[gmx-users] Error: Lost Particles while sorting

[Szilárd Páll]

On Thu, Mar 31, 2016 at 9:25 PM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> 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.
>

I don't think the machine needs to be offline just to install a version of
GROMACS. ;)


> -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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