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

[Justin A. Lemkul]

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 
intervention).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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