Re: [changed subject to] pkgsrc in scientific computing

[Jason Bacon <jwbacon%tds.net@localhost>]

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.

    http://acadix.biz/pkgsrc.php

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.

Regards,

    Jason

On 7/7/15 2:04 PM, Thomas Orgis wrote:
> Am Tue, 07 Jul 2015 09:52:12 -0500
> schrieb Jason Bacon <jwbacon%tds.net@localhost>:
>
> > 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,
>
> Thomas


--
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  Jason W. Bacon
  jwbacon%tds.net@localhost

  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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