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

8 February 2023

Test Maintainer

Michael Larabel 

Test Type

System

Average Install Time

2 Minutes, 28 Seconds

Average Run Time

2 Hours, 28 Minutes, 11 Seconds

Test Dependencies

C/C++ Compiler Toolchain + CMake + OpenMPI

Accolades

60k+ Downloads

Supported Platforms

Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.022019.042019.062019.082019.102019.122020.022020.042020.062020.082020.102020.122021.022021.042021.062021.082021.102021.122022.022022.042022.062022.082022.102022.122023.022023.042023.062023.082023.106K12K18K24K30K
* 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 28 November 2023.

Revision History

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 2023

Implementation: MPI CPU - Input: water_GMX50_bare

OpenBenchmarking.org metrics for this test profile configuration based on 701 public results since 8 February 2023 with the latest data as of 30 November 2023.

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)
2 x AMD EPYC 9754 128-Core
100th
6
21.04 +/- 1.36
2 x AMD EPYC 9684X 96-Core
100th
7
19.51 +/- 1.21
2 x AMD EPYC 9654 96-Core
98th
29
18.90 +/- 0.68
2 x AMD EPYC 9554 64-Core
95th
7
17.79 +/- 0.94
2 x Intel Xeon Platinum 8490H
93rd
19
14.93 +/- 0.48
2 x AMD EPYC 9534 64-Core
91st
3
12.88 +/- 0.63
2 x Intel Xeon Max 9468
91st
6
12.31 +/- 1.21
AMD EPYC 9754 128-Core
91st
3
12.20
2 x Intel Xeon Max 9480
90th
9
11.97 +/- 0.88
AMD EPYC 9684X 96-Core
89th
10
11.61 +/- 0.35
2 x AMD EPYC 7773X 64-Core
84th
15
10.75 +/- 0.80
AMD Ryzen Threadripper PRO 7995WX 96-Cores
84th
8
10.70 +/- 0.19
AMD EPYC 9554 64-Core
82nd
3
9.65
2 x Intel Xeon Platinum 8380
81st
10
9.23 +/- 0.05
2 x AMD EPYC 7573X 32-Core
78th
5
8.25 +/- 0.04
Intel Xeon Platinum 8480
77th
7
7.98 +/- 0.84
Intel Xeon Max 9480
76th
6
7.51 +/- 0.77
Mid-Tier
75th
< 7.30
AMD EPYC 7773X 64-Core
75th
7
7.30 +/- 0.01
AMD Ryzen Threadripper 7980X 64-Cores
74th
9
7.02 +/- 1.05
2 x Intel Xeon Gold 6342
74th
3
6.76
AMD EPYC 8534P 64-Core
72nd
3
6.22 +/- 0.02
AMD EPYC 7763 64-Core
71st
4
5.71 +/- 0.02
AMD Ryzen Threadripper 7970X 32-Cores
70th
9
5.63 +/- 0.33
2 x Intel Xeon Gold 6346
69th
3
5.39
2 x AMD EPYC 7373X 16-Core
68th
4
5.22 +/- 0.03
AMD EPYC 7713P 64-Core
67th
6
5.12 +/- 0.03
Intel Xeon Gold 6421N
67th
5
5.04 +/- 0.41
AMD EPYC 7R13 48-Core
65th
7
4.70 +/- 0.05
ARMv8 Neoverse-N1 128-Core
64th
6
4.67 +/- 0.02
AMD EPYC 8534PN 32-Core
63rd
3
4.25 +/- 0.03
AMD EPYC 7543 32-Core
61st
3
4.00
AMD Ryzen Threadripper 3990X 64-Core
60th
5
3.79 +/- 0.10
AMD EPYC 7513 32-Core
58th
7
3.55 +/- 0.01
AMD Ryzen Threadripper 3970X 32-Core
57th
5
3.36 +/- 0.13
AMD Ryzen Threadripper PRO 5965WX 24-Cores
56th
9
3.20 +/- 0.41
AMD EPYC 7413 24-Core
56th
3
3.01
AMD Ryzen 9 7950X3D 16-Core
52nd
23
2.61 +/- 0.10
Median
50th
2.60
AMD Ryzen 9 7950X 16-Core
49th
19
2.56 +/- 0.08
AMD Ryzen Threadripper 3960X 24-Core
48th
3
2.43 +/- 0.01
ARMv8 Neoverse-V1 32-Core
44th
9
2.26 +/- 0.06
AMD Ryzen 9 7900X3D 12-Core
43rd
18
2.20 +/- 0.10
AMD Ryzen 9 7900X 12-Core
43rd
22
2.18 +/- 0.08
AMD Ryzen 9 7900 12-Core
38th
21
1.96 +/- 0.06
AMD Ryzen 7 7800X3D 8-Core
35th
13
1.72 +/- 0.05
Intel Core i9-10980XE
33rd
4
1.58 +/- 0.01
AMD Ryzen 7 7700X 8-Core
31st
15
1.49 +/- 0.05
AMD Ryzen 7 7700 8-Core
29th
8
1.42 +/- 0.04
AMD Ryzen 9 5950X 16-Core
29th
11
1.42 +/- 0.17
AMD Ryzen 7 5800X3D 8-Core
27th
13
1.27 +/- 0.05
AMD EPYC 7F32 8-Core
27th
4
1.26 +/- 0.02
Low-Tier
25th
< 1.23
AMD Ryzen 9 3900XT 12-Core
23rd
4
1.15
Intel Core i9-14900K
22nd
9
1.15
AMD Ryzen 5 7600X 6-Core
22nd
13
1.14 +/- 0.04
Intel Core i9-13900K
21st
15
1.14 +/- 0.04
AMD Ryzen 7 5800X 8-Core
18th
4
1.04 +/- 0.09
Intel Core i5-12600K
17th
3
0.97 +/- 0.01
AMD Ryzen 7 6800U
17th
3
0.87
Intel Core i5-12400
16th
3
0.85
AMD Ryzen 7 3800XT 8-Core
16th
3
0.81
Intel Xeon E-2388G
14th
7
0.79
Intel Core i7-5960X
14th
3
0.79
Intel Core i7-8700K
13th
3
0.78
AMD Ryzen 7 PRO 6850U
13th
6
0.78 +/- 0.03
AMD Ryzen 9 5900HX
11th
3
0.67
AMD Ryzen 7 PRO 5850U
10th
4
0.67 +/- 0.01
Intel Xeon E-2336
10th
7
0.67
Intel Core i7-10700T
9th
3
0.64
AMD Ryzen 5 5500U
8th
4
0.60
Intel Core i7-1185G7
7th
3
0.56
Intel Core i7-1165G7
6th
3
0.53
AMD Ryzen 7 4700U
5th
4
0.52
AMD Ryzen 5 4500U
5th
3
0.48
AMD Ryzen 7 4800U
4th
3
0.43
Intel Core i7-1065G7
3rd
3
0.36 +/- 0.02
Apple M2
3rd
4
0.22
ARMv8 Cortex-A72 4-Core
2nd
3
0.06
OpenBenchmarking.orgDistribution Of Public Results - Implementation: MPI CPU - Input: water_GMX50_bare697 Results Range From 0 To 23 Ns Per Day2468101214161820222460120180240300

Based on OpenBenchmarking.org data, the selected test / test configuration (GROMACS 2023 - Implementation: MPI CPU - Input: water_GMX50_bare) has an average run-time of 6 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-Time918273645Min: 1 / Avg: 5.33 / Max: 44

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: 0.06 / 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_bare4681216326412848121620

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
aarch64
ARMv8 Cortex-A53 24-Core, ARMv8 Cortex-A72 4-Core, ARMv8 Neoverse-N1, ARMv8 Neoverse-N1 128-Core, ARMv8 Neoverse-V1, ARMv8 Neoverse-V1 32-Core, Apple M2

Recent Test Results

OpenBenchmarking.org Results Compare

4 Systems - 153 Benchmark Results

Intel Xeon Gold 6414U - Supermicro X13SEW-F v1.02 - 256GB

Rocky Linux 9.2 - 5.14.0-284.11.1.el9_2.x86_64 - GCC 11.3.1 20221121

1 System - 566 Benchmark Results

ARMv8 Cortex-A72 - BCM2835 Raspberry Pi 4 Model B Rev 1.5 - Broadcom BCM2711

Arch Linux ARM - 6.1.58-2-rpi-ARCH - GCC 12.1.0 + Clang 16.0.6

2 Systems - 452 Benchmark Results

ARMv8 Neoverse-N1 - GIGABYTE MP32-AR2-00 v01000100 - Ampere Computing LLC Altra PCI Root Complex A

Ubuntu 22.04 - 5.15.0-89-generic - 1.3.238

1 System - 484 Benchmark Results

ARMv8 Neoverse-N1 - GIGABYTE MP32-AR2-00 v01000100 - Ampere Computing LLC Device e100

Ubuntu 20.04 - 5.4.0-167-generic - 1.1.182

2 Systems - 8 Benchmark Results

Intel Xeon w9-3495X - ASUS Pro WS W790E-SAGE SE - Intel Device 7aa7

Ubuntu 22.04 - 6.3.0-060300-generic - GNOME Shell 42.9

1 System - 4 Benchmark Results

Intel Xeon w9-3495X - ASUS Pro WS W790E-SAGE SE - Intel Device 7aa7

Ubuntu 22.04 - 6.3.0-060300-generic - GNOME Shell 42.9

4 Systems - 415 Benchmark Results

AMD Ryzen Threadripper 7980X 64-Cores - ASUS Pro WS TRX50-SAGE WIFI - AMD Device 14a4

Ubuntu 23.10 - 6.5.0-9-generic - GNOME Shell 45.0

4 Systems - 106 Benchmark Results

AMD EPYC 7B12 - Google Compute Engine n2d-standard-8 - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 6.2.0-1018-gcp - 1.3.238

4 Systems - 106 Benchmark Results

AMD EPYC 7B12 - Google Compute Engine n2d-standard-8 - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 6.2.0-1018-gcp - 1.3.238

4 Systems - 106 Benchmark Results

Intel Xeon Platinum 8481C - Google Compute Engine c3-standard-8 - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 6.2.0-1018-gcp - 1.3.238

3 Systems - 106 Benchmark Results

AMD EPYC 9B14 - Google Compute Engine c3d-standard-8 - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 6.2.0-1018-gcp - 1.3.238

2 Systems - 106 Benchmark Results

AMD EPYC 9B14 - Google Compute Engine c3d-standard-8 - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 6.2.0-1018-gcp - 1.3.238

1 System - 1 Benchmark Result

AMD EPYC 7R13 48-Core - Supermicro H12SSL-I v1.02 - AMD Starship

EndeavourOS rolling - 6.6.1-zen1-1-zen - Xfce 4.18

1 System - 1 Benchmark Result

AMD EPYC 7R13 48-Core - Supermicro H12SSL-I v1.02 - AMD Starship

EndeavourOS rolling - 6.6.1-zen1-1-zen - Xfce 4.18

1 System - 1 Benchmark Result

AMD EPYC 7R13 48-Core - Supermicro H12SSL-I v1.02 - AMD Starship

EndeavourOS rolling - 6.6.1-zen1-1-zen - Xfce 4.18

Most Popular Test Results

OpenBenchmarking.org Results Compare

5 Systems - 396 Benchmark Results

AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 23.04 - 6.2.0-060200rc8daily20230213-generic - GNOME Shell 43.2

5 Systems - 10 Benchmark Results

2 x AMD EPYC 9654 96-Core - AMD Titanite_4G - AMD Device 14a4

Ubuntu 22.10 - 6.2.0-rc3-phx-tip-x86-cpu - GNOME Shell 43.1

2 Systems - 201 Benchmark Results

AMD Ryzen 7 5800X3D 8-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 22.04 - 5.17.0-1019-oem - GNOME Shell 42.2

3 Systems - 151 Benchmark Results

Intel Core i7-10700T - Logic Supply RXM-181 - Intel Comet Lake PCH

Ubuntu 22.04 - 5.15.0-56-generic - GNOME Shell 42.2

2 Systems - 111 Benchmark Results

AMD Ryzen 7 6800U - System76 Pangolin - AMD Device 14b5

Pop 22.04 - 6.2.6-76060206-generic - GNOME Shell 42.5

2 Systems - 328 Benchmark Results

AMD Ryzen 9 3900XT 12-Core - MSI MEG X570 GODLIKE - AMD Starship

Ubuntu 22.04 - 5.15.0-53-generic - GNOME Shell 42.2

3 Systems - 231 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Ice Lake IEH

Ubuntu 22.10 - 6.2.0-rc5-phx-dodt - GNOME Shell 43.0

2 Systems - 608 Benchmark Results

5 Systems - 203 Benchmark Results

2 x AMD EPYC 9654 96-Core - AMD Titanite_4G - AMD Device 14a4

Ubuntu 23.04 - 5.19.0-21-generic - GNOME Shell 43.1

3 Systems - 191 Benchmark Results

Intel Core i5-12600K - ASUS PRIME Z690-P WIFI D4 - Intel Device 7aa7

Ubuntu 22.04 - 5.19.0-051900rc6daily20220716-generic - GNOME Shell 42.1
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