[gmx-users] help: load imbalance

申昊 shenhao at mail.bnu.edu.cn
Wed Apr 10 16:50:49 CEST 2013

   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? 

; 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%

           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


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