[gmx-users] Problems with IMD in Gromacs 2016.3
Charles Laughton
Charles.Laughton at nottingham.ac.uk
Thu Jun 15 19:41:42 CEST 2017
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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