On Thursday, August 28, 2003, at 11:25 PM, Bill Barnard wrote: > 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. R would be a great package to add. The instructions to add rpms to make your own customized distro are in the Rocks User's Guide. But I can go over them with you if you have any questions. > > 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. This is what I have planned. I plan to release a vanilla base distro, Callident Rx, that people can customize to their hearts' content. But I'm holding off until I have a few more features ready. Should only be another month or so. > 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 > know... It's easier than you think. Just take a look at the Rocks User's Guide. > > 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... I will probably write a script that will pull down, build, and install software that I'm not allowed to redistribute, like TCoffee, from remote sites. Glen