[gmx-users] High load imbalance: 31.8%

[Nash, Anthony]

Hi Mark,

Many thanks for looking into this.

One of the log files (the job hasn’t finished running) is here:
https://www.dropbox.com/s/zwrro54yni2uxtn/umb_3_umb.log?dl=0

The system is a soluble collagenase in water with a collagen substrate and
two zinc co-factors. There are 287562 atoms in the system.

Please let me know if you need to know anything else. Thanks!

Anthony





On 20/08/2015 11:39, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

>Hi,
>
>In cases like this, it's good to describe what's in your simulation, and
>share the full .log file on a file-sharing service, so we can see both the
>things mdrun reports early and late.
>
>Mark
>
>On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>
>> Hi all,
>>
>> I appear to have a very high load imbalance on some of my runs. Values
>> starting from approx. 7% up to 31.8% with reported vol min/aver of
>>around
>> 0.6 (I haven¹t found one under half yet).
>>
>> When I look through the .log file at the start of the run I see:
>>
>> Initializing Domain Decomposition on 8 ranks
>> Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>     two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123
>>   multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123
>> Minimum cell size due to bonded interactions: 0.472 nm
>> Maximum distance for 5 constraints, at 120 deg. angles, all-trans:
>>0.862 nm
>> Estimated maximum distance required for P-LINCS: 0.862 nm
>> This distance will limit the DD cell size, you can override this with
>>-rcon
>> Using 0 separate PME ranks, as there are too few total
>>  ranks for efficient splitting
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 8 cells with a minimum initial size of 1.077
>>nm
>> The maximum allowed number of cells is: X 12 Y 12 Z 12
>> Domain decomposition grid 4 x 2 x 1, separate PME ranks 0
>> PME domain decomposition: 4 x 2 x 1
>> Domain decomposition rank 0, coordinates 0 0 0
>> Using 8 MPI processes
>> Using 1 OpenMP thread per MPI process
>>
>>
>>
>>
>> Having a quick look through the documentation and I see that I should
>> consider implementing the verlet cut-off (which I am) and adjust the
>> number of PME nodes/cut-off and PME grid spacing. Would this simply be a
>> case of throwing more cores at the simulation or must I play around with
>> P-LINCS parameters?
>>
>> Thanks
>> Anthony
>>
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