According to computational scientists at Stanford who develop the distributed protein folding package ‘Folding at Home‘ (FAH), the Cell processor in Sony’s Playstation 3 (PS3) provides computational power in the 20 gigaflop range. They calculate that 50,000 PS3’s would acheive performance on the petaflop scale.

Armed with this power FAH hopes to explore related diseases, including Alzheimer’s, Huntington’s, and certain forms of cancer. What type of calculations the PS3 client is capable of running? The FAH/FAQ answers:

The PS3 currently runs what are called implicit solvation calculations (see also), including some simple ones (sigmodal dependent dielectric) and some more sophisticated ones (AGBNP, a type of Generalized Born method from Prof. Ron Levy’s group at Rutgers). In this respect, the PS3 client is much like our GPU client. However, the PS3 client is more flexible, in that it can also run explicit solvent calculations as well, although not at the same speed increase relative to PC’s. We are working to increase the speed of explicit solvent on the PS3 and would then run these calculations on the PS3 as well. In a nutshell, the PS3 takes the middle ground between GPU’s (extreme speed, but at limited types of WU’s) and CPU’s (less speed, but more flexibility in types of WU’s).

Under load, the PS3 consumes around 200 watts. Folding at Home is available on PS3 system version 1.6 or later.

I’m interested in using Cell processors for bioscience processing. If these systems are as fast as they appear it could be cost effective to create clusters of PS3s. One possible method might be to install a version of LINUX and treat them as clustered PCs. Yellow Dog and Gentoo are currently available, others are on the way. LinuxDevices reported in December 2006 that Sony contributed LINUX patches for machine-specific features and they were merged into the 2.6.20 kernel tree.

A press release on HPCwire describes Terra Soft’s intention to build the ‘World’s First Cell-based Supercomputer‘. Glen Otero, Director of Life Sciences Research for Terra Soft Solutions explains,:

This cluster represents a two-fold opportunity: to optimize a suite of open-source life science applications for the Cell processor; to develop a hands-on community around this world-first cluster whereby researchers and life science studies at all levels may benefit. Once up and running with our first labs engaged, we will expand the community through invitations and referrals, supporting a growing knowledge base and library of Cell optimized code, open and available to life science researchers everywhere.

Tera Soft offers for sale a six node PS3 cluster, boasting Teraflop performance for less than $20,000 ($18,325). 32 nodes offer a potential 5TF for just over $40,000. These PS3 clusters are built from the following components:

– IBM p5 185 dual-core 970 head node.
– Sony PLAYSTATION 3s (PS3).
– Gigabit switch & cables.
– Mouse, Keyboard, Benq 19″ Display.
– Yellow Dog Linux v5.0 with Cell SDK pre-installed.
– Moab Cluster Management Suite
– Y-HPC Cluster Construction suite pre-installed.
– RapidMind Cell Development Toolkit, pre-installed.
– include 20 Hours of technical support.

Does anyone have recent benchmark numbers for PS3 systems running open-source life sciences applications under LINUX? Glen?

(See also: ScienceDaily: Engineer Creates First Academic Playstation 3 Computing Cluster)

While at IBM, John W. Backus proposed an alternative to assembly language for programming the IBM 704 mainframe computer in 1953. A draft specification for The IBM Mathematical Formula Translating System was completed mid-1954. The first optimizing FORTRAN compiler was delivered in April 1957.

The language was extremely efficient and widely adopted for writing numerically intensive programs. The inclusion of complex number data types in the language made Fortran especially suited to technical applications such as engineering and scientific simulation. It also provided a solution to two primary problems in computing at that time: making programming easier for humans and providing a structured higher level framework for the creation of mathematical solutions to algebraic systems. It is in use in high performance computing (HPC) to this day.

He worked closely with Peter Naur (see also), from Denmark, to develop a system for describing programming languages. It is now known as Backus-Naur form (BNF).

He had an informal style and an aptitude for problem solving skills. He was one of the hackers of his day.

In their article ‘Shock and Awe: How Installing Apple’s Updates can Render Your Mac Unbootable and How You Can Prevent it’ they offer the following explanation of the prebinding problem:

When you see the “Optimizing System Performance” phase of a software update, Mac OS X is really updating prebinding. Updating prebinding has a very, very nasty bug in it (look at _dyld_update_prebinding). If multiple processes are updating prebinding at the same time, then it is possible for a system file to be completely zero’d out. Basically, all data in the file is deleted and it is replaced with nothing. This bug is usually triggered when updating Mac OS X and every update to Mac OS X has the potential to render your system unbootable depending on if the “right” file is deleted or not. It’s triggered during the “Optimizing System Performance” phase of installing an update. This phase is actually just running update_prebinding. If you launch an application that links to libraries that are not yet prebound, there is a chance one of those files will be zero’d out as dyld automatically redoes the prebinding on that file.

…Every single time you install an update to Mac OS X whether it be an iTunes update, a QuickTime update, an update for daylight saving time, a security update, an Airport update, or an actual Mac OS X update, you can be hit by this bug. In order to prevent yourself from being smacked in the face by this bug, follow this simple rule: When “Optimize System Performance” appears during the update process do not touch your computer and definitely do not launch any applications. Just back away from your computer box as if it were a swarm of bees.

Daniel Hellerich, friend and NLC tenor, runs the site piday.org.

Pi, Greek letter (pi), is the symbol for the ratio of the circumference of a circle to its diameter. It is approximately 22/7 and is usually calculated to 3 digits, 3.14. With the use of computers, Pi has been caculated to over 51 billion decimal places. Pi is an irrational number meaning it will continue infinitely without repeating. The symbol for pi, was first used in 1737 by William Jones, but was popular after it was adopted by the Swiss mathematician Leonhard Euler in 1737.

Check out Dan’s page of Pi to a million digits. How many can you recall? Send a friend an eCard.

The Weisman was the first of the curving stainless steel facades for which Frank Gehry has become famous. Though the design is meant to flow it is disturbed by the implementation of individual stainless steel panels. Later Gehry buildings, such as the Guggenheim Museum in Bilbao, Spain and the Walt Disney Concert Hall in Los Angeles, CA are considerably more elegant though acknowledged variations on the Weisman theme.

The addition to the Weisman may be the first addition to one of his own designs. Considered ‘more organic’ the addition will add 11,000-square feet including a cafe.

The Weisman Art Museum is a teaching museum located on the campus of the University of Minnesota. Construction on the addition is set to begin in 2007 and complete in 2009.

All photos were taken at the press announcement with my Blackberry 8100.