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Re: [lammps-users] Scaling with PMMM
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Re: [lammps-users] Scaling with PMMM


From: Vasily Pisarev <pisarevvv@...24...>
Date: Thu, 22 Jun 2017 16:28:22 +0300

Your number of atoms?
If you have 1000 atoms or less, more time is wasted on interprocess communications than you gain from parallelization (see Amdahl's law).

 Yours,
Vasily

2017-06-22 11:29 GMT+03:00 <jony.castagna@...3299...>:

Hi LAMMPS users,

I am pretty new to LAMMPS and I am trying to benchmark it on a simple case.

 

I have the attached input file (it’s a lj case with different PMMM parameter values) and run with different number of cores. Here the results:

 

-----------------1 core

Performance: 4565.958 tau/day, 10.569 timesteps/s

Performance: 2182.186 tau/day, 5.051 timesteps/s

Performance: 1774.433 tau/day, 4.107 timesteps/s

Performance: 2543.834 tau/day, 5.889 timesteps/s

Performance: 772.765 tau/day, 6.203 timesteps/s

 

-----------------2 core

Performance: 4225.783 tau/day, 9.782 timesteps/s

Performance: 2094.889 tau/day, 4.849 timesteps/s

Performance: 1816.108 tau/day, 4.204 timesteps/s

Performance: 2326.414 tau/day, 5.385 timesteps/s

Performance: 703.687 tau/day, 5.593 timesteps/s

 

 

-----------------4 core

Performance: 3504.945 tau/day, 8.113 timesteps/s

Performance: 1787.126 tau/day, 4.137 timesteps/s

Performance: 1635.585 tau/day, 3.786 timesteps/s

Performance: 1892.753 tau/day, 4.381 timesteps/s

Performance: 546.831 tau/day, 4.529 timesteps/s

 

-----------------8 core

Performance: 2593.201 tau/day, 6.003 timesteps/s

Performance: 1404.663 tau/day, 3.252 timesteps/s

Performance: 1284.628 tau/day, 2.974 timesteps/s

Performance: 1394.353 tau/day, 3.228 timesteps/s

Performance: 433.404 tau/day, 3.308 timesteps/s

 

 

-----------------16 core

Performance: 1172.032 tau/day, 2.713 timesteps/s

Performance: 926.618 tau/day, 2.145 timesteps/s

Performance: 892.738 tau/day, 2.067 timesteps/s

Performance: 931.408 tau/day, 2.156 timesteps/s

Performance: 270.925 tau/day, 2.157 timesteps/s

 

-----------------32 core

Performance: 652.883 tau/day, 1.511 timesteps/s

Performance: 601.613 tau/day, 1.393 timesteps/s

Performance: 598.401 tau/day, 1.385 timesteps/s

Performance: 618.035 tau/day, 1.431 timesteps/s

Performance: 167.245 tau/day, 1.451 timesteps/s

 

 

Results are still odd: I would expect a larger simulation time using more cores, not lower! In any case there is a poor scaling from 1 to 8 cores, better from 8 to 32.

 

Any suggestions? Thanks.

 

Best,

Jony

 

 

Dr Jony Castagna

Sci-Tech Daresbury

Keckwick Lane

Daresbury

Warrington

WA4 4AD

Tel.: +44 (0)1925 603682

 

From: Axel Kohlmeyer [mailto:akohlmey@...24...]
Sent: 21 June 2017 14:06
To: Castagna, Jony (STFC,DL,HC)
Cc: LAMMPS Users Mailing List
Subject: Re: [lammps-users] Problem with PPPM

 

 

 

On Wed, Jun 21, 2017 at 8:42 AM, <jony.castagna@...3299...> wrote:

Hi there,

  I tried to run the attached input file with1-32 cores, but I get the following error (see also the putput.txt file attached):

“ERROR on proc 1: Out of range atoms - cannot compute PPPMDisp (../pppm_disp.cpp:4300)”

 

Any idea?

 

too infrequent neighbor list updates?

 

axel

 

 

 

Best Regards,

Jony

 

Dr Jony Castagna

Sci-Tech Daresbury

Keckwick Lane

Daresbury

Warrington

WA4 4AD

Tel.: +44 (0)1925 603682

 


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Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.


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