[gmx-users] Efficiently running multiple simulations

Zimmerman, Maxwell mizimmer at wustl.edu
Tue Sep 15 23:37:36 CEST 2015


I am having some troubles efficiently running simulations in parallel on a gpu-cluster. The cluster has 8 GPUs and 16 CPUs. Currently, the command that I am using is:

mpirun -np 8 mdrun_mpi -multi 8 -nice 4 -s md -o md -c after_md -v -x frame -pin on

Per-simulation, the performance I am getting with this command is significantly lower than running 1 simulation that uses 1 GPU and 2 CPUs alone. This command seems to use all 8 GPUs and 16 CPUs on the 8 parallel simulations, although I think this would be faster if I could pin each simulation to a specific GPU and pair of CPUs. The -gpu_id option does not seem to change anything when I am using the mpirun. Is there a way that I can efficiently run the 8 simulations on the cluster by specifying the GPU and CPUs to run with each simulation?

Thank you in advance!



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