[gmx-users] load imbalance

[Mark Abraham]

On 17/06/2011 12:44 PM, E. Nihal Korkmaz wrote:
> Hi all,
>
> I am trying to run GB model simulation of a small protein. I keep 
> getting these errors for every step printed to the log file.
>
> DD  load balancing is limited by minimum cell size in dimension X
> DD  step 35999  vol min/aver 0.799! load imb.: force 154.9%

Not all systems can efficiently parallelize on arbitrary numbers of 
processors for a given implementation. There's an analysis at the top of 
the .log file that describes the issues leading to the minimum cell 
size. Possibly there's an issue there, but more likely you've got not 
enough work for your processors.

Mark

> Below i copied my mdp parameters. I'd appreciate any suggestion to 
> help me fix this.
>
> Thanks,
> Nihal
>
>
> integrator               = sd
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 5000000
> simulation_part          = 1
> init_step                = 1 %start from 5ns
>
>
> nstxout                  = 5000
> nstvout                  = 5000
> nstenergy                = 500
> nstxtcout                = 500
> nstlog                   = 500
>
> xtc_grps                 = System
> energygrps               = System
> comm_mode                = Linear
> ; neighbor searching and vdw/pme setting up
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 2.0
>
> coulombtype              = pme
> fourierspacing           = 0.1
> pme_order                = 6
> rcoulomb                 = 2.0
>
> vdwtype                  = Cut-off
> rvdw_switch              = 1.0
> rvdw                     = 2.0
>
> ; cpt control
> tcoupl                   = Berendsen
> tc-grps                  = System
> tau_t                    = 0.1
> ref_t                    = 300.0
> Pcoupl                   = Berendsen
> pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> ; velocity & temperature control
> gen_vel                  = yes
> gen_temp                 = 300.0
> annealing                = no
> constraints              = hbonds
> constraint_algorithm     = lincs
> morse                    = no
>
>
> -- 
> Elif Nihal Korkmaz
>
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email: korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>
>
>

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