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Re: science category

On 04/19/17 03:14, Jonathan Perkin wrote:
* On 2017-04-19 at 07:18 BST, Jason Bacon wrote:

I did a poll among XSEDE campus champions about a year ago and at that time
about 80% of HPC clusters were running CentOS or a derivative such as
Scientific Linux.  Most of the remaining clusters were running RHEL.

I cited HPC and CentOS because pkgsrc serves an unmet need there.  However,
many scientists who don't need HPC or commercial software (and are probably
running Ubuntu now) will also warm up to pkgsrc as the scientific software
collection grows.  It will simply make sense for them to use the same
package manager as their collaborators who have to use RHEL derivatives.
Are they aware of the EL6 and EL7 binary packages that we provide?
They are updated daily from pkgsrc trunk so should always have the
latest software available:

If not, I'd appreciate getting the word out.  I advertised them on
some of the CentOS/Scientific lists a while ago but didn't get many


Thanks, Jonathan!  These will be a big help.

The fact that the collection is continuously updated actually makes it unsuitable for a lot of scientific research, though. Many researchers need to keep a software installation static for the duration of a study since newer versions might alter results.

One of the beauties of pkgsrc, though, is the inherent ability to install multiple snapshots on the same machine under a prefix of your choosing. For research tools, we have snapshots available over NFS in /sharedapps/pkg-2017Q1, etc. to provide continuity. Users just load the module for a particular snapshot and they're on their way. This is a lighter and simpler solution than containers or other methods people often use.

On my clusters, I also keep a pkgsrc tree on the local disk of each node in /usr/pkg for system tools (SLURM, subversion, git, editors, etc). Your binary packages should work well for this once the necessary packages are committed and vetted.

My plan is to build packages for the /sharedapps snapshots and provide them to the community. It's all approved and in the works, but it's just a matter of man-hours. I'm 1 of 1.5 FTEs supporting research computing for most of the university and I spend most of my time responding to immediate needs. The project is inching forward, though...



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