[gmx-users] load imbalance

[E. Nihal Korkmaz]

Thanks for the reply.

Would that cause any problems in the simulation? It says force 154.9%, does
that mean it is applying the wrong force? Is it safe to proceed to
simulation like that?

Thanks,
Nihal

On Thu, Jun 16, 2011 at 9:54 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> **
> 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
>
>
>
>
> --
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-- 
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
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