Hi Mark, I dont think i need to play with npme at all.
Amit On Fri, Feb 19, 2010 at 2:41 PM, Amit Choubey <kgp.a...@gmail.com> wrote: > Hi Mark, > > I am not using PME calculation. > > I was hoping mdrun will do the cell allocation itself. > > Thanks, > Amit > > > On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> ----- Original Message ----- >> From: Amit Choubey <kgp.a...@gmail.com> >> Date: Saturday, February 20, 2010 8:51 >> Subject: [gmx-users] domain decomposition and load balancing >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> >> > Hi Everyone, >> > I am trying to run a simulation with the option "pbc=xy" turned on. I am >> using 64 processors for the simulation. The mdrun_mpi evokes the following >> error message before starting the md steps >> > >> > There is no domain decomposition for 64 nodes that is compatible with >> the given box and a minimum cell size of 0.889862 nm> Change the number of >> nodes or mdrun option -rdd or -dds> >> Look in the log file for details on the domain decomposition> >> > This has to do with the load balancing in the domain decomposition >> version of mdrun. Can anyone suggest me how to set the option -rdd or -dds? >> >> Those options are not normally the problem - but see the log file for info >> and mdrun -h for instructions. >> >> You should read up in the manual about domain decomposition, and see about >> choosing npme such that 64-npme is a number that is suitably composite that >> you can make a reasonably compact 3D grid so that the minimum cell size is >> not a constraint. Cells have to be large enough that all nonbonded >> interactions can be resolved in consultation with at most nearest-neighbour >> cells (and some other constraints). >> >> I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45 >> gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the >> cells to have the smallest diameter possible. Of course if your simulation >> box is so small that the 2D DD for pbc=xy will always lead to slabs that are >> too small in one dimension then you can't solve this problem with DD. >> >> If pbc=xy permits a 3D DD, then the same considerations apply. npme=19 >> gives 5x3x3 but npme=28 allows 4x3x3 >> >> > Also the simulation runs fine on one node (with domain decomposition) >> and with particle decomposition but both of them extremely slow.> >> >> Well, that's normal... >> >> Mark >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > >
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