[BioBrew Users] separate biobrew install?

Bill Barnard bill at barnard-engineering.com
Fri Aug 29 02:25:15 EDT 2003

On Thu, 2003-08-28 at 13:01, Glen Otero wrote: 
> I actually intend to create other 'Brews' for computational chemistry, 
> climate modeling, etc. A domain agnostic package structure makes sense 
> for distribution of applications, and the Rocks folks are experimenting 
> with this idea in their upcoming 3.0 release. So I may adopt that 
> structure in the future. But for right now, since the bio packages that 
> are included in BioBrew are just rpms that I've built, it's trivial 
> (for me) to integrate them with a Rocks release to create BioBrew. I 
> save people a lot of time and frustration by doing this. Installing 
> BioBrew saves one the trouble of installing Rocks, and then downloading 
> all the individual bio rpms, building and installing them on the 
> Frontend, and then installing them on the compute nodes. I understand 
> that if the cluster were to be used for more than just bio, like bio 
> and physics, that doing a regular Rocks install and then grabbing the 
> desired bio and physics packages would make the cluster a little more 
> customizable. I have been kicking around the idea of making the 
> individual bio SRPMS available in the biopackage repository so that 
> folks can pick just the ones that they want. Is that something you 
> would be interested in?

As we get our cluster working I'm interested in learning how to add new
rpms for various packages I'm interested in which are not currently part
of BioBrew, R and some R software like Bioconductor. It seems likely
we'll also want to add other non-bio software, though I don't know what
at this time.

I would probably most like to be able to install the Rocks distribution,
then pick and choose other rpms as needed to build a particular cluster.
I don't yet know what work is required to add rpms to a frontend node to
enable shoot-node of a new BioChemoDynoSimYouNameItBrew, but I'm
guessing I'll be learning fairly soon. Seems to me the most flexible
approach would be most useful to the most cluster admins. I like having
all the packages you've selected for the BioBrew distro, but I already
know I want to roll my own. Possibly some tools can be developed to make
this easy (easier?) Maybe it's really easy already and I just don't

That said, there is a big advantage to someone starting out to know that
some community of users has already used a set of packages together (mpi
plus blast, plus ??) and that the set is available with a sensible
starting configuration. Simply providing the srpms is not going to
address that.

Maybe srpms plus scripts to assemble a set of srpms into a particular
Brew would be a useful way to structure things. It could get complicated
if you try to then combine two or more Brews into one distro; dependency
checking could be difficult, or you could end up with incompatible
configurations somewhere. I don't know...

Anyway I do know I like what you've put together so far. Now I need to
delve into it so I can start complaining!

Bill Barnard <bill at barnard-engineering.com>

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