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, 58 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/gromacs2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042021.055001000150020002500
* 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 Mon, 10 May 2021 21:53:32 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 461 public results since 9 February 2021 with the latest data as of 9 May 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
10
9.753 +/- 0.053
99th
3
8.919 +/- 0.002
98th
6
8.293 +/- 0.047
96th
6
8.175 +/- 0.085
95th
10
7.379 +/- 0.078
92nd
7
5.724 +/- 0.028
89th
8
5.642 +/- 0.050
88th
5
5.526 +/- 0.011
86th
6
5.257 +/- 0.117
85th
6
5.023 +/- 0.114
85th
4
4.904 +/- 0.036
83rd
5
4.713 +/- 0.084
82nd
4
4.544 +/- 0.023
81st
3
4.416 +/- 0.008
80th
4
4.379 +/- 0.015
79th
8
4.322 +/- 0.026
77th
3
4.129 +/- 0.040
76th
8
4.086 +/- 0.032
Mid-Tier
75th
< 4.045
74th
5
3.969 +/- 0.016
72nd
5
3.445 +/- 0.081
72nd
5
3.435 +/- 0.004
69th
3
3.322 +/- 0.008
69th
4
3.258 +/- 0.004
68th
4
3.148 +/- 0.015
65th
5
2.657 +/- 0.006
62nd
7
2.357 +/- 0.033
61st
6
1.819 +/- 0.015
58th
5
1.700 +/- 0.002
57th
4
1.678 +/- 0.006
56th
9
1.579 +/- 0.008
54th
4
1.530 +/- 0.051
52nd
4
1.412 +/- 0.009
51st
4
1.351 +/- 0.005
Median
50th
1.345
50th
3
1.343 +/- 0.005
49th
11
1.265 +/- 0.004
46th
10
1.255 +/- 0.015
46th
3
1.216 +/- 0.004
43rd
5
1.127 +/- 0.009
43rd
4
1.118 +/- 0.004
42nd
4
0.965 +/- 0.006
41st
8
0.955 +/- 0.006
40th
3
0.951 +/- 0.002
39th
4
0.932 +/- 0.139
38th
4
0.844 +/- 0.003
37th
4
0.842 +/- 0.002
36th
7
0.822 +/- 0.008
34th
4
0.800 +/- 0.001
33rd
4
0.781 +/- 0.001
32nd
3
0.779 +/- 0.001
31st
3
0.776 +/- 0.002
31st
3
0.772 +/- 0.015
31st
3
0.752 +/- 0.001
30th
3
0.715 +/- 0.001
29th
3
0.681 +/- 0.006
28th
3
0.651 +/- 0.003
28th
5
0.650 +/- 0.003
27th
8
0.633 +/- 0.064
26th
3
0.624 +/- 0.003
Low-Tier
25th
< 0.611
24th
3
0.582 +/- 0.004
24th
3
0.566 +/- 0.001
23rd
3
0.557 +/- 0.001
22nd
4
0.548 +/- 0.007
22nd
4
0.544 +/- 0.001
21st
3
0.519 +/- 0.004
20th
3
0.516 +/- 0.001
20th
3
0.516 +/- 0.001
19th
3
0.498 +/- 0.002
17th
4
0.471 +/- 0.008
16th
4
0.456 +/- 0.003
16th
4
0.438 +/- 0.003
14th
4
0.407 +/- 0.002
13th
3
0.399 +/- 0.003
13th
3
0.399 +/- 0.002
12th
3
0.391 +/- 0.016
11th
8
0.377 +/- 0.002
10th
3
0.357 +/- 0.002
9th
3
0.355 +/- 0.004
9th
4
0.355 +/- 0.001
7th
3
0.334 +/- 0.004
6th
4
0.296 +/- 0.004
5th
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_bare461 Results Range From 0 To 10 Ns Per Day00.8331.6662.4993.3324.1654.9985.8316.6647.4978.339.1639.9964080120160200

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2021 - Input: water_GMX50_bare) has an average run-time of 10 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-Time918273645Min: 1 / Avg: 9.34 / Max: 46

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_bare4681216243264128714212835

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