mpiHMMer update

Well, we now have a mailing list and a repository up in addition to the main page. There are some binary RPMs available. My question to the teaming masses of mpiHMMer users (current or future), what platforms/architectures/OSes are you interested in binary builds for? And support for? Please either answer in a response to this … Read morempiHMMer update

Sun buys Mysql

So Sun continues their buying spree. First with CFS, and now Mysql. This is quite relevant to HPC for a variety of reasons.
Customers have been telling me that they are quite worried about Lustre as a result of the Sun acquisition. There is a lot of speculation about its (likely) limited future outside of Solaris.

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DragonFly update: humming along …

Haven’t updated this in a while. Done lots of code/function clean up. Still have more to do, but to get it to a usable beta state is very much closer than it was a month ago. Lots of items are working … in a cool web 2.0 ajaxy sorta kinda way. And if we did it right, it gracefully degrades to average everyday HTML in the event that you want to shun javascript (sometimes a good idea in and of itself).
Whats working:

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Why use Linux?

There are many reasons. Some economic and TCO, some performance, some development, some stability. Well, that last one is interesting. We hear occasionally about systems stability, ability to withstand withering loads, ability to function and multifunction with ease.
The machine that this blog has been running on, shared with multiple other websites, and other functions, is running Linux. Patches relevant for its functionality have been applied with none of the “you must reboot now” garbage that other OSes impose.
And it has been up for 1 year today.

1 >uptime
 12:24:43 up 365 days, 23:04, 15 users,  load average: 0.03, 0.13, 0.15

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Update on file formats

Robin Harris noted that he might have misinterpreted what happened. There is a blog which explains it here. Yes, Robin is correct, Microsoft does inspire strong reactions. Allow me to be blunt about it and say not all of them are deserved. The HPC people I have met and spoken with are good people. I … Read moreUpdate on file formats

Interesting thoughts on CS education

We haven’t covered CS education as such in this blog, as rather surprisingly, most of high performance computing is not being done/driven by CS people. This is probably unfortunate for several reasons, most of which is that many HPC practitioners are taking localized utilitarian views of HPC, and not looking at bigger pictures which may net them additional benefit.
That said, the authors of this article imply that the state of CS education is in decline, that CS departments are not creating the computer scientists we need, rather they are creating java programmers, and others well insulated from a deeper understanding of the machine.

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Fortran version of the compiler quality test

Quite a few people asked offline for a fortran version of the tests I indicated in the last post on this subject. So here is the basic code and its performance. What is interesting is that, for the same inputs as the C code, with no heroic loop unrolling/unwinding, the Fortran is about 3x faster than the C. Well, except for ifort. But we will get into that more later on.

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MPI-HMMer site is now live

MPI-HMMer, the implementation of Professor Eddy’s HMMer code built for MPI clusters, is now live on the net. will get you there, as will There are some nice nuggets buried within … the papers, and a short discussion of MPI-HMMer-boost, which is a multi-layer parallel-accelerated implementation of HMMer. As usual, we are in … Read moreMPI-HMMer site is now live