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? Definitely. > >>> 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: http://www.mathworks.com/matlabcentral/fileexchange/ loadFile.do?objectId=1216 > 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! Glen