CUDA GPGPU Parallel Computing Newsletter - Issue 52

Wed., April 13, 2011, Issue #52 - Newsletter Home

WELCOME
Welcome to CUDA: Week in Review, an online news summary for the worldwide CUDA, GPU computing and parallel programming ecosystem.

CUDA TOP STORIES

GPU Computing at Microway

Update on Keeneland

GPUs and Econophysics

Scobleizer YouTube Video: GPUs for Datacenters

New GPU Computing Overviews and Training

CONTENTS

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GPU Computing Momentum at Microway

This week’s Spotlight is on Stephen Fried, founder of Microway and veteran technology inventor. Steve is a former space scientist and FAA flight examiner who can be found on weekends soaring in his sailplane over the Green Mountains of Vermont.

We caught up with Steve after learning that BioStack-LS — a CUDA/Tesla-based Microway product — was named "Best of Show" finalist at the Bio-IT World Conference in Boston this week. Here’s an extract from our interview:

Steve Fried in his Schleicher ASH-26 E sailplane

NVIDIA: Steve, tell us about Microway.

Steve: We develop x86-based Linux clusters whose nodes each employ a pair of NVIDIA Tesla GPUs. For the past four years, we’ve been providing customers with well-designed and cooled GPU platforms.

NVIDIA: Where are you seeing the most momentum in GPU computing?

Steve: Applications that manipulate matrices or rely on linear algebra techniques are excellent candidates for a system of parallel GPGPUs.

For example, we believe that GPUs are ideal for executing the parallel vector applications that dominate much of the bio-informatics world. This week we are at Bio-IT World demonstrating BioStack-LS. BioStack-LS includes seven GPU compute nodes, each with two Tesla C2070s.

BioStack-LS represents an innovation for the bio-medical community because it’s delivered pre-configured for life sciences software, including AMBER, MATLAB, NAMD and VMD.

NVIDIA: Why are people embracing the CUDA parallel programming model?

Steve: CUDA automatically solves many annoying problems.... It hides the bits and pieces of kernel control, data flow and task synchronization from the user. It reduces the user’s task to writing a single piece of C code that executes on the host, which automatically loads and calls the kernels that are embedded within the CUDA application in the order that they are to be executed....

- Read the complete interview here

(Would you like to be in the CUDA Spotlight? Email: cuda_week_in_review@nvidia.com)

Update on Keeneland

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The Keeneland Project is a five-year, $12 million grant awarded by the NSF for creation of an experimental high-performance system. Georgia Tech and its partners, the University of Tennessee at Knoxville and Oak Ridge National Lab, are deploying an HP system powered by Tesla GPUs. A Keeneland Workshop will be held April 14-15 in Atlanta.
- For more info, visit: http://keeneland.gatech.edu/
- Watch Prof. Jeff Vetter speak about Keeneland (SC09): http://is.gd/HuMNEr

GPUs and Econophysics - New Article in European Physical Journal
Tobias Preis has authored an article on GPU computing in econophysics/statistical physics in the European Physical Journal - Special Topics.
- See abstract: http://dx.doi.org/10.1140/epjst/e2011-01398-x
- Contact info: www.tobiaspreis.de

Scobleizer YouTube Video: GPUs for Datacenters
Watch tech blogger Robert Scoble interview Jack Levin of ImageShack/YFrog about GPUs, CUDA and datacenters (7 mins).
- See: http://www.youtube.com/watch?v=UPUJUa4XgUs

New GPU Computing Overviews and Training Seminars
Microsoft, Acceleware and NVIDIA will host complimentary "GPU Computing Overviews" next month. Breakfast and lunch will be served.

May 3, Boston

May 4, New York

May 19, San Francisco

May 20, Chicago

In addition, Microsoft and Acceleware are offering 4-day CUDA/OpenCL training courses using Microsoft Visual Studio and NVIDIA Parallel Nsight (early bird and group discounts available).

Reminders
- CUDA Toolkit 4.0 is publicly available: http://developer.nvidia.com/cuda-downloads
- GTC 2011 Call for Submissions is open until May 3: www.nvidia.com/object/call_for_submissions.html

NEW: Each week we highlight sessions from GTC 2010 and SC10. Here are our picks for this week:

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      Using GPUs for Real–Time Brain–Computer Interfaces (GTC10)
      Adam Wilson - University of Cincinnati
      http://nvidia.fullviewmedia.com/gtc2010/0922-c-2122.html (51 mins)

      Faster, Cheaper, Better: Biomolecular Sim w/ NAMD, VMD, CUDA (SC10)
      John Stone - University of Illinois at Urbana-Champaign
      http://www.nvidia.com/content/PDF/sc_2010/theater/Stone_SC10.pdf

The Stockholm Environment Center, University of York, is funding a summer scholarship in biodiversity and conservation research. Aim of project is to develop GPGPU application to interface with R programming language, MATLAB and GNU Octave. Prototype will be tested on NVIDIA-based server.
Dates: July 11-Sept. 16, 2011. Project number: 201107
- Apply: http://www.york.ac.uk/res/yccsa/research/transit/scholarships.html
- More info:
http://www.york.ac.uk/res/yccsa/research/transit/scholarships2011/201107.pdf

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NVIDIA’s Andy Walsh blogged this week about how OpenEye Scientific Software is tackling the challenges of drug discovery:

"A key path to drug discovery over the past decade has been the process of determining "shared bioactivity" between molecules, that is, determining the similarity of one molecule to another based on its three-dimensional shape.

There’s always been a catch, though. If you’re a large pharmaceutical company doing research in this area, you probably have a collection of more than a hundred million molecule shapes or conformations. In the rush to find new cures, how do you even begin to get through this much data in a reasonable timeframe, even in a lifetime?

Enter an innovative company called OpenEye Scientific Software, and its revolutionary new application called FastROCS."

- Read the full blog post: http://blogs.nvidia.com/2011/04/a-molecule-matching-star-is-born/

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Featured GPU Webinars:	back to the top

- Live Q&A on CUDA-gdb and memcheck - Webinar

Wed., April 13, 2011, 10:00-11:00 am pacific

Presented by senior engineering team, NVIDIA

https://www2.gotomeeting.com/register/337468450

- Bright Cluster Manager/Advanced Clusters Made Easy - Webinar

Thurs., April 21, 2011, 9:00-10:00 am pacific

https://www2.gotomeeting.com/register/687856658

Featured GPU Meetups:

- Meetup: Brisbane GPU Users

April 21, 2011, 6:00 pm, Brisbane, Australia

http://www.meetup.com/Brisbane-GPU-Users/events/17151901/

- Meetup: HPC & GPU Supercomputing Group of Silicon Valley

May 2, 2011, 6:00 pm, Carnegie Mellon Silicon Valley/NASA, Mountain View, Calif.

http://www.meetup.com/HPC-GPU-Supercomputing-Group-of-Silicon-Valley/

- Meetup: HPC & GPU Supercomputing Group of Boston

May 4, 2011, 6:00 pm, Microsoft NERD Center, Cambridge, Mass.

http://www.meetup.com/HPC-GPU-Supercomputing-Group-of-Boston/

Upcoming Events:

April 2011

BIO-IT WORLD 2011

April 12-14, Boston, Mass.

Note: Presentation by Bob Tolbert, OpenEye Scientific Software, April 13

http://www.bio-itworldexpo.com/

NAB 2011

April 11-14, 2011, Las Vegas, Nev.

http://www.nabshow.com/2011/index.asp

Fluid-Structure Interaction 2011: Workshop on the Advances in
Computational Methods

April 27-29, 2011, Singapore

Note: Session by Srinivas Kodiyalam, NVIDIA, on April 29

www.fsi-singapore.com/

May 2011

-GPU Computing Overview - Microsoft, Acceleware, NVIDIA

May 3, 2011, 9:00 am-5:00 pm, Boston, Mass.

https://msevents.microsoft.com/CUI/EventDetail.aspx?EventID=1032479956&Culture=en-US

-GPU Computing Overview - Microsoft, Acceleware, NVIDIA

May 4, 2011, 9:00 am-5:00 pm, New York, New York

https://msevents.microsoft.com/CUI/EventDetail.aspx?EventID=1032479952&Culture=en-US

-NEW: GTC Workshop Singapore

May 12, 2011, Singapore

Note: The GPU Technology Conference enters South East Asia with this new GTC Workshop. Co-sponsored by NVIDIA and NOVATTE.

http://www.novatte.com/press-room/gtc2011/

-NEW: Spring CUDA Training by Tech-X Corporation

May 16-18, 2011, Boulder, Colo.

Note: Lead by Dr. Peter Messmer, Dr. Paul Mullowney and Dr. Michael Galloy

http://www.txcorp.com/products/GPULib/cuda_training/index.php

-Parallel CFD Conference (ParCFD 2011)

May 16-20, 2011, Barcelona, Spain

Note: Tutorial by Tom Reed, NVIDIA, on May 16

http://parcfd2011.bsc.es/

-Workshop on High Performance Computational Biology - IEEE

May 16, 2011, Anchorage, Alaska

Note: Held with International Parallel & Distributed Processing Symposium

www.hicomb.org/

-GPU Computing Overview - Microsoft, Acceleware, NVIDIA

May 19, 2011, 9:00 am-5:00 pm, San Francisco, Calif.

https://msevents.microsoft.com/CUI/EventDetail.aspx?EventID=1032479960&Culture=en-US

-GPU Computing Overview - Microsoft, Acceleware, NVIDIA

May 20, 2011, 9:00 am-5:00 pm, Chicago, Ill.

https://msevents.microsoft.com/CUI/EventDetail.aspx?EventID=1032479956&Culture=en-US

-NEW: GPGPU Computing for Scientific Applications

May 23-27, 2011, Cordoba, Argentina

Held in FaMAF, National University of Cordoba

Note: Sessions by Robert Strzodka (MPI-Saarbrücken) and Ross Walker (SDSC, CUDA Fellow) www.famaf.unc.edu.ar/grupos/GPGPU/EscuelaGPGPU2011

-NAFEMS World Congress: Promoting Adoption of HPC for Engineering Simulation

May 23-26, 2011, Boston, Mass.

Note: Session by Stan Posey, NVIDIA, on May 25

http://www.nafems.org/congress

-LS-DYNA 8th European Users Conference

May 23-24, 2011, Strasbourg, France

Note: Paper and talk by Stan Posey and Srinivas Kodiyalam, NVIDIA

http://www.lsdynaeuc.alyotech.fr/

-NEW: Computer Simulations on GPU - International Symposium

May 30-June 1, 2011, Mainz, Germany

Note: Axel Koehler, NVIDIA, will present

www.cond-mat.physik.uni-mainz.de/~weigel/GPU2011/home/

June 2011

-25th International Conference on Supercomputing

June 1-4, 2011, Tucson, Ariz.

http://ics11.cs.arizona.edu/

-Intelligent Vehicles Conference - IEEE

June 5-9, 2011, Baden-Baden, Germany

Note: Session by Jeff Ota, NVIDIA, on Parallel Computing in Intelligent Vehicles

www.mrt.uni-karlsruhe.de/iv2011/

-Internat’l. Supercomputing Conference (ISC)

June 19-23, 2011, Hamburg, Germany

www.supercomp.de/isc11/Take-Part/Call-for-Papers

-Internat’l. Conference on Computer Systems and Applications

June 27-30, 2011, Sharm El-Sheikh, Egypt

http://aiccsa2011.hpcl.gwu.edu/

July – Dec. 2011

-2011 World Congress on Engineering (WCE 2011)

July 6-8, 2011, London, England

http://www.iaeng.org/WCE2011/ICPDC2011.html

-Genetic and Evolutionary Computation Conference (GECCO)

July 12-16, 2011 Dublin, Ireland

www.sigevo.org/gecco-2011/index.html

-World Congress in C.S., Computer Engineering, Applied Computing (WORLDCOMP’11)

July 18-21, 2011, Las Vegas, Nevada

www.world-academy-of-science.org/worldcomp11/ws

-Application Accelerators in High Performance Computing (SAAHPC 2011)

(Call for papers: May 6)

July 19-21, 2011, Univ. of Tennessee, Knoxville, Tennessee

http://illinois.edu/lb/article/2100/45663

-Advanced Numerical Methods on GPUs

Mini-symposium at ENUMATH 2011

Sept. 5-9, Univ. of Leicester, Leicester, UK

http://www2.le.ac.uk/departments/mathematics/research/enumath2011
/minisymposia

-Parallel Processing and Applied Mathematics (PPAM 2011)

Sept. 11-14, 2011, Torun, Poland

Note: Scientific Computing with GPUs tutorial, incl. session by Tim Schroeder, NVIDIA

http://ppam.pl/tutorials/21

-Geospatial Summit

Sept. 13-14, 2011, Herndon, Virginia

http://cfp.foseinstitute.org/gis2011

-SPIE Conference on High-Performance Computing in Remote Sensing

Sept. 19-22, 2011, Prague, Czech Republic

http://spie.org/rs11

-SEG (Society of Exploration Geophysicists) Annual Meeting

Sept 18-23, 2011, San Antonio, Tex.

(Deadline for abstracts: April 6, 2011)

http://www.seg.org/events/annual-meeting/sanantonio2011/am2011techprogram

-GPU Technology Conference (GTC 11)

Oct. 11-14, 2011, San Jose, Calif.

www.gputechconf.com

-SC11

Nov. 12-18, 2011, Seattle, Wash.

http://sc11.supercomputing.org/?pg=techprogram.html

(To list an event, email: cuda_week_in_review@nvidia.com)

CUDA Downloads	back to the top
– Download CUDA: www.nvidia.com/getcuda – Download Parallel Nsight: www.nvidia.com/object/parallel-nsight.html – Get developer guides and docs: http://developer.nvidia.com/object/gpucomputing.html

CUDA Registered Developer Program

– Sign up: www.nvidia.com/paralleldeveloper

CUDA GPUs

– List of CUDA-enabled GPUs: www.nvidia.com/object/cuda_gpus.html

CUDA Libraries Performance Report

– Download: http://bit.ly/ehR5az

CUDA on the Web

– See previous issues of CUDA: Week in Review: http://is.gd/cBXbg
– Follow CUDA & GPU Computing on Twitter: www.twitter.com/gpucomputing
– Network with other developers: www.gpucomputing.net
– Stayed tuned to GPGPU news and events: www.gpgpu.org
– Learn more about CUDA on CUDA Zone: www.nvidia.com/cuda
– Check out the NVIDIA Research page: www.nvidia.com/research

CUDA Recommended Reading

– Kudos for CUDA: www.hpcwire.com/features/Kudos-for-CUDA-97889444.html
– Supercomputing for the Masses, Part 21: http://is.gd/f9o6o
– CUDA books: http://www.nvidia.com/object/cuda_books.html

CUDA Recommended Viewing

– Third Pillar of Science: www.nvidia.com/object/race-for-better-science.html

– GTC 2010 presentations: www.nvidia.com/gtc

– SC10 presentations: www.nvidia.com/object/sc10_theater.html

CUDA is NVIDIA’s parallel computing hardware architecture. NVIDIA provides a complete toolkit for programming on the CUDA architecture, supporting standard computing languages such as C, C++ and Fortran as well as APIs such as OpenCL and DirectCompute. Send comments and suggestions to: cuda_week_in_review@nvidia.com

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