[gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

Hi,

Good to know. I'll ask the supercomputing folks to update gromacs from 5.0.4 to 5.0.7 at the next scheduled downtime. 

-Micholas

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Thursday, March 31, 2016 3:22 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Error: Lost Particles while sorting

Hi,

I was thinking of http://redmine.gromacs.org/issues/1153 but on general
principles that should not have showed up in 5.0. Nonetheless the early 5.0
versions had enough GPU-related issues that you still want to follow my
suggestion and see how you go.

Mark

On Thu, 31 Mar 2016 20:11 Smith, Micholas D. <smithmd at ornl.gov> wrote:

> Thanks, Mark. I didn't see this bug noted in the bug list so I thought I
> was just going crazy
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: Thursday, March 31, 2016 2:57 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error: Lost Particles while sorting
>
> Hi,
>
> Starting a new series of calculations on the earliest of a series of patch
> releases means you have chosen to accept all the bugs that have been fixed
> since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.
>
> Mark
>
> On Thu, 31 Mar 2016 19:40 Smith, Micholas D. <smithmd at ornl.gov> wrote:
>
> > Dear other users (and developers)
> >
> >
> > I moved some simulations that were working pretty well on one
> > supercomputer to another (the previous one did not have gpu nodes) to
> take
> > advantage of some gpus, but I am now getting a sporadic error:
> >
> >
> > ----
> >
> > Program gmx_mpi, VERSION 5.0
> > Source code file:
> > /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> > acs/mdlib/nbnxn_search.c, line: 728
> >
> > Software inconsistency error:
> > Lost particles while sorting
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > -----
> >
> >
> > in one of my simulations (but not the others), when I start to use more
> 16
> > MPI processes per simulation. I should note that I am using mdrun
> -multidir
> > in order to launch these simulations at the same time, and it doesn't
> seem
> > to be a specific simulation that it causing the issue. Additionally, it
> is
> > rather sporadic, sometimes the simulations will run with no problems,
> other
> > times it run for 2 minutes and then fails (and I get stuck back in the
> > queue). Any ideas?
> >
> >
> >
> > ===================
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> > --
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