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Re: [lammps-users] Improved performance for setup on large numbers of MPI ranks
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Re: [lammps-users] Improved performance for setup on large numbers of MPI ranks


From: "Moore, Stan" <stamoor@...3...>
Date: Thu, 26 Oct 2017 21:05:49 +0000

Chris, I just updated the PR on GitHub with an example input deck. It looks like an issue with triclinic boxes (orthogonal boxes such as the rhodo benchmark work great).

Stan

-----Original Message-----
From: Christopher Knight [mailto:cjknight2009@...24...] 
Sent: Thursday, October 26, 2017 1:39 PM
To: Moore, Stan <stamoor@...3...>
Cc: akohlmey@...24...; lammps-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [lammps-users] Improved performance for setup on large numbers of MPI ranks

Hi Stan,

Yup, sure thing. Just did a quick test with the remotes/origin/comm-nprocs-opt branch and the rhodo input replicated 30x30x30 OK for me on 4,096 ranks. 

When writing this, not assigning atoms correctly was usually because the overlap criteria wasn’t robust, so my first guess is that’s the issue in your case (assuming it’s not because I simply omitted support/testing for something, e.g. triclinic).

Can you share details of what you ran and/or inputs (if not readily accessible)? I didn’t see description on github of inputs that crashed.

chris


=========

LAMMPS (23 Oct 2017)
  using 1 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines Reading data file ...
  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
  16 by 16 by 16 MPI processor grid
  reading atoms ...
  32000 atoms
…
Replicating atoms ...
  orthogonal box = (-27.5 -38.5 -36.3646) to (1622.5 2271.5 2145.42)
  16 by 16 by 16 MPI processor grid
Replicate::bounding box image: lo= -1 -1 -1  hi= 1 1 1
Replicate:: buf_all memory allocating       8.02 MB
Replicate: average # of replicas added to proc= 111.458252 out of 27000 (0.412808 %)
  864000000 atoms
  748521000 bonds
  1092609000 angles
  1534383000 dihedrals
  27918000 impropers
…



On Oct 26, 2017, at 12:54 PM, Moore, Stan <stamoor@...3...> wrote:

Chris,
 
Axel added your code as a PR on LAMMPS GitHub: https://github.com/lammps/lammps/pull/713. I tried out the replicate memory command but got a crash, can you take a look?
 
Thanks,
 
Stan