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, 6 Seconds

Average Run Time

38 Minutes, 19 Seconds

Test Dependencies

C/C++ Compiler Toolchain + CMake + OpenMPI

Accolades

30k+ Downloads

Supported Platforms

* 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 3 July 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

Molecular Dynamics

HPC - High Performance Computing

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 225 public results since 19 May 2022 with the latest data as of 2 July 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)

2 x AMD EPYC 7773X 64-Core

100th

10.94 ^{+/- 0.10}

2 x Intel Xeon Platinum 8380

96th

9.22 ^{+/- 0.28}

2 x AMD EPYC 75F3 32-Core

92nd

7.36 ^{+/- 0.08}

2 x Intel Xeon Platinum 8280

90th

5.83 ^{+/- 0.02}

2 x AMD EPYC 7601 32-Core

88th

4.04 ^{+/- 0.05}

AMD Ryzen Threadripper 3990X 64-Core

86th

3.68 ^{+/- 0.01}

2 x Intel Xeon Gold 5220R

84th

3.38 ^{+/- 0.01}

AMD Ryzen Threadripper 3970X 32-Core

83rd

3.25 ^{+/- 0.01}

AMD Ryzen Threadripper 3960X 24-Core

81st

2.52

Intel Xeon Gold 6226R

77th

1.86 ^{+/- 0.01}

Mid-Tier

75th

< 1.81

Intel Core i9-12900K

75th

1.77 ^{+/- 0.03}

Intel Core i9-10980XE

73rd

1.54 ^{+/- 0.04}

AMD Ryzen Threadripper 2970WX 24-Core

70th

1.44 ^{+/- 0.02}

Intel Xeon Silver 4216

68th

1.32 ^{+/- 0.01}

AMD Ryzen 9 5900X 12-Core

65th

1.26

AMD Ryzen 9 3950X 16-Core

63rd

1.22

AMD EPYC 7F32 8-Core

62nd

1.17 ^{+/- 0.09}

AMD Ryzen 9 3900XT 12-Core

59th

1.12 ^{+/- 0.05}

AMD Ryzen 9 3900X 12-Core

58th

1.12

Intel Core i9-11900K

53rd

1.00 ^{+/- 0.01}

Median

50th

0.99

Intel Core i5-12600K

50th

0.99

Intel Core i5-12400

48th

0.94 ^{+/- 0.09}

Intel Core i9-9900K

45th

0.85 ^{+/- 0.01}

AMD Ryzen 7 5700G

43rd

0.84 ^{+/- 0.01}

Intel Core i7-5960X

41st

0.80 ^{+/- 0.02}

Intel Core i7-8700K

38th

0.77 ^{+/- 0.01}

AMD Ryzen 7 3700X 8-Core

38th

0.77

AMD Ryzen 7 PRO 5850U

35th

0.67

AMD Ryzen 9 5900HX

34th

0.66 ^{+/- 0.01}

Intel Core i7-10700T

33rd

0.62

Intel Core i3-12100

28th

0.59 ^{+/- 0.01}

Intel Core i7-1185G7

26th

0.56 ^{+/- 0.01}

Low-Tier

25th

< 0.56

AMD Ryzen 3 3300X 4-Core

23rd

0.55

Intel Xeon E3-1275 v6

22nd

0.55 ^{+/- 0.01}

AMD Ryzen 5 5500U

21st

0.53 ^{+/- 0.06}

Intel Core i7-1165G7

21st

0.53 ^{+/- 0.01}

Intel Core i3-8100

18th

0.51

Intel Core i3-10100

17th

0.51 ^{+/- 0.01}

AMD Ryzen 5 4500U

13th

0.47 ^{+/- 0.01}

Intel Core i3-7100

9th

0.31

Intel Core i3-1005G1

6th

0.21

Apple M1

5th

0.19

AMD Ryzen 3 3200U

2nd

0.11

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 12 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.

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.

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-A72, ARMv8 Neoverse-N1, ARMv8 Neoverse-V1, Ampere ARMv8 Neoverse-N1 160-Core, Apple M1

june skylake 3 Systems - 110 Benchmark Results	Intel Xeon E3-1280 v5 - MSI Z170A SLI PLUS - Intel Xeon E3-1200 v5 Ubuntu 20.04 - 5.13.0-051300-generic - GNOME Shell 3.36.9
epyc extra Featured Processor Comparison	AMD EPYC 7773X 64-Core - AMD EPYC 7763 64-Core
Laptop Benchmarks 1 System - 323 Benchmark Results	AMD Ryzen 7 PRO 5850U - HP 8A78 - AMD Renoir Ubuntu 22.04 - 5.18.8-051808-generic - GNOME Shell 42.2
AMD EPYC Milan-X Mid-2022 Refresh Performance Benchmarks 2 Systems - 577 Benchmark Results	2 x AMD EPYC 7773X 64-Core - AMD DAYTONA_X - AMD Starship Ubuntu 22.04 - 5.19.0-051900rc4daily20220628-generic - GNOME Shell 42.2
3960x-june-2022 4 Systems - 157 Benchmark Results	AMD Ryzen Threadripper 3960X 24-Core - MSI Creator TRX40 - AMD Starship Ubuntu 20.04 - 5.12.0-051200rc2daily20210307-generic - GNOME Shell 3.36.4
10700T Summer 2022 4 Systems - 166 Benchmark Results	Intel Core i7-10700T - Logic Supply RXM-181 - Intel Comet Lake PCH Ubuntu 22.04 - 5.15.0-27-generic - GNOME Shell 42.2
3700X June 2022 AMD 3 Systems - 138 Benchmark Results	AMD Ryzen 7 3700X 8-Core - Gigabyte A320M-S2H-CF - AMD Starship Ubuntu 20.04 - 5.13.0-39-generic - GNOME Shell 3.36.4
june 3 Systems - 143 Benchmark Results	Intel Core i7-8700K - ASUS TUF Z370-PLUS GAMING - Intel 8th Gen Core Ubuntu 20.04 - 5.9.0-050900rc6daily20200923-generic - GNOME Shell 3.36.4
AMD EPYC Milan-X Mid-2022 Refresh Benchmarks 1 System - 643 Benchmark Results	2 x AMD EPYC 7773X 64-Core - AMD DAYTONA_X - AMD Starship Ubuntu 22.04 - 5.19.0-051900rc4daily20220628-generic - GNOME Shell 42.2
Core i3 7100 Ubuntu 22.04 3 Systems - 45 Benchmark Results	Intel Core i3-7100 - Gigabyte B250M-DS3H-CF - Intel Xeon E3-1200 v6 Ubuntu 22.04 - 5.15.0-40-generic - GNOME Shell 42.2
1275-june-2022 3 Systems - 200 Benchmark Results	Intel Xeon E3-1275 v6 - ASUS P10S-M WS - Intel Xeon E3-1200 v6 Ubuntu 20.04 - 5.9.0-050900rc8daily20201007-generic - X Server 1.20.8
dual-7551-gromacs-bench-22-06-29-channel-tdp-250w-setting-smt-on 1 System - 1 Benchmark Result	2 x AMD EPYC 7551 32-Core - Supermicro H11DSi-NT v2.00 - AMD 17h Ubuntu 22.04 - 5.15.0-40-generic - GNOME Shell 42.2
Core i5 12600K Kernel Build Optimizations Featured Kernel Comparison	5.19.0-rc4-phx-two - 5.19.0-rc4-phx-three
zen1 epyc 4 Systems - 119 Benchmark Results	2 x AMD EPYC 7601 32-Core - Dell 02MJ3T - AMD 17h Ubuntu 22.04 - 5.15.0-40-generic - GNOME Shell 42.2
3950X Summer 2022 3 Systems - 144 Benchmark Results	AMD Ryzen 9 3950X 16-Core - ASUS ROG CROSSHAIR VII HERO - AMD Starship Ubuntu 20.04 - 5.11.0-43-generic - GNOME Shell 3.36.4

Amazon EC2 Graviton3 Benchmark Comparison 5 Systems - 94 Benchmark Results	ARMv8 Neoverse-N1 - Amazon EC2 c6g.4xlarge - Amazon Device 0200 Ubuntu 22.04 - 5.15.0-1004-aws - GCC 11.2.0
cascade may Featured Vulkan Comparison	Intel Core i9-10980XE - ASRock X299 Steel Legend - Intel Sky Lake-E DMI3 Registers Ubuntu 22.04 - 5.15.0-23-generic - GNOME Shell 40.5
cascade lake summer 2022 3 Systems - 178 Benchmark Results	2 x Intel Xeon Platinum 8280 - GIGABYTE MD61-SC2-00 v01000100 - Intel Sky Lake-E DMI3 Registers Ubuntu 21.04 - 5.11.0-40-generic - GNOME Shell 3.38.4
xeon june 2 Systems - 86 Benchmark Results	Intel Xeon Silver 4216 - TYAN S7100AG2NR - Intel Sky Lake-E DMI3 Registers Debian 11 - 5.10.0-10-amd64 - X Server
Amazon EC2 c7g.4xlarge Graviton3 4 Systems - 102 Benchmark Results	Apple M1 - Apple MacBook Air - 16GB macOS 12.4 - 21.5.0 - GCC 13.0.0 + Clang 13.0.0
Neoverse-V1 Compiler Tests 2 Systems - 121 Benchmark Results	ARMv8 Neoverse-V1 - Amazon EC2 c7g.8xlarge - Amazon Device 0200 Ubuntu 22.04 - 5.15.0-1004-aws - GCC 12.0.0 20220117
epyc-7f32-may 3 Systems - 45 Benchmark Results	AMD EPYC 7F32 8-Core - ASRockRack EPYCD8 - AMD Starship Debian 11 - 5.10.0-10-amd64 - GNOME Shell 3.38.6
EPYC Milan-X Linux 5.19 Benchmarks Featured Kernel Comparison	2 x AMD EPYC 7773X 64-Core - AMD DAYTONA_X - AMD Starship Ubuntu 21.04 - 5.17.0-051700-generic - GNOME Shell 3.38.4
june 5960X 3 Systems - 86 Benchmark Results	Intel Core i7-5960X - Gigabyte X99-UD4-CF - Intel Xeon E7 v3 Debian 11 - 5.10.0-10-amd64 - 1.0.2
tuxedo extra 2 Systems - 32 Benchmark Results	AMD Ryzen 5 5500U - NB01 NL5xNU - AMD Renoir Root Complex Ubuntu 20.04 - 5.15.0-10025-tuxedo - Budgie
new tests eo may epyc 4 Systems - 71 Benchmark Results	2 x AMD EPYC 7773X 64-Core - AMD DAYTONA_X - AMD Starship Ubuntu 21.04 - 5.18.0-clocksource-patch - GNOME Shell 3.38.4
tigerlake-renaissance 4 Systems - 12 Benchmark Results	Intel Core i7-1165G7 - Dell 0GG9PT - Intel Tiger Lake-LP Ubuntu 21.10 - 5.13.0-40-generic - GNOME Shell 40.5
gromacs ren 3 Systems - 18 Benchmark Results	AMD Ryzen Threadripper 3990X 64-Core - Gigabyte TRX40 AORUS PRO WIFI - AMD Starship Pop 22.04 - 5.17.5-76051705-generic - GNOME Shell 42.0
tr 3970X May 4 Systems - 48 Benchmark Results	AMD Ryzen Threadripper 3970X 32-Core - ASUS ROG ZENITH II EXTREME - AMD Starship Ubuntu 21.10 - 5.15.5-051505-generic - GNOME Shell 40.5
4500u may 4 Systems - 45 Benchmark Results	AMD Ryzen 5 4500U - LENOVO LNVNB161216 - AMD Renoir Ubuntu 21.10 - 5.16.0-051600rc8daily20220108-generic - GNOME Shell 40.5