[gmx-users] Avoiding domain decomposition error

[Carsten Kutzner]

Hi,

On Nov 19, 2013, at 5:53 PM, Ricardo Oliveira dos Santos Soares <rsoares at fcfrp.usp.br> wrote:

> Hello fellow users, 
> is there a direct way of checking the domain decomposition viability before running a job, thus avoiding wasting large queue times on a shared cluster only to receive the attached error? 
> Is this something that can be done with aid of g_tune_pme? 
well, if there is a decomposition that works on a given number of nodes, then g_tune_pme
will be able to find it! With g_tun_pme -s x.tpr -launch you can then directly after
tuning launch your simulation (The only time 'wasted' then is the couple of minutes
for tuning).

Carsten

> 
> Here's the link to this well know issue: 
> 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 
> 
> Thanks, 
> 
> Ricardo. 
> 
> 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa