SC’05 sessions

We had wanted to see several of the sessions including the ClawHmmer, and various others. I spent most of my time talking with various vendors and others on the show floor.

ClawHmmer is interesting as it is a GPU version of HMMer, and on good GPU hardware, you can get quite a performance boost on HMMer. The only problem we see is that most servers don’t have good hardware accelerated GPUs. Adding such cards in is usually non-trivial, as you would need PCI versions of the card. Most of the servers we have seen rarely have an AGP slot (or even a PCI-e slot) for graphics (again, since these are 1U servers, you would need a riser card at a right angle in most cases). So this may be more appropriate for desktop users whom happen to have a good graphics card.

There are other hardware accelerators possible. What we observe here is that there is lots of interest from suppliers of FPGA systems in finding customers for these systems. FPGA board sales volumes are large when they hit hundreds of units. FPGAs of course can do all sorts of interesting integer calculations that you need to express in terms of a circuit. If you can design that circuit well, you can in some cases hit 100x faster performance than you can with the general purpose CPU.

Nothing good in life is free.

To program these FPGA’s, you need to convert your program into such a circuit. Or better put, you need to express the computationally expensive portion of your program as a circuit, and then adjust your program to call you new hardware subroutine or method. This can be done either by hand coding the VHDL expression of your algorithm, or using tools that convert C code into VHDL. Doing the VHDL by hand, you typically get a higher density of circuits per unit area, and the circuit tends to be quite a bit faster than with the codes that convert C code to VHDL. Of course, programming in VHDL is non-trivial.

There is much hype surrounding the FPGAs right now. They are the hot thing in supercomputing, well hot in the sense of the most attention getting. They tend to run quite cool, even under load.

On other fronts: Clusters clusters everywhere. Of all shapes and sizes. Orion now has competition from Penguin Computing, and others. Blades were all the rage a few years ago appear to be somewhat less in the forefront.

There are a number of innovative vendors there with some really interesting things. You need to see the LightSpace Technologies display in the ASC booth. This is a true 3D display. Words and pictures cannot do this justice. Compare this to every other 3D display on the show floors. You can walk around the “image” in a wide angle. With one of the displayed items, a molecule with something that looks like an ion channel, you can orient the channel in such a way that you cannot see down it from the front, but moving 45 degrees off the axis (that is, you move, and leave the display alone), you can look down the channel. This is absolutely incredible. Applications for this range from medical imaging, volume visualization of large/complex 3D systems, through entertainment.

I’ll continue gathering information and snapping pictures. Feel free to email/comment on what stuff you might like to see.

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