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High Performance Computing – What Accessibility to TFlops Can Offer Scientists: PlayStations and the Cell Broadband Engine

14 Nov

I subscribe to Scientific Computing so that it drops into my email inbox. I read Rob Farber’s article this week entitled “The Future Looks Bright for Teraflop Computing “. His opening question was “Wouldn’t it be great to have a teraflop of computing power sitting in your lab, desktop workstation, or remote instrument server?” What would that mean to your work?

For those of you using ChemSpider you will know that we have about 20 million compounds on the database. With that many compounds population of the database with properties such as InChIStrings, InChIKeys, physchem properties and systematic names can take many days if not weeks. With three computers only in our hands, one of them a web server and one of them the database server, we are limited to one system. Even that dual processor system provides slow throughput. Oh the joys of having access to teraflop processors!!!

In my previous post on focused libraries I commented on ongoing discussions regarding the potential to perform online docking. Evangelists such as Jean-Claude Bradley (on our advisory group) have been talking about this possibility as part of his approach to Open Notebook Science. Docking can be very time consuming and the speed of calculations is very important. I have been working on a project regarding the value of porting docking software to the Cell Broadband Engine processor from IBM. The development of that processor is an interesting story in itself since it was driven specifically by the needs of the gaming industry for better performance in their calculations. Now SimBioSys are porting their docking software to the Cell processor as described in this White Paper. The improvement in performance is quite amazing!!!

While working for a commercial software company we saw productivity gains moving to clusters. Dual processors in our laptops and annual performance gains from the general technology shifts offer faster calculations every year. Teraflops on the desktop (and even laptop) are likely a few years away…but GFlops are here..

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on November 14, 2007 in Vision

 

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