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, 8 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/gromacs2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042021.052021.062021.072021.082021.092021.1011002200330044005500
* 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 16 October 2021.
MPI CPU66.4%NVIDIA CUDA GPU33.6%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 403 public results since 13 May 2021 with the latest data as of 12 October 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
10
10.15 +/- 0.08
2 x Intel Xeon Platinum 8380
93rd
37
8.99 +/- 0.13
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
87th
3
5.87 +/- 0.07
2 x Intel Xeon Platinum 8280
86th
4
5.71 +/- 0.02
AMD EPYC 7763 64-Core
85th
4
5.66 +/- 0.03
2 x AMD EPYC 7443 24-Core
84th
4
5.18 +/- 0.01
AMD EPYC 7713 64-Core
82nd
4
5.11 +/- 0.01
2 x AMD EPYC 7453 28-Core
81st
8
5.08 +/- 0.08
Intel Xeon Platinum 8380
79th
9
5.02
2 x AMD EPYC 7601 32-Core
77th
3
4.11 +/- 0.04
Mid-Tier
75th
< 3.80
AMD EPYC 7543 32-Core
72nd
26
3.70 +/- 0.07
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
2 x Intel Xeon Gold 5220R
68th
3
3.38 +/- 0.02
AMD Ryzen Threadripper 3970X 32-Core
67th
3
3.34
AMD EPYC 74F3 24-Core
67th
3
3.28 +/- 0.02
AMD Ryzen Threadripper 3960X 24-Core
64th
3
2.53
Intel Xeon Gold 6226R
62nd
3
1.83
Intel Core i9-7980XE
62nd
3
1.69
Intel Core i9-10980XE
60th
6
1.58 +/- 0.01
AMD Ryzen Threadripper 2970WX 24-Core
59th
4
1.42 +/- 0.03
Intel Xeon Silver 4216
57th
4
1.33 +/- 0.01
AMD Ryzen 9 5950X 16-Core
53rd
13
1.28 +/- 0.01
AMD Ryzen 9 5900X 12-Core
53rd
8
1.28 +/- 0.02
AMD Ryzen 9 3950X 16-Core
53rd
5
1.28 +/- 0.12
Median
50th
1.22
AMD Ryzen Threadripper 2950X 16-Core
50th
4
1.13
AMD Ryzen 9 3900X 12-Core
48th
3
1.12 +/- 0.01
AMD Ryzen 9 3900XT 12-Core
47th
5
1.11 +/- 0.03
Intel Core i9-11900K
46th
8
1.01 +/- 0.01
Intel Core i9-10900K
45th
3
0.96
Intel Core i9-9900KS
44th
3
0.95 +/- 0.01
AMD Ryzen 7 5800X 8-Core
43rd
5
0.91 +/- 0.01
AMD Ryzen 5 5600X 6-Core
41st
5
0.84 +/- 0.01
Intel Core i5-10600K
41st
4
0.84
Intel Xeon E-2288G
39th
4
0.82
AMD Ryzen 7 3800XT 8-Core
39th
4
0.80
AMD Ryzen 7 5700G
37th
6
0.80
AMD Ryzen 7 3700X 8-Core
36th
3
0.78
Intel Core i7-8700K
35th
3
0.78
Intel Core i7-8086K
35th
3
0.77 +/- 0.01
AMD Ryzen 5 5600G
34th
4
0.75
Intel Core i5-8400
32nd
6
0.71
AMD Ryzen 5 3600XT 6-Core
31st
3
0.68
AMD Ryzen 9 5900HX
30th
4
0.66 +/- 0.02
Intel Core i7-10700T
29th
3
0.63
Intel Core i7-7700K
28th
4
0.62
Intel Core i7-9750H
27th
3
0.58
AMD Ryzen 3 3300X 4-Core
27th
3
0.56
Intel Xeon E3-1275 v6
26th
4
0.55 +/- 0.01
Low-Tier
25th
< 0.55
AMD Ryzen 7 2700 Eight-Core
25th
3
0.54
AMD Ryzen 7 1700 Eight-Core
24th
3
0.53
Intel Core i3-10100
22nd
3
0.52
Intel Core i3-8100
21st
3
0.52 +/- 0.01
Intel Xeon E3-1245 v5
20th
4
0.51
Intel Xeon E3-1280 v5
19th
4
0.50
Intel Core i7-1165G7
18th
8
0.48 +/- 0.05
AMD Ryzen 5 4500U
18th
3
0.48 +/- 0.01
Intel Core i5-6500
17th
3
0.47
Intel Xeon E3-1260L v5
16th
3
0.44
Intel Xeon E3-1270 v5
14th
4
0.41
Intel Xeon E3-1235L v5
13th
3
0.40
Intel Core i5-7600K
13th
4
0.40
Intel Core i7-8550U
11th
3
0.37
AMD Ryzen 5 3400G
11th
3
0.37
Intel Xeon E3-1231 v3
11th
3
0.37
AMD Ryzen 5 2400G
9th
4
0.35 +/- 0.01
Intel Core i7-1065G7
9th
3
0.35 +/- 0.02
Intel Core i7-8565U
7th
3
0.33
AMD Ryzen 3 2200G
7th
3
0.33 +/- 0.01
Intel Core i3-7100
6th
4
0.30
Intel Core i7-4770K
5th
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_bare403 Results Range From 0 To 11 Ns Per Day00.9171.8342.7513.6684.5855.5026.4197.3368.2539.1710.08711.0044080120160200

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-Time1122334455Min: 1 / Avg: 7.36 / Max: 53

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: 0.15 / 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_bare4681216243264612182430

Recent Test Results

OpenBenchmarking.org Results Compare

3 Systems - 210 Benchmark Results

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6 Systems - 103 Benchmark Results

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CentOS Linux 8 - 4.18.0-240.10.1.el8_3.x86_64 - GCC 8.3.1 20191121

1 System - 1 Benchmark Result

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Fedora 34 - 5.14.9-200.fc34.x86_64 - GCC 11.2.1 20210728 + Clang 12.0.1 + LLVM 12.0.1

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3 Systems - 185 Benchmark Results

2 x AMD EPYC 7601 32-Core - Dell 02MJ3T - AMD 17h

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1 System - 149 Benchmark Results

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Ubuntu 19.10 - 5.3.0-18-generic - GNOME Shell 3.34.1

8 Systems - 111 Benchmark Results

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

Ubuntu 20.04 - 5.11.0-37-generic - GNOME Shell 3.36.9

7 Systems - 110 Benchmark Results

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

Debian 11 - 5.10.0-8-amd64 - 1.0.2

6 Systems - 186 Benchmark Results

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

Arch Linux - 5.14.9-arch2-1 - GCC 11.1.0

5 Systems - 64 Benchmark Results

Intel Core i7-1165G7 - Dell 0GG9PT - Intel Tiger Lake-LP

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4 Systems - 64 Benchmark Results

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Arch Linux - 5.14.9-arch2-1 - GNOME Shell 40.5

5 Systems - 186 Benchmark Results

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openSUSE Tumbleweed 20210929 - 5.14.6-1-default - KDE Plasma

5 Systems - 103 Benchmark Results

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CentOS Linux 8 - 4.18.0-193.19.1.el8_2.x86_64 - GCC 8.3.1 20191121

3 Systems - 64 Benchmark Results

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Ubuntu 21.04 - 5.11.0-34-generic - GNOME Shell 3.38.4

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