Striving for greatness

Thoughts on emerging tech, open source, and life

[Gentoo] Still alive and kicking

It’s been a while since I posted. I’ve discovered that the more time I spend blogging, the less actual work I get done. And I don’t have any bosses or employees who I need to convince I’ve been working.

Lots of work has gone into improving the Gentoo scientific computing experience. I’ve written new, more flexible eselect modules for BLAS and LAPACK, a couple of very commonly used linear algebra libraries. They’re in my overlay now, and they will enter the Portage tree soon.

I’m trying to make Gentoo the distribution of choice for my day job — protein X-ray crystallography. This means packaging all the weird Fortran stuff with even weirder, broken build systems. I’m waiting on a patch to go into Portage 2.1.1 to fix RESTRICT=stricter, then I’ll be able to add the remaining apps chilling in my overlay — primarily CCP4 and Coot. I’ve recently added packages for CNS, SHELX and ABINIT. Ghemical-2’s ability to run GAMESS-US also helps quite a bit, and I hope to find some time to work on the WebMO package that’s hard-masked in Portage.

The entrance of GCC 4.1 into testing has made a lot possible, but also requires a lot of fixing. This is particularly the case in scientific computing, where there’s an entirely new Fortran compiler — gfortran. Please note that gfortran is NOT a renamed g77. It accepts different options, and it compiles different code. Only gfortran will compile Fortran90 and Fortran95 code. Only g77 will accept common options such as -fno-globals. Do not assume they are the same.

I’ve also gotten back into trying to do some work on the cluster project, prompted by a couple of active cluster builders in the #gentoo-cluster IRC channel. I hope to be able to set up a test cluster this summer and rework the high-performance computing documentation. It’s currently a bit of a hack, outdated and incomplete but better than nothing. I’d like to create a clean cluster setup using diskless nodes with UnionFS, PXELinux, etc. Also on this list is getting OpenMPI into the tree and creating some sort of ‘eselect mpi’ module that will allow not just system-level switching but also changes on a per-user level.

Also, X.Org 7.1 has entered testing a bit under a month ago. Look to see this stable well before the 2006.1 release, which is in August. Now that Portage 2.1 is stable, the last major blocker appears to be gone. Perhaps we can get it stabilized around the beginning of July. That would be a nice Independence Day present.


Written by Donnie Berkholz

June 16, 2006 at 1:02 am

Posted in Uncategorized

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