sounds very very good :) and very very helpful for many people in lab! :) On Sep 22, 2011, at 12:31 AM, Daniel Russel wrote:
> It might make sense to set up a ccache for the cluster, like we have for the lab. The old netapp seems like a good place. That way only the first person has to wait around while a new checkout is being built. And we can provide some standard config.py files to make everything just work. Make sense? > > > On Sep 21, 2011, at 2:19 PM, Dave Barkan wrote: > >> I was able to successfully build IMP on the cluster in fast mode. Right >> now, I believe IMP is built daily in release mode on /diva1 for people >> to use, but not in fast. Until we have something automated for that I >> think people are doing it on their own. >> >> The only thing that gave me trouble was the hdf5 stuff, which I >> corrected by adding Daniel's hdf5 into my config file: >> >> libpath="/netapp/sali/drussel/production/hdf5/lib" >> cxxflags="-m64 -mmmx -msse -msse2 -isystem >> /netapp/sali/drussel/production/hdf5/include" >> >> (I'm actually not sure if I needed both those lines or just one). >> >> I asked Josh about updating hdf5 to version 1.8 on the cluster and he >> said that there will soon be a major OS change and he'll do it after >> that. For now it had dependencies which probably need to be updated >> before hdf5 itself, and unless it's a priority, he'll wait until after >> the OS change and do it all at once. >> >> Maybe this is obvious to people, but since I had to ask around, here is >> what I did to build IMP-fast, maybe it will be useful for others: >> 1. Check out IMP on the head node (the svn repository is accessible from >> there) >> 2. Update the config file to include Daniel's hdf5 stuff (also he has >> links to bullet and CGAL if you need those) >> 3. login to an interactive node and build there to avoid abusing the >> head node. Since the disks are the same on the interactive node and the >> head node, you can build on one and have it available on the other one. >> >> Thanks to Dr. Rogers for helping me out with this. >> >> db >> >> >> >> On 9/21/11 7:37 AM, Daniel Russel wrote: >>> On Sep 21, 2011, at 6:18 AM, Keren Lasker wrote: >>> >>> >>>> thanks. >>>> so how do you think others are running things on the cluster these days? :) >>>> is everyone using your production version or installed things locally? >>>> >>> I know of various combinations of using mine, using others, Charles was going to ask Josh to update some build machines or not using it at all. I like my production setup since you know there are no other libraries that are non-standard that are required. And I intent to keep things stable (most of the libraries there have version numbers in their paths). >>> >>> >>>> also, you can answer to that offline if more appropriate, but how do one link your hdf5 version with imp? is there a flag in the config file or something like that? >>>> >>> As with all dependencies, just make sure the includepath, libpath, and perhaps, ldlibpath includes the library. >>> >>> >>>> On Sep 21, 2011, at 4:16 PM, Daniel Russel wrote: >>>> >>>> >>>>> I don't think hdf5 or at least appropriate versions of hdf5 is installed on the cluster as a whole. I suggest building against the version in ~drussel/production/hdf5 (you can copy that to your home dir if you want). >>>>> >>>>> On Sep 21, 2011, at 3:41 AM, Keren Lasker wrote: >>>>> >>>>> >>>>>> hi: >>>>>> running jobs on our shared cluster i am getting an error: >>>>>> "ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory" >>>>>> things are running ok on baton2, the problem occurs on the nodes of the cluster. >>>>>> any idea how to resolve that? >>>>>> >>>>>> thanks, keren. >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev