[gmx-users] help: load imbalance

[Justin Lemkul]

On Wed, Apr 10, 2013 at 10:50 AM, 申昊 <shenhao at 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?
>
>
No. You're making ad hoc changes to nonbonded cutoffs (which can completely
invalidate the force field model) and you're making the PME grid less
accurate.

-Justin


> ; 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
>     2.60082e-05
>
>
>
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-- 

========================================

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

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