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

5 May 2021

Test Maintainer

Andrew Schofield 

Test Type

Processor

Average Install Time

1 Minute, 56 Seconds

Average Run Time

24 Minutes, 20 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

150k+ Downloads

Supported Platforms


Public Result Uploads *Reported Test Completions **Reported Installs **Test Profile Page Views ***OpenBenchmarking.orgEventsTimed MrBayes Analysis Popularity Statisticspts/mrbayes2010.122011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.042021.086K12K18K24K30K
* 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 22 September 2021.

Revision History

pts/mrbayes-1.5.0   [View Source]   Wed, 05 May 2021 14:34:45 GMT
Increase ngen size.

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

HPC - High Performance Computing

MPI Benchmarks

Bioinformatics


Performance Metrics

Analyze Test Configuration:

Timed MrBayes Analysis 3.2.7

Primate Phylogeny Analysis

OpenBenchmarking.org metrics for this test profile configuration based on 360 public results since 5 May 2021 with the latest data as of 10 September 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
# Compatible Public Results
Seconds (Average)
98th
44
82 +/- 10
80th
3
105 +/- 1
Mid-Tier
75th
> 112
74th
3
112 +/- 1
74th
3
115 +/- 1
65th
3
131 +/- 3
64th
4
136 +/- 5
63rd
7
137 +/- 6
57th
6
141 +/- 1
54th
5
143 +/- 8
53rd
3
144 +/- 2
Median
50th
145
48th
3
151 +/- 2
46th
6
154 +/- 2
42nd
6
156 +/- 1
40th
4
158 +/- 1
39th
8
160 +/- 16
35th
3
173 +/- 1
33rd
3
176 +/- 4
30th
3
178 +/- 1
28th
3
179 +/- 1
28th
4
179 +/- 3
Low-Tier
25th
> 184
25th
6
184 +/- 2
23rd
3
189 +/- 5
17th
4
196 +/- 6
16th
5
202 +/- 10
16th
4
205 +/- 6
12th
3
217 +/- 4
11th
4
218 +/- 2
5th
3
328 +/- 3
OpenBenchmarking.orgDistribution Of Public Results - Primate Phylogeny Analysis360 Results Range From 46 To 4425 Seconds4613422231039848657466275083892610141102119012781366145415421630171818061894198220702158224623342422251025982686277428622950303831263214330233903478356636543742383039184006409441824270435844464080120160200

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 8 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-Time918273645Min: 2 / Avg: 7.4 / Max: 42

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.3%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsPrimate Phylogeny AnalysisDeviation246810Min: 0 / Avg: 0.29 / Max: 3

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.

AMDIntelOpenBenchmarking.orgRelative Core Scaling To BaseTimed MrBayes Analysis CPU Core ScalingPrimate Phylogeny Analysis46812160.74681.49362.24042.98723.734

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 VINSERTF128 VBROADCASTSD VBROADCASTSS VPERM2F128 VPERMILPD VBROADCASTF128 VMASKMOVPS
Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).

 
VEXTRACTI128 VPBROADCASTQ VPBROADCASTD VINSERTI128 VPERMQ VPERM2I128 VPERMD VPMASKMOVQ VPMASKMOVD VPERMPD VPGATHERQD VPGATHERDD VPGATHERQQ VGATHERQPD VPBLENDD VGATHERDPD
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: 10 May 2021

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

Recent Test Results

OpenBenchmarking.org Results Compare

12 Systems - 121 Benchmark Results

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6 Systems - 133 Benchmark Results

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AMD Ryzen 3 PRO 4350G - ASRock B450M Pro4 - AMD Renoir Root Complex

Clear Linux OS 34550 - 5.10.32-1035.native - GNOME Shell 40.0

1 System - 1 Benchmark Result

AMD Ryzen 3 3200G - GALAX A320M DRAGON GENERAL Ver1.0 - AMD Raven

Ubuntu 21.10 - 5.13.0-14-generic - GNOME Shell 40.2

1 System - 17 Benchmark Results

Intel Core i3-7100 - FUJITSU D3433-S2 - Intel Xeon E3-1200 v6

Ubuntu 21.04 - 5.11.0-25-generic - GCC 10.3.0

1 System - 1 Benchmark Result

Intel Xeon W3503 - LENOVO - Intel 5520

Arch Linux - 5.12.15-arch1-1 - X Server 1.20.12

1 System - 1 Benchmark Result

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Arch Linux - 5.13.6-arch1-1 - X Server 1.20.13

1 System - 113 Benchmark Results

4 x Intel Xeon E5-4657L v2 - Dell 04K5X5 - Intel Xeon E7 v2

Ubuntu 20.04 - 5.8.0-59-generic - GNOME Shell 3.36.9

4 Systems - 51 Benchmark Results

AMD EPYC 7J13 64-Core - (1.4.1 BIOS) - 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16384 + 16128 0MHz

Microsoft Windows Server 2019 Standard Build 17763 - 10.0 - 9.25.36.24

1 System - 179 Benchmark Results

AMD Ryzen Threadripper 1920X 12-Core - Gigabyte X399 AORUS PRO-CF - AMD 17h

Ubuntu 20.04 - 5.8.0-63-generic - GNOME Shell 3.36.9

3 Systems - 253 Benchmark Results

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Ubuntu 20.04 - 5.9.0-050900rc7daily20201003-generic - GNOME Shell 3.36.9

3 Systems - 272 Benchmark Results

4 x Intel Xeon Gold 6254 - HPE ProLiant DL560 Gen10 - Intel Sky Lake-E DMI3 Registers

RedHatEnterpriseServer 7.9 - 3.10.0-1160.31.1.el7.x86_64 - GNOME Shell 3.28.3

1 System - 17 Benchmark Results

Intel Pentium G2030 - American Megatrends 4.6.5 - Intel Xeon E3-1200 v2

Ubuntu 21.04 - 5.11.0-22-generic - GCC 10.3.0

1 System - 31 Benchmark Results

ARMv8 Neoverse-N1 - GIGABYTE MP32-AR0-00 v01000100 - Ampere Computing LLC Device e100

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1 System - 130 Benchmark Results

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Microsoft Windows 10 Pro Build 19042 - 10.0 - 27.20.100.9664

Most Popular Test Results

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3 Systems - 37 Benchmark Results

Intel Core i5-10600K - ASUS PRIME Z490M-PLUS - Intel Comet Lake PCH

Ubuntu 20.10 - 5.11.0-051100rc2daily20210106-generic - GNOME Shell 3.38.1

6 Systems - 36 Benchmark Results

AMD Ryzen 9 3950X 16-Core - ASUS ROG CROSSHAIR VII HERO - AMD Starship

Ubuntu 20.04 - 5.9.0-050900rc6daily20200922-generic - GNOME Shell 3.36.4

4 Systems - 82 Benchmark Results

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Ubuntu 20.04 - 5.9.0-050900rc7daily20200929-generic - GNOME Shell 3.36.4

3 Systems - 117 Benchmark Results

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Ubuntu 20.10 - 5.8.0-48-generic - GNOME Shell 3.38.1

3 Systems - 178 Benchmark Results

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4 Systems - 172 Benchmark Results

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Ubuntu 20.04 - 5.9.0-050900rc8daily20201007-generic - X Server 1.20.8

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Ubuntu 20.04 - 5.11.6-051106-generic - GNOME Shell 3.36.4

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4 Systems - 11 Benchmark Results

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3 Systems - 164 Benchmark Results

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Ubuntu 20.04 - 5.9.0-050900rc6daily20200926-generic - GNOME Shell 3.36.2

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AMD Ryzen 7 3700X 8-Core - Gigabyte A320M-S2H-CF - AMD Starship

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