[gmx-users] MD simulation stops without any error/warning message

[Michele Pellegrino]

Alessandra, no core file was generated: I 'only' have the trajectory, the checkpoint state, the .edr file and the md.log file; none of them report an error message whatsoever.
The only thing that comes to my mind is a crash because of a failure of the SIMD (I have set AVX2_128 when building GROMACS), could it be?
Thank you for the suggestion by the way.

Cheers,
Michele
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alessandra Villa <alessandra.villa.biosim at gmail.com>
Sent: 23 January 2020 14:38
To: gmx-users at gromacs.org; gromacs.org_gmx-users
Subject: Re: [gmx-users] MD simulation stops without any error/warning  message

Hi,

On Thu, Jan 23, 2020 at 2:04 PM Michele Pellegrino <micpel at kth.se> wrote:

> Hi,
>
>
> today I was running a MD simulation and it stopped without any
> error/warning message.
>
> It just stopped: the md.log file reported everything till the last time
> step, and no information on the nature of the termination can be found in
> the standard output and the standard error.
>
> I tried to restart the simulation using the last checkpoint but I got the
> error message:
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2019.4
> Source file: src/gromacs/fileio/checkpoint.cpp (line 2435)
>
> Fatal error:
> Failed to lock: md.log. Already running simulation?
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> So, I double-checked if the simulation was still running in the background
> (and exponentially slowed down, for some reason) or if I accidentally
> stopped the process in background (without killing it, though): no trace of
> the process to be found.
> I run gmx energy with the default ener.edr file to see if it stopped
> because of some unphysical values for the temperature or the total energy,
> but everything seems to have stayed bounded.
> It is actually the second time I find myself in this situation: is there
> another way to what find out could have gone wrong?
>
>
If  a core file was generated , you could look at it

Best regards
Alessandra

>
> Thank you.
>
>
> Cheers,
>
> Michele
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