[gmx-users] Error while scaling mdrun for more number of nodes.

vivek sharma viveksharma.iitb at gmail.com
Fri Sep 25 11:09:27 CEST 2009

Hi There,
I was trying to rum mdrun on large number of nodes. When I tried the run on
57 nodes, I got an error which is pasted below.
Program mpi_mdrun_d, VERSION 4.0.3
Source code file: domdec_setup.c, line: 147

Fatal error:
Could not find an appropriate number of separate PME nodes. i.e. >=
0.409991*#nodes (44) and <= #nodes/2 (57) and reasonable performance wise
(grid_x=63, grid_y=63).
Use the -npme option of mdrun or change the number of processors or the PME
grid dimensions, see the manual for details.
then I tried with -npme option as "-npme 20", this time it failed with the
following error.
Program mpi_mdrun_d, VERSION 4.0.3
Source code file: domdec.c, line: 5858

Fatal error:
There is no domain decomposition for 94 nodes that is compatible with the
given box and a minimum cell size of 1.025 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
Look in the log file for details on the domain decomposition
Same system was running fine when I tried it on 4 nodes.
I havn't used gromacs4.0 very well, so i don't understand these errors.
Please suggest me a way to get out of these errors, It will be really
helpful if anybody can explain me these errors.

With thanks in advance.

Thanks & Regards,
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