[gmx-users] MPI_BCAST : Message truncated [when restarting from checkpoint]
gmx3 at hotmail.com
Thu Nov 5 09:47:04 CET 2009
I can vaguely remember an issue like this which I have fixed.
But I don't recall if this was in 4.0.5 or in git master.
Do you continue on exactly the same number of nodes?
Do you use separate PME nodes?
Which integrator do you use?
> Date: Thu, 5 Nov 2009 18:37:07 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] MPI_BCAST : Message truncated [when restarting from checkpoint]
> Vasilii Artyukhov wrote:
> > Dear colleagues,
> > I encountered the following error messages when trying out the
> > checkpoint continuation functionality with MPI:
> > Reading file topol.tpr, VERSION 4.0.5 (single precision)
> > Reading checkpoint file state.cpt generated: Tue Oct 27 22:37:23 2009
> > 8 - MPI_BCAST : Message truncated
> >   Aborting Program!
> > Abort signaled by rank 8: Aborting program !
> > Exit code -3 signaled from [node address]
> > Killing remote processes...
> > From a short google search I've come under the impression that this has
> > to do with sending messages between the nodes that are larger than the
> > receive buffer (note my total lack of practical experience with MPI
> > programming). However, I have no idea where, if this is true, it might
> > be happening.
> > My system has 44091 atoms, and the .cpt file size is 1.1M, which doesn't
> > seems too large. Restarting works seemingly fine with serial mdrun.
> Hmm, that's an issue I've not seen before. Perhaps your MPI is
> configured with quite a small buffer for such things. What MPI style and
> version is it? Checking about this with your system admins is a good idea.
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