LAMMPS Molecular Dynamics Simulator

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark lammps.

Project Site

lammps.sandia.gov

Test Created

10 June 2012

Last Updated

12 January 2021

Test Maintainer

Michael Larabel 

Test Type

Processor

Average Install Time

1 Minute, 48 Seconds

Average Run Time

7 Minutes, 13 Seconds

Test Dependencies

Fortran + OpenMPI + FFTW + CMake + C/C++ Compiler Toolchain

Accolades

100k+ Downloads

Supported Platforms


Public Result UploadsTest Completions*Reported Installs*OpenBenchmarking.orgEventsLAMMPS Molecular Dynamics Simulator Popularity Statisticspts/lammps2012.062012.092012.122013.032013.062013.092013.122014.032014.062014.092014.122015.032015.062015.092015.122016.032016.062016.092016.122017.032017.062017.092017.122018.032018.062018.092018.122019.032019.062019.092019.122020.032020.062020.092020.122021.0316003200480064008000
* Data based on those opting to upload their test results to OpenBenchmarking.org and users enabling the opt-in anonymous statistics reporting while running benchmarks from an Internet-connected platform.
Data current as of Fri, 09 Apr 2021 19:42:07 GMT.
Rhodopsin Protein64.6%20k Atoms35.4%Model Option PopularityOpenBenchmarking.org

Revision History

pts/lammps-1.3.2   [View Source]   Tue, 12 Jan 2021 10:27:58 GMT
LAMMPS works fine on macOS.

pts/lammps-1.3.1   [View Source]   Sun, 10 Jan 2021 20:50:23 GMT
Update download mirror that is iffy.

pts/lammps-1.3.0   [View Source]   Thu, 29 Oct 2020 10:11:23 GMT
Update against LAMMPS 29Oct2020.

pts/lammps-1.2.1   [View Source]   Fri, 18 Sep 2020 21:09:08 GMT
Add back Rhodopsin Protein for those wanting the easier model.

pts/lammps-1.2.0   [View Source]   Fri, 18 Sep 2020 20:40:07 GMT
Update against LAMMPS 24Aug2020 latest release, also add more intense input file for working better on modern systems.

pts/lammps-1.1.0   [View Source]   Fri, 10 Jan 2020 20:05:05 GMT
Update against latest upstream lammps and other improvements to the script.

pts/lammps-1.0.1   [View Source]   Tue, 01 Mar 2016 08:59:37 GMT
Update download links.

pts/lammps-1.0.0   [View Source]   Sun, 10 Jun 2012 21:13:02 GMT
Initial commit of the MPI LAMMPS program from the Sandia National Laboratories.

Suites Using This Test

C/C++ Compiler Tests

Multi-Core

CPU Massive

Molecular Dynamics

Scientific Computing

MPI Benchmarks

HPC - High Performance Computing


Performance Metrics

Analyze Test Configuration:

LAMMPS Molecular Dynamics Simulator 29Oct2020

Model: Rhodopsin Protein

OpenBenchmarking.org metrics for this test profile configuration based on 1,035 public results since 29 October 2020 with the latest data as of 10 April 2021.

Below is an overview of the generalized performance for components where there is sufficient statistically significant data based upon user-uploaded results. It is important to keep in mind particularly in the Linux/open-source space there can be vastly different OS configurations, with this overview intended to offer just general guidance as to the performance expectations.

Component
Percentile Rank
# Matching Public Results
ns/day (Average)
100th
7
29.6 +/- 0.4
99th
5
27.3 +/- 0.1
99th
5
26.6 +/- 0.1
95th
3
24.4 +/- 0.1
94th
12
23.6 +/- 0.6
94th
24
23.6 +/- 1.3
91st
4
22.4 +/- 2.0
91st
4
21.8 +/- 0.1
90th
4
21.4 +/- 0.1
89th
3
20.3 +/- 0.1
88th
4
19.6 +/- 0.1
88th
4
19.4 +/- 0.1
88th
7
19.1 +/- 1.2
87th
4
18.5 +/- 0.1
85th
8
16.8 +/- 0.1
84th
4
15.7 +/- 0.1
83rd
7
15.3 +/- 1.2
82nd
9
14.8 +/- 1.4
81st
9
14.5 +/- 0.5
81st
9
14.4 +/- 1.0
80th
6
13.9 +/- 0.4
77th
19
12.9 +/- 0.5
76th
4
12.5 +/- 1.2
Mid-Tier
75th
< 12.1
73rd
10
11.4 +/- 0.2
72nd
19
11.0 +/- 1.3
68th
8
10.7 +/- 0.1
68th
60
10.6 +/- 0.5
67th
4
10.4 +/- 0.1
65th
11
9.8 +/- 0.7
57th
6
7.6 +/- 0.3
56th
11
7.4 +/- 0.4
55th
9
6.9 +/- 0.1
53rd
7
6.8 +/- 0.9
53rd
14
6.8 +/- 0.2
Median
50th
6.5
50th
8
6.4 +/- 0.1
49th
11
6.0 +/- 0.1
49th
8
5.9 +/- 0.1
46th
16
5.6 +/- 0.1
45th
24
5.3 +/- 0.5
45th
7
5.3 +/- 0.1
39th
6
4.9 +/- 0.2
36th
4
4.5 +/- 0.3
36th
6
4.4 +/- 0.3
33rd
4
4.0 +/- 0.1
29th
7
3.1 +/- 0.1
26th
12
3.0 +/- 0.4
Low-Tier
25th
< 2.9
20th
9
2.7 +/- 0.1
19th
11
2.7 +/- 0.1
16th
10
2.6 +/- 0.1
15th
10
2.6 +/- 0.2
13th
6
2.5 +/- 0.3
9th
6
2.1 +/- 0.1
9th
6
2.1 +/- 0.1
OpenBenchmarking.orgDistribution Of Public Results - Model: Rhodopsin Protein1035 Results Range From 0 To 43 ns/day0481216202428323640444870140210280350

Based on OpenBenchmarking.org data, the selected test / test configuration (LAMMPS Molecular Dynamics Simulator 29Oct2020 - Model: Rhodopsin Protein) has an average run-time of 2 minutes. By default this test profile is set to run at least 3 times but may increase if the standard deviation exceeds pre-defined defaults or other calculations deem additional runs necessary for greater statistical accuracy of the result.

OpenBenchmarking.orgMinutesTime Required To Complete BenchmarkModel: Rhodopsin ProteinRun-Time246810Min: 1 / Avg: 1.08 / Max: 3

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 2.3%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsModel: Rhodopsin ProteinDeviation3691215Min: 0 / Avg: 2.28 / Max: 12

Does It Scale Well With Increasing Cores?

Yes, based on the automated analysis of the collected public benchmark data, this test / test settings does generally scale well with increasing CPU core counts. Data based on publicly available results for this test / test settings, separated by vendor, result divided by the reference CPU clock speed, grouped by matching physical CPU core count, and normalized against the smallest core count tested from each vendor for each CPU having a sufficient number of test samples and statistically significant data.

AMDIntelOpenBenchmarking.orgRelative Core Scaling To BaseLAMMPS Molecular Dynamics Simulator CPU Core ScalingModel: Rhodopsin Protein4681216243248643691215

Notable Instruction Set Usage

Notable instruction set extensions supported by this test, based on an automatic analysis by the Phoronix Test Suite / OpenBenchmarking.org analytics engine.

Instruction Set
Support
Instructions Detected
SSE2 (SSE2)
Used by default on supported hardware.
 
MOVUPD ADDPD MOVAPD MAXSD MOVD PSHUFD MOVDQA UNPCKLPD DIVSD COMISD MULSD SUBSD CVTSI2SD ADDSD UCOMISD SQRTSD XORPD MOVDQU PUNPCKLQDQ ANDPD CVTTSD2SI PMULUDQ PADDQ PSRLDQ MINSD ANDNPD CMPNLESD ORPD CMPNLTSD SHUFPD MULPD MOVHPD CVTSD2SS CVTSS2SD SUBPD MOVLPD DIVPD UNPCKHPD CVTDQ2PD CMPLESD CMPLTSD CVTTPD2DQ PUNPCKHQDQ CMPLTPD CMPNEQPD MINPD CMPNLEPD CVTPD2PS MOVMSKPD PSLLDQ
Requires passing a supported compiler/build flag (verified with targets: sandybridge, skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Sandy Bridge (2011).
Found on AMD processors since Bulldozer (2011).

 
VZEROUPPER VINSERTF128 VPERM2F128 VEXTRACTF128 VBROADCASTSD VBROADCASTSS VPERMILPD
Requires passing a supported compiler/build flag (verified with targets: skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).

 
VPGATHERQQ VPGATHERQD VPBROADCASTD VPBROADCASTQ VPERMQ VINSERTI128 VEXTRACTI128 VPMASKMOVD VPGATHERDQ VPERM2I128 VGATHERQPD VPERMPD VPGATHERDD VPBLENDD VPBROADCASTW VPBROADCASTB VPERMD
FMA (FMA)
Requires passing a supported compiler/build flag (verified with targets: skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Haswell (2013).
Found on AMD processors since Bulldozer (2011).

 
VFMADD213SD VFMADD231SD VFMADD132SD VFNMADD132SD VFMSUB231SD VFMSUB132SD VFMADD132PD VFMADD213PD VFMSUB213SD VFNMADD231SD VFNMADD132PD VFNMADD213SD VFNMADD231PD VFMSUB231PD VFMSUB132PD VFNMSUB132SD VFMADD231PD VFNMSUB231PD VFNMSUB132PD VFNMSUB231SD VFNMADD213PD VFNMSUB213SD VFMSUB213PD VFNMSUB213PD
The test / benchmark does honor compiler flag changes.
Last automated analysis: 30 January 2021

This test profile binary relies on the shared libraries libmpi.so.40, libjpeg.so.8, libpng16.so.16, libz.so.1, libfftw3.so.3, libm.so.6, libpthread.so.0, libc.so.6, libopen-rte.so.40, libopen-pal.so.40, libhwloc.so.15, libgomp.so.1, libevent-2.1.so.7, libdl.so.2, libutil.so.1, libudev.so.1.

Recent Test Results

OpenBenchmarking.org Results Compare

5 Systems - 67 Benchmark Results

Intel Celeron G5900 - Gigabyte B460M DS3H - Intel Device 9b73

Debian 10 - 4.19.0-9-amd64 - X Server 1.20.4

1 System - 272 Benchmark Results

26 Systems - 438 Benchmark Results

AMD EPYC 7702 64-Core - ASRockRack EPYCD8 - AMD Starship

Ubuntu 20.04 - 5.11.0-051100rc6daily20210201-generic - GNOME Shell 3.36.4

1 System - 272 Benchmark Results

4 Systems - 160 Benchmark Results

Intel Core i5-4670 - ASUS Z87-A - Intel 4th Gen Core DRAM

Clear Linux OS 34220 - 5.10.10-1017.native - GNOME Shell 3.38.3

3 Systems - 136 Benchmark Results

Intel Core i5-4670 - ASUS Z87-A - Intel 4th Gen Core DRAM

Clear Linux OS 34440 - 5.10.19-1032.native - GNOME Shell 3.38.4

25 Systems - 438 Benchmark Results

AMD EPYC 7713 64-Core - TYAN S8030GM2NE - AMD Starship

Fedora 33 - 5.11.7-200.fc33.x86_64 - GNOME Shell 3.38.4

4 Systems - 179 Benchmark Results

Intel Core i5-11600K - ASUS ROG MAXIMUS XIII HERO - Intel Device 43ef

Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4

5 Systems - 74 Benchmark Results

Intel Celeron G5900 - Gigabyte B460M DS3H - Intel Device 9b73

Debian 10 - 4.19.0-9-amd64 - X Server 1.20.4

1 System - 119 Benchmark Results

AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Fedora 34 - 5.11.9-300.fc34.x86_64 - GNOME Shell 40.0

3 Systems - 179 Benchmark Results

Intel Core i5-11600K - ASUS ROG MAXIMUS XIII HERO - Intel Device 43ef

Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4

3 Systems - 179 Benchmark Results

AMD Ryzen 5 5600X 6-Core - ASRock X570 Taichi - AMD Starship

Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4

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