[gmx-users] Re: Re: help: load imbalance

[申昊]

> > 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.
> 
Thank you for your reply. As mentioned above, what i need to do is either increase coulomb cut-off or increase the FFT grid spacing. However, the Vmd 
cut-off should longer than the coulomb cut-off. According to what justin had said, this kind of changes are nor reasonable. Now i trun the cut-offs to 
1.4 nm and grid spacing to 0.16. 


> >
> > ; 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
> 
The system i simulated is about a short peptide with 2300 water molecules. It is absolute not the case i). Anyway, is seems not
a inhomogeneous system for case iii). I can sure that this simulation is running on totally one cluster node.
Does PP-PME helpful for the different cluster nodes? 

Best wishes!
Hao
> >
> >            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
> >
> >
> >
> > --
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>