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Re: [changed subject to] pkgsrc in scientific computing

In case you missed it last time I mentioned it in a different thread, I developed a pkgsrc bootstrap wrapper called auto-pkgsrc-setup to facilitate creating and maintaining multiple independent trees, e.g. /sharedapps/pkg-1, /sharedapps/pkg-2, /sharedapps/pkg-2, etc.

For selecting a tree, it generates startup scripts suitable for sourcing from other scripts or placement in /etc/profile.d as well as environment module files. To use /sharedapps/pkg-3, for example, a user simply would run on of the following in their [SLURM in our case] submit script.

source /sharedapps/pkg-3/etc/cshrc
module load /sharedapps/pkg-3/etc/modulefiles/pkgsrc/3

Auto-pkgsrc-setup also adds safety features, like wrapping bmake to verify that you're in the correct source tree.

On our HPC clusters, I simply bootstrap a whole new tree about every 6 to 12 months to make newer software versions available. Older trees are left in place so researchers can finish up projects using the same version of a package, but eventually deprecated.

I have a lot of scientific packages in wip and more coming, but too little time to devote to it. One of my colleagues here is learning to package and may join pkgsrc-wip soon. There's a lot of work to be done in categories like math and biology, though. Fortran support needs some work as well.



On 7/7/15 2:04 PM, Thomas Orgis wrote:
Am Tue, 07 Jul 2015 09:52:12 -0500
schrieb Jason Bacon <>:

I'm trying to promote the use of pkgsrc in computational science,
because I think it offers the best
foundation of any conceivable method for managing scientific software:
That's where I come from: We want to manage the main userspace and
assorted libraries for some of those scientific software packages that
depend on lots of open source libraries with pkgsrc. This is on an
install that shall live 6 years minimum and be updated but at the same
time keep old versions of stuff around and working.

I hope that pkgsrc will serve us well in that function. And this might
also explain why I'm still fiddling with 2014Q3 while transitioning
from an older installation (it's the freshest there).

Alrighty then,


  Jason W. Bacon

  If a problem can be solved,
  there's no need to worry.
If it cannot be solved, then
  worrying will do no good.

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