[gmx-users] Problems with IMD in Gromacs 2016.3

[Kutzner, Carsten]

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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