The IBM folks have turned the Blue Gene into what they claim is the worlds fastest blast engine. Interesting read. They use our A. thaliana data in the Bioinformatics Benchmark System v3 (BBS) to perform their measurement, as well as data from Aaron Darling for mpiBLAST. Our data had been in a mislabeled file for years, and I never took the time to rename the S. lycopersicum for the original Arabidopsis.

I haven’t seen it yet. Eventually when I get more time, I want play with it, but from what I have heard it is not ready for prime time yet. That said, I would like note that the Cygwin tools are really good. I just built LAM-7.1.1 using them. Tried it out and it works quite nicely (at least on this box). A major coup for Microsoft would be if they tossed their existing SFU bit and used Cygwin.

More reflections on the differences between architectures and products. Beowulf and most cluster systems are architectures to be built. Many vendors attempt to freeze the architecture, or restrict variations of it in order to build a polished product. Polished products are finished. They have a finished feel to them. Someone went through and actually made stuff work, identified broken stuff, and had someone fix them. Well, not all clusters are like this, some feel like stacked boxes that the cluster vendor could get at a low price, as the cluster vendor knows how to spell HPC, but not do it.

High performance computing is a tough business. Customers always want more performance. Few want to pay more for this performance. Many vendors want to serve this market but precious few are pushing more than boxes. Its easy to push boxes, and the really low end vendors, likely having been burned as suppliers of low end windows machines, decided to work on clusters. Occasionally there are some good ideas. Some really good ones.

I have noticed a tendency for technologists, programmers, and others to fall in love with their projects, their tools, … . Why this happens, I am not sure. I don’t love my hammer, my circular saw, my computers, the languages I use. They are tools. They are the means to a goal. Sure, I like some tools more than others, but I am also not going to waste my time misusing a tool for a purpose ill suited for it.

At the excellent Cluster Monkey Doug Eadline mused on a number of topics of interest, specifically on why Cluster HPC is hard. There were some excellent points made. The OSC is working on an initiative to increase access to high performance computing resources for end users. Their effort is in part by making access to HPC hardware easier, and in part by helping people (users and commercial entities) make better use of computational gear.

This will be a short comment on something I have noticed with engineering led startups. The hardware oriented ones tend to have really neat architectures. Everything is technically beautiful. One problem though. They are not products. A product is finished. It has all the features one might expect out of a product. Yeah, this is a tautology. You don’t buy a car with the engine inserted, but no fuel lines hooked up, no instrumentation attached.

I remain consistently amused by the makefiles we see. Some of them are broken beyond repair. If I told you where I found them, and the profile of the projects that they were in, you would have a hard time stopping laughing. No, I am not talking about the auto-generated monstrosities from the GNU auto-tools. I am talking about hand written, and for the most part, borked beyond simple repair. Since I get to teach a nice class on HPC applications shortly, I plan to cover the do’s and don’ts of makefiles.

Please see [http://www.scalableinformatics.com/metadot/index.pl?iid=2179&#jobsfor more details.

This took me a while to post in part due to heavy year end load, but also, that I wanted to think through what I did see, and what I didn’t. It is important in many processes to take a moment, step back from where you are, and try to assemble the bigger picture of the situation. This introspection can yield invaluable insights. Failing to do it can blind you to what was there, with you focusing mostly on the minutae.