We have recently developed a system with Xeon E5-2699 v3 processors in two sockets and an RTX 2080 Super. We are running GROMACS 2020.2.

The problem is, we are observing a serious decline in performance when two simulations are run simultaneously even with -pin on and -pinoffset mentioned. Our logical core maps are like:

Socket 0- Cores 0-17, 36-54

Socket 1- Cores 18-35, 55-72

Also, when a single simulation is run with -nb gpu -bonded gpu -pme gpu, gpu usage does not exceed 70%. In our previous workstation with the same GPU and E5-1680 v2, we used to get 1.8 times of the present performance.

Thanks in advance.

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