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MPI continues to be the dominant programming model on all large-scale parallel machines, such as IBM Blue Gene/P and Cray XT5, as well as on Linux and Windows clusters of all sizes. Another important trend is the widespread availability of multicore chips, as a result of which the individual nodes of parallel machines are increasingly multicore. This tutorial will cover several advanced features of MPI that can help users program such machines and architectures effectively. Topics to be covered include parallel I/O, multithreaded communication, one-sided communication, dynamic processes, and new features being added in MPI-3 for hybrid programming, RMA, fault tolerance, and tools. In all cases, we will introduce concepts by using code examples based on scenarios found in real applications. Attendees will leave the tutorial with an understanding of how to use these advanced features of MPI and guidelines on how they might perform on different platforms and architectures.

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In the last decade, agent-based modeling and simulation (ABMS) has been successfully applied to a variety of domains, demonstrating the potential of this technique to advance operations research, social science, physical science, engineering, and policy analysis. However, realizing the full potential of agent-based modeling to find breakthrough research results requires far greater computing capability than is available through current desktop and small cluster tools. The Repast Simphony for C++ (Repast SC++) project addresses this need by developing a next generation ABMS system explicitly focusing on large scale distributed computing platforms. The first part of this tutorial will consist of a working introduction to the Repast SC++ toolkit as a useful and usable framework. The second part will focus on the implementation of an ABMS model including hands-on exercises.

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InfiniBand (IB) and High-speed Ethernet (HSE) technologies are generating a lot of excitement towards building next generation High-End Computing (HEC) systems. This tutorial will provide an overview of these emerging technologies, their offered features, their current market standing, and their suitability for prime-time HEC. It will start with a brief overview of IB, HSE, and their architectural features. An overview of the emerging OpenFabrics stack which encapsulates both IB and HSE in a unified manner will be presented. IB and HSE hardware/software solutions and the market trends will be highlighted. Finally, sample performance numbers highlighting the performance these technologies can achieve in different environments will be shown.

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I/O on HPC systems is a black art. This tutorial sheds light on the state-of-the-art in parallel I/O and provides the knowledge necessary for attendees to best leverage I/O resources available to them. We cover the entire I/O software stack from parallel file systems at the lowest layer, to intermediate layers (such as MPI-IO), and finally high-level I/O libraries (such as HDF-5). We emphasize ways to use these interfaces that result in high performance, and benchmarks on real systems are used throughout to show real-world results. This tutorial first discusses parallel file systems in detail (PFSs). We cover general concepts and examine four examples: GPFS, Lustre, PanFS, and PVFS. We examine the upper layers of the I/O stack, covering POSIX I/O, MPI-IO, Parallel netCDF, and HDF5. We discuss interface features, show code examples, and describe how application calls translate into PFS operations. Finally we discuss I/O best practice.

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Python, a high-level portable multi-paradigm interpreted programming language, is becoming increasingly popular with the scientific and HPC communities due to ease of use, large collection of modules, adaptability, and strong support from vendors and community alike. This tutorial provides an introduction to Python focused on HPC and scientific computing. Throughout, we provide concrete examples, hands-on examples, and links to additional sources of information. The result will be a clear sense of possibilities and best practices using Python in HPC environments. We will cover several key concepts: language basics, NumPy and SciPy, parallel programming, performance issues, integrating C and Fortran, basic visualization, large production codes, and finding resources. While it is impossible to address all libraries and application domains, at the end participants should be able to write a simple application making use of parallel programming techniques, visualize the output, and know how to confidently proceed with future projects with Python.

SPEAKERS:
3:30pm – 04:00pm
Outsourcing IT Complexity: Moving Ultraviz Management from the Laboratory to the Cloud
Ian Foster, University of Chicago and Argonne National Laboratory

04:30pm – 05:00pm
A Flexible Framework for Simulation-time Data Analysis at Extreme Scale
Venkatram Vishwanath, Argonne National Laboratory

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The output from leading-edge scientific simulations and experiments is so voluminous and complex that advanced visualization techniques are necessary to interpret the calculated results. Even though visualization technology has progressed significantly in recent years, we are barely capable of exploiting petascale data to its full extent, and exascale datasets are on the horizon. This workshop aims at addressing this pressing issue by fostering communication between visualization researchers and the users of visualization. Attendees will be introduced to the latest and greatest research innovations in large data visualization, and also learn how these innovations impact scientific supercomputing and discovery process.

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ABSTRACT:
High performance computing (HPC) has become an essential tool used to study real world problems of significant scale and detail across a wide range of fields. However, successfully applying HPC can be a challenging undertaking to newcomers. This workshop provides graduate students who are adopting HPC an opportunity to present early stage research and gain valuable feedback. A panel of expert reviewers with significant experience will be invited to critique students’ work and provide constructive critique. The goal of this workshop is to help students identify shortcomings, introduce new approaches, discuss new technology, learn about relevant literature or define their future research goals.

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As InfiniBand (IB) and High-speed Ethernet (HSE) technologies mature in their support for next generation high-end Computing (HEC) systems, many scientists, engineers and researchers are becoming interested in learning the details of these technologies. Large-scale deployments of these technologies are also bringing new challenges in terms of performance, scalability, portability and reliability. This tutorial will provide details about the advanced features of these emerging technologies. It will start with an overview of the current large-scale deployments of clusters and the associated challenges being faced. Advanced hardware and software features and their capabilities to alleviate the bottlenecks will be emphasized. Challenges in designing next generation systems with these advanced features will be focused. Finally, case studies and experiences in designing HPC clusters (with MPI-1 and MPI-2), parallel file and storage systems, multi-tier datacenters, and cloud computing systems (including virtualization schemes) will be presented together with the associated performance numbers and comparisons.

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The 3rd workshop on Many-Task Computing on Grids and Supercomputers (MTAGS10) will provide the scientific community a dedicated forum for presenting new research, development, and deployment efforts of large-scale many-task computing (MTC) applications on large scale clusters, Grids, Supercomputers, and Cloud Computing infrastructure. MTC, the theme of the workshop encompasses loosely coupled applications, which are generally composed of many tasks (both independent and dependent tasks) to achieve some larger application goal. This workshop will cover challenges that can hamper efficiency and utilization in running applications on large-scale systems, such as local resource manager scalability and granularity, efficient utilization of raw hardware, parallel file system contention and scalability, data management, I/O management, reliability at scale, and application scalability. This workshop encourages interaction and cross-pollination between those developing applications, algorithms, software, hardware and networking, emphasizing many-task computing for large-scale distributed systems.

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Bringing together a wide range of systems administrators, the Petascale Systems management BOF aims to: identify the issues that commonly arise with the management of petascale systems, such as Blue Gene /P, Blue Waters class systems, and extremely large clusters; share solutions and approaches to issues; introduce members of the systems administration community to one another.

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The Coordinated Infrastructure for Fault Tolerant Systems (CIFTS) initiative provides a standard framework, through the Fault Tolerance Backplane (FTB), where any component of the system, whether hardware or software, can report or be notified of faults through a common interface – thus enabling coordinated fault tolerance and recovery. SC’07, SC’08 and SC’09 saw an enthusiastic audience of industry leaders, academia, and research participate in the CIFTS BOF. Expanding on our previous success, the objectives of the SC’10 BOF are: 1. Discuss the experiences gained and challenges faced in comprehensive fault management on petascale leadership machines, and the impact of the CIFTS framework in these environments. Teams working on integrating CIFTS in high-end computing environments such as the Cray XT and IBM Blue Gene machines will share their experiences. Teams developing CIFTS-enabled applications and other popular and widely-used software such as MPICH2, Open MPI, MVAPICH2, BLCR, Math libraries like FT-LA etc. will also share their experiences. 2. Discuss the recent enhancements and planned developments for CIFTS and solicit audience feedback. Discussion will also focus on how system hardware and software, including high-level applications, can adapt to coordinated fault tolerance infrastructures such as CIFTS and how/what services should be provided by such frameworks for emerging extreme-scale architectures. 3. Bring together individuals responsible for exascale computing infrastructures, who have an interest in developing fault tolerance specifically for these environments.

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Advances in genome sequencing have made it possible to sequence over 1,000 species, and during the next 5-10 years it should become routine to sequence humans as part of medical diagnostics and to sequence thousands more organisms important to energy, industry, and science. Genome analysis methods powered by petascale systems will make it possible to quickly go from DNA sequence to functional knowledge and predictive models. Making this a real-time process will radically change the uses of genomic sequencing data. Uncovering individual gene history and protein families will reveal the factors that influence molecular evolution, refine our strategies for databases of protein structures, and lay the foundation for understanding the role of horizontal gene transfer in evolution. Mathematical techniques and large-scale computing are revealing how to reconstruct cell networks, map them from one organism to another, and ultimately develop predictive models to shed light on evolution, ecosystems, development, and disease.

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Current leadership-class machines suffer from a significant imbalance between their computational power and their I/O bandwidth. I/O forwarding is a paradigm that attempts to bridge the increasing performance and scalability gap between the compute and I/O components of leadership-class machines to meet the requirements of data intensive applications by shipping I/O calls from compute nodes to dedicated I/O nodes. I/O forwarding is a critical component of the I/O subsystem of the IBM Blue Gene P supercomputer currently deployed at several leadership computing facilities. We evaluate the performance of the existing I/O forwarding mechanisms for BG / P and identify the performance bottlenecks in the current design. We augment the I/O forwarding with two approaches: I/O scheduling using a work-queue model and asynchronous data staging. We evaluate the efficacy of our approaches using micro-benchmarks and application-level benchmarks on leadership-class systems.

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ABSTRACT:
The issues surrounding HPC work-force development are many fold, which makes them appropriate for a panel discussion approach. Specific issues will include development of future researchers and experienced support staff, including resource access, position instability, salary, and required educational and professional experiences. HR issues range from retention problems due to soft monies to quality of life enticements. HPC staffing requires a reliable pipe-line of candidate personnel with appropriate combinations of general and specialized knowledge relating to multiple machine architectures, operating systems, and methods. Education requirements include appropriate numerical methods, machine properties, and general principles of computational thinking. The panel members will include representatives from organizations supporting HPC, including funding/oversight (Ed Seidel), curriculum development (Thomas Sterling), research enablement (Daniel S. Katz), management (Jim Lupo, HPC@LSU User Services Manager) and human resources (Laurie Rea, LSU).

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Over the last twenty years, the international open source community has increasingly provided the software at the heart of the world’s high-performance computing systems. The community provides everything from operating system components to compilers and advanced math libraries. As an international community, however, we have only loosely coordinated activities and plans for development. The new rapidly changing technologies in multicore, power consumption, GPGPUs, and memory architectures creates an opportunity for the community to work together and build an international program to design, build, and deliver the software so critical the science goals of our institutions. To help plan how the international community could build a partnership to provide the next generation of HPC software to support scientific discovery, we have had a series of workshops. We would like to hold a BOF at SC10 to report on the effort and solicit feedback from the community.

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The need for parallel IO is becoming ever more pressing – With several libraries available, some more established than others, and some seemingly filling niche roles for particular scientific domains, the developer has a difficult time choosing the right library, and getting the best performance from it. If parallel file systems can be scaled up to support more and more IO nodes and metadata servers, then is the issue of raw bandwidth a ’solved’ problem? If so, how can library developers ensure that scientific applications get the maximum performance without requiring extensive understanding of the underlying methods and issues. In this panel, we bring together developers of some of the leading parallel IO libraries used in the scientific computing community and ask how they can be best used by developers (such as climate modelers) producing prodigious amounts of data and how will the libraries change to meet future needs.

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The relationship between our ability to analyze and extract insights from visualization of climate model output and the capability of the available resources to make those visualizations has reached a crisis point. The large volume of data currently produced by climate models is overwhelming the current, decades-old visualization workflow. The traditional methods for visualizing climate output also have not kept pace with changes in the types of grids used, the number of variables involved, and the number of different simulations performed with a climate model or the feature-richness of high-resolution simulations. In this BOF, producers of climate data and developers of climate visualization and analysis platforms will meet to discuss these challenges.

[.ics calendar file] MPICH is a popular, open-source implementation of the MPI message passing standard. It has been ported to many platforms and used by several vendors and research groups as the basis for their own MPI implementations. This BoF session will provide a forum for users of MPICH as well as developers of MPI implementations derived from MPICH to discuss experiences and issues in using and porting MPICH. Future plans for MPI-3 support will be discussed. Representatives from MPICH-derived implementations will provide brief updates on the status of their efforts. MPICH developers will also be present for an open forum discussion. All those interested in MPICH usage, development, and future directions are encouraged to attend.

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Our experiences with High Performance Computing are highly varied and often exhibit great examples of achievement, technical and scientific ability, unmitigated disaster, and of course – humor. This BOF is a story slam in which individuals will have the opportunity to share their own true High Performance and Scientific Computing themed story. All stories will be limited to no more than five minutes, and while we permit names to be changed, all stories should be based on real life experiences. Session leaders will provide an introduction, guide speakers, and lead audience members in voting for their favorite stories at the close of the session. Those participants who shared favorite stories will be awarded New Orleans themed gag-prizes.