[gmx-users] multi threads pinning problem

Zhenyu Meng fdmm1989 at gmail.com
Fri Jul 24 05:53:08 CEST 2015

Dear all,
When I'm running gromacs with mdrun, I always receive such message:

The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto: will not pin thread to cores.
This can lead to significant performance degradation.
Consider using -pin on (and -pinoffset in case you run multiple jobs).

The server I use has 128 cores, and usually I use mdrun with flag -nt 32 or
-nt 64 to specify the threads, I also notice there's large performance lost
in each run.
I wonder what's the difference between '-pin on' and '-pinoffset'. I
usually run multi jobs on the server so will '-pin on' or '-pinoffset'
affect the other jobs? If I use '-pinoffset' what value I should
set(suppose I have already use 32 cores for other jobs)?

Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University

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