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

Source Repository

github.com

Test Created

15 June 2019

Last Updated

16 February 2024

Test Maintainer

Michael Larabel 

Test Type

System

Average Install Time

2 Minutes, 41 Seconds

Average Run Time

2 Hours, 28 Minutes, 11 Seconds

Test Dependencies

C/C++ Compiler Toolchain + CMake + OpenMPI

Accolades

70k+ Downloads

Supported Platforms


Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.022019.042019.062019.082019.102019.122020.022020.042020.062020.082020.102020.122021.022021.042021.062021.082021.102021.122022.022022.042022.062022.082022.102022.122023.022023.042023.062023.082023.102023.122024.026K12K18K24K30K
* 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 updated weekly as of 25 March 2024.

Revision History

pts/gromacs-1.9.0   [View Source]   Fri, 16 Feb 2024 13:53:43 GMT
Update against GROMACS 2024 upstream.

pts/gromacs-1.8.0   [View Source]   Wed, 08 Feb 2023 07:24:57 GMT
Update against GROMACS 2023 upstream.

pts/gromacs-1.7.0   [View Source]   Thu, 19 May 2022 08:03:09 GMT
Update against GROMACS 2022.1 upstream.

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

HPC - High Performance Computing

Molecular Dynamics

NVIDIA GPU Compute

Scientific Computing

MPI Benchmarks


Performance Metrics

Analyze Test Configuration:

GROMACS 2021

Input: water_GMX50_bare

OpenBenchmarking.org metrics for this test profile configuration based on 476 public results since 9 February 2021 with the latest data as of 11 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
# Compatible 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
94th
11
7.368 +/- 0.082
91st
7
5.724 +/- 0.028
89th
8
5.642 +/- 0.050
87th
5
5.526 +/- 0.011
86th
6
5.257 +/- 0.117
85th
6
5.023 +/- 0.114
84th
4
4.904 +/- 0.036
82nd
6
4.688 +/- 0.097
82nd
3
4.608 +/- 0.018
81st
4
4.544 +/- 0.023
80th
3
4.416 +/- 0.008
80th
4
4.379 +/- 0.015
78th
9
4.324 +/- 0.025
77th
3
4.129 +/- 0.040
76th
8
4.086 +/- 0.032
Mid-Tier
75th
< 4.080
74th
6
3.964 +/- 0.018
71st
5
3.445 +/- 0.081
71st
6
3.436 +/- 0.005
68th
3
3.322 +/- 0.008
68th
4
3.258 +/- 0.004
67th
4
3.148 +/- 0.015
64th
6
2.659 +/- 0.007
61st
7
2.357 +/- 0.033
60th
6
1.819 +/- 0.015
57th
5
1.700 +/- 0.002
56th
4
1.678 +/- 0.006
55th
9
1.579 +/- 0.008
53rd
4
1.530 +/- 0.051
52nd
4
1.412 +/- 0.009
51st
4
1.351 +/- 0.005
Median
50th
1.348
50th
3
1.343 +/- 0.005
47th
13
1.263 +/- 0.007
46th
10
1.255 +/- 0.015
45th
3
1.216 +/- 0.004
42nd
5
1.127 +/- 0.009
42nd
4
1.118 +/- 0.004
40th
4
0.965 +/- 0.006
39th
8
0.955 +/- 0.006
39th
3
0.951 +/- 0.002
38th
4
0.932 +/- 0.139
36th
4
0.844 +/- 0.003
36th
4
0.842 +/- 0.002
34th
7
0.822 +/- 0.008
33rd
4
0.800 +/- 0.001
32nd
4
0.781 +/- 0.001
31st
3
0.779 +/- 0.001
30th
3
0.776 +/- 0.002
30th
3
0.772 +/- 0.015
30th
3
0.752 +/- 0.001
29th
3
0.715 +/- 0.001
28th
3
0.681 +/- 0.006
27th
3
0.651 +/- 0.003
27th
5
0.650 +/- 0.003
26th
8
0.633 +/- 0.064
26th
3
0.624 +/- 0.003
Low-Tier
25th
< 0.620
24th
3
0.582 +/- 0.004
23rd
3
0.566 +/- 0.001
23rd
3
0.557 +/- 0.001
22nd
4
0.548 +/- 0.007
21st
4
0.544 +/- 0.001
20th
3
0.519 +/- 0.004
20th
3
0.516 +/- 0.001
20th
3
0.516 +/- 0.001
18th
3
0.498 +/- 0.002
17th
4
0.471 +/- 0.008
16th
4
0.456 +/- 0.003
15th
4
0.438 +/- 0.003
13th
4
0.407 +/- 0.002
12th
3
0.399 +/- 0.003
12th
3
0.399 +/- 0.002
12th
3
0.391 +/- 0.016
11th
8
0.377 +/- 0.002
9th
3
0.357 +/- 0.002
9th
4
0.355 +/- 0.001
9th
3
0.355 +/- 0.004
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_bare476 Results Range From 0 To 10 Ns Per Day0.8331.6662.4993.3324.1654.9985.8316.6647.4978.339.1639.9964080120160200

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2021 - Input: water_GMX50_bare) has an average run-time of 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: 2 / Avg: 10.61 / 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: 0.17 / 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_bare4681216243248641281020304050

Tested CPU Architectures

This benchmark has been successfully tested on the below mentioned architectures. The CPU architectures listed is where successful OpenBenchmarking.org result uploads occurred, namely for helping to determine if a given test is compatible with various alternative CPU architectures.

CPU Architecture
Kernel Identifier
Verified On
Intel / AMD x86 64-bit
x86_64
(Many Processors)