[gmx-users] nodes error

[Terry]

Hi,

You should start from here:

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

Terry


On Fri, Jan 6, 2012 at 12:49 PM, Albert <mailmd2011 at gmail.com> wrote:

>  Hello:
>   I found that each time I would like to increase my nodes for MD run, my
> job always failed. it said:
>
> Will use 192 particle-particle and 64 PME only nodes
> This is a guess, check the performance at the end of the log file
>
> -------------------------------------------------------
> 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
> -------------------------------------------------------
>
> "Ohne Arbeit wird das Leben Oede" (Wir Sind Helden)
>
>
> Does anybody have any idea for this? here is my scrips for submitting jobs;
> # @ job_name = I213A
> # @ class = kdm-large
> # @ account_no = G07-13
> # @ error = gromacs.err
> # @ output = gromacs.out
> # @ environment = COPY_ALL
> # @ wall_clock_limit = 12:00:00
> # @ notification = error
> # @ notify_user = albert at icm.edu.pl
> # @ job_type = bluegene
> # @ bg_size = 64
> # @ queue
> mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v
> -s npt.tpr" -mode VN -np 256
>
>
> if I change the bg_size=32 and -np=128, everything goes well....
>
>
> THX
>
>
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