Sun Computational Biology SIG Newsletter - 20 July 2004
Sun Fire V20z AMD Opteron Servers Check out this brief (8 minute) webcast with audio, outlining the benefits of the Sun Fire V20z AMD Opteron servers, presented by Steve Perrenod, Group Mgr for Science & Engineering, Sun Global Education and Research. The webcast includes Opteron reference customers in Edu and info on special offers for V20z individual units and Compute Grid rack solutions for Edu customers. This web cast is available 24 x7 at this URL: July 2004 Update on Sun's High Performance Technical Computing Strategy A number of stories about Sun's High Performance Technical Computing (HPTC) and Grid business and strategy have circulated in the press recently and many of you have asked about the future of HPTC and Grid computing at Sun. The truth is, Sun's HPTC business is alive and well and our strategy continues to be based on delivering not just great products, but total HPTC and Grid solutions incorporating compute nodes, storage systems, data visualization, software, and services meeting our customer's business needs. As Client Services Director, I am responsible not only for ensuring Sun's HPTC and Grid solutions meet the needs of our Education and Research customers, but also for ensuring Sun collaborates with our academic customers to transform their innovation and research into future solutions which can be used across our entire customer base. Following are several updates on HPTC and Grid related developments at Sun. Over the last two years, Sun's Asia Pacific Science and Technology Center, http://apstc.sun.com.sg, in collaboration with key schools across Asia Pacific, has created a number of HPTC and Grid solutions including:
I've asked Dr. Simon See, director of APSTC, to expand his successful "franchise" into a worldwide network, which will be named the Sun Global Science and Technology Network, driving collaborations and joint development projects with some of the leading schools around the world. Simon has already signed up his first European and US schools which will be formally announced in the next few weeks. Sun's V20z dual processor Opteron server is shipping in volume, with specially discounted single server and cluster rack solutions available to our Edu customers, http://www.sun.com/edu/promotions/hardware.html Several new Opteron based servers and workstations will be announced soon, all qualified to run Solaris x86, Linux, and Microsoft Windows. While many customers are using Solaris x86 on the V20z today, there has been tremendous anticipation of our full 64 bit implementation of Solaris x86 for Opteron which will start shipping via the Solaris Software Express program in August. This will make available, for the first time, 64 bit versions of advanced features such as N1 Grid Containers, Solaris Dynamic Tracing, and the Solaris Dynamic File System on the Opteron platform. Sun is working on a number of second and third generation Opteron server designs, so continue to look for Sun innovations in the 1 to 8 CPU space based on Opteron CPU technology. Last month, Sun announced a major expansion of our long standing relationship with Fujitsu which will bring to market in 2006 a new family of "large SMP" enterprise servers dubbed the "Advanced Product Line" or APL. However, the traditional definition of "large SMP" is starting to change. APL servers will utilize several advanced SPARC CPUs, including Sun's first aggressive Chip Multi Threading, or CMT design. If you can run 32 threads on one CPU, how many CPUs do you need to be a "large SMP" by today's standards? Stay tuned. On the software front, besides the exciting new Solaris features mentioned above, Solaris 10 includes a total re-write of the TCP/IP stack to enable the types of high performance I/O required for 10 Gb ethernet and future high performance storage networks. After all, lots of compute cycles are not very useful if you can't feed data into your cluster and store the results afterwards. To manage all of that storage, Sun's customers are using solutions based on Sun's Storage Resource Broker, StorEdge QFS, and StorEdge SAM-FS software. Sun's latest Grid Engine 6 software continues to be available as an open source product, at http://gridengine.sunsource.net while the Sun branded version, N1 Grid Engine 6 adds a host of new enterprise management features including new accounting and reporting functionality. Sun Studio 8 includes Sun's latest released C, C++, and Fortran compilers while early versions of Sun Studio 9 are already available through the Sun Studio 9 Customer Acceptance program, http://developers.sun.com/prodtech/cc/ea/ss9/index.html Besides Solaris and Solaris-x86 support, Studio 9 introduces new Linux support for Sun's award winning developer tools. Finally, Sun continues work on our DARPA HPCS project, designing a Petaflop class supercomputer planned for later this decade. At the core of our design is the same Chip Multi Threading technology designed for our commercial servers, with breakthrough new technologies from Sun Labs such as capacitive coupling which allows electrical signals to flow between adjacent CPUs without the use of connecting wires or pins. The HPCS project is led by Dr. Jim Mitchell, who previously oversaw many of these developments as head of Sun Labs. So, in summary, not only is HPCS and Grid technology and innovation alive and well at Sun, but our client services organization is better prepared than ever to help translate these innovations into solutions meeting our customer's business needs. Please feel free to contact me directly if you have any questions about items in this update or would like more information about Sun's HPTC and Grid solutions. Marc Hamilton Workshop for PhD Students in Biostatistics, Lyngby, Denmark, 27 Sept - 1 Oct, 2004 DTU (in Lyngby, near Copenhagen, Denmark) is organizing a workshop targetting Phd students in biostatistics. The theme of the workshop is "High Performance Computing in Biostatistics". The workshop will be held September 27 - October 1. Part of this 5 day event will be filled with a 'Sun Application Tuning Seminar'. The fee is 1000 DK (~150 Euro) only. More information at Seminar: Integrating Knowledge in the Life Sciences Product Life Cycle, online, 18-29 Oct 2004 Sun is co-sponsoring a first-of-its-kind virtual conference, "Integrating Knowledge in the Life Sciences Product Life Cycle" to be held online Oct 18-29, 2004 and comprising over forty topics covering progressive knowledge and information management tools and practices from drug discovery through to healthcare delivery. We have arranged for you to get a 20% discount on the registration fee of $300 - that's only $6/seminar! To take advantage of this, contact Nicki Douglas (kmls@douglasconnect.com) and mention the code "Sun_plc04". Dr JohnRobert Gardner of Sun will be speaking on knowledge-sharing tools in his talk, "Tracking what you know, Finding what you don't, Putting it all Together" within the session, Supporting Innovation in Life Science Product Development. Please visit the conference site at http://km.colayer.net/, register and get involved! Case Study: Grids in Computational Biology
http://www.sun.com/solutions/infrastructure/grid/grid_ Integrating Sun N1 Grid Engine with Globus Toolkit
This article describes how to integrate grid computing with Globus Toolkit software for a site using Sun N1 Grid Engine software (formerly Sun Grid Engine) as a local resource manager. This article provides
background information and step-by-step instructions for installing, configuring, integrating, and testing Globus Toolkit software with Sun N1 Grid Engine software on x86 architecture using the Solaris 9 Operating System (Solaris 9 OS). Human Genome Project at Los Alamos National Laboratory Runs on Sun
Solaris[tm] Operating System (SPARC¨ Platform Edition) Provides Stable Base Call for Papers: CB-SIG Meeting, RTP, NC, 28-29 October 2004 Please send a short proposal for a 30 minute presentation to stefan.unger@sun.com This CB-SIG meeting will be held in conjunction with the "Bridging the Gaps in Computational Biology" meeting being planned with our RTP COE. It is a separate event, however. By the way, we had about 30 attendees at our meeting in Heidelberg, which is very good since the HPC Consortium is not a "bio" event. The proceedings will be published to our web site in the near future. Watch for some interesting announcements from Sun and partners at ISMB, Glasgow
We will be at the ISMB in Glasgow with a large booth and a large number of activities. Be sure to stop by!
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