[DFTB-Plus-User] Problem of parallel computing with openmpi

[yokoi-mp.pse]

Dear Dr. Ben,

Thank you very much for your advice.

With the option you advised the computational time has greatly 
decreased, from 47 sec. with 1 node to 13 sec. with 4 nodes, per MD step!!

Thank you very much again.

Best regards,
Tatsu

On 2017/05/12 0:41, Ben Hourahine wrote:
>
> Hello Tatsu,
>
> to add to Bálint's comment, you might be able to improve the 
> scalability by using parallelization over the k-points in your 
> calculation. Either running on the 8 cores with two separate groups of 
> points:
>
> Parallel = {
>   Groups = 2
> }
>
> Or running only on 7 of the total number of cores by using Groups = 7, 
> might improve the scalability.
>
> Regards
>
> Ben
>
>
> On 11/05/17 15:23, Bálint Aradi wrote:
>> Dear Tatsu,
>>
>>> When I perform a MD calculation on 4 cores in one node, computational
>>> time effectively decreases compared to a single-core calculation.
>>> However, when the same MD calculation is done on 8 cores of two nodes,
>>> its computational time become 2-3 times longer than the case of 4 cores
>>> in one node.
>>>
>>> I think that the calculated simulation box contains relatively a large
>>> number of atoms (496 Si atoms) and the number of nodes is just two, and
>>> thus communication overhead is not a cause. Would you give me advice
>>> about possible causes of this problem?
>>>
>> It depends pretty much on the interconnect between your nodes. I could
>> get 1000 atoms scaling up to 4 nodes, when using nodes with 8 cores each
>> and connected by infiniband. Your system is rather small (you have
>> roughly half of the orbitals I used), but I still would accept scaling
>> to 2 nodes, provided you have a low latency interconnect.
>>
>>    Best regards,
>>
>>    Bálint
>>
>>
>>
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>
> -- 
>        Dr. B. Hourahine, SUPA, Department of Physics,
>      University of Strathclyde, John Anderson Building,
>              107 Rottenrow, Glasgow G4 0NG, UK.
>      +44 141 548 2325,benjamin.hourahine at strath.ac.uk
>
> 2013/4 THE Awards Entrepreneurial University of the Year
>        2012/13 THE Awards UK University of the Year
>
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>          registered in Scotland, number SC015263
>
>
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