Re: [gmx-users] mdrun -rdd and -dds flag
On 11/04/2013 11:17, "manara r. (rm16g09)" wrote: >Dear gmx-users, > >I am having a problem with a periodic molecule and the domain >decomposition, I wish to use a high number of processors (circa 180, but >can obviously be reduced) and therefore need to use the -rdd or -dds >flags (I believe), how do these value effect the simulation? This is well documented and can be easily viewed by running mdrun -h In general these will be set automatically and do not need to be altered. > >The box size is 11.5 x 11.5 x 45. > >The polymer contains charged groups every repeating unit. Depending on how these are setup this might be where your problem lies. Charge groups are generally be small neutral groups of atoms say CH3 and CH2 in a polyethylene molecule or CH in benzene. If your monomer is large and treated as 1 charge group that could cause some problems. The exact setup depends on how they were parameterised in the forcefield. If you are using gromacs 4.6 or 4.6.1 with the verlet-cutoff charge groups have no effect anyway. > >The error I'm getting is (note this is a test run on my home machine, not >the cluster): >Fatal error: >There is no domain decomposition for 4 nodes that is compatible with the >given box and a minimum cell size of 61.7923 nm >Change the number of nodes or mdrun option -rdd or -dds Since that is larger than your box size it suggests something is dramatically wrong with your setup. The two things I know of that could potentially cause this are strange constraints in the topology combined with LINCS, or inappropriate choice of charge groups in the topology. My guess is the latter. > >Regards > >Rich Manara >PhD Student >Chemistry >Southampton University >UK >-- >gmx-users mailing listgmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >* Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun -rdd and -dds flag
On Thu, Apr 11, 2013 at 6:17 AM, manara r. (rm16g09) wrote: > Dear gmx-users, > > I am having a problem with a periodic molecule and the domain > decomposition, I wish to use a high number of processors (circa 180, but > can obviously be reduced) and therefore need to use the -rdd or -dds flags > (I believe), how do these value effect the simulation? > > The box size is 11.5 x 11.5 x 45. > > The polymer contains charged groups every repeating unit. > > The error I'm getting is (note this is a test run on my home machine, not > the cluster): > Fatal error: > There is no domain decomposition for 4 nodes that is compatible with the > given box and a minimum cell size of 61.7923 nm > Change the number of nodes or mdrun option -rdd or -dds > > There is no amount of hacking of -rdd or -dds that will "solve" this problem. DD cell size should be on the order of the longest cutoff. Your minimum size is huge, indicating you probably have either a bad topology or incorrect .mdp settings. 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun -rdd and -dds flag
Dear gmx-users, I am having a problem with a periodic molecule and the domain decomposition, I wish to use a high number of processors (circa 180, but can obviously be reduced) and therefore need to use the -rdd or -dds flags (I believe), how do these value effect the simulation? The box size is 11.5 x 11.5 x 45. The polymer contains charged groups every repeating unit. The error I'm getting is (note this is a test run on my home machine, not the cluster): Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 61.7923 nm Change the number of nodes or mdrun option -rdd or -dds Regards Rich Manara PhD Student Chemistry Southampton University UK -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
