Timed MrBayes Analysis

This test performs a bayesian analysis of a set of primate genome sequences in order to estimate their phylogeny.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark mrbayes.

Project Site

github.com

Test Created

6 December 2010

Last Updated

11 October 2019

Test Maintainer

Andrew Schofield 

Test Type

Processor

Average Install Time

1 Minute, 52 Seconds

Average Run Time

12 Minutes, 41 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

150k+ Downloads

Supported Platforms


Public Result UploadsTest Completions*Reported Installs*OpenBenchmarking.orgEventsTimed MrBayes Analysis Popularity Statisticspts/mrbayes2011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.044K8K12K16K20K
* 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 Sat, 10 Apr 2021 06:08:42 GMT.

Revision History

pts/mrbayes-1.4.0   [View Source]   Fri, 11 Oct 2019 11:45:36 GMT
Update against upstream, add Windows support.

pts/mrbayes-1.3.2   [View Source]   Sun, 26 Aug 2018 17:06:48 GMT
Update download links.

pts/mrbayes-1.3.1   [View Source]   Wed, 07 Feb 2018 13:41:43 GMT
Use built-in mpich/mpi, add SHA256 for download file.

pts/mrbayes-1.3.0   [View Source]   Sat, 09 Sep 2017 14:07:59 GMT
Fix for higher core count CPUs

pts/mrbayes-1.2.0   [View Source]   Mon, 06 Dec 2010 14:57:53 GMT
Initial import into OpenBenchmarking.org

Suites Using This Test

C/C++ Compiler Tests

CPU Massive

Scientific Computing

MPI Benchmarks

Bioinformatics

HPC - High Performance Computing


Performance Metrics

Analyze Test Configuration:

Timed MrBayes Analysis 3.2.7

Primate Phylogeny Analysis

OpenBenchmarking.org metrics for this test profile configuration based on 1,175 public results since 11 October 2019 with the latest data as of 10 April 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
Seconds (Average)
96th
13
58 +/- 2
91st
26
64 +/- 1
77th
10
74 +/- 2
Mid-Tier
75th
> 77
75th
4
79 +/- 1
68th
4
87 +/- 2
65th
3
90 +/- 13
64th
10
91 +/- 12
56th
11
99 +/- 12
53rd
25
103 +/- 2
51st
3
104 +/- 1
Median
50th
105
48th
5
107 +/- 1
46th
20
109 +/- 5
41st
16
112 +/- 6
41st
13
113 +/- 4
37th
5
118 +/- 16
36th
10
121 +/- 16
36th
7
121 +/- 11
Low-Tier
25th
> 140
22nd
5
147 +/- 15
22nd
3
149 +/- 20
21st
7
150 +/- 4
21st
5
156 +/- 15
11th
4
243 +/- 35
OpenBenchmarking.orgDistribution Of Public Results - Primate Phylogeny Analysis1158 Results Range From 45 To 18923 Seconds454238011179155719352313269130693447382542034581495953375715609364716849722776057983836187399117949598731025110629110071138511763121411251912897132751365314031144091478715165155431592116299166771705517433178111818918567189452004006008001000

Based on OpenBenchmarking.org data, the selected test / test configuration (Timed MrBayes Analysis 3.2.7 - Primate Phylogeny Analysis) has an average run-time of 9 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 BenchmarkPrimate Phylogeny AnalysisRun-Time20406080100Min: 1 / Avg: 8.56 / Max: 119

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.5%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsPrimate Phylogeny AnalysisDeviation3691215Min: 0 / Avg: 0.5 / Max: 12

Does It Scale Well With Increasing Cores?

No, based on the automated analysis of the collected public benchmark data, this test / test settings does not 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 BaseTimed MrBayes Analysis CPU Core ScalingPrimate Phylogeny Analysis4812163248640.39790.79581.19371.59161.9895

Notable Instruction Set Usage

Notable instruction set extensions supported by this test, based on an automatic analysis by the Phoronix Test Suite / OpenBenchmarking.org analytics engine.

Instruction Set
Support
Instructions Detected
SSE 4.2 (SSE4_2)
Used by default on supported hardware.
Found on Intel processors since at least 2010.
Found on AMD processors since Bulldozer (2011).

 
POPCNT
Used by default on supported hardware.
Found on Intel processors since Sandy Bridge (2011).
Found on AMD processors since Bulldozer (2011).

 
VZEROUPPER VEXTRACTF128 VBROADCASTSD VINSERTF128 VPERMILPD VBROADCASTSS VPERM2F128 VMASKMOVPS
Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).

 
VEXTRACTI128 VPBROADCASTQ VINSERTI128 VPBROADCASTD VPERMQ VPERM2I128 VPERMD VPMASKMOVQ VPMASKMOVD VPERMPD VPGATHERQD VPGATHERDD VPGATHERQQ VGATHERQPD VPBLENDD VGATHERDPD VPBROADCASTB
FMA (FMA)
Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Bulldozer (2011).

 
VFMADD132PS VFMADD231PS
The test / benchmark does honor compiler flag changes.
Last automated analysis: 30 January 2021

This test profile binary relies on the shared libraries libm.so.6, libreadline.so.8, libc.so.6, libtinfo.so.6.

Recent Test Results

OpenBenchmarking.org Results Compare

12 Systems - 453 Benchmark Results

Intel Core i9-11900K - ASUS ROG MAXIMUS XIII HERO - Intel Tiger Lake-H

Ubuntu 21.04 - 5.12.0-051200rc3daily20210315-generic - GNOME Shell 3.38.3

1 System - 4 Benchmark Results

AMD Ryzen Threadripper 3970X 32-Core - ASRock TRX40 Creator - AMD Starship

Debian 10 - 4.19.0-16-amd64 - GNOME Shell 3.30.2

1 System - 115 Benchmark Results

Intel Xeon E3-1225 v6 - (2.002 BIOS) - Intel Xeon E3-1200 v6

Ubuntu 20.04 - 5.4.0-70-generic - 1.2.145

1 System - 115 Benchmark Results

Intel Xeon E3-1225 v5 - INTEL H110 - Intel Xeon E3-1200 v5

Ubuntu 20.04 - 5.4.0-66-generic - 1.2.145

1 System - 105 Benchmark Results

Intel Core - Red Hat RHEL-AV - Intel 82G33

Debian 9.12 - 4.9.0-12-amd64 - GCC 6.3.0 20170516

1 System - 108 Benchmark Results

2 x Intel Xeon Gold 5218R - Supermicro X11DPX-T - Intel Device 2020

Ubuntu 16.04 - 4.15.0-140-generic - Unity 7.4.0

1 System - 212 Benchmark Results

Intel Core i5-8250U - LENOVO 20L7CTO1WW - Intel Xeon E3-1200 v6

Debian testing - 5.10.0-5-amd64 - GNOME Shell 3.38.4

9 Systems - 442 Benchmark Results

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

Ubuntu 21.04 - 5.12.0-051200rc3daily20210315-generic - GNOME Shell 3.38.3

1 System - 272 Benchmark Results

1 System - 272 Benchmark Results

1 System - 323 Benchmark Results

Intel Core i9-11900K - ASUS ROG MAXIMUS XIII HERO - Intel Tiger Lake-H

Ubuntu 21.04 - 5.12.0-051200rc3daily20210315-generic - GNOME Shell 3.38.3

Most Popular Test Results

OpenBenchmarking.org Results Compare

3 Systems - 268 Benchmark Results

Intel Core i5-2520M - HP 161C - Intel 2nd Generation Core DRAM

Ubuntu 18.04 - 4.18.0-20-generic - GNOME Shell 3.28.3

16 Systems - 119 Benchmark Results

2 x Intel Xeon Platinum 8280 - GIGABYTE MD61-SC2-00 v01000100 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.4.0-18-generic - GNOME Shell 3.36.0

11 Systems - 217 Benchmark Results

AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 20.04 - 5.9.0-050900-generic - GNOME Shell 3.36.4

8 Systems - 360 Benchmark Results

Intel Core i9-7980XE - ASUS PRIME X299-A - Intel Sky Lake-E DMI3 Registers

Ubuntu 19.10 - 5.4.0-999-generic - GNOME Shell 3.34.1

3 Systems - 301 Benchmark Results

Intel Core i5-4670 - MSI B85M-P33 - Intel 4th Gen Core DRAM

Ubuntu 20.04 - 5.4.0-40-generic - GNOME Shell 3.36.3

18 Systems - 115 Benchmark Results

Intel Core i9-7980XE - ASUS PRIME X299-A - Intel Sky Lake-E DMI3 Registers

Ubuntu 19.10 - 5.3.0-18-generic - GNOME Shell 3.34.1

3 Systems - 143 Benchmark Results

AMD EPYC 7742 64-Core - AMD DAYTONA_X - AMD Starship

Ubuntu 20.04 - 5.4.0-31-generic - GNOME Shell 3.36.1

3 Systems - 173 Benchmark Results

AMD Ryzen Threadripper 3970X 32-Core - 64GB - 931GB

Ubuntu 20.04 - 4.4.0-19041-Microsoft - GCC 9.3.0

2 Systems - 269 Benchmark Results

AMD Ryzen Threadripper 3990X 64-Core - System76 Thelio Major - AMD Starship

Ubuntu 20.04 - 5.4.0-29-generic - GNOME Shell 3.36.1

2 Systems - 150 Benchmark Results

AMD Ryzen 7 4700U - LENOVO LNVNB161216 - AMD Renoir Root Complex

Ubuntu 20.04 - 5.7.0-999-generic - GNOME Shell 3.36.1

Find More Test Results