[gmx-users] sequential simulations with mdrun -multi option

[Mark Abraham]

You're choosing 240 ranks for 20 simulations, so that is 12 ranks per
simulation. Start 20 ranks for your position-restrained simulation, to
avoid this historical mal-implementation.

Mark

On Wed, 24 May 2017 17:15 Debdip Bhandary <debdip.bhandary at mv.uni-kl.de>
wrote:

>
> Dear Users,
> I am trying to perform n number of simulations in parallel using -multi
> option with mdrun (version 5.0.4). I want to simulate the system at
> different conditions in parallel using '-multi' option. The process
> involves nvt followed by NpT step. The jobscript is as following:
>
> #---------------------------------------------------
> for ((i=0;i<20;i++)) do
> aprun -n 1 grompp_mpi -f nvt$i.mdp -c emin.gro -p topol.top -n index.ndx
> -o topol$i.tpr
> done
> aprun -n 240 mdrun_mpi -multi 20 -s topol -pf pullf
> #---------------------------------------------------
> for ((i=0;i<20;i++)) do
> aprun -n 1 grompp_mpi -f npt$i.mdp -c confout$i.gro -t state$i.cpt -p
> topol.top -n index.ndx -o topol$i.tpr
> done
> aprun -n 240 mdrun_mpi -multi 20 -s topol -pf pulf
> #---------------------------------------------------
>
> With this script, the nvt step is performed. The simulation stops when
> it is executing the npt step. the error is following:
> ----
> Time or ensemble averaged or multiple pair distance restraints do not
> work (yet) with domain decomposition, use a single MPI rank per simulation.
> ----
>
> Is there any suggestion for this? I could not able to figure out how to
> use a single mpi rank per simulations.
>
> Thanks in advance.
> with regards,
> Debdip Bhandary
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