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

19 May 2022

Test Maintainer

Michael Larabel 

Test Type

System

Average Install Time

4 Minutes, 11 Seconds

Average Run Time

1 Hour, 48 Minutes, 59 Seconds

Test Dependencies

C/C++ Compiler Toolchain + CMake + OpenMPI

Accolades

30k+ Downloads

Supported Platforms


Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.022019.042019.062019.082019.102019.122020.022020.042020.062020.082020.102020.122021.022021.042021.062021.082021.102021.122022.022022.042022.062022.082022.103K6K9K12K15K
* 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 29 November 2022.

Revision History

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

Scientific Computing

NVIDIA GPU Compute

MPI Benchmarks


Performance Metrics

Analyze Test Configuration:

GROMACS 2022.1

Implementation: MPI CPU - Input: water_GMX50_bare

OpenBenchmarking.org metrics for this test profile configuration based on 663 public results since 19 May 2022 with the latest data as of 19 November 2022.

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
8
19.26 +/- 0.61
100th
8
17.74 +/- 0.68
98th
8
12.05 +/- 0.97
98th
4
11.59 +/- 0.24
96th
19
11.00 +/- 0.13
93rd
12
10.05 +/- 0.04
92nd
8
9.99 +/- 0.38
90th
24
9.09 +/- 0.26
85th
14
8.19 +/- 0.09
83rd
3
7.46 +/- 0.14
82nd
8
7.39 +/- 0.11
81st
12
7.18 +/- 0.05
79th
6
6.83 +/- 0.06
79th
4
6.18 +/- 0.34
77th
12
5.70 +/- 0.05
Mid-Tier
75th
< 5.66
74th
10
5.13 +/- 0.03
73rd
6
5.06 +/- 0.03
71st
12
4.96 +/- 0.07
68th
5
4.05 +/- 0.06
64th
6
3.50 +/- 0.02
62nd
4
3.38 +/- 0.01
59th
5
2.54 +/- 0.02
59th
9
2.54 +/- 0.05
53rd
3
1.86 +/- 0.01
51st
9
1.73 +/- 0.05
Median
50th
1.72
49th
7
1.56 +/- 0.03
48th
8
1.54 +/- 0.01
48th
4
1.53 +/- 0.01
45th
14
1.47 +/- 0.04
43rd
4
1.32 +/- 0.01
43rd
10
1.31 +/- 0.15
39th
10
1.24 +/- 0.01
38th
10
1.22 +/- 0.01
36th
4
1.17 +/- 0.09
36th
6
1.13 +/- 0.02
35th
4
1.12 +/- 0.05
32nd
14
1.02 +/- 0.09
32nd
9
1.02 +/- 0.02
27th
5
0.96 +/- 0.01
27th
3
0.96 +/- 0.01
27th
8
0.95 +/- 0.09
Low-Tier
25th
< 0.86
25th
3
0.85 +/- 0.01
23rd
6
0.84 +/- 0.01
23rd
4
0.84 +/- 0.01
22nd
3
0.80 +/- 0.02
21st
3
0.77 +/- 0.01
19th
3
0.66 +/- 0.01
16th
6
0.59 +/- 0.01
15th
5
0.56 +/- 0.01
14th
3
0.55 +/- 0.01
13th
11
0.53 +/- 0.06
13th
3
0.53 +/- 0.01
11th
4
0.51 +/- 0.01
9th
4
0.47 +/- 0.01
5th
4
0.30 +/- 0.01
5th
7
0.23
OpenBenchmarking.orgDistribution Of Public Results - Implementation: MPI CPU - Input: water_GMX50_bare663 Results Range From 0 To 20 Ns Per Day2468101214161820222470140210280350

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2022.1 - Implementation: MPI CPU - Input: water_GMX50_bare) has an average run-time of 7 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-Time816243240Min: 1 / Avg: 6.25 / Max: 37

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 RunsImplementation: MPI CPU - Input: water_GMX50_bareDeviation246810Min: 0 / Avg: 0.19 / Max: 4

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.

IntelAMDOpenBenchmarking.orgRelative Core Scaling To BaseGROMACS CPU Core ScalingImplementation: MPI CPU - Input: water_GMX50_bare4681216246412848121620

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)
ARMv8 64-bit
arm64
Apple M1
ARMv8 64-bit
aarch64
ARMv8 Cortex-A72, ARMv8 Neoverse-N1, ARMv8 Neoverse-N1 64-Core, ARMv8 Neoverse-N1 80-Core, ARMv8 Neoverse-V1, Ampere ARMv8 Neoverse-N1 128-Core, Ampere ARMv8 Neoverse-N1 160-Core, Ampere ARMv8 Neoverse-N1 256-Core, Apple M1, Apple M2

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CentOS Stream 8 - 4.18.0-358.el8.x86_64 - NVIDIA

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CentOS Stream 8 - 4.18.0-358.el8.x86_64 - NVIDIA

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