[gmx-users] About usage of node in mpi calculation

Justin A. Lemkul jalemkul at vt.edu
Thu May 31 18:11:31 CEST 2012

On 5/31/12 12:00 PM, vidhya sankar wrote:
> Dear justin ,
> Very very thanks for your previous patience reply
> When i run the mpi calculation using more than one node (each node have 16
> processor) which option do i need to use in the following command may i use
> -npme option?
> mpirun -np 19 mdrun_mpi_d -s toplo.tpr

The above command will not work on 16 processors, since it specifies 19. 
Assuming that is a typo, there's nothing necessarily wrong with that command at 
all.  The -npme option is only necessary when you need to override whatever 
mdrun detects as being optimal (which is usually fine and does not require 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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