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GPU
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March 17-20, 2015 | San Jose, California
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S5185 - A CUDA Implementation of the High Performance Conjugate Gradient (HPCG) Benchmark

Everett Phillips HPC Software Engineer, NVIDIA
Everett works on HPC applications in the Tesla Performance Group at NVIDIA.

This talk will present the details of a CUDA implementation of the HPCG benchmark, including key optimization strategies and performance results on a wide range of GPU systems: from the smallest CUDA capable platform - the Jetson TK1, to the largest GPU supercomputers - Titan (Cray XK7 at ORNL) and Piz Daint (Cray XC30 at CSCS). HPCG was recently proposed as a complement to the High Performance Linpack (HPL) benchmark currently used to rank supercomputers in the Top500 list. HPCG solves a large sparse linear system of equations using a multigrid preconditioned conjugate gradient algorithm, and is designed to represent modern application workloads.

Level: Intermediate
Type: Talk
Tags: Supercomputing; Data Center, Cloud Computing & HPC; Developer - Algorithms

Day: Tuesday, 03/17
Time: 16:00 - 16:25
Location: Room 212B
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S5371 - VMD: Visualization and Analysis of Biomolecular Complexes with GPU Computing

John Stone Senior Research Programmer, University of Illinois at Urbana-Champaign
Highly-Rated Speaker
John Stone
John Stone is a Senior Research Programmer in the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology, and Associate Director of the NVIDIA CUDA Center of Excellence at the University of Illinois. Mr. Stone is the lead developer of VMD, a high performance molecular visualization tool used by researchers all over the world. His research interests include molecular visualization, GPU computing, parallel processing, ray tracing, haptics, and virtual environments. Mr. Stone was awarded as an NVIDIA CUDA Fellow in 2010. Mr. Stone also provides consulting services for projects involving computer graphics, GPU computing, and high performance computing.

This talk will showcase recent successes in the use of GPUs to accelerate challenging molecular visualization and analysis tasks on hardware platforms ranging from commodity desktop computers to the latest Cray supercomputers. This presentation will highlight the use of in-place OpenGL rendering and GPU ray tracing for interactive and batch mode rendering of images and movies, CUDA just-in-time (JIT) compilation for increasing the performance of data-driven visualization and analysis algorithms, and GPU accelerated analysis of results of hybrid structure determination methods that combine data from cryo-electron microscopy and X-ray crystallography with all-atom molecular dynamics simulations.

Level: Intermediate
Type: Talk
Tags: Visualization - In-Situ & Scientific; Life & Material Science; Big Data Analytics

Day: Wednesday, 03/18
Time: 09:00 - 09:50
Location: Room LL21C
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S5149 - Attacking HIV with Petascale Molecular Dynamics Simulations on Titan and Blue Waters

James Phillips Senior Research Programmer, University of Illinois at Urbana-Champaign
Highly-Rated Speaker
James Phillips
James Phillips is a Senior Research Programmer in the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. He has a Ph.D. in Physics from the University of Illinois. Since 1999, James has been the lead developer of the highly scalable parallel molecular dynamics program NAMD, for which he received a Gordon Bell Award in 2002. His research interests include improving the performance and accuracy of biomolecular simulations through parallelization, optimization, hardware acceleration, better algorithms, and new methods.

The highly parallel molecular dynamics code NAMD was was one of the first codes to run on a GPU cluster when G80 and CUDA were introduced in 2007, and is now used to perform petascale biomolecular simulations, including a 64-million-atom model of the HIV virus capsid, on the GPU-accelerated Cray XK7 Blue Waters and ORNL Titan machines. Come learn the opportunities and pitfalls of taking GPU computing to the petascale, the importance of CUDA 6.5 and Kepler/Maxwell features in combining multicore host processors and GPUs in a legacy message-driven application, and the promise of remote graphics for improving productivity and accessibility in petascale biology.

Level: Intermediate
Type: Talk
Tags: Life & Material Science; Supercomputing; Graphics Virtualization

Day: Wednesday, 03/18
Time: 10:00 - 10:50
Location: Room 212A
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S5386 - VMD: Publication-Quality Ray Tracing of Molecular Graphics with OptiX

John Stone Senior Research Programmer, University of Illinois at Urbana-Champaign
Highly-Rated Speaker
John Stone
John Stone is a Senior Research Programmer in the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology, and Associate Director of the NVIDIA CUDA Center of Excellence at the University of Illinois. Mr. Stone is the lead developer of VMD, a high performance molecular visualization tool used by researchers all over the world. His research interests include molecular visualization, GPU computing, parallel processing, ray tracing, haptics, and virtual environments. Mr. Stone was awarded as an NVIDIA CUDA Fellow in 2010. Mr. Stone also provides consulting services for projects involving computer graphics, GPU computing, and high performance computing.

This session will describe the adaptation of the popular molecular graphics program VMD to support both batch and interactive ray tracing using NVIDIA OptiX, on computers ranging from laptops all the way up to large scale Cray XK7 supercomputers such as Blue Waters and Titan. We will describe the benefits of custom VMD-specific geometric primitives and memory layouts, and relate our experiences adapting the Tachyon CPU-based ray tracing engine used by VMD, to NVIDIA's OptiX GPU ray tracing framework. The session will present performance data for workstation and supercomputer class visualizations, integration of OptiX into VMD, interactive ray tracing, many example movies and visualizations, and avenues for further improvement.

Level: Intermediate
Type: Talk
Tags: Rendering & Ray Tracing; Media & Entertainment; Visualization - In-Situ & Scientific

Day: Thursday, 03/19
Time: 09:00 - 09:25
Location: Room LL21E
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S5202 - Porting Computational Physics Applications to the Titan Supercomputer with OpenACC and OpenMP (Presented by Cray)

Aaron Vose Benchmark and Application Analyst, Cray Inc.
Aaron Vose
Aaron Vose is a benchmark and application analyst with the Cray Center of Excellence at the U.S. Department of Energy's Oak Ridge National Laboratory, where he helps domain scientists achieve maximum performance and scalability of their applications on the Titan supercomputer.

This session presents valuable "lessons learned" during the process of porting computational physics applications to the Titan supercomputer with hybrid OpenACC and OpenMP. Specifically, three real-world HPC codes are enhanced with OpenACC directives to take advantage of the Kepler GPUs and OpenMP directives to target the CPUs of the Titan supercomputer. The first application is TACOMA, a computational fluid dynamics code which solves finite-volume, block-structured, compressible flows. The second application is Delta5D, a Monte Carlo fusion code which follows particle orbits in Boozer space using Hamiltonian guiding center equations solved with an adaptive time step integrator. Finally, the third application is NekCEM, a high-fidelity electromagnetics solver based on spectral element methods. While the science behind these applications may differ significantly, the same porting process and lessons learned apply to each.

Level: Intermediate
Type: Talk
Tags: OpenACC; Developer - Programming Languages; Computational Physics; Developer - Performance Optimization

Day: Thursday, 03/19
Time: 15:00 - 15:25
Location: Room 220C
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S5382 - OpenACC 2.5 and Beyond

Michael Wolfe Compiler Engineer, NVIDIA
Highly-Rated Speaker
Michael Wolfe
Michael Wolfe works on the Portland Group compilers at NVIDIA. He has over 35 years of experience developing languages and compilers for high performance and parallel computers in industry and academia. He has published one textbook, "High Performance Compilers for Parallel Computing," and a number of technical papers.

Learn about the new features being added to OpenACC in the upcoming 2.5 version, and the new data management features being designed for the subsequent version. OpenACC is the popular directive-based API for GPU and accelerator programming, first released in 2011, supported by the Cray and PGI commercial products, and being implemented by numerous open-source compilers. The latest OpenACC release includes several simplifications and exposes some new behavior that programmers should be aware of. This presentation will also discuss the continuing work on deep data structure management features being designed for the subsequent release.

Level: Intermediate
Type: Talk
Tags: OpenACC; Developer - Programming Languages; Supercomputing

Day: Thursday, 03/19
Time: 15:30 - 15:55
Location: Room 220C
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S5259 - Optimizing High-Dimensional Dynamic Stochastic Economic Models for MPI+GPU Clusters

Simon Scheidegger Postdoc, University of Zurich
Simon Scheidegger
Dr. Simon Scheidegger is a Postdoc at the Department of Banking and Finance in the Group of F. Kübler, where he works since 2012. In 2010, he obtained his PhD in theoretical physics at the University of Basel (Supervisors: Prof. Dr. M. Liebendörfer, Prof. Dr. F-K. Thielemann), being awarded with the Faculty prize of the Department of Science. From 2010 to 2012, he worked as a Credit Risk Modeler at Credit Suisse. His current research activities cover high performance computing in finance & economics, the numerical solution of real business cycle models, overlapping generation models and optimal taxation problems.

In our talk we will present programming and optimization techniques for exposing the potential of CSCS's Cray XC30 "Piz Daint" cluster for economic modelling. Macroeconomic phenomena are often modeled as constrained optimization problems. Targeting limited level of detail, it is often possible to find local solutions to such problems, useful only for examining the macro-economy dynamics around a steady state. Solving globally a model with high heterogeneity (different types of consumers, sectors, or countries) yields into dramatic increase of computational and storage costs. In our solver we combine adaptive sparse grids with MPI+GPU implementation, which allows to compute global solutions for e.g. international real business cycle models with unprecedentedly high heterogeneity.

Level: Intermediate
Type: Talk
Tags: Finance; Developer - Performance Optimization; Supercomputing

Day: Thursday, 03/19
Time: 16:00 - 16:25
Location: Room 210C
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S5871 - Realizing GPU Computation at Scale (Presented by Cray)

John Lee VP - Product Management, Cray Cluster Solutions, Inc.
John Lee
John Lee has been in the HPC industry for the past 15 years. John provides product leadership & strategic direction to Cray's Cluster Solutions. In this role, he heads the Product Group planning, coordination and growth initiatives for Cray's cluster products and complex supercomputing solutions. This portfolio provides the foundation for Cray's converged HPC cluster solutions, the company's strategy for next-generation clustered supercomputers that enable customers to increase agility, lower costs of operations and drive innovation into their businesses.
Maria Iordache Product Management Director, Cray Inc.
Dr. Maria Iordache is a Product Management Director at Cray, responsible for Cray’s CS-Storm high-density GPU systems and for the HPC cluster software stack. Previous to Cray, Maria worked for BlueArc (acquired by Hitachi Data Systems), Brocade, and IBM in Product Management, Business Development and Alliances, covering the areas of HPC systems, storage, networking and virtualization. Maria has a computational mechanics background and was a developer at Abaqus Inc., specialized in non-linear finite element models for materials and structures. She holds a Ph.D. from CU Boulder in Computational Mechanics, and an MBA from the MIT Sloan School of Management.

GPUs deliver compelling performance in a very energy efficient and compact package. However, a number of requirements have to be satisfied in order to extract this performance. This talk will discuss Cray's experience with scaling behavior on systems built from 8 GPU servers, using K40 or K80 GPUs, as a function of algorithm, data flow and interconnect. Some of these examples were validated on systems ranging up to the 10th fastest supercomputer in the world (#10 on the Top500 list) and the 4th greenest supercomputer (#4 on the Green500).

Level: Intermediate
Type: Talk
Tags: Supercomputing; Data Center, Cloud Computing & HPC

Day: Thursday, 03/19
Time: 18:00 - 18:50
Location: Room 212B
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Talk