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, 49 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 Uploads *Reported Test Completions **Reported Installs **Test Profile Page Views ***OpenBenchmarking.orgEventsLAMMPS Molecular Dynamics Simulator Popularity Statisticspts/lammps2012.062012.092012.122013.032013.062013.092013.122014.032014.062014.092014.122015.032015.062015.092015.122016.032016.062016.092016.122017.032017.062017.092017.122018.032018.062018.092018.122019.032019.062019.092019.122020.032020.062020.092020.122021.032021.0617003400510068008500
* Uploading of benchmark result data to OpenBenchmarking.org is always optional (opt-in) via the Phoronix Test Suite for users wishing to share their results publicly.
** 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.
*** Test profile page view reporting began March 2021.
Data current as of 15 June 2021.
Rhodopsin Protein62.6%20k Atoms37.4%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

HPC - High Performance Computing

MPI Benchmarks


Performance Metrics

Analyze Test Configuration:

LAMMPS Molecular Dynamics Simulator 29Oct2020

Model: Rhodopsin Protein

OpenBenchmarking.org metrics for this test profile configuration based on 1,217 public results since 29 October 2020 with the latest data as of 14 June 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
# Compatible Public Results
ns/day (Average)
99th
13
29.9 +/- 1.3
98th
6
27.5 +/- 1.8
97th
9
26.9 +/- 0.9
97th
11
26.9 +/- 0.5
96th
5
26.3 +/- 0.7
96th
3
26.1 +/- 0.1
95th
6
25.5 +/- 2.7
94th
3
25.0 +/- 0.8
91st
12
23.6 +/- 0.6
91st
24
23.6 +/- 1.3
89th
4
23.1 +/- 1.1
87th
7
22.2 +/- 1.5
87th
4
22.0 +/- 0.4
87th
4
21.8 +/- 0.1
86th
4
21.4 +/- 0.1
85th
5
20.6 +/- 0.3
85th
3
20.5 +/- 0.4
85th
3
20.3 +/- 0.1
84th
9
19.5 +/- 0.2
83rd
4
19.4 +/- 0.1
83rd
7
19.1 +/- 1.2
82nd
4
18.5 +/- 0.1
80th
6
16.9 +/- 0.4
80th
8
16.8 +/- 0.1
80th
3
16.6 +/- 0.4
78th
4
15.7 +/- 0.1
77th
6
15.7 +/- 0.1
77th
7
15.3 +/- 1.2
76th
9
14.8 +/- 1.4
Mid-Tier
75th
< 14.6
75th
9
14.5 +/- 0.5
75th
3
14.4 +/- 0.9
75th
9
14.4 +/- 1.0
74th
6
13.9 +/- 0.4
71st
25
12.9 +/- 0.4
71st
6
12.7 +/- 0.1
70th
4
12.5 +/- 1.2
67th
10
11.4 +/- 0.2
65th
19
11.0 +/- 1.3
62nd
8
10.7 +/- 0.1
62nd
61
10.6 +/- 0.5
61st
4
10.4 +/- 0.1
59th
11
9.8 +/- 0.7
54th
20
8.2 +/- 0.3
51st
6
7.6 +/- 0.3
Median
50th
7.4
50th
12
7.4 +/- 0.4
49th
6
7.0 +/- 0.1
49th
9
6.9 +/- 0.1
47th
7
6.8 +/- 0.9
47th
14
6.8 +/- 0.2
45th
11
6.4 +/- 0.1
43rd
11
6.0 +/- 0.1
43rd
9
6.0 +/- 0.2
41st
16
5.6 +/- 0.1
40th
24
5.3 +/- 0.5
40th
7
5.3 +/- 0.1
35th
6
5.0 +/- 0.1
34th
6
4.9 +/- 0.2
32nd
4
4.5 +/- 0.3
32nd
6
4.4 +/- 0.3
29th
5
4.0 +/- 0.1
Low-Tier
25th
< 3.1
25th
7
3.1 +/- 0.1
23rd
13
3.0 +/- 0.4
18th
9
2.7 +/- 0.1
17th
11
2.7 +/- 0.1
14th
11
2.6 +/- 0.2
14th
10
2.6 +/- 0.1
12th
6
2.5 +/- 0.3
8th
6
2.1 +/- 0.1
8th
6
2.1 +/- 0.1
OpenBenchmarking.orgDistribution Of Public Results - Model: Rhodopsin Protein1217 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: 1.07 / Max: 3

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 2.2%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsModel: Rhodopsin ProteinDeviation3691215Min: 0 / Avg: 2.19 / Max: 11

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.
 
MAXSD MINSD ADDSD MULSD UNPCKLPD MOVD PSHUFD MOVDQA MOVDQU PUNPCKLQDQ UCOMISD COMISD MOVAPD DIVSD ANDPD SUBSD SQRTSD CVTTSD2SI CVTSI2SD PMULUDQ PADDQ PSRLDQ MOVUPD ADDPD ANDNPD CMPNLESD ORPD SHUFPD MULPD CVTSD2SS CVTSS2SD XORPD SUBPD DIVPD UNPCKHPD CMPNLTSD MOVHPD CVTDQ2PD CVTTPD2DQ CMPLESD PUNPCKHQDQ MOVLPD CMPLTPD CMPNEQPD MINPD CMPNLEPD CVTPD2PS MOVMSKPD CMPLTSD SQRTPD PSLLDQ
Requires passing a supported compiler/build flag (verified with targets: sandybridge, skylake, tigerlake, cascadelake, 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, 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 VPERMD
FMA (FMA)
Requires passing a supported compiler/build flag (verified with targets: skylake, tigerlake, cascadelake, znver2, znver3).
Found on Intel processors since Haswell (2013).
Found on AMD processors since Bulldozer (2011).

 
VFMADD231SD VFMADD132SD VFNMADD132SD VFMSUB231SD VFMSUB132SD VFMADD132PD VFMADD213SD VFMADD213PD VFMSUB213SD VFNMADD213SD VFNMADD231SD VFNMSUB231SD VFNMSUB132SD VFMADD231PD VFNMSUB213SD VFMSUB132PD VFNMADD132PD VFNMADD213PD VFNMADD231PD VFMSUB231PD VFNMSUB132PD VFNMSUB231PD VFMSUB213PD VFNMSUB213PD
The test / benchmark does honor compiler flag changes.
Last automated analysis: 10 May 2021

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

Recent Test Results

OpenBenchmarking.org Results Compare

1 System - 372 Benchmark Results

2 x AMD EPYC 7763 64-Core - AMD DAYTONA_X - AMD Starship

Ubuntu 21.04 - 5.13.0-051300rc4-generic - X Server 1.20.11

12 Systems - 214 Benchmark Results

AMD EPYC 7713 64-Core - AMD DAYTONA_X - AMD Starship

Ubuntu 21.04 - 5.13.0-051300rc4-generic - X Server 1.20.11

2 Systems - 118 Benchmark Results

Intel Core i9-11900K - ASUS ROG MAXIMUS XIII HERO - Intel Tiger Lake-H

Fedora 34 - 5.12.9-300.fc34.x86_64 - GNOME Shell 40.1

1 System - 240 Benchmark Results

2 x Intel Xeon - OpenStack Foundation Nova v21.0.0 - Intel 440FX 82441FX PMC

Ubuntu 20.04 - 5.4.0-74-generic - GCC 9.3.0

1 System - 241 Benchmark Results

2 x Intel Xeon - OpenStack Foundation Nova v21.0.0 - Intel 440FX 82441FX PMC

Ubuntu 20.04 - 5.4.0-74-generic - GCC 9.3.0

1 System - 369 Benchmark Results

2 x AMD EPYC 7713 64-Core - AMD DAYTONA_X - AMD Starship

Ubuntu 21.04 - 5.13.0-051300rc4-generic - X Server 1.20.11

4 Systems - 214 Benchmark Results

Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4

3 Systems - 214 Benchmark Results

Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4

5 Systems - 67 Benchmark Results

ARMv7 Cortex-A72 - BCM2711 Raspberry Pi 4 Model B Rev 1.1 - 2048MB

Raspbian 10 - 5.4.51-v7l+ - LXDE 0.10.0

1 System - 485 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4

5 Systems - 148 Benchmark Results

ARMv8 Cortex-A72 - BCM2835 Raspberry Pi 400 Rev 1.0 - 4096MB

Debian 10 - 5.4.51-v8+ - LXDE 0.10.0

1 System - 206 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4

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