[gmx-users] MDrun -maxh option

Akshay akshays.sridhar at gmail.com
Sat Jul 1 15:44:54 CEST 2017

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?


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