[gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

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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