On Wed, Apr 10, 2013 at 4:50 PM, 申昊 <shen...@mail.bnu.edu.cn> wrote: > Hello, > I wanna ask some questions about load imbalance. > 1> Here are the messages resulted from grompp -f md.mdp -p topol.top -c > npt.gro -o md.tpr > > NOTE 1 [file md.mdp]: > The optimal PME mesh load for parallel simulations is below 0.5 > and for highly parallel simulations between 0.25 and 0.33, > for higher performance, increase the cut-off and the PME grid spacing > > therefore, i changed the md.mdp as whrited below, then used the command > grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr , then there is no NOTE > printed. So if i change the cut-offs to 2.0 nm and increase the grid spacing > to 0.30, does the calculated results reasonable?
You can shift work between short- and long-range electrostatics by adjusting the *coulomb* cut-off freely, but *not* the VdW cut-off. However, 2.0 nm sounds like a *very* long cut-off. > > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > rlist = 2 ; short-range neighborlist cutoff (in nm) > rcoulomb = 2 ; short-range electrostatic cutoff (in nm) > rvdw = 2 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.3 ; grid spacing for FFT > > 2> and how about no changes, just simulate it with the original mdp. Is the > results still reasonable? Here are the messages without any changes: > > DD load balancing is limited by minimum cell size in dimension X > DD step 2933999 vol min/aver 0.189! load imb.: force 124.7% You are simply pushing your simulation to the limit of how far it can be parallelized. As you can see from the above output, to compensate for the imbalance, the load balancing shrunk DD cells to the extent that the volume ratio of the smallest and average DD cell size is 0.189, meaning that the smallest DD cells are ~5.3x smaller than the average cell size - and the run is still *hugely* imbalanced. The "!" indicates what the line before says, that the DD load-balancing is limited and can't shrink cells further. Some aspects that might be limiting your simulation are: i) running with just a few hundred atoms/core; ii) running on multiple very different cluster nodes; iii) using a very inhomogeneous system. If you're using the group scheme (which i assume you are, otherwise the automated PP-PME balancing would have kicked in), you should be able to get better performance at high parallelization with the verlet scheme. Cheers, -- Szilard > > Step Time Lambda > 2934000 5868.00000 0.00000 > > Energies (kJ/mol) > Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 > 2.99315e+02 2.13778e+01 1.74659e+02 2.22024e+02 2.02466e+03 > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential > -1.68074e+02 -2.09809e-01 -1.80294e+03 -3.28155e+03 -2.51074e+03 > Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) > 1.69264e+04 1.44156e+04 2.95552e+02 -1.33866e-04 1.51489e+00 > Constr. rmsd > 2.60082e-05 > > > > -- > 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/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 list gmx-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
