[gmx-users] queue up simulations

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 26 08:26:14 CEST 2007

sarbani chattopadhyay wrote:
>   hi,
>     I want to know is there any way to 'queue up mdrun jobs' so that 
> once one job is
> finished, the next starts automaticaly?

The same way you might any other command :-) This question is not 
strictly a GROMACS one... However if your queuing system requires you to 
write a shell script, then it is easy to have as your last command

qsub scriptname.sh

which will achieve serial resubmission. Note that you will eventually 
have to kill a job by hand to stop this, so you might like to consider 
some fancier logic, like testing for the existence of a file named 
"continue". See the manual for your shell for info here. Also you should 
test for successful completion of the previous job before resubmitting 
another one, otherwise you'll annoy your admin people in no time flat. 
Infinite loops are good for that!


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