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

Test Created

15 June 2019

Last Updated

13 May 2021

Test Maintainer

Michael Larabel 

Test Type

System

Average Install Time

4 Minutes, 8 Seconds

Average Run Time

34 Minutes, 26 Seconds

Test Dependencies

C/C++ Compiler Toolchain + CMake + OpenMPI

Accolades

20k+ Downloads

Supported Platforms


Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042021.052021.062021.072021.082021.092021.1011002200330044005500
* 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 16 October 2021.
MPI CPU66.4%NVIDIA CUDA GPU33.6%Implementation Option PopularityOpenBenchmarking.org

Revision History

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

Molecular Dynamics

Scientific Computing

HPC - High Performance Computing

MPI Benchmarks

NVIDIA GPU Compute


Performance Metrics

Analyze Test Configuration:

GROMACS 2021.2

Implementation: MPI CPU - Input: water_GMX50_bare

OpenBenchmarking.org metrics for this test profile configuration based on 403 public results since 13 May 2021 with the latest data as of 12 October 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
10.15 +/- 0.08
93rd
37
8.99 +/- 0.13
90th
4
8.53 +/- 0.02
89th
3
8.50 +/- 0.02
87th
3
5.87 +/- 0.07
85th
4
5.66 +/- 0.03
84th
4
5.18 +/- 0.01
82nd
4
5.11 +/- 0.01
81st
8
5.08 +/- 0.08
77th
3
4.11 +/- 0.04
Mid-Tier
75th
< 3.80
72nd
26
3.70 +/- 0.07
72nd
6
3.69 +/- 0.52
68th
3
3.38 +/- 0.02
67th
3
3.28 +/- 0.02
60th
6
1.58 +/- 0.01
57th
4
1.33 +/- 0.01
53rd
13
1.28 +/- 0.01
53rd
8
1.28 +/- 0.02
53rd
5
1.28 +/- 0.12
Median
50th
1.22
48th
3
1.12 +/- 0.01
47th
5
1.11 +/- 0.03
46th
8
1.01 +/- 0.01
44th
3
0.95 +/- 0.01
43rd
5
0.91 +/- 0.01
41st
5
0.84 +/- 0.01
35th
3
0.77 +/- 0.01
30th
4
0.66 +/- 0.02
26th
4
0.55 +/- 0.01
Low-Tier
25th
< 0.55
21st
3
0.52 +/- 0.01
18th
8
0.48 +/- 0.05
18th
3
0.48 +/- 0.01
9th
4
0.35 +/- 0.01
9th
3
0.35 +/- 0.02
7th
3
0.33 +/- 0.01
4th
3
0.17 +/- 0.01
OpenBenchmarking.orgDistribution Of Public Results - Implementation: MPI CPU - Input: water_GMX50_bare403 Results Range From 0 To 11 Ns Per Day00.9171.8342.7513.6684.5855.5026.4197.3368.2539.1710.08711.0044080120160200

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2021.2 - Implementation: MPI CPU - Input: water_GMX50_bare) has an average run-time of 8 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-Time1122334455Min: 1 / Avg: 7.36 / Max: 53

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.1%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsImplementation: MPI CPU - Input: water_GMX50_bareDeviation246810Min: 0 / Avg: 0.15 / Max: 2

Does It Scale Well With Increasing Cores?

No, based on the automated analysis of the collected public benchmark data, this test / test settings does not 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 ScalingImplementation: MPI CPU - Input: water_GMX50_bare4681216243264612182430

Recent Test Results

OpenBenchmarking.org Results Compare

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6 Systems - 103 Benchmark Results

Intel Xeon Gold 6238R - Supermicro X11SPL-F v1.02 - Intel Sky Lake-E DMI3 Registers

CentOS Linux 8 - 4.18.0-240.10.1.el8_3.x86_64 - GCC 8.3.1 20191121

1 System - 1 Benchmark Result

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Fedora 34 - 5.14.9-200.fc34.x86_64 - GCC 11.2.1 20210728 + Clang 12.0.1 + LLVM 12.0.1

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AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 20.04 - 5.11.0-37-generic - GNOME Shell 3.36.9

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Ubuntu 19.10 - 5.3.0-18-generic - GNOME Shell 3.34.1

8 Systems - 111 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Ubuntu 20.04 - 5.11.0-37-generic - GNOME Shell 3.36.9

7 Systems - 110 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Debian 11 - 5.10.0-8-amd64 - 1.0.2

6 Systems - 186 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Arch Linux - 5.14.9-arch2-1 - GCC 11.1.0

5 Systems - 64 Benchmark Results

Intel Core i7-1165G7 - Dell 0GG9PT - Intel Tiger Lake-LP

Ubuntu 21.10 - 5.13.0-16-generic - GNOME Shell 40.5

4 Systems - 64 Benchmark Results

Intel Core i7-1165G7 - Dell 0GG9PT - Intel Tiger Lake-LP

Arch Linux - 5.14.9-arch2-1 - GNOME Shell 40.5

5 Systems - 186 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

openSUSE Tumbleweed 20210929 - 5.14.6-1-default - KDE Plasma

5 Systems - 103 Benchmark Results

Intel Xeon Gold 6238R - Supermicro X11SPL-F v1.02 - Intel Sky Lake-E DMI3 Registers

CentOS Linux 8 - 4.18.0-193.19.1.el8_2.x86_64 - GCC 8.3.1 20191121

3 Systems - 64 Benchmark Results

Intel Core i7-1165G7 - Dell 0GG9PT - Intel Tiger Lake-LP

Ubuntu 21.04 - 5.11.0-34-generic - GNOME Shell 3.38.4

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