[BioBrew Users] separate biobrew install?

Glen Otero gotero at linuxprophet.com
Thu Aug 28 19:20:56 EDT 2003

On Thursday, August 28, 2003, at 02:04  PM, Kip Lubliner wrote:

> 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.

Do you use MATLAB?  Here is a package that is supposed to help with  
running MATLAB on a cluster:


> An example of a software program that we will probably use is LISSOM
> http://www.cs.utexas.edu/users/jbednar/rflissom_small.html
> 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".

Are you volunteering to create NeuralBrew? ; ) I'll build an rpm of  
LISSOM and incorporate it into BioBrew when I get a chance. What other  
software are you using? What software do you think people in your field  
would find useful?

> 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.

Glad to hear it!


More information about the BioBrew-Users mailing list