[gmx-users] Re: nodes error

[Terry]

"The minimum cell size is controlled by the size of the largest charge
group or bonded interaction and the largest of rvdw, rlist and rcoulomb,
some other effects of bond constraints, and a safety margin. *Thus it is
not possible to run a small simulation with large numbers of processors.*"

Based on the information you provided, the only thing I can say is, MAYBE
your system is "too small" to run with 256 processors.

Cheers

Terry


On Fri, Jan 6, 2012 at 3:45 PM, Albert <mailmd2011 at gmail.com> wrote:

> thank you very much for kind reply.
>
> I change my command as following:
>
> mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_**mpi_bg -args "-nosum -dlb yes
> -v -s npt.tpr -nt 1" -mode VN -np 256
>
> the "-nt 1" option has been added above. but it still doesn't work and
> here is the log file
>
>
>
>
> Initializing Domain Decomposition on 256 nodes
> Dynamic load balancing: yes
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>    two-body bonded interactions: 0.435 nm, LJ-14, atoms 1853 1861
>  multi-body bonded interactions: 0.435 nm, Proper Dih., atoms 1853 1861
> Minimum cell size due to bonded interactions: 0.478 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm
> Estimated maximum distance required for P-LINCS: 0.819 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Guess for relative PME load: 0.21
>
> Will use 192 particle-particle and 64 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 64 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 192 cells with a minimum initial size of 1.024
> nm
> The maximum allowed number of cells is: X 7 Y 7 Z 7
>
>
> ------------------------------**-------------------------
> Program mdrun_mpi_bg, VERSION 4.5.5
> Source code file: ../../../src/mdlib/domdec.c, line: 6436
>
> Fatal error:
> There is no domain decomposition for 192 nodes that is compatible with the
> given box and a minimum cell size of
>  1.02425 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS
> settings
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
> ------------------------------**-------------------------
>
> "It's So Fast It's Slow" (F. Black)
>
>
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