White Papers

Ready Solutions Engineering Test Results

LAMMPS Four Node Comparative Performance

Analysis on Skylake Processors

Author: Joseph Stanfield

The purpose of this blog is to provide a comparative performance analysis of the Intel® Xeon® Gold 6150 processor (architecture code

named “Skylake”) and the previous generation Xeon® E5-2697 v4 processor using the LAMMPS benchmark. The Xeon® Gold 6150

CPU features 18 cores or 36 when utilizing hyper threading. Intel significantly increased the L2 cache per core from 256 KB on previous

generations of Xeon to 1 MB. The new processor also touts 24.75 MB of L3 cache and a six channel DDR4 memory interface.

LAMMPS, or Large Scale Atom/Molecular Massively Parallel Simulator, is an open-source molecular dynamics program originally

developed by Sandia National Laboratories, Temple University, and the United States Department of Energy. The main function of

LAMMPS is to model particles in a gaseous, liquid, or solid state.

Test cluster configuration:

Dell EMC PowerEdge

C6420

Dell EMC PowerEdge C6320

CPU

2x Xeon® Gold 6150 18c 2.7 GHz

(Skylake)

2x Xeon® E5-2697 v4 16c 2.3 GHz

(Broadwell)

RAM

12x 16GB @2666 MT/s 8x 16GB @2400 MT/s

HDD

1TB SATA 1 TB SATA

RHEL 7.3 RHEL 7.3

InfiniBand

EDR ConnectX-4 EDR ConnectX-4

BIOS Options

Settings

System Profile

Performance Optimized

Logical Processor

Disabled

Virtualization Technology

Disabled

The LAMMPS version used for testing release was lammps-6June-17. The in.eam dataset was used for the analysis on both

configurations. In.eam is a dataset that simulates a metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45 neighbors per atom),

NVE integration. The simulation was executed using 100 steps with 32,000 atoms.

The first series of benchmarks conducted were to measure performance in units of timesteps/s. The test environment consisted of four

servers interconnected with InfiniBand EDR, and tests were run on a single node, two nodes, and four nodes with LAMMPS, three times

for each configuration. Average results from a single node showed 106 time steps per second while a two node result nearly doubled

performance with 216 time steps per second. This trend remained consistent as the environment was scaled to four nodes as seen in

Figure 1.

PAGE 1
Ready Solutions Engineering Test Results LAMMPS Four Node Comparative Performance Analysis on Skylake Processors Author: Joseph Stanfield The purpose of this blog is to provide a comparative performance analysis of the Intel® Xeon® Gold 6150 processor (architecture code named “Skylake”) and the previous generation Xeon® E5-2697 v4 processor using the LAMMPS benchmark. The Xeon® Gold 6150 CPU features 18 cores or 36 when utilizing hyper threading.
PAGE 2
Xeon Gold 6150 in.eam 800 120% 96% 700 79% 100% 600 80% 500 387 400 300 216 200 60% 40% 110 20% 100 0 0% 1 Node 2 Node SCALING PERFORMANCE SPEED INCREASE TIME STEPS/SECOND (HIGHER IS BETTER) Ready Solutions Engineering Test Results 4 Node Figure 1. lammps in.eam 450 117% 123% 97% 387 400 TIMESTEPS (HIGHER IS BETTER) 140% 120% 350 100% 300 250 80% 216 196 200 150 100 50 110 60% 40% 100 49 20% 0 0% 1 Node 2 Node Xeon E5-2697 v4 4 Node Xeon Gold 6150 Figure 2.
PAGE 3
Ready Solutions Engineering Test Results 3 Conclusion In this blog, we analyzed and presented the performance of a Dell EMC PowerEdge C6420 cluster scaling from a single node to four nodes running the LAMMPS benchmark. Results show that performance of LAMMPS scales linearly with the increased number of nodes. A comparative analysis was also conducted with the previous generation Dell EMC PowerEdge C6320 server with a Xeon ® E5 v4 (Broadwell) processor.