[gmx-users] load imbalance

[Mark Abraham]

On 18/06/2011 10:36 AM, E. Nihal Korkmaz wrote:
> Thanks for the reply.
>
> Would that cause any problems in the simulation?

No.

> It says force 154.9%, does that mean it is applying the wrong force?

No, it means calculating the forces is taking an amount of time that is 
significantly different from a calculation that had ideal load balance.

> Is it safe to proceed to simulation like that?

Yes. Whether you care about efficiency vs throughput is your call to make.

Mark

> Thanks,
> Nihal
>
> On Thu, Jun 16, 2011 at 9:54 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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 <tel:608-265-3644>
>>     Email: korkmaz at wisc.edu <mailto: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 <mailto:korkmaz at wisc.edu>
>
>

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