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 + Recently Updated Test Profile

Supported Platforms


Public Result UploadsReported Installs*Test Completions*OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.026001200180024003000
* 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 Fri, 26 Feb 2021 11:12:20 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 274 public results since 9 February 2021 with the latest data as of 27 February 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
4
5.229 +/- 0.139
96th
5
4.101 +/- 0.026
93rd
3
3.386 +/- 0.012
87th
5
2.345 +/- 0.029
85th
3
1.832 +/- 0.007
84th
5
1.700 +/- 0.002
82nd
5
1.576 +/- 0.001
79th
4
1.530 +/- 0.051
76th
3
1.343 +/- 0.005
Mid-Tier
75th
< 1.337
73rd
7
1.263 +/- 0.003
70th
10
1.255 +/- 0.015
69th
3
1.216 +/- 0.004
65th
5
1.127 +/- 0.009
64th
4
1.118 +/- 0.004
62nd
4
0.965 +/- 0.006
62nd
3
0.961 +/- 0.001
60th
3
0.951 +/- 0.002
60th
4
0.932 +/- 0.139
57th
4
0.844 +/- 0.003
57th
4
0.842 +/- 0.002
54th
7
0.822 +/- 0.008
52nd
4
0.800 +/- 0.001
Median
50th
0.790
50th
4
0.781 +/- 0.001
48th
3
0.779 +/- 0.001
46th
3
0.776 +/- 0.002
46th
3
0.772 +/- 0.015
46th
3
0.752 +/- 0.001
44th
3
0.715 +/- 0.001
43rd
3
0.681 +/- 0.006
42nd
3
0.651 +/- 0.003
41st
5
0.650 +/- 0.003
39th
8
0.633 +/- 0.064
39th
3
0.624 +/- 0.003
35th
3
0.582 +/- 0.004
34th
3
0.557 +/- 0.001
33rd
4
0.548 +/- 0.007
32nd
4
0.544 +/- 0.001
30th
3
0.519 +/- 0.004
30th
3
0.516 +/- 0.001
28th
3
0.498 +/- 0.002
27th
3
0.475 +/- 0.002
Low-Tier
25th
< 0.459
25th
4
0.456 +/- 0.003
24th
4
0.438 +/- 0.003
21st
4
0.407 +/- 0.002
19th
3
0.399 +/- 0.002
19th
3
0.399 +/- 0.003
18th
3
0.391 +/- 0.016
16th
8
0.377 +/- 0.002
14th
3
0.355 +/- 0.004
14th
4
0.355 +/- 0.001
10th
3
0.334 +/- 0.004
9th
4
0.296 +/- 0.004
8th
3
0.253 +/- 0.002
5th
3
0.188 +/- 0.003
4th
3
0.169 +/- 0.005
4th
3
0.166 +/- 0.001
3rd
3
0.143 +/- 0.001
OpenBenchmarking.orgDistribution Of Public Results - Input: water_GMX50_bare270 Results Range From 0 To 6 Ns Per Day00.511.522.533.544.555.5620406080100

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2021 - Input: water_GMX50_bare) has an average run-time of 15 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-Time1122334455Min: 2 / Avg: 14.07 / Max: 53

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.3%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsInput: water_GMX50_bareDeviation246810Min: 0 / Avg: 0.26 / Max: 3

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_bare46812161.0352.073.1054.145.175

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4 Systems - 15 Benchmark Results

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Most Popular Test Results

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AMD Ryzen 3 1300X - ASRock AB350 Pro4 - AMD 17h

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