CUDA GPGPU Parallel Computing Newsletter - Issue 61

GPU-Accelerated Biophotonics & Biomedical Optics
This week’s spotlight is on Alexander Doronin, a PhD candidate in the Biophotonics & Biomedical Imaging Research Group at the University of Otago in New Zealand.

His research interests include biophotonics, light-tissue interaction, Monte Carlo (MC) computational modeling and parallel programming on GPUs using CUDA.

NVIDIA: Alex, what is biophotonics?

Alex: Biophotonics refers to the interaction between biology and photonics. Photonics is a science that deals with the particle properties of light. A number of revolutionary applications have arisen in the field of photonics as a result of advancements in high technology and the miniaturization of solid-state optical/laser devices. A recent trend is the mapping of photonics technologies to the life sciences and medicine -- hence the term "biophotonics" was coined. It is a fast moving and very exciting area of research.

NVIDIA: What’s an example of an application that could benefit from biophotonics?

Alex: One example is cancer diagnostics. The current, most widely-used methodology for cancer diagnosis is histological analysis with microscopy. However, morphological variations (and especially morphological changes associated with early grades of cancer tissue) are difficult to resolve regarding what type or sub-type of cancer is present.

In our research, we are investigating the use of circular polarized light -- and the manipulation of the coherent properties of light -- to improve cancer diagnostics. The technique has the potential to revolutionize the ability to detect cancer at the very early stage.

NVIDIA: Tell us about the online Monte Carlo tool developed by your group.

Alex: With the rapid growth of the Internet, rich, browser-based applications have become more and more popular. Solutions such as Google Apps, Google Docs, online video sharing and gaming portals have become a large part of our everyday life.

Leveraging modern, web-based technology, we have created a free online MC computational tool for researchers in the area of biophotonics and biomedical optics. On the server side, the tool is accelerated by CUDA GPUs. On the client side, a lightweight, user-friendly web interface allows multiple clients to set up optical system parameters, perform modeling, and download results in a typical journal paper format.

We are currently extending our GPU cluster with additional M2090s and are expecting even more performance. The online MC tool is made available to the worldwide biophotonics community through the Biophotonics & Biomedical Imaging Research Group, which is headed up by my supervisor, Dr. Igor Meglinski.

- Read the complete interview here

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

GTC Asia Announced

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NVIDIA announced GTC Asia, the next major event in NVIDIA’s international series of GPU Technology Conference (GTC) events. GTC Asia will take place on Dec. 14-15, 2011 at the China National Convention Center in Beijing. www.gputechconf.cn

GTC Worldwide Call for Submissions
NVIDIA is now accepting poster proposals for the following events:
- GTC Express Live Theater @ SC11 (Nov. 12-18, 2011)
- GTC Asia 2011 (Dec. 14-15, 2011)
- GTC U.S. 2012 (May 14-17, 2012)
See: http://www.gputechconf.com

Project Maximus Update
NVIDIA’s ‘Project Maximus’ is an initiative to build a technology platform that enables workstation applications to take advantage of multi-GPU computing. By adding the computational power of a Tesla GPU with the advanced graphics capability of Quadro, users will be able to experience the highest level of productivity. Read what AnandTech’s Ryan Smith says about it: http://bit.ly/rpxoE6

A GPU Mini-Supercomputer for Every Scientist
The new GPU Starter Kit from HP is a pre-configured system that provides researchers with a ready-to-use GPU computing cluster, straight out of the box. It combines eight HP ProLiant SL390 G7 servers (containing 24 Tesla M2070 GPUs) with 16 CPUs. It is pre-configured with CUDA 4.0. For info, read Roy Kim’s recent blog on A GPU Mini-Supercomputer for Every Scientist or send an email to: Hpc-sales@hp.com

MAGMA v1.0 Supports Tesla GPUs
The Innovative Computing Laboratory (ICL) at University of Tennessee has released MAGMA v1.0 with support for NVIDIA Tesla GPUs. The MAGMA (Matrix Algebra for GPU and Multicore Architectures) Project aims to create a next generation of linear algebra libraries on heterogeneous systems. The ICL is directed by Dr. Jack Dongarra. http://icl.cs.utk.edu/magma/software/index.html

Gaussian to Support GPU Acceleration
NVIDIA, Gaussian, Inc., and The Portland Group (PGI) will develop a GPU-accelerated release of Gaussian, the quantum chemistry software app. Dr. Michael Frisch, president of Gaussian, said: "By coordinating the development of hardware, compiler technology and application software, the new app will bring the speed and cost-effectiveness of GPUs to the challenging problems and applications that Gaussian’s customers need to address." http://www.nvidia.com/object/newsroom.html

A GPU Mini-Supercomputer for Every Scientist, by Roy Kim

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NEW: Each week we highlight sessions from GTC 2010 and ISC 2011. Here are our picks for this week:

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      Enabling On Demand Value-At-Risk for Financial Markets (GTC 10)
      Matthew Dixon – UC Davis and Jike Chong – Parasians
      http://nvidia.fullviewmedia.com/gtc2010/0923-a7-2098.html

      Texture Unit in 3D Volume Reconstruction (ISC 2011)
      Karl Schwartz – Siemens AG
      http://www.nvidia.com/content/PDF/isc-2011/Schwarz.pdf

NEW: Dell is seeking a systems engineer for its HPC engineering team in Austin, TX. Experience with GPUs, CUDA and/or OpenCL required. http://bit.ly/nSzOVD

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If you are travelling to any of these locations, feel free to drop in to a GPU Meetup. Visitors are welcome.

- United States
        Boston GPU Meetup – Sept. 1, 6:00 pm
        New York GPU Meetup – (Special Meeting) September 8, 6:00 pm
        Silicon Valley GPU Meetup – Sept. 12, 6:15 pm
        New York GPU Meetup – Sept. 26, 6:00 pm
        Boston GPU Meetup – Oct. 6, 6:00 pm

- Australia
        Sydney GPU Meetup – Sept. 15, 6:00 pm
        Brisbane GPU Meetup – Sept. 15, 6:00 pm

August 2011	back to the top

- In-Depth CUDA Training (Presented by Acceleware, with Microsoft)

Aug. 30-Sept. 2, 2011, Chicago, Illinois

http://acceleware.com/aug30chicago

- NEW: ANSYS Regional Conference

Aug. 30, 2011, Chicago, Illinois

http://ansys.com/Conference/Chicago/

- NEW: ANSYS Regional Conference

Aug. 31-Sept. 1, 2011, Houston, Texas

http://ansys.com/Conference/Houston/

September 2011

- Advanced Numerical Methods on GPUs

Mini-symposium at ENUMATH 2011

Sept. 5-9, 2011, Univ. of Leicester, Leicester, UK

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

- NEW: GPU Direct and Unified Virtual Addressing (Webinar)

Sept. 6, 2011

Presented by Timothy Schroeder, NVIDIA

https://www2.gotomeeting.com/register/410023659

- 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

- Rapid Problem Solving Using Thrust (Webinar)

Sept. 14, 2011

Presented by Nathan Bell, NVIDIA

Note: Thrust is a library that enables programmers to develop high-performance applications on CUDA with minimal effort.

http://www.gputechconf.com/object/gtc-express-webinar.html

- CUDA Course (Presented by SagivTech)

Sept. 18-20, 2011, Ramat Gan, Israel

Hands-on sessions and optimization techniques.

http://www.sagivtech.com/24054.html

- SEG (Society of Exploration Geophysicists) Annual Meeting

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

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

- CUDA Course (Presented by Tech-X)

Sept. 19-21, Boulder, Colorado

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

- Russian-German HPC School

Sept. 19-30, Novosibirsk

http://conf.nsc.ru/hpcschool

- SPIE Conference on High-Performance Computing in Remote Sensing

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

http://spie.org/rs11

- NEW: CUDA Optimization: Memory Bandwidth Limited Kernels (Webinar)

Sept. 20, 2011

Presented by Timothy Schroeder, NVIDIA

https://www2.gotomeeting.com/register/936728978

- NEW: CUDA Optimization: Instruction Limited Kernels (Webinar)

Sept. 27, 2011

Presented by Gernot Ziegler, NVIDIA

https://www2.gotomeeting.com/register/260445946

- NEW: GPU-Accelerated Derivative Pricing Models

Sept. 27, 2011, New York

Presented by SciComp, NVIDIA, Dell, Microsoft

http://www.scicomp.com/seminars/2011/signup

October 2011

- NEW: CUDA Optimization: Register Spilling and Local Memory Usage (Webinar)

Oct. 4, 2011

Presented by Paulius Micikevicius, NVIDIA

https://www2.gotomeeting.com/register/273766338

- NEW: GPU-Accelerated Derivative Pricing Models

Presented by SciComp, NVIDIA, Dell, Microsoft

Oct. 17, 2011, London, UK

http://www.scicomp.com/seminars/2011/signup

November 2011

- NEW: Supercomputing 2011 (SC11)

Nov. 12-18, Seattle, Washington

http://sc11.supercomputing.org/

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

Downloads	back to the top
– CUDA 4.0: www.nvidia.com/getcuda – Parallel Nsight: http://developer.nvidia.com/nvidia-parallel-nsight
Webinars
– CUDA: www.nvidia.com/webinars – Parallel Nsight: http://developer.nvidia.com/developer-webinars

CUDA Registered Developer Program

– Sign up: www.nvidia.com/paralleldeveloper

CUDA GPUs

– List of CUDA-enabled GPUs: http://developer.nvidia.com/cuda-gpus

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

– Future of Computing Performance: http://bit.ly/hYqH2H
– Supercomputing for the Masses, Part 21: http://is.gd/Fj56gf
– CUDA books: http://www.nvidia.com/object/cuda_books.html

CUDA Recommended Viewing

– The 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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