126.lammps
SPEC MPI2007 Benchmark Description

Benchmark Name

126.lammps

Benchmark Author

Sandia, Steve Plimpton, sjplimp@sandia.gov

Benchmark Program General Category

Molecular dynamics simulation

Benchmark Description

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

MPI Usage

LAMMPS divides 3d space into 3d sub-volumes, e.g. a AxBxC grid of procs, where P = total # of procs = A * B * C. It tries to make the sub-volumes as cubic as possible, since the volume of data exchanged is proportional to the surface are of the sub-volume. The routines MPI_Irecv and MPI_Send are primary means to achieve the communication.

The code has been modified to run at rank counts that show generally increasing performance. What this means is that if you ask for 35 ranks, 3 of the ranks will idle and 32 will continue on processing. The optimal rank counts are: 140, 135, 132, 128, 126, 125, 124, 120, 114, 112, 110, 108, 105, 102, 99, 96, 90, 84, 80, 72, 70, 64, 63, 60, 56, 54, 50, 48, 45, 44, 42, 36, 32, 30, 28, 27, 24, 20, 18, 16, 12, 8, 4

Input Description

General description of input to lammps can be found in Section_start.html. The input for the mref dataset is a 3d Lennard-Jones melt problem. 
variable        x index 202
variable        y index 202
variable        z index 202

units           lj
atom_style      atomic

lattice         fcc 0.8442
region          box block 0 $x 0 $y 0 $z
create_box      1 box
create_atoms    1
mass            1 1.0

velocity        all create 1.44 87287 loop geom

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0 2.5

neighbor        0.3 bin
neigh_modify    every 20 check no

fix             1 all nve

thermo          100

run             500

Output Description

For a full discussion of the output, see Section_start.html.

The validated output of the mref dataset is a set of steps, temperature, energy and pressure.

Programming Language

C++

Known portability issues

Version and Licensing

This is the LAMMPS (17 Jan 2005) software package.

Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License.

References

Last updated: February 6, 2007