Dell High Performance Computing Solution Resources Owner's manual

Dell
Brand
Dell
Model
High Performance Computing Solution Resources
Type
Owner's manual

Dell High Performance Computing Solution Resources provide unparalleled performance and scalability for demanding workloads. With powerful processors, high-speed memory, and cutting-edge accelerators, these solutions are ideal for scientific research, engineering simulations, and data analytics. Tackle complex problems faster, accelerate time to discovery, and gain valuable insights with Dell High Performance Computing Solutions.

Dell High Performance Computing Solution Resources provide unparalleled performance and scalability for demanding workloads. With powerful processors, high-speed memory, and cutting-edge accelerators, these solutions are ideal for scientific research, engineering simulations, and data analytics. Tackle complex problems faster, accelerate time to discovery, and gain valuable insights with Dell High Performance Computing Solutions.

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.
Ready Solutions Engineering Test Results
2
Figure 1.
The second series of benchmarks were run to compare the Xeon® Gold against the previous generation, Xeon® E5 v4. The same
dataset, in.eam, was used with 32,000 atoms and 100 steps per run. As you can see below in Figure 2, the Xeon® Gold CPU outperforms
the Xeon® E5 v4 by about 120% with each test, but the performance increase drops slightly as the cluster is scaled.
Figure 2.
110
216
387
96%
79%
0%
20%
40%
60%
80%
100%
120%
0
100
200
300
400
500
600
700
800
1 Node 2 Node 4 Node
SCALING PERFORMANCE SPEED INCREASE
TIME STEPS/SECOND (HIGHER IS BETTER)
Xeon Gold 6150
in.eam
49
100
196
110
216
387
123%
117%
97%
0%
20%
40%
60%
80%
100%
120%
140%
0
50
100
150
200
250
300
350
400
450
1 Node 2 Node 4 Node
SCALED PERFORMANCE IMPROVEMENT WITH
SKYLAKE
TIMESTEPS (HIGHER IS BETTER)
lammps in.eam
Xeon E5-2697 v4 Xeon Gold 6150
Ready Solutions Engineering Test Results
Copyright © 2017 Dell Inc. or its subsidiaries. All Rights Reserved. Dell, EMC, and other trademarks are trademarks of Dell Inc. or its subsidiaries. Other trademarks may be
the property of their respective owners. Published in the USA. Dell EMC believes the information in this document is accurate as of its publication date. The information is
subject to change without notice.
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. As with the first test, as node count was increased the linear scaling of the application was observed on Xeon®
E5 v4, results similar to the Xeon® Gold.. But the Xeon® Gold processor outperformed the previous generation CPU by about 120%
each run.
Resources
Intel LAMMPS Recipe: https://software.intel.com/en-us/articles/recipe-lammps-for-intel-xeon-phi-processors
LAMMPS USER-INTEL Package: http://lammps.sandia.gov/doc/accelerate_intel.html
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Dell High Performance Computing Solution Resources Owner's manual

Dell
Brand
Dell
Model
High Performance Computing Solution Resources
Type
Owner's manual

Dell High Performance Computing Solution Resources provide unparalleled performance and scalability for demanding workloads. With powerful processors, high-speed memory, and cutting-edge accelerators, these solutions are ideal for scientific research, engineering simulations, and data analytics. Tackle complex problems faster, accelerate time to discovery, and gain valuable insights with Dell High Performance Computing Solutions.

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