[BioBrew Users] separate biobrew install?

Kip Lubliner kip at camelot.mssm.edu
Thu Aug 28 17:04:08 EDT 2003

Glen Otero wrote:

> This is true, for the most part.  One major difference is that I've 
> dumped PBS for SGE. Technically, you would need to get a license for 
> PBS to use it, so I won't include it. SGE is completely open source, 
> freely redistributable, easier to use, and more robust IMHO.

I researched both PBS and SGE, and I agree with you, SGE is the one to 
go with.  I thought that I read that mainline Rocks was headed towards 
using SGE.  Is this the case?

>> There are many other possible application areas, e.g. chemistry, 
>> physics, etc.  Wouldn't it make more sense to have some sort of 
>> 'package' structure that could be installed on the rocks front-end 
>> directly after the regular Rocks install?  That way if someone wanted 
>> to run bioinformatics programs and physics programs, they could just 
>> install both 'packages'.  With the current situation, going to rocks 
>> 3.0.0 would require Glen to release an updated BioBrew.
> 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?

I'm not interested in *stripping down* BioBrew.  I am thinking about the 
other direction - the other 'Brews' that you mention.  Personally, the 
cluster that I am building will support mathematicians studying 
neuroscience, so I am primarily interested in math software.

An example of a software program that we will probably use is LISSOM
This program is for simulating the visual cortex.  It seems that the 
software that you have assembled is more focused towards DNA, gene 
sequencing, and the like.  This could be a part of a "NeuralBrew".

As I said, I am a Rocks newbie, and I don't really have a strong opinion 
on how all this should work.  In any case, using BioBrew is making my 
life *much* easier.  If only openCM were as easy to set up...


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