[gmx-users] Error: Cannot set thread affinities on the current platform

[Mark Abraham]

Hi,

Unfortunately Cygwin isn't a supported platform for GROMACS. Setting such
affinities is very important for performance, but doing so on cygwin
requires doing things outside of Cygwin, I believe. There are some blog
posts around that might help.

Mark

On Sun, Nov 11, 2018 at 6:45 PM Neena Susan Eappen <
neena.susaneappen at mail.utoronto.ca> wrote:

> Hello GROMACS users,
>
>
> I am running GROMACS version 5.1.1 on windows using cygwin (latest
> version).After the following command: gmx mdrun -deffnm nvt
>
> Error message: Compiled SIMD instructions: SSE4.1, GROMACS could use
> AVX2_256 on this machine, which is better
>
> Reading file nvt.tpr, VERSION 5.1.1 (single precision)
> Changing nstlist from 10 to 20, rlist from 1 to 1.029
>
> Using 1 MPI thread
> Using 4 OpenMP threads
>
> NOTE: Cannot set thread affinities on the current platform.
> starting mdrun 'Protein in water'
> 50000 steps,    100.0 ps.
>
> Could there be anything incompatible between Cygwin and Gromacs here? Any
> insight would be appreciated, Many thanks,
>
>
> Neena Eappen
> Graduate Student
> Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
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