[gmx-users] Reg: Parallel run

[Justin A. Lemkul]

Rohit Farmer wrote:
> Dear Users,
> 
> I am trying to run my simulation in parallel using above 40 threads on a 
> cluster using qsub system but i am getting the following errors
> 
> Fatal error:
> The number of nodes you selected (43) contains a large prime factor 43. 
> In most cases this will lead to bad performance. Choose a number with 
> smaller prime factors or set the decomposition (option -dd) manually.
> For more information and tips for troubleshooting, please check the GROMACS
> 
> Fatal error:
> There is no domain decomposition for 40 nodes that is compatible with 
> the given box and a minimum cell size of 1.02425 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS 
> settings
> Look in the log file for details on the domain decomposition
> 
> The above two errors are on changing to different number of threads.
> 
> Any help??
> 

You can't necessarily split any system into an arbitrary number of 
processors/threads.  See:

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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