[gmx-users] load imbalance

[Justin A. Lemkul]

E. Nihal Korkmaz wrote:
> 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?
> 

It just means that one (or maybe more) processors are doing a whole lot more 
work than others.  There's nothing wrong with the force calculation itself.

For small proteins in an implicit solvent, DD parallelization doesn't offer much 
benefit.  There are optimized settings for non-periodic systems that may even 
result in better performance when there are serious balance issues, in which 
case your performance likely isn't very good since the DLB algorithm is clearly 
struggling.

-Justin

> 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>
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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