GROMACS

The GROMACS (GROningen MAchine for Chemical Simulations) molecular dynamics package testing with the water_GMX50 data. This test profile allows selecting between CPU and GPU-based GROMACS builds.

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

Project Site

gromacs.org

Test Created

15 June 2019

Last Updated

13 May 2021

Test Maintainer

Michael Larabel 

Test Type

System

Average Install Time

4 Minutes, 12 Seconds

Average Run Time

34 Minutes, 26 Seconds

Test Dependencies

C/C++ Compiler Toolchain + CMake + OpenMPI

Accolades

20k+ Downloads

Supported Platforms

Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042021.052021.062021.0710002000300040005000
* 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 26 July 2021.
MPI CPU90.4%NVIDIA CUDA GPU9.6%Implementation Option PopularityOpenBenchmarking.org

Revision History

pts/gromacs-1.6.0   [View Source]   Thu, 13 May 2021 18:29:24 GMT
Update GROMACS against GROMACS 2021.2 upstream, add GPU CUDA build as part of this test profile rather than prior separate gromacs-gpu.

pts/gromacs-1.5.0   [View Source]   Tue, 09 Feb 2021 10:51:38 GMT
Update against GROMACS 2021 upstream.

pts/gromacs-1.4.1   [View Source]   Fri, 13 Nov 2020 09:09:25 GMT
Enable macOS support.

pts/gromacs-1.4.0   [View Source]   Sat, 26 Sep 2020 14:18:28 GMT
Update against GROMACS 2020.3 upstream to workaround compiler issues on newer distros like Fedora.

pts/gromacs-1.3.0   [View Source]   Tue, 14 Apr 2020 11:26:15 GMT
Update against gromacs 2020.1 upstream.

pts/gromacs-1.2.1   [View Source]   Wed, 26 Feb 2020 18:41:29 GMT
Add external dependencies that were missing/

pts/gromacs-1.2.0   [View Source]   Wed, 26 Feb 2020 15:24:53 GMT
Update against new GROMACS 2020 upstream, add allow run as root for mpirun.

pts/gromacs-1.1.1   [View Source]   Sat, 09 Nov 2019 14:16:00 GMT
Fix for the run sometimes failing, delete the previous tpr files before running.

pts/gromacs-1.1.0   [View Source]   Sat, 09 Nov 2019 13:57:57 GMT
Update against GROMACS 2019.4 upstream.

pts/gromacs-1.0.0   [View Source]   Sat, 15 Jun 2019 10:41:11 GMT
Been meaning to add this, very similar to existing gromacs-gpu test profile but this test profile only subject to running on CPU.

Suites Using This Test

C/C++ Compiler Tests

Multi-Core

Molecular Dynamics

Scientific Computing

HPC - High Performance Computing

MPI Benchmarks

NVIDIA GPU Compute


Performance Metrics

Analyze Test Configuration:

GROMACS 2021.2

Implementation: MPI CPU - Input: water_GMX50_bare

OpenBenchmarking.org metrics for this test profile configuration based on 304 public results since 13 May 2021 with the latest data as of 26 July 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 Per Day (Average)
2 x AMD EPYC 7763 64-Core
100th
8
10.17 +/- 0.04
2 x Intel Xeon Platinum 8380
94th
25
9.00 +/- 0.10
2 x AMD EPYC 7713 64-Core
90th
4
8.53 +/- 0.02
2 x AMD EPYC 7663 56-Core
89th
3
8.50 +/- 0.02
2 x AMD EPYC 74F3 24-Core
88th
3
5.87 +/- 0.07
AMD EPYC 7763 64-Core
87th
4
5.66 +/- 0.03
2 x AMD EPYC 7443 24-Core
85th
4
5.18 +/- 0.01
AMD EPYC 7713 64-Core
83rd
4
5.11 +/- 0.01
2 x AMD EPYC 7453 28-Core
83rd
7
5.10 +/- 0.03
Intel Xeon Platinum 8380
79th
9
5.02
Mid-Tier
75th
< 3.76
AMD EPYC 7543 32-Core
73rd
20
3.71 +/- 0.06
AMD Ryzen Threadripper 3990X 64-Core
72nd
3
3.70 +/- 0.01
2 x AMD EPYC 7343 16-Core
72nd
6
3.69 +/- 0.52
AMD Ryzen Threadripper 3970X 32-Core
68th
3
3.34
AMD Ryzen Threadripper 3960X 24-Core
65th
3
2.53
Intel Core i9-7980XE
63rd
3
1.69
Intel Core i9-10980XE
62nd
6
1.58 +/- 0.01
AMD Ryzen Threadripper 2970WX 24-Core
60th
4
1.42 +/- 0.03
Intel Xeon Silver 4216
58th
4
1.33 +/- 0.01
AMD Ryzen 9 5950X 16-Core
54th
10
1.28 +/- 0.01
AMD Ryzen 9 5900X 12-Core
53rd
6
1.27 +/- 0.02
AMD Ryzen 9 3950X 16-Core
51st
4
1.22
Median
50th
1.22
AMD Ryzen 9 3900X 12-Core
50th
3
1.12 +/- 0.01
AMD Ryzen 9 3900XT 12-Core
49th
3
1.09 +/- 0.04
Intel Core i9-11900K
48th
4
1.00
Intel Core i9-10900K
47th
3
0.96
Intel Core i9-9900KS
46th
3
0.95 +/- 0.01
AMD Ryzen 5 5600X 6-Core
44th
3
0.83
Intel Xeon E-2288G
43rd
4
0.82
AMD Ryzen 7 3800XT 8-Core
42nd
4
0.80
AMD Ryzen 7 3700X 8-Core
40th
3
0.78
Intel Core i7-8086K
39th
3
0.77 +/- 0.01
Intel Core i5-8400
38th
6
0.71
AMD Ryzen 5 3600XT 6-Core
36th
3
0.68
AMD Ryzen 9 5900HX
35th
4
0.66 +/- 0.02
Intel Core i7-10700T
34th
3
0.63
Intel Core i7-7700K
32nd
4
0.62
Intel Core i7-9750H
31st
3
0.58
AMD Ryzen 3 3300X 4-Core
30th
3
0.56
Intel Xeon E3-1275 v6
29th
4
0.55 +/- 0.01
AMD Ryzen 7 2700 Eight-Core
28th
3
0.54
AMD Ryzen 7 1700 Eight-Core
27th
3
0.53
Low-Tier
25th
< 0.52
Intel Core i3-10100
25th
3
0.52
Intel Core i3-8100
24th
3
0.52 +/- 0.01
Intel Xeon E3-1245 v5
23rd
4
0.51
Intel Xeon E3-1280 v5
22nd
4
0.50
AMD Ryzen 5 4500U
20th
3
0.48 +/- 0.01
Intel Core i5-6500
20th
3
0.47
Intel Xeon E3-1260L v5
18th
3
0.44
Intel Core i7-1165G7
17th
3
0.43
Intel Xeon E3-1270 v5
16th
4
0.41
Intel Xeon E3-1235L v5
15th
3
0.40
Intel Core i7-8550U
14th
3
0.37
AMD Ryzen 5 3400G
13th
3
0.37
Intel Xeon E3-1231 v3
13th
3
0.37
Intel Core i7-1065G7
11th
3
0.35 +/- 0.02
AMD Ryzen 5 2400G
11th
4
0.35 +/- 0.01
Intel Core i7-8565U
8th
3
0.33
AMD Ryzen 3 2200G
8th
3
0.33 +/- 0.01
Intel Core i3-7100
7th
4
0.30
Intel Core i7-4770K
6th
4
0.26
Intel Core i3-4130
4th
3
0.17 +/- 0.01
Intel Core i7-3770K
3rd
3
0.17
AMD Ryzen 3 3200U
2nd
3
0.14
OpenBenchmarking.orgDistribution Of Public Results - Implementation: MPI CPU - Input: water_GMX50_bare302 Results Range From 0 To 11 Ns Per Day00.9171.8342.7513.6684.5855.5026.4197.3368.2539.1710.08711.004306090120150

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2021.2 - Implementation: MPI CPU - Input: water_GMX50_bare) has an average run-time of 8 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 BenchmarkImplementation: MPI CPU - Input: water_GMX50_bareRun-Time918273645Min: 1 / Avg: 7.46 / Max: 46

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.1%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsImplementation: MPI CPU - Input: water_GMX50_bareDeviation246810Min: 0 / Avg: 0.14 / Max: 2

Does It Scale Well With Increasing Cores?

No, based on the automated analysis of the collected public benchmark data, this test / test settings does not 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 BaseGROMACS CPU Core ScalingImplementation: MPI CPU - Input: water_GMX50_bare46812163264612182430

Recent Test Results

OpenBenchmarking.org Results Compare

4 Systems - 78 Benchmark Results

AMD Ryzen 9 5900HX - ASUS G513QY v1.0 - AMD Renoir

Fedora 34 - 5.13.4-200.fc34.x86_64 - GNOME Shell 40.3

3 Systems - 78 Benchmark Results

AMD Ryzen 9 5900HX - ASUS G513QY v1.0 - AMD Renoir Root Complex

Ubuntu 21.04 - 5.13.2 - GNOME Shell 3.38.4

3 Systems - 116 Benchmark Results

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

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

2 Systems - 75 Benchmark Results

AMD Ryzen 9 5900HX - ASUS G513QY v1.0 - AMD Renoir Root Complex

Arch Linux - 5.13.4-arch1-1 - GNOME Shell 40.3

1 System - 2 Benchmark Results

AMD Ryzen 9 5900X 12-Core - ASUS TUF GAMING B550M-PLUS - AMD Starship

Ubuntu 20.04 - 5.8.0-63-generic - GNOME Shell 3.36.9

1 System - 1 Benchmark Result

AMD Ryzen 9 5900X 12-Core - ASUS TUF GAMING B550M-PLUS - AMD Starship

Ubuntu 20.04 - 5.8.0-63-generic - GNOME Shell 3.36.9

1 System - 1 Benchmark Result

2 x Intel Xeon Gold 6130 - Supermicro X11DPG-OT-CPU v1.01 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.4.0-80-generic - X Server 1.20.9

3 Systems - 253 Benchmark Results

AMD Ryzen 7 4700U - LENOVO LNVNB161216 - AMD Renoir Root Complex

Ubuntu 20.04 - 5.9.0-050900rc7daily20201003-generic - GNOME Shell 3.36.9

1 System - 162 Benchmark Results

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

Ubuntu 21.04 - 5.14.0-rc1-vanilla - X Server 1.20.11

1 System - 1 Benchmark Result

AMD Ryzen 7 3700X 8-Core - MSI MPG X570 GAMING PLUS - AMD Starship

Ubuntu 20.04 - 5.8.0-59-generic - GNOME Shell 3.36.4

1 System - 1 Benchmark Result

AMD Ryzen 9 3900X 12-Core - ASUS PRIME X570-PRO - AMD Starship

Ubuntu 20.04 - 5.8.0-36-generic - GNOME Shell 3.36.4

1 System - 1 Benchmark Result

AMD Ryzen 9 5900X 12-Core - Gigabyte B550 AORUS ELITE V2 - AMD Starship

Ubuntu 20.04 - 5.8.0-59-generic - GNOME Shell 3.36.4

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