[gmx-users] GROMACS Domain decomposition

[John Whittaker]

> Dear gmx-users,
>
> Would you mind giving me some instruction on this.
>
> I am learning Gromacs tutorial #1 of mdtutotials.com. However to the 5th
> step: EM,  http://www.mdtutorials.com/gmx/lysozyme/05_EM.html
> I got the error:
> "Domain decomposition does not support simple neighbor searching, use grid
> searching or run with one MPI rank"

Did you use the .mdp file in the tutorial
(http://www.mdtutorials.com/gmx/lysozyme/Files/minim.mdp)? You can see
that the "ns-type" (neighbor search type) parameter is set to "grid" in
that file. Whatever you had in your .mdp file set the ns-type to "simple",
which does not support domain decomposition and thus cannot be run on more
than one thread.

Best,

John

>
> Running on 1 thread of PC by changing from
> gmx mdrun -v -deffnm em
> to
> gmx mdrun -nt 1 -s -v -deffnm em
> gives no problem but it's too slow, (50k steps, 2seconds/1step)
>
> Thank you very much for your kind helps,
> Best regards,
>
> The full log is as follows
> -------------------------------------------------------------------------------------
> GROMACS:      gmx mdrun, VERSION 5.1.1
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>   gmx mdrun -s -deffnm em
>
> Back Off! I just backed up em.log to ./#em.log.33#
>
> Running on 1 node with total 12 cores, 24 logical cores
> Hardware detected:
>   CPU info:
>     Vendor: GenuineIntel
>     Brand:  Intel(R) Xeon(R) CPU           X5650  @ 2.67GHz
>     SIMD instructions most likely to fit this hardware: SSE4.1
>     SIMD instructions selected at GROMACS compile time: SSE4.1
>
> Reading file em.tpr, VERSION 5.1.1 (single precision)
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.1
> Source code file:
> /home/nguyenduyvy/Downloads/gromacs-5.1.1/src/gromacs/domdec/domdec.cpp,
> line: 6542
>
> Fatal error:
> Domain decomposition does not support simple neighbor searching, use grid
> searching or run with one MPI rank
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> -------------------------------------------------------------------------------------
>
> Yours sincerely,
> Nguyen Duy Vy
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