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


Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsGROMACS Popularity Statisticspts/gromacs2018.122019.012019.022019.032019.042019.052019.062019.072019.082019.092019.102019.112019.122020.012020.022020.032020.042020.052020.062020.072020.082020.092020.102020.112020.122021.012021.022021.032021.042021.052021.062021.072021.082021.092021.102021.112021.122022.012022.022022.032022.042022.052022.062022.073K6K9K12K15K
* 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)
100th
11
10.94 +/- 0.10
92nd
5
7.36 +/- 0.08
88th
4
4.04 +/- 0.05
84th
4
3.38 +/- 0.01
77th
3
1.86 +/- 0.01
Mid-Tier
75th
< 1.81
75th
3
1.77 +/- 0.03
73rd
3
1.54 +/- 0.04
68th
4
1.32 +/- 0.01
62nd
4
1.17 +/- 0.09
59th
4
1.12 +/- 0.05
53rd
3
1.00 +/- 0.01
Median
50th
0.99
48th
7
0.94 +/- 0.09
45th
3
0.85 +/- 0.01
43rd
4
0.84 +/- 0.01
41st
3
0.80 +/- 0.02
38th
3
0.77 +/- 0.01
34th
3
0.66 +/- 0.01
28th
5
0.59 +/- 0.01
26th
5
0.56 +/- 0.01
Low-Tier
25th
< 0.56
22nd
3
0.55 +/- 0.01
21st
11
0.53 +/- 0.06
21st
3
0.53 +/- 0.01
17th
3
0.51 +/- 0.01
13th
4
0.47 +/- 0.01
5th
5
0.19
OpenBenchmarking.orgDistribution Of Public Results - Implementation: MPI CPU - Input: water_GMX50_bare189 Results Range From 0 To 12 Ns Per Day012345678910111220406080100

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.

OpenBenchmarking.orgMinutesTime Required To Complete BenchmarkImplementation: MPI CPU - Input: water_GMX50_bareRun-Time918273645Min: 1 / Avg: 11.65 / Max: 42

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_bare481216641.753.55.2578.75

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

Recent Test Results

OpenBenchmarking.org Results Compare

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

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

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

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

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

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

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

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

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

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

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

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

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

Most Popular Test Results

OpenBenchmarking.org Results Compare

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

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

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

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

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

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

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

2 Systems - 32 Benchmark Results

AMD Ryzen 5 5500U - NB01 NL5xNU - AMD Renoir Root Complex

Ubuntu 20.04 - 5.15.0-10025-tuxedo - Budgie

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

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

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

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

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

Find More Test Results