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)
2 x AMD EPYC 7F72 24-Core
100th
4
5.229 +/- 0.139
2 x AMD EPYC 7601 32-Core
96th
5
4.101 +/- 0.026
AMD Ryzen Threadripper 3990X 64-Core
95th
5
3.795 +/- 0.001
2 x Intel Xeon Gold 5220R
93rd
3
3.386 +/- 0.012
AMD Ryzen Threadripper 3970X 32-Core
92nd
4
3.343 +/- 0.001
AMD Ryzen Threadripper 3960X 24-Core
88th
3
2.534 +/- 0.004
AMD EPYC 7F52 16-Core
87th
5
2.345 +/- 0.029
Intel Xeon Gold 6226R
85th
3
1.832 +/- 0.007
Intel Core i9-7980XE
84th
5
1.700 +/- 0.002
Intel Core i9-10980XE
82nd
5
1.576 +/- 0.001
AMD EPYC 7551 32-Core
79th
4
1.530 +/- 0.051
AMD Ryzen Threadripper 2970WX 24-Core
79th
3
1.457 +/- 0.035
Intel Xeon Silver 4216
76th
3
1.343 +/- 0.005
Mid-Tier
75th
< 1.337
AMD Ryzen 9 5950X 16-Core
73rd
7
1.263 +/- 0.003
AMD Ryzen 9 5900X 12-Core
70th
10
1.255 +/- 0.015
AMD Ryzen 9 3950X 16-Core
69th
3
1.216 +/- 0.004
AMD Ryzen Threadripper 2950X 16-Core
67th
3
1.142 +/- 0.002
AMD Ryzen 9 3900XT 12-Core
65th
5
1.127 +/- 0.009
AMD Ryzen 9 3900X 12-Core
64th
4
1.118 +/- 0.004
Intel Core i9-10900K
62nd
4
0.965 +/- 0.006
AMD Ryzen 7 5800X 8-Core
62nd
3
0.961 +/- 0.001
Intel Core i9-9900KS
60th
3
0.951 +/- 0.002
Intel Core i9-9900K
60th
4
0.932 +/- 0.139
Intel Core i5-10600K
57th
4
0.844 +/- 0.003
AMD Ryzen 5 5600X 6-Core
57th
4
0.842 +/- 0.002
Intel Xeon E-2288G
54th
7
0.822 +/- 0.008
AMD Ryzen 7 3800XT 8-Core
52nd
4
0.800 +/- 0.001
Median
50th
0.790
Intel Core i7-8086K
50th
4
0.781 +/- 0.001
AMD Ryzen 7 3700X 8-Core
48th
3
0.779 +/- 0.001
Intel Core i7-8700K
46th
3
0.776 +/- 0.002
AMD Ryzen 7 PRO 4750G
46th
3
0.772 +/- 0.015
Intel Xeon E5-1680 v3
46th
3
0.752 +/- 0.001
Intel Core i5-8400
44th
3
0.715 +/- 0.001
AMD Ryzen 5 3600XT 6-Core
43rd
3
0.681 +/- 0.006
Intel Core i5-9400F
42nd
3
0.651 +/- 0.003
Intel Core i7-10700T
41st
5
0.650 +/- 0.003
Intel Core i9-10885H
39th
8
0.633 +/- 0.064
Intel Core i7-7700K
39th
3
0.624 +/- 0.003
Intel Core i7-9750H
35th
3
0.582 +/- 0.004
AMD Ryzen 3 3300X 4-Core
34th
3
0.557 +/- 0.001
Intel Xeon E3-1275 v6
33rd
4
0.548 +/- 0.007
AMD Ryzen 7 2700 Eight-Core
32nd
4
0.544 +/- 0.001
Intel Core i3-8100
30th
3
0.519 +/- 0.004
Intel Core i3-10100
30th
3
0.516 +/- 0.001
Intel Xeon E3-1280 v5
28th
3
0.498 +/- 0.002
AMD Ryzen 5 4500U
27th
3
0.475 +/- 0.002
Low-Tier
25th
< 0.459
Intel Xeon E5-2609 v4
25th
4
0.456 +/- 0.003
Intel Core i7-1165G7
24th
4
0.438 +/- 0.003
Intel Xeon E3-1270 v5
21st
4
0.407 +/- 0.002
Intel Xeon E3-1235L v5
19th
3
0.399 +/- 0.002
Intel Core i5-7600K
19th
3
0.399 +/- 0.003
Intel Xeon E3-1231 v3
18th
3
0.391 +/- 0.016
AMD Ryzen 5 3400G
16th
8
0.377 +/- 0.002
AMD Ryzen 3 1300X
14th
3
0.355
Intel Core i7-8565U
14th
3
0.355 +/- 0.004
Intel Core i7-4960X
14th
4
0.355 +/- 0.001
Intel Core i7-1065G7
10th
3
0.334 +/- 0.004
Intel Core i3-7100
9th
4
0.296 +/- 0.004
Intel Core i7-4770K
8th
3
0.253 +/- 0.002
Intel Core i5-3470
7th
3
0.252
Intel Core i7-5600U
5th
3
0.188 +/- 0.003
Intel Core i3-4130
4th
3
0.169 +/- 0.005
Intel Core i7-3770K
4th
3
0.166 +/- 0.001
AMD Ryzen 3 3200U
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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