Re: [AMBER] bash scripting for MD tasks

From: James Starlight <>
Date: Mon, 29 Sep 2014 09:06:17 +0200

Hi Ross,

thank you very much for the ideas!
I think the task of the scripting (some brief concepts and examples) should
be included to the future Amber workshops as the integral part of any
computational research :).
Regarding my question: I've also considered 2 nested loops example - outer
(run sh file in the background assosiated with simulation_i) inner (set k
as GPU number)+wait (not sure fow to assosiate this delay to the outer loop
but I should to check syntax first).

But probably in my case the problem must be really simplifier because I
need to run each simulation of each free GPU in parallel (to use n GPU for
the same number of simulations):

#so just to define at the beginning of the script
nvidia-smi -c 3
 for sim in $simulations/* ; do
   simulation=$(basename "$sim")
   echo "Simulation of ${simulation} is in a progress!"
   cd $sim
   chmod +x ./${simulation}.Sh
  ./${simulation}.Sh &

I think it should run not very big ( for instance 3-5) number of the
simulation in parallel using free GPU for each md, shouldn't it? BYW what
will be in case of the missmatch beetween number of available GPUs and
simulations to run (e.g if I have 2 GPU and 10 Sh files) in this case?

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Received on Mon Sep 29 2014 - 00:30:04 PDT
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