GROMACS

The GROMACS (GROningen MAchine for Chemical Simulations) molecular dynamics package testing on the CPU with the water_GMX50 data.

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

9 February 2021

Test Maintainer

Michael Larabel 

Test Type

System

Average Install Time

3 Minutes, 56 Seconds

Average Run Time

34 Minutes, 26 Seconds

Test Dependencies

C/C++ Compiler Toolchain + CMake + OpenMPI

Accolades

20k+ Downloads

Supported Platforms


Public Result UploadsReported Installs*Test Completions*OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.045001000150020002500
* 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 Wed, 14 Apr 2021 07:31:04 GMT.

Revision History

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

MPI Benchmarks

HPC - High Performance Computing


Performance Metrics

Analyze Test Configuration:

GROMACS 2021

Input: water_GMX50_bare

OpenBenchmarking.org metrics for this test profile configuration based on 400 public results since 9 February 2021 with the latest data as of 15 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 Per Day (Average)
100th
7
9.754 +/- 0.057
99th
4
8.292 +/- 0.048
98th
6
8.175 +/- 0.085
96th
7
7.399 +/- 0.079
94th
6
5.728 +/- 0.029
92nd
6
5.637 +/- 0.059
89th
6
5.257 +/- 0.117
88th
4
5.013 +/- 0.146
88th
4
4.904 +/- 0.036
86th
4
4.544 +/- 0.023
85th
3
4.416 +/- 0.008
85th
4
4.379 +/- 0.015
83rd
5
4.329 +/- 0.029
82nd
3
4.129 +/- 0.040
81st
8
4.086 +/- 0.032
77th
5
3.445 +/- 0.081
Mid-Tier
75th
< 3.344
75th
3
3.322 +/- 0.008
74th
4
3.258 +/- 0.004
73rd
4
3.148 +/- 0.015
68th
7
2.357 +/- 0.033
67th
6
1.819 +/- 0.015
64th
5
1.700 +/- 0.002
63rd
4
1.678 +/- 0.006
61st
7
1.575 +/- 0.002
60th
4
1.530 +/- 0.051
58th
4
1.412 +/- 0.009
57th
4
1.351 +/- 0.005
56th
3
1.343 +/- 0.005
54th
7
1.263 +/- 0.003
52nd
10
1.255 +/- 0.015
51st
3
1.216 +/- 0.004
Median
50th
1.144
49th
5
1.127 +/- 0.009
48th
4
1.118 +/- 0.004
47th
4
0.965 +/- 0.006
46th
8
0.955 +/- 0.006
45th
3
0.951 +/- 0.002
44th
4
0.932 +/- 0.139
42nd
4
0.844 +/- 0.003
42nd
4
0.842 +/- 0.002
40th
7
0.822 +/- 0.008
38th
4
0.800 +/- 0.001
37th
4
0.781 +/- 0.001
36th
3
0.779 +/- 0.001
35th
3
0.776 +/- 0.002
34th
3
0.772 +/- 0.015
34th
3
0.752 +/- 0.001
33rd
3
0.715 +/- 0.001
32nd
3
0.681 +/- 0.006
31st
3
0.651 +/- 0.003
31st
5
0.650 +/- 0.003
30th
8
0.633 +/- 0.064
29th
3
0.624 +/- 0.003
27th
3
0.582 +/- 0.004
26th
3
0.557 +/- 0.001
Low-Tier
25th
< 0.553
25th
4
0.548 +/- 0.007
25th
4
0.544 +/- 0.001
24th
3
0.519 +/- 0.004
23rd
3
0.516 +/- 0.001
23rd
3
0.516 +/- 0.001
21st
3
0.498 +/- 0.002
20th
4
0.471 +/- 0.008
19th
4
0.456 +/- 0.003
18th
4
0.438 +/- 0.003
16th
4
0.407 +/- 0.002
14th
3
0.399 +/- 0.003
14th
3
0.399 +/- 0.002
14th
3
0.391 +/- 0.016
13th
8
0.377 +/- 0.002
11th
3
0.357 +/- 0.002
10th
3
0.355 +/- 0.004
10th
4
0.355 +/- 0.001
8th
3
0.334 +/- 0.004
7th
4
0.296 +/- 0.004
6th
3
0.253 +/- 0.002
4th
3
0.188 +/- 0.003
3rd
3
0.169 +/- 0.005
3rd
3
0.166 +/- 0.001
2nd
3
0.143 +/- 0.001
OpenBenchmarking.orgDistribution Of Public Results - Input: water_GMX50_bare399 Results Range From 0 To 10 Ns Per Day00.8331.6662.4993.3324.1654.9985.8316.6647.4978.339.1639.996306090120150

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2021 - Input: water_GMX50_bare) has an average run-time of 11 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 BenchmarkInput: water_GMX50_bareRun-Time1020304050Min: 1 / Avg: 10.12 / Max: 47

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.2%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsInput: water_GMX50_bareDeviation246810Min: 0 / Avg: 0.18 / Max: 2

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 BaseGROMACS CPU Core ScalingInput: water_GMX50_bare46812163264128714212835

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