrophe Is Upon Us! Are the Largest HPC Machines Ever Up?
- Introduction
- Defining a Resilient System
- Difficulties in Obtaining and Comparing Data
- Reliability of Kraken at the National Institute for Computational Sciences
- Cray XT Architecture Description
- NICS Kraken System Description
- Data Collection
- Kraken Node Failure Data
- Comparison of Large Cray Systems Resiliency
- Data Collection
- The Machines
- Future Work
- Conclusions
- References
- Simulating Application Resilience at Exascale
- Introduction
- Requirements
- Future Systems
- Simulation and Modeling
- Design of Our Simulation Infrastructure
- The Structural Simulation Toolkit (SST)
- Router Model
- Storage Component
- Communication Pattern Generators and Applications
- Implementing Pattern Generators
- Tying It All Together
- Work in Progress
- References
- Framework for Enabling System Understanding
- Introduction
- Approaches
- Numeric Information Collection and Storage
- Text Based Information Collection and Storage
- Numeric Analysis
- Text Based Analysis
- Applications
- Related Work
- Conclusions
- References
- Cooperative Application/OS DRAM Fault Recovery
- Introduction
- DRAM Failures
- Fault and Recovery Model
- Fault Model
- Recovery Model
- Application / OS Interface
- Design
- Implementation
- Testing Support
- Fault-Tolerant GMRES
- Initial Results
- Related Work
- DRAM Error Handling
- Fault Tolerant Algorithms
- Conclusions and Future Work
- References
- A Tunable, Software-Based DRAM Error Detection and Correction Library for HPC
- Introduction
- Design
- Extensions for Error Correction
- Assumptions and Limitations
- Implementation
- Handling User Pointers with System Calls
- Results
- Related Work
- Conclusions and Future Work
- References
- Reducing the Impact of Soft Errors on Fabric-Based Collective Communications
- Introduction
- Fabric-Based Collectives
- Handling Soft Errors on InfiniBand
- Collective Replication Approaches
- Spatial Replication
- Temporal Replication
- Experiments
- Results
- Related Work
- Conclusions
- References
- Evaluating Application Vulnerability to Soft Errors in Multi-level Cache Hierarchy
- Introduction
- Graphite Simulator and Bit Error Injection
- Fast Processor Simulation
- Cache Error Injection
- Multiple Cell Upset and Bit Error Patterns
- Simulation Setup
- Applications
- Simulation Parameters
- Simulation Results
- Application Response to Fault Injections
- Conclusions
- References
- Experimental Framework for Injecting Logic Errors in a Virtual Machine to Profile Applications for Soft Error Resilience
- Introduction
- Overview of Methodology
- Startup
- Probe
- Fault Injection
- Experiments
- Floating Point Multiply Fault Injection
- Floating Point Addition Fault Injection
- Intended Uses
- Related Work
- Future Work
- Conclusion
- References
- High Availability on Cloud with HA-OSCAR
- Introduction
- Related Work
- HA-OSCAR 2.0
- HA-OSCAR Software Architecture
- System Architecture
- OSCAR-V Cluster Architecture
- HA-OSCAR-V Cluster Architecture
- Case Study: HA-OSCAR-Enabled Nimbus
- System Model
- OSCAR-V Cluster System Model
- HA-OSCAR-V Cluster System Model
- Availability Analysis
- OSCAR-V Cluster System Analysis
- HA-OSCAR-V Cluster System Analysis
- HA Comparison
- Conclusions and Future Work
- References
- On the Viability of Checkpoint Compression for Extreme Scale Fault Tolerance
- Introduction
- Checkpoint Compression
- A Checkpoint Compression Viability Model
- Previous Work
- Evaluating Checkpoint Compression
- The Applications
- The Checkpoint Library
- The Compression Algorithms
- The Tests
- Compression Results
- Discussion
- Current Limitations
- References
- Can Checkpoint/Restart Mechanisms Benefit from Hierarchical Data Staging?
- Introduction
- Background
- Detailed Design
- Experimental Evaluation
- Experimental Testbed
- Profiling of a Stand-Alone Staging Server
- Scalability Analysis
- Evaluation with Applications
- Related Work
- Conclusion and Future Work
- References
- Impact of Over-Decomposition on Coordinated Checkpoint/Rollback Protocol
- Introduction
- Background
- Over-Decomposition for Rollback
- Over-Decomposition for Global Restart
- Over-Decomposition for Partial Restart
- Experimental Results
- Global Restart
- Partial Restart
- Related Works
- Conclusion and Future Work
- References
- UCHPC 2011: Fourth Workshop on UnConventional High-Performance Computing
- UCHPC 2011: Fourth Workshop on UnConventional High Performance Computing
- PACUE: Processor Allocator Considering User Experience
- Introduction
- Designing PACUE
- Dynamic Compute Device Redirection
- System Resource Management
- Evaluation
- Evaluation Policy
- Results
- Analysis
- Conclusions and Future Work
- References
- Workload Balancing on Heterogeneous Systems: A Case Study of Sparse Grid Interpolation
- Introduction
- Related Work
- Optimizing Programs for Heterogeneous Computing
- Sparse Grid Interpolation
- Interpolation and Heterogeneous Computing
- Dynamic Task Based Load Balancing
- Static Load Balancing
- Evaluation
- Conclusion
- References
- Performance Evaluation of a Multi-GPU Enabled Finite Element Method for Computational Electromagnetics
- Introduction
- The Physical Problem and Its Numerical Treatment
- Implementation Aspects
- DGTD CUDA Kernels
- Multi-GPU Strategy
- Performance Results
- Weak Scalability
- Strong Scalability
- Conclusion
- References
- Study of Hierarchical N-Body Methods for Network-on-Chip Architectures
- Introduction
- Modeling of the Network-on-Chip
- The Hierarchical N-Body Methods
- Experimental Evaluation
- Experiment Setup
- Result Analysis
- Conclusion
- References
- Extending a Highly Parallel Data Mining Algorithm to the Intel R Many Integrated Core Architecture
- Introduction
- Intel MIC Architecture in Comparison to NVIDIA Fermi Architecture
- Data Mining Using Sparse Grids
- Implementation and Performance Measurements
- Conclusion
- References
- VHPC 2011: 6th Workshop on Virtualization in High-Performance Cloud Computing
- VHPC 2011: 6th Workshop on Virtualization in High-Performance Cloud Computing
- Group-Based Memory Deduplication for Virtualized Clouds
- Introduction
- Background and Motivation
- Memory Deduplication
- Performance Isolation in Clouds
- Limitations of Memory Deduplication in Clouds
- Group-Based Memory Deduplication
- Design
- Implementation
- Evaluation
- Experimental Environments
- Effects of Group-Based Memory Deduplication
- Discussion
- VM Colocation
- Grouping Policies
- Per-group Deduplication Customization
- Conclusions and Future Work
- References
- A Smart HPC Interconnect for Clusters of Virtual Machines
- Introduction
- Background and Related Work
- Design and Implementation
- Performance Evaluation
- Results
- Conclusions
- References
- Coexisting Scheduling Policies Boosting I/O Virtual Machines
- Introduction
- Background
- Motivation
- Related Work
- Default Setup
- Co-existing Scheduling Polices
- Monitoring Tool
- The Driver Domain Pool
- Decoupling vCPUs Based on Workload Characteristics
- Discussion
- Credit Vulnerabilities to I/O Service
- Exotic Scenarios
- Dynamic Instead of Static
- Conclusions
- References
- PIGA-Virt: An Advanced Distributed MAC Protection of Virtual Systems
- Introduction
- Motivation
- Architecture of PIGA-Virt
- In-Depth End-to-End Mandatory Protection
- Experimentations
- Related Works
- Conclusion
- References
- An Economic Approach for Application QoS Management in Clouds
- Introduction
- Architecture
- Use Cases
- Adapting the Agent's Spending Rate
- Adapting the Virtual Cluster Size
- Related Work
- Conclusions
- References
- Evaluation of the HPC Challenge Benchmarks in Virtualized Environments
- Introduction
- Related Work
- Setup
- Self-monitoring Results
- Statistical Methods
- Hardware and Software Used in Tests
- Disparity between CPU and Wall Clock Timers
- Accuracy-Drift of Timers with VM State Accumulation
- Results
- Conclusions and Future Work
- References
- DISCOVERY, Beyond the Clouds
- Introduction
- Related Work
- The DISCOVERY Proposal
- Architecture Overview
- The DISCOVERY Agent
- DISCOVERY in a Nutshell
- Conclusion
- References
- Cooperative Dynamic Scheduling of Virtual Machines in Distributed Systems
- Introduction
- Related Work
- Proposal Overview
- Main Characteristics
- The Iterative Scheduling Procedure
- Implementation
- Current State
- Node Agent
- Experiments
- Future Work
- Conclusion
- References
- Large-Scale DNA Sequence Analysis in the Cloud: A Stream-Based Approach
- Introduction
- Large-Scale DNA Sequence Analysis
- A Stream-Based Approach
- Incremental Data Processing with an SPE
- Use Case Implementation
- Initial Evaluation
- Conclusions and Future Work
- References
- Author Index
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