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.abra...@gmail.com> > Para: "Discussion list for GROMACS users" > <gromacs.org_gmx-users@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 < > rsoa...@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. > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.