[gmx-users] Restarting a simulation when checkpoint files are corrupted

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 17 18:11:41 CET 2017


On Fri, Mar 17, 2017 at 6:00 PM David Dotson <dldotson at asu.edu> wrote:

> Greetings,
> I have a simulation that has been running for a long time, with many
> trajectory segments (counting up to about 190). One of the segments ran on
> a cluster that experienced a filesystem outage such that some of the files
> for that run were corrupted, including its checkpoint files (both the *.cpt
> and *_prev.cpt, somehow).

Yeah, that's a recurring problem. mdrun tells the filesystem to flush to
disk, but if it doesn't actually do that, then all we can suggest is that
you request more conservative settings from your sysadmins.

> Since I only have checkpoint files for the most recent run, I need to do
> something like a manual restart.
> I'm aware I can do this with `gmx convert-tpr` using an existing TPR and
> the most recent uncorrupted TRR and EDR file, but starting a run from this
> restarts counting for the output files from `0001`. Is there some way to
> make counting start from another value (like `0191`)?

Somehow it never got documented (I will fix that), but there is an .mdp
field that lets you set "simulation-part = 191" that would let you take
matters suitably into your own hands.


> If not, I can work around this I think by concatenating the existing parts
> and moving forward with restarted counting, but being able to do this would
> be the cleanest solution for me in this particular case to maintain some
> consistency with other runs.
> Thanks!
> David
> --
> David L. Dotson * david.dotson at asu.edu
> Beckstein Lab
> Center for Biological Physics
> Arizona State University
> becksteinlab.physics.asu.edu
> --
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