[gmx-developers] gromacs VERSION 4.0.7-There is no domain decomposition.....

Hamid Mosaddeghi hamid592004m at yahoo.com
Sat Mar 9 23:05:42 CET 2013

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?

I get this error in NVT (Em run without error).

Best Regards.

Hamid Mosaddeghi

View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-VERSION-4-0-7-There-is-no-domain-decomposition-tp5006246.html
Sent from the GROMACS Developers Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-developers mailing list