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

[Mark Abraham]

Hi,

That suggests something is wrong with the pthreads infrastructure on your
machine. I would strongly advise checking that your cygwin is up to date.
It's supposed to just work because the cygwin library implements the
pthreads interface that GROMACS expects to find (and checks for, leading to
this message). But we don't regularly test on Cygwin or officially support
it, so it's possible there's some issue arisen that nobody else has
reported.

If you can update cygwin and try a fresh install of GROMACS and still get
this message from mdrun, please tarball your build directory and email it
to me off-list and I can perhaps see where the problem might lie.

Your major alternative would be to install openmpi under cygwin and use the
GROMACS MPI build, but I suspect you'll run into similar performance issues.

Mark

On Mon, Jan 23, 2017 at 4:44 AM liming_52 <liming_52 at 163.com> wrote:

> 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
> --
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