[gmx-users] Running two separate mdrun instances on a single workstation

Deva Priya devapriyachem at gmail.com
Fri Sep 18 11:59:48 CEST 2015

Hello gmx users,

I have a two-socket (8 physical cores each, and with hyperthreading 32
cores system) with 2 gpus. I want to run two independent simulations using
16 threads and a single GPU.

I tried the -pin on and -pinoffset  0 for the first instance of mdrun and
-pin on and -pinoffset 8 for the second instance.

However, that did not show all 32 threads active in htop.

Then I tried -pin on -pinoffset 0 and -pin on -pinoffset 16, but still the
same result.

I noticed in the log file that mdrun selected a logical core stride of 2.

I have attached a snapshot of htop.


 I hope I can get some advice on how to fix this, so that both simulations
can share the hardware efficiently.


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