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

[liming_52]

Dear gmx users,
I ran a md in Cygwin. Howerver, when I ran "gmx mdrun -deffnm nvt". There were errors as follows:

$ gmx mdrun -deffnm nvt

:-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:

GROMACS is written by:

Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar

Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch

Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen

Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner

Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff

Erik Marklund Teemu Murtola Szilard Pall Sander Pronk

Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers

Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf

and the project leaders:

Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2015, The GROMACS development team at

Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it

under the terms of the GNU Lesser General Public License

as published by the Free Software Foundation; either version 2.1

of the License, or (at your option) any later version.

GROMACS: gmx mdrun, VERSION 5.1.4

Executable: /usr/local/gromacs/bin/gmx.exe

Data prefix: /usr/local/gromacs

Command line:

gmx mdrun -deffnm nvt

　

Running on 1 node with total 24 logical cores

Hardware detected:

CPU info:

Vendor: GenuineIntel

Brand: Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz

SIMD instructions most likely to fit this hardware: AVX_256

SIMD instructions selected at GROMACS compile time: AVX_256

Reading file nvt.tpr, VERSION 5.1.4 (single precision)

Changing nstlist from 10 to 20, rlist from 1 to 1.03

　

Will use 18 particle-particle and 6 PME only ranks

This is a guess, check the performance at the end of the log file

Using 24 MPI threads

Using 1 OpenMP thread per tMPI thread

　

　

　

　

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.NOTE: Cannot set thre ad affinities on the current platform.NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.NOTE: Cannot set thre ad affinities on the current platform.

　

　

　

　

　

NOTE: Cannot set thread affinities on the current platform.NOTE: Cannot set thre ad affinities on the current platform.

　

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

NOTE: Cannot set thread affinities on the current platform.

　

　

NOTE: Cannot set thread affinities on the current platform.NOTE: Cannot set thre ad affinities on the current platform.NOTE: Cannot set thread affinities on the current platform.

　

　

NOTE: Cannot set thread affinities on the current platform.

And the cpus were not used for calculation, the md will be continued without stopping. How should I solve this problem?
Any reply will be appreciated.





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China