[gmx-users] Re: gromacs VERSION 4.0.7-There is no domain decomposition.....

[Christoph Junghans]

Dear Hamid,

please post these kind of questions on the users and not the developers list.

2013/3/9 Hamid Mosaddeghi <hamid592004m at yahoo.com>:
> Dear users
>
> I used gromacs for my system include CNT-water-ion-protein (400,000atom), I
> used grompp without error.
>
> after used mdrun with 16 node on cluster, I get this error:
>
> Reading file nvt.tpr, VERSION 4.0.7 (single precision)
> Loaded with Money
>
>
> NOTE: Periodic molecules: can not easily determine the required minimum
> bonded cut-off, using half the non-bonded cut-off
>
>
> Will use 15 particle-particle and 1 PME only nodes
> This is a guess, check the performance at the end of the log file
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.7
> Source code file: domdec.c, line: 5888
>
> Fatal error:
> There is no domain decomposition for 15 nodes that is compatible with the
> given box and a minimum cell size of 3.75 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> -------------------------------------------------------
>
> "Good Music Saves your Soul" (Lemmy)
>
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun on CPU 0 out of 16
>
> ---------------------------------------
>
> my box size is 14*14*18.
>
> I used mdrun -rdd 1 , gromacs run without error is it correct or not?
If you are sure that the maximum distance of your bonded interactions
is 1nm, you can do that.

It seems like mdrun was not able to find a decomposition
automatically, try to give one by hand:
$ mdrun -dd 2 2 4

Btw, your gromacs is 2 major versions behind, it might be a good idea to update.

Christoph
>
> I get this error in NVT (Em run without error).
>
> Best Regards.
>
> Hamid Mosaddeghi
>
>
>
> --
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--
Christoph Junghans
Web: http://www.compphys.de