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-- Thank you, B. Sangeetha On Sat, Mar 10, 2012 at 11:54 PM, Thomas Cheatham <tec3.utah.edu> wrote: > > Please try to avoid sending the same question multiple times to the > reflector. > > > I have been running simulations using Amber 11 on a GPU Tesla C2050 > > since a year. I would be running simulations with systems as large as > > 1,00,000 atoms. > > Fantastic. Given this experience, you already know the relative > performance of GPUs and also presumably the clusters you have access to. > Given this knowledge, you should be able to answer these questions > yourself. If not, I would suggest looking at the benchmarks on the AMBER > WWW page. You should at least verify that what you were seeing (on your > GPUs / clusters) in the 1,00,000 atom simulations is consistent with what > is reported on the AMBER page. > > > 1. If I set up a cluster with the following configurations, what would > > be the performance for a parallel run using Sander? > > Use your experience and also look at the AMBER benchmarks. Performance > will depend on how you utilize the resources. > > > 2. How many jobs can I run in parallel at a time without affecting the > > performance? > > This depends on how you run your job. The description of the resources > you provide is confusing. As I read it, the configutation is: > > 1 master node. 12-core, 3 TB RAID. Infiniband. > 2 compute nodes. Each 12-core. Infiniband. > > So, you have one front-end node, and a back-end with two 12-core nodes (or > 24 processors total). This will likely be ~1/2 the performance of one of > the GPUs you were running on previously. On this setup, you could likely > run two 12 processor jobs or one 24 processor job. If I had this setup, I > would runit as three nodes rather than dedicating a front-end/master. > > If you are only buying three nodes, look at buying two and adding GPU > cards to each. If it was a typo on the number of nodes, and you are > actually buying 10's to 100's of nodes, look at the balanced cost of GPUs > vs. cores. In my experience with the current GPUs, they match ~48-60 > cores. > > --tec3 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Mar 11 2012 - 08:30:03 PDT