[gmx-users] Avoiding domain decomposition error

[Ricardo Oliveira dos Santos Soares]

Thanks for Carsten and Mark for the useful suggestions, that helps a lot. 

Cheers 

--- 
Biological Chemistry and Physics 
Faculty of Pharmaceutical Sciences at Ribeirão Preto 
University of São Paulo - Brazil 
----- Mensagem original -----

> De: "Mark Abraham" <mark.j.abraham at gmail.com>
> Para: "Discussion list for GROMACS users"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Enviadas: Terça-feira, 19 de Novembro de 2013 15:39:22
> Assunto: Re: [gmx-users] Avoiding domain decomposition error

> Sure, using mpirun -np x mdrun_mpi will check for this. You don't
> want to
> actually compute on the head node (your sysadmins know where I
> live!), but
> all you need to do to trigger the check is to spawn an MPI job with
> that
> many ranks, and then kill it immediately if there was no error. (Not
> sure
> if adding -nsteps 0 will get the job done, but -nsteps 1 certainly
> will.) You don't need those ranks to be spawned across a real compute
> system for this test - over-subscribing any machine is fine.

> Mark

> On Tue, 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?
> >
> > 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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