[gmx-users] MDrun -maxh option

Mark Abraham mark.j.abraham at gmail.com
Sat Jul 1 16:20:02 CEST 2017


Inter-simulation signalling for coordinating stuff like mdrun -maxh for
replica exchange has not had a great history. I believe it finally works
properly in 2016, but haven't actually tried it.


On Sat, Jul 1, 2017 at 3:45 PM Akshay <akshays.sridhar at gmail.com> wrote:

> Hello All,
> The cluster of my University uses a queuing system with a maximum wall-time
> of 12 hours. So, I run mdrun with the option -maxh 11.9 and subsequently
> restart the simulation using the output checkpoint files iteratively.
> However, the -maxh option has not been killing the jobs when I run replica
> exchange jobs across nodes (4 replicas with 2 nodes for each replica (16
> cores per node)). I only get an output error with the job scheduler killing
> the job at the 12 hour mark.
> I would love to have suggestions on how to begin my troubleshooting. Could
> it be an installation issue on specific nodes? Or should I reduce the -maxh
> value further to allow time for mdrun to write all the checkpoint files?
> Thanks,
> Akshay
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