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

Supported Platforms

Public Result UploadsReported Installs*Test Completions*OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042021.055001000150020002500
* 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 Mon, 10 May 2021 21:53:32 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 461 public results since 9 February 2021 with the latest data as of 9 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
# Matching Public Results
Ns Per Day (Average)
2 x AMD EPYC 7763 64-Core
100th
10
9.753 +/- 0.053
2 x Intel Xeon Platinum 8380
99th
3
8.919 +/- 0.002
2 x AMD EPYC 7713 64-Core
98th
6
8.293 +/- 0.047
2 x AMD EPYC 7742 64-Core
96th
6
8.175 +/- 0.085
2 x AMD EPYC 75F3 32-Core
95th
10
7.379 +/- 0.078
2 x Intel Xeon Platinum 8280
92nd
7
5.724 +/- 0.028
AMD EPYC 7763 64-Core
89th
8
5.642 +/- 0.050
2 x AMD EPYC 7513 32-Core
88th
5
5.526 +/- 0.011
2 x AMD EPYC 7F72 24-Core
86th
6
5.257 +/- 0.117
AMD EPYC 7713 64-Core
85th
6
5.023 +/- 0.114
AMD EPYC 7742 64-Core
85th
4
4.904 +/- 0.036
2 x AMD EPYC 73F3 16-Core
83rd
5
4.713 +/- 0.084
AMD EPYC 7662 64-Core
82nd
4
4.544 +/- 0.023
2 x AMD EPYC 7F52 16-Core
81st
3
4.416 +/- 0.008
AMD EPYC 7702 64-Core
80th
4
4.379 +/- 0.015
AMD EPYC 75F3 32-Core
79th
8
4.322 +/- 0.026
AMD EPYC 7642 48-Core
77th
3
4.129 +/- 0.040
2 x AMD EPYC 7601 32-Core
76th
8
4.086 +/- 0.032
Mid-Tier
75th
< 4.045
AMD EPYC 7543 32-Core
74th
5
3.969 +/- 0.016
AMD Ryzen Threadripper 3990X 64-Core
74th
5
3.795 +/- 0.001
2 x Intel Xeon Gold 5220R
72nd
5
3.445 +/- 0.081
AMD EPYC 74F3 24-Core
72nd
5
3.435 +/- 0.004
AMD EPYC 7542 32-Core
69th
3
3.322 +/- 0.008
AMD EPYC 7532 32-Core
69th
4
3.258 +/- 0.004
AMD EPYC 7502P 32-Core
68th
4
3.148 +/- 0.015
AMD EPYC 73F3 16-Core
65th
5
2.657 +/- 0.006
AMD Ryzen Threadripper 3960X 24-Core
64th
3
2.534 +/- 0.004
AMD EPYC 7F52 16-Core
62nd
7
2.357 +/- 0.033
Intel Xeon Gold 6226R
61st
6
1.819 +/- 0.015
AMD Ryzen Threadripper 2990WX 32-Core
59th
4
1.780 +/- 0.007
Intel Core i9-7980XE
58th
5
1.700 +/- 0.002
AMD EPYC 7282 16-Core
57th
4
1.678 +/- 0.006
Intel Core i9-10980XE
56th
9
1.579 +/- 0.008
AMD EPYC 7551 32-Core
54th
4
1.530 +/- 0.051
AMD Ryzen Threadripper 2970WX 24-Core
53rd
3
1.457 +/- 0.035
AMD EPYC 7272 12-Core
52nd
4
1.412 +/- 0.009
AMD EPYC 7F32 8-Core
51st
4
1.351 +/- 0.005
Median
50th
1.345
Intel Xeon Silver 4216
50th
3
1.343 +/- 0.005
AMD Ryzen 9 5950X 16-Core
49th
11
1.265 +/- 0.004
AMD Ryzen 9 5900X 12-Core
46th
10
1.255 +/- 0.015
AMD Ryzen 9 3950X 16-Core
46th
3
1.216 +/- 0.004
AMD Ryzen Threadripper 2950X 16-Core
44th
3
1.142 +/- 0.002
AMD Ryzen 9 3900XT 12-Core
43rd
5
1.127 +/- 0.009
AMD Ryzen 9 3900X 12-Core
43rd
4
1.118 +/- 0.004
Intel Core i9-10900K
42nd
4
0.965 +/- 0.006
AMD Ryzen 7 5800X 8-Core
41st
8
0.955 +/- 0.006
Intel Core i9-9900KS
40th
3
0.951 +/- 0.002
Intel Core i9-9900K
39th
4
0.932 +/- 0.139
Intel Core i5-10600K
38th
4
0.844 +/- 0.003
AMD Ryzen 5 5600X 6-Core
37th
4
0.842 +/- 0.002
Intel Xeon E-2288G
36th
7
0.822 +/- 0.008
AMD Ryzen 7 3800XT 8-Core
34th
4
0.800 +/- 0.001
Intel Core i7-8086K
33rd
4
0.781 +/- 0.001
AMD Ryzen 7 3700X 8-Core
32nd
3
0.779 +/- 0.001
Intel Core i7-8700K
31st
3
0.776 +/- 0.002
AMD Ryzen 7 PRO 4750G
31st
3
0.772 +/- 0.015
Intel Xeon E5-1680 v3
31st
3
0.752 +/- 0.001
Intel Core i5-8400
30th
3
0.715 +/- 0.001
AMD Ryzen 5 3600XT 6-Core
29th
3
0.681 +/- 0.006
Intel Core i5-9400F
28th
3
0.651 +/- 0.003
Intel Core i7-10700T
28th
5
0.650 +/- 0.003
Intel Core i9-10885H
27th
8
0.633 +/- 0.064
Intel Core i7-7700K
26th
3
0.624 +/- 0.003
Low-Tier
25th
< 0.611
Intel Core i7-9750H
24th
3
0.582 +/- 0.004
Intel Core i7-6800K
24th
3
0.566 +/- 0.001
AMD Ryzen 3 3300X 4-Core
23rd
3
0.557 +/- 0.001
Intel Xeon E3-1275 v6
22nd
4
0.548 +/- 0.007
AMD Ryzen 7 2700 Eight-Core
22nd
4
0.544 +/- 0.001
Intel Core i3-8100
21st
3
0.519 +/- 0.004
Intel Core i3-10100
20th
3
0.516 +/- 0.001
AMD Ryzen 7 1700 Eight-Core
20th
3
0.516 +/- 0.001
Intel Xeon E3-1280 v5
19th
3
0.498 +/- 0.002
AMD Ryzen 5 4500U
17th
4
0.471 +/- 0.008
Intel Xeon E5-2609 v4
16th
4
0.456 +/- 0.003
Intel Core i7-1165G7
16th
4
0.438 +/- 0.003
Intel Xeon E3-1270 v5
14th
4
0.407 +/- 0.002
Intel Core i5-7600K
13th
3
0.399 +/- 0.003
Intel Xeon E3-1235L v5
13th
3
0.399 +/- 0.002
Intel Xeon E3-1231 v3
12th
3
0.391 +/- 0.016
AMD Ryzen 5 3400G
11th
8
0.377 +/- 0.002
Intel Core i5-4670
10th
3
0.357 +/- 0.002
AMD Ryzen 3 1300X
9th
3
0.355
Intel Core i7-8565U
9th
3
0.355 +/- 0.004
Intel Core i7-4960X
9th
4
0.355 +/- 0.001
Intel Core i7-1065G7
7th
3
0.334 +/- 0.004
Intel Core i3-7100
6th
4
0.296 +/- 0.004
Intel Core i7-4770K
5th
3
0.253 +/- 0.002
Intel Core i5-3470
5th
3
0.252
Intel Core i7-5600U
4th
3
0.188 +/- 0.003
Intel Core i3-4130
3rd
3
0.169 +/- 0.005
Intel Core i7-3770K
3rd
3
0.166 +/- 0.001
AMD Ryzen 3 3200U
2nd
3
0.143 +/- 0.001
OpenBenchmarking.orgDistribution Of Public Results - Input: water_GMX50_bare461 Results Range From 0 To 10 Ns Per Day00.8331.6662.4993.3324.1654.9985.8316.6647.4978.339.1639.9964080120160200

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2021 - Input: water_GMX50_bare) has an average run-time of 10 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-Time918273645Min: 1 / Avg: 9.34 / Max: 46

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: 0.18 / 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_bare4681216243264128714212835

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