[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
> >
> >
> >
> >
> >
> > This message and any attachment are intended solely for the addressee
> > and may contain confidential information. If you have received this
> > message in error, please send it back to me, and immediately delete
> it.
> >
> > Please do not use, copy or disclose the information contained in this
> > message or in any attachment. Any views or opinions expressed by the
> > author of this email do not necessarily reflect the views of the
> > University of Nottingham.
> >
> > This message has been checked for viruses but the contents of an
> > attachment may still contain software viruses which could damage your
> > computer system, you are advised to perform your own checks. Email
> > communications with the University of Nottingham may be monitored as
> > permitted by UK legislation.
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
>
>
>
> This message and any attachment are intended solely for the addressee
> and may contain confidential information. If you have received this
> message in error, please send it back to me, and immediately delete it.
>
> Please do not use, copy or disclose the information contained in this
> message or in any attachment. Any views or opinions expressed by the
> author of this email do not necessarily reflect the views of the
> University of Nottingham.
>
> This message has been checked for viruses but the contents of an
> attachment may still contain software viruses which could damage your
> computer system, you are advised to perform your own checks. Email
> communications with the University of Nottingham may be monitored as
> permitted by UK legislation.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list