This web log is the product of the collaborative, innovative, virtual minds of the editors of the IBM developerWorks Multicore acceleration (Cell/B.E. SDK) zone.

Faster than a speeding bullet: Big Blue competition looks less-than-super in latest Green500

Faster than a speeding bullet: What does supercomputing bring to science?

Method transformation?
New modeling abilities can lead to new methods: Can the ability to do simulations -- massively complex, multivariate simulations -- at unheard of speeds change how science is performed? According to scientists at the recent SC08 conference, absolutely.

• "The scientific method has changed for the first time since Galileo invented the telescope. It's getting to the point where simulation is actually the third branch of science. We say that nature is always the arbiter of truth, but it turns out our ability to observe nature is fundamentally limited," said computer scientist Mark Seager of LLNL.
• "The new capability allows you to do fundamentally new physics and tackle new problems and it will accelerate the transition from basic research to applied technology," said Thomas Zacharia of ORNL.

Different testing?
Briefer Top500 tests may be called for: Even some of the organizers of the Top500 list think the benchmarks used to test supercomputer performance is getting too top heavy to handle -- and they are looking for input to see how they might modify the test. At the recent SC08, Jack Dongarra, one of the Top500 officials, noted: "It's clear this is a problem. It is getting out of control at this point, so we have to do something. We'll make some changes to the benchmarks. We don't know what those changes are, yet. We're looking for feedback from the community to determine what those changes should be." Changes like maybe only running a portion of the full Linpack test.

Better software?
SW blurs the lines between super- and regular computing: One visitor to the recent SC08 conference, Stacey Higginbotham, made the connection that "since supercomputers can be built with commodity chips and networking gear, high-performance computing isn't really about the hardware like it was back in the days of Cray ... today it's all about the software." She goes on to postulate that it is the software that will enable the supercomputer to jump from the science-only realm to the workstation arena (and probably even further, into the device market). One other area in which software will be of extreme importance to supercomputing is in bolstering labor -- for many current supercomputer installations, there are hired programmers (science/government installations) and volunteer programmers (universities) to tune and keep the systems running. Many businesses cannot afford this cost -- that's where the appropriate software comes in.

"Red"-hot technology library: Configure the Monte Carlo random number generator library

Monte Carlo Library Programmer's Guide and API Reference: This publication describes in detail how to configure the Monte Carlo random number generator library and how to program applications using it on the IBM SDK for Multicore Acceleration. It contains detailed reference information about the APIs for the library as well as sample applications showing usage of these APIs. (PDF version | Information Center version)

Product watch: YDL 6.1 launches

Giving you the "Advanced Cell Experience": From booth 1915 at the recent SC08, Fixstars released Yellow Dog Linux 6.1 for the G4/G5, the PS3, the PowerStation, and IBM Power Systems; 6.1 hopes to shine in its mix of desktop and development environments. For end users it offers an updated Firefox and OpenOffice.org, an improved graphical wireless configuration tool, and ps3vram functionality which enables use of PS3 video RAM for temporary storage or swap. For developers it offers the latest stable kernel, an updated GCC, the open portion of the IBM Cell SDK v3.1, and the new BSC Cell Superscalar. Other improvements include

• X.org 1.4.999 with xrandr 1.2.2.
• GUI configuration tool for YDL.net.
• Bluetooth support for the PS3 Sixaxis controller.

Programming with Cell/B.E. Security SDK: Your guide to mini-guides

Faster than a speeding bullet: And still the champ ...

... at half the energy: Or, to paraphrase another cartoon, the cat tried but couldn't catch the bird. The IBM-constructed LANL Roadrunner (see disclaimer on name use) is still No. 1 on the Top500 Supercomputing Sites list, the ninth time in a row an IBM machine grabbed the top spot. At 1.105pflops, the LANL Roadrunner just beat out the Cray XT5 QC Jaguar (at 1.059pflops), the second plus-pflops machine. LANL Roadrunner also was roughly twice as energy-efficient as No. 2 (IBM took the energy effiency prize in the list -- the 20 top systems belonged to Big Blue).

Securing an energy future with performance
Grabbing the advantage through the ability to simulate: Besides cutting the cost of finding oil, the Repsol Kaleidoscope project is also hoping to demonstrate that the ability to rapidly develop and display complex simulations (like the company's doing with its Cell/B.E.-based system) can be the key to securing the world's energy future. Repsol just fired up its system to add some speed to advanced seismic imaging so the company can better visualize oil accumulations lying deep beneath the ocean floor.

Games people play: PS3 in the "terrific" twos

November 17 the birthday: According to Sony Insider, there are nearly 17 million PS3 systems around the world. That's an installed base!

Clear conference calendars: SC08 about fast networking

Going on right now: SC08 (November 15-21, Austin, Texas) is all about fast interconnects, including

• QLogic's quad-rate Infiniband switches based on a new ASIC with 36 ports running at up to 40Gbps.
• Alacritech's upgraded 10Gb Ethernet adapter card that can be used for partial offload of TCP/IP processing.

There's also a posting session by the LANL authors of "Entering the Petaflop Era: The Architecture and Performance of Roadrunner," plus scads of papers detailing programming and networking techniques to leverage a massively parallel, multicore system and that demonstrate practical uses of supercomputing power, from tire development to electron transport systems. It is a bonanza of knowledge!

It came from the Lab: Non-genetic use for DNA

Turning DNA strands into fiber optical cables: ChalmersUofTech researchers want to praise their new technique because it allows them to easily convert strands of DNA into very small fibre optic cables. The key is assembling chromophores (molecules that absorb and pass light) in a chain. The group used a YO chromophore that has a strong affinity for DNA molecules -- it hungrily jams itself in between the basepair rungs of DNA strands. Just like that, you've got a 20nm long/1-2nm wide optical wire, the perfect size for microchip interconnects. They placed a molecule that would accept light on one end and one that would emit light at the other.

A downside is that in early testing, it shows the strands naturally transmit about 30 percent of the light received; also, since they are naturally replicating, precise positioning along the strand can't be acertained so variations could exist. On the extraplus side, though, if one chromophore gets damaged, another will naturally take its place so they are self-healing. Some uses: Artificial photosynthesis to replace solar panels, optical computers.

All the antimatter you can eat
Cooking with lasers: Lawrence Livermore researchers have a recipe for antimatter -- shoot an intense laser through a pinhead-size gold bit and whooosh! 100 billion particles of antimatter (positrons). The laser drives accelerated ions (loose electrons) through the gold where they interact with the gold nuclei. The interaction makes the electrons emit pure energy packets which decay into matter and antimatter. It's the concentration of energy and mass that produces the copious amounts of antiparticles -- researchers have done this trick before but they'd only tried it with thin sheets of gold and less-intense lasers.

Conventional wisdom alert: Evolution just happens, man

Guess what? Evolution evolves: Princeton scientists looking at a group of proteins that help cells burn energy found something else -- evidence that evolutionary changes don't take place gradually and randomly under pressure from natural selection. In other words, the changes evolution engenders may be more directed than scientists originally thought -- but unlike "intelligent design," the "intelligence" comes from within the organism itself. (Intelligent design believers can stop reading now ... the group says this is not evidence of an exterior intelligence driving evolution; also, it is not evidence that the DNA itself is "thinking.")

What they are proposing is that evolution isn't as random as originally thought. They discovered that their electron transport chain proteins were self-correcting imbalance imposed on them via artifical mutation. A math analysis showed that these proteins were making tiny corrections all the time, pushing the organism to a more fit state.

Are semi makers really software companies?
Opinion: Software is the elephant in the room: Michel Genard thinks that if semiconductor manufacturers reinvented themselves as software-centric companies, they would be able to solve many of their biggest operational problems and to add the differentiating qualities to their individual organizations they will need to stand out in the future of the semi business. Genard says that if you examine semi industry constraints, you'll see that software glitches are the basis of most problems like product delays and budget overruns. Virtual software development could give a semi company a jump on the competition by allowing them to find and eliminate problems before they happen by working with their RTOS partners, long before the silicon is ready. (One product produced this way was the new Freescale QorIQ P4080 multicore processor.)

Oddments: Zapping refuse

Heating your home with plasma-vaporized garbage: We've discussed it before -- plasma gassification -- now it seems Florida's St. Lucie County and company Geoplasma are developing the first US plasma gasification plant to vaporize 1,500 tons of trash a day and product 60mW of turbine-spun electricity (50K homes worth of juice). The plasma involved is 10K degrees F (5,500ish C/5,800ish K).

For those without, fast Internet over powerlines
IBM and energy company rethink an old idea: IBM and International Broadband Electric Communications have agreed to have IBM install Broadband over Power Line (BPL) networks at electric cooperatives in the eastern US so IBEC can provide broadband services to underserved residents in rural America.

A step closer to the flying car?
New from the military mad scientist division: Darpa announces the Personal Air Vehicle Technology project, an attempt to build a working prototype of a two-to-four-passenger, military-suitable flying car that can drive on roads or take off like a helicopter. Darpa is shooting for 60/150MPH (land/air) with a flight time of two hours on a single tank. The group figures it'll need "morphing wings" for a smooth transition from road to sky; "optimized disk loading" propulsion (whatever that is); and strong flight control software (a wing and a prayer and a programmer?). At least actor Avery Brooks can relax -- he will probably get that flying car.

Cell/B.E. Security SDK: Six programming examples

ISO_ENCRYPT_SEC := ALL
ISO_KERN_KEY = /etc/pki/cell-spu-isolation/loader/loader.app_encrypt_key.public.pem

Faster than a speeding bullet: LANL Roadrunner makes TIME Top Ten list ...

... of technology for 2008: Yes, the LANL Roadrunner (see disclaimer for name usage) is number 10 on TIME magazine's "Best Inventions of 2008" list:

On May 26, at 3:30 in the morning, a $133 million supercomputer nicknamed Roadrunner broke the long-sought-after petaflop barrier: 1 quadrillion calculations per second. Built by IBM for Los Alamos National Laboratory, Roadrunner will be used primarily to simulate the effects of aging on nuclear weapons. Next up: the exaflop barrier.

The other nine before LANL Roadrunner:

1. The Retail DNA Test.
2. The Tesla Roadster.
3. The Lunar Reconnaissance Orbiter.
4. Hulu.com.
5. The Large Hadron Collider.
6. The Global Seed Vault.
7. The Chevy Volt.
8. Bullets That Shoot Bullets.
9. The Orbital Internet.

LANL Roadrunner takes a Tekne Award
A win for superior computing in Minnesota: IBM-Rochester received a Tekne Award for the LANL Roadrunner supercomputer (see disclaimer for name usage). Specifically, the company won the IT-Software & Hardware, Communications and Infrastructure award for the hybrid that is the first computer to break the petaflop barrier. (A Tekne Award acknowledges companies and individuals who have demonstrated superior technology advancement and leadership in Minnesota. There is no requirement that this superiority has to also manifest itself outside of MN, but it usually does.)

Catching up with LANL Roadrunner?
Is Cray closing in?: Oak Ridge National Labs just tested its newly installed AMD-based Cray XT5 supercomputer ("Jaguar") and it peaked out at 1.64pflops, just under the 1.7pflops peak for the Cell/B.E.-/Opteron hybrid LANL Roadrunner (see disclaimer for name usage), in essence making it the world's fastest computer for (non-military) science research.

Design on a dime: Folding@home awarded for its good design

PS3 at heart of distributed, sharing system: The StanfordU Folding@home project has just grabbed the Japanese Ministry of International Trade and Industry's Good Design Award for outstanding design in industrial and consumer products. (Folding@home is a distributed PS3 network, chock full of Cell/B.E. processors and visualizer software, designed to let users share idle PS3 time with scientists studying protein folding.) According to the jury: "Analysis of proteins for the purpose of shedding light on diseases is just one example of solution design for social issues, a stance that indicates the direction that design should take in the future. Motivating the people who will be involved in these studies will be the key to success, but the program functions well as an idea for making participation in this project visible on a global scale."

Games people play: Two perspectives on simulation performance

Per cost and raw performance: In the excellent ars technica thinkpiece "Putting the PS3's brain to work," Matt Ford details an article from the Journal of Physical Review E: Statistical, Nonlinear, and Soft Matter Physics ("Accuracy of the lattice-Boltzmann method using the Cell processor") that discusses the computer simulation transition from faster and faster single processors to large multiprocessing systems. The article compares how two Cell/B.E. systems -- the PS3 (best performance per cost) and an IBM QS20/QS21 blade server (best for raw performance) -- handles simulations. The group was trying to determine whether the Cell/B.E. processor's inability to accurately represent floating-point numbers caused a significant loss of precision in the simulations.

(Lattice Boltzmann is a relatively new simulation technique for complex fluid systems. Traditional methods solve the conservation equations of macroscopic properties -- mass, momentum, and energy -- numerically; LB models the fluid consisting of fictive particles and such particles perform consecutive propagation and collision processes over a discrete lattice mesh. Because of its particulate nature and local dynamics, LB has advantages in dealing with complex boundaries, incorporating of microscopic interactions, and parallelization of the algorithm.)