[gmx-users] job failed. Too many CPU?

[Albert]

Hello:

I am trying to run a Gromacs job with command line:

mpirun -np 1 gmx_mpi grompp -f step6.0_minimization.mdp -o 60.tpr -n -c 
step5_charmm2gmx.pdb -maxwarn -1
mpirun -np 56 mdrun_mpi -s 60.tpr -g  60.log -c 60.gro >& 60.info


I am using Charmm36 FF for my system which contains 60,000 atoms.

The box size is:

CRYST1  73.607065  73.607065  109.376  90.0  90.0  90.0


Here is the log file. I googled similar errors and found that this 
normally happen to a small system with large no. of CPU. However, I 
don't think 56 cores CPU are too many for my system....



Reading file 60.tpr, VERSION 5.1.1 (single precision)

Will use 40 particle-particle and 16 PME only ranks
This is a guess, check the performance at the end of the log file

-------------------------------------------------------
Program mdrun_mpi, VERSION 5.1.1
Source code file: 
/icm/home/memar/topola/gromacs-5.1.1/src/gromacs/domdec/domdec.cpp, 
line: 6987

Fatal error:
There is no domain decomposition for 40 ranks that is compatible with 
the given box and a minimum cell size of 6.76123
  nm
Change the number of ranks or mdrun option -rdd
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
-------------------------------------------------------



THX a lot