[gmx-users] mdrun domain decomposition in GROMACS 5 and GROMACS 4

[Rebeca García Fandiño]

Dear Gromacs users,
I am trying to carry out a mdrun simulation (mdrun -v -deffnm prod ) and depending on the version and on the number of processors I use, I am having these errors:

1) Using GROMACS 5.0.4 (AMD architecture) and 2 or 4 processors, the calculation is OK.

2) Using GROMACS 4.6.2 (Sandy architecture) and 2, 4, 8 processors, the calculation is also OK.

3) Using GROMACS 5.0.4 (AMD architecture) and 8 processors, I get this error:

Program mdrun, VERSION 5.0.4
Source code file: /root/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 6902

Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the given box and a minimum cell size of 0.959375 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings


4) Using GROMACS 4.6.2 (Sandy architecture) and 16 processors, I get this error, too:

Fatal error:
There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.959375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings

Which could be the reason of the errors? I assume this is not due to the system, since for a lower number of processors, it works well.

Thanks a lot in advance,

Best wishes,

Rebeca

Dr. Rebeca Garcia
Santiago de Compostela University
Spain