[gmx-users] Problems with IMD in Gromacs 2016.3

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 15 20:10:36 CEST 2017


Hi,

Redmine.gromacs.org is the place. Please add enough inputs to reproduce the
problem!

Mark

On Thu, 15 Jun 2017 20:42 Charles Laughton <
Charles.Laughton at nottingham.ac.uk> wrote:

> Hi Carsten,
>
> Can you explain how I file a bug report? Do I need to be subscribed to the
> gmx-developers list or something?
>
> Regards,
>
> Charlie
>
> On 15/06/2017, 13:50, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> on behalf of Kutzner, Carsten" <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> ckutzne at gwdg.de> wrote:
>
>     Hi Charlie,
>
>     I just made a quick check with 5.1 and 2016 and I also see the problem
> that you
>     described. For me IMD works with 5.1, but not with 2016, but I don't
> know why.
>     Could you file a bug report?
>
>     Thank you,
>       Carsten
>
>
>     > On 14. Jun 2017, at 18:05, Charles Laughton <
> Charles.Laughton at nottingham.ac.uk> wrote:
>     >
>     > Hi,
>     >
>     > I have been using the IMD facility in Gromacs 5.1.4 for some time
> without problems, but I have now updated to Gromacs 2016.3 and there are
> errors (I can’t connect to mdrun from e.g. VMD).
>     >
>     > Possibly it has something to do with endian-ness issues?
>     >
>     > Here are snippets of a job run with 5.1.4:
>     > % gmx mdrun –deffnm test –imdwait imdport 0
>     >
>     >                   :-) 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<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/remote/gromacs/5.1.4/bin/gmx
>     > Data prefix:  /usr/remote/gromacs/5.1.4
>     > Command line:
>     >  gmx mdrun -deffnm test -imdwait -imdport 0
>     >
>     > (…etc..)
>     > IMD: Enabled. This simulation will accept incoming IMD connections.
>     > IMD: You chose a port number < 1. Will automatically assign a free
> port.
>     > IMD: You chose a port number < 1. Will automatically assign a free
> port.
>     >
>     > Back Off! I just backed up test.xvg to ./#test.xvg.7#
>     > IMD: Pausing simulation while no IMD connection present (-imdwait).
>     > IMD: Turning on IMD - port for incoming requests is 0.
>     > IMD: Setting up incoming socket.
>     > IMD: Listening for IMD connection on port 13134.
>     > IMD: Will wait until I have a connection and IMD_GO orders.
>     >
>     > In another window I then check the port:
>     > % netstat -lntp | grep gmx
>     > (Not all processes could be identified, non-owned process info
>     > will not be shown, you would have to be root to see it all.)
>     > tcp        0      0 0.0.0.0:13134           0.0.0.0:*
>  LISTEN      308137/gmx
>     >
>     > All looks healthy – gmx is listening on port 13134.
>     >
>     >
>     >
>     > Now the same with 2016.3:
>     >
>     >                      :-) GROMACS - gmx mdrun, 2016.3 (-:
>     >
>     >                            GROMACS is written by:
>     >     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
> Bjelkmar
>     > Aldert van Buuren   Rudi van Drunen     Anton Feenstra    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) 2001-2017, The GROMACS development team at
>     > Uppsala University, Stockholm University and
>     > the Royal Institute of Technology, Sweden.
>     > check out http://www.gromacs.org<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 2016.3
>     > Executable:   /usr/remote/gromacs/2016.3/bin/gmx
>     > Data prefix:  /usr/remote/gromacs/2016.3
>     > Working dir:  /users/charlie/tios/examples
>     > Command line:
>     >  gmx mdrun -deffnm test -imdwait -imdport 0
>     >
>     > (..etc..)
>     > IMD: Enabled. This simulation will accept incoming IMD connections.
>     > IMD: You chose a port number < 1. Will automatically assign a free
> port.
>     > IMD: You chose a port number < 1. Will automatically assign a free
> port.
>     >
>     > Back Off! I just backed up test.xvg to ./#test.xvg.8#
>     > IMD: Pausing simulation while no IMD connection present (-imdwait).
>     > IMD: Turning on IMD - port for incoming requests is 0.
>     > IMD: Setting up incoming socket.
>     > IMD: Listening for IMD connection on port 52434.
>     > IMD: Will wait until I have a connection and IMD_GO orders.
>     >
>     > But in the other window:
>     >
>     > % netstat -lntp | grep gmx
>     > (Not all processes could be identified, non-owned process info
>     > will not be shown, you would have to be root to see it all.)
>     > tcp        0      0 0.0.0.0:53964           0.0.0.0:*
>  LISTEN      308199/gmx
>     >
>     > i.e. gmx is actually listening on port 53964. Not 52434.
>     >
>     > Interestingly:
>     >
>     > % python -c 'import socket; print socket.htons(53964)'
>     > 52434
>     >
>     > It makes me wonder if some endianness issues have got into the code
> somehow?
>     >
>     > Many thanks in advance for any help.
>     >
>     > Regards,
>     >
>     > Charlie Laughton
>     >
>     >
>     >
>     >
>     >
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