Hi all, I am running a water/surfactant system with just under 100000 atoms using MPI on a local cluster and not getting the scaling I was hoping for. The cluster consists of 8 core xeon nodes and I'm running gromacs 4.5 with mpich2-gnu. I've tried running a few benchmarks using 100ps runs and get the following results:
*Threads: 8 16 24 32 40 48 56 64* *hr/ns: 15 18 53 54 76 117 98 50 * * * *Each set of 8 threads is being sent to one node and the 8 threaded run was performed without MPI. I have tried changing the -npme settings for all permissible values on runs with 16 threads. In every instance the results were worse than if I didn't specify anything.* * * *The fact that I am getting negative scaling leads me to believe that something is wrong with my set up. Any tips on what I could try?* * * *Many thanks,* *--* Christoph Klein University of Virginia B.S. Chemical Engineering
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