[gmx-users] gromacs in parallel

Marcela Madrid mmadrid at psc.edu
Wed Sep 10 23:06:48 CEST 2014


can you recommend a test for gromacs v. 5.0.1 that works in parallel?
I see the tutorials but there are no output files. The distribution says that the test is not working.

I have installed on an  SGI UV 1000cc-NUMA shared-memory system comprising 256 blades. Each blade holds 2 Intel Xeon X7560 (Nehalem) eight-core processors, for a total of 4096 cores across the whole machine.

I did not use the MPI option because I read in the manual that this is not necessary, that gromacs
uses built-in ThreadMPI, but I am not sure.

thanks, Marcela

Marcela Madrid, Ph.D.
Senior Computational Scientist
Pittsburgh Supercomputing Center

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