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, 4 Seconds

Average Run Time

24 Minutes, 20 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

200k+ Downloads

Supported Platforms


Public Result Uploads *Reported Test Completions **Reported Installs **Test Profile Page Views ***OpenBenchmarking.orgEventsTimed MrBayes Analysis Popularity Statisticspts/mrbayes2010.122011.052011.102012.032012.082013.012013.062013.112014.042014.092015.022015.072015.122016.052016.102017.032017.082018.012018.062018.112019.042019.092020.022020.072020.122021.052021.102022.032022.082023.012023.062023.116K12K18K24K30K
* 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 3 December 2023.

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

HPC - High Performance Computing

CPU Massive

Scientific 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 1,007 public results since 5 May 2021 with the latest data as of 2 December 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
Seconds (Average)
91st
3
84 +/- 2
86th
4
91 +/- 3
76th
3
105 +/- 1
Mid-Tier
75th
> 105
71st
14
112 +/- 3
71st
3
112 +/- 1
70th
3
115 +/- 1
65th
4
125 +/- 1
63rd
3
128 +/- 1
60th
17
133 +/- 8
59th
4
136 +/- 5
59th
7
137 +/- 6
56th
6
140 +/- 3
54th
6
141 +/- 1
53rd
5
143 +/- 8
53rd
3
143 +/- 5
52nd
3
144 +/- 2
Median
50th
145
49th
8
148 +/- 12
48th
3
151 +/- 2
44th
6
156 +/- 1
39th
4
165 +/- 4
35th
3
173 +/- 1
33rd
3
176 +/- 4
32nd
3
178 +/- 1
31st
3
179 +/- 1
31st
4
179 +/- 3
30th
6
184 +/- 2
27th
3
192 +/- 2
Low-Tier
25th
> 194
25th
4
196 +/- 6
25th
6
196 +/- 22
24th
5
202 +/- 10
21st
3
217 +/- 4
21st
4
218 +/- 2
18th
5
242 +/- 2
15th
3
302 +/- 1
13th
3
328 +/- 3
8th
6
495 +/- 7
8th
5
537 +/- 6
7th
3
572 +/- 7
OpenBenchmarking.orgDistribution Of Public Results - Primate Phylogeny Analysis1006 Results Range From 46 To 4868 Seconds4614324033743453162872582291910161113121013071404150115981695179218891986208321802277237424712568266527622859295630533150324733443441353836353732382939264023412042174314441145084605470247994896100200300400500

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 13 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-Time1632486480Min: 2 / Avg: 12.89 / Max: 82

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 AnalysisDeviation48121620Min: 0 / Avg: 0.5 / Max: 14

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 Analysis46812162432641280.47920.95841.43761.91682.396

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 VBROADCASTSD VPERMILPD VBROADCASTSS VEXTRACTF128 VINSERTF128
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 VPERMD VPERM2I128 VPERMPD VPGATHERQD VPGATHERDD VPGATHERQQ VGATHERQPD VGATHERDPD VPBROADCASTB
Advanced Vector Extensions 512 (AVX512)
Used by default on supported hardware.
 
(ZMM REGISTER USE)
FMA (FMA)
Used by default on supported hardware.
Found on Intel processors since Haswell (2013).
Found on AMD processors since Bulldozer (2011).

 
VFMADD231PS
The test / benchmark does honor compiler flag changes.
Last automated analysis: 18 January 2022

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

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)
Itanium 64-bit
ia64
2 x Madison
ARMv7 32-bit
armv7l
ARMv7 Cortex-A72 4-Core
ARMv8 64-bit
arm64
Apple M1, Apple M1 Pro
DEC Alpha
alpha
Alpha
ARMv8 64-bit
aarch64
ARMv8, ARMv8 Cortex-A72, ARMv8 Cortex-A72 4-Core, ARMv8 Neoverse-N1, ARMv8 Neoverse-N1 160-Core, ARMv8 Neoverse-N1 80-Core, ARMv8 Neoverse-V1, Ampere ARMv8 Neoverse-N1 160-Core, Ampere ARMv8 Neoverse-N1 256-Core, Ampere Altra ARMv8 Neoverse-N1 160-Core, Ampere eMAG ARMv8 32-Core, Apple M2, Rockchip ARMv8 Cortex-A76 4-Core

Recent Test Results

OpenBenchmarking.org Results Compare

1 System - 7 Benchmark Results

Intel Core i5-13600K - MSI MPG Z690 EDGE WIFI - 2 x 16384 MB 6600MHz Corsair CMK32GX5M2X6600C32

Microsoft Windows 10 Pro Build 19045 - 10.0.19045.2251 - 537.42

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

1 System - 99 Benchmark Results

Intel Core i7-1370P - LENOVO 21HGS21V00 - 8 x 4096 MB 4800MHz H58G66BK7BX067

Microsoft Windows 10 Enterprise Build 19045 - 10.0.19045.3570 - 31.0.101.4575

13 Systems - 102 Benchmark Results

Intel Core i5-4690K - ASUS Z97-A-USB31 - Intel 4th Gen Core DRAM

ManjaroLinux 18.0.1 - 4.19.12-1-MANJARO - Xfce 4.13

17 Systems - 119 Benchmark Results

Intel Xeon Platinum 8375C - Supermicro X12DPi-N6 v1.00 - Intel Device 0998

Ubuntu 19.10 - 5.3.0-64-generic - GNOME Shell 3.34.1

1 System - 621 Benchmark Results

AMD Ryzen 7 PRO 4750G - LENOVO 318E - AMD Renoir

Arch Linux - 6.1.59-1-lts - GCC 13.2.1 20230801 + Clang 16.0.6

1 System - 1 Benchmark Result

2 x Intel Xeon E5-2680 v3 - Dell 0CN7X8 - Intel Xeon E7 v3

Ubuntu 22.04 - 5.15.0-82-generic - GNOME Shell 42.9

1 System - 1 Benchmark Result

2 x Intel Xeon E5-2680 v3 - Dell 0CN7X8 - Intel Xeon E7 v3

Ubuntu 22.04 - 5.15.0-82-generic - GNOME Shell 42.9

1 System - 591 Benchmark Results

Intel Core i7-4790 - ASUS H97M-PLUS - Intel 4th Gen Core DRAM

Arch Linux - 6.1.57-1-lts - GCC 13.2.1 20230801 + Clang 16.0.6

1 System - 598 Benchmark Results

Intel Core i7-4770 - Mouse H87M-S01 v1.0 - Intel 4th Gen Core DRAM

Arch Linux - 6.1.55-1-lts - GCC 13.2.1 20230801 + Clang 16.0.6

1 System - 12 Benchmark Results

Intel Core i5-4570 - Dell 04YP6J - Intel 4th Gen Core DRAM

ManjaroLinux 23.0.4 - 6.5.5-1-MANJARO - KDE Plasma 5.27.8

1 System - 10 Benchmark Results

Intel Core i5-4570 - Dell 04YP6J - Intel 4th Gen Core DRAM

ManjaroLinux 23.0.4 - 6.5.5-1-MANJARO - KDE Plasma 5.27.8

1 System - 3 Benchmark Results

Intel Core i5-4570 - Dell 04YP6J - Intel 4th Gen Core DRAM

ManjaroLinux 23.0.4 - 6.5.5-1-MANJARO - KDE Plasma 5.27.8

7 Systems - 263 Benchmark Results

AMD Ryzen 9 7950X 16-Core - ASUS TUF GAMING X670E-PLUS WIFI - AMD Device 14d8

EndeavourOS rolling - 6.1.12-arch1-1 - Cinnamon 5.6.7

1 System - 1 Benchmark Result

2 x Intel Xeon E5-2680 v3 - Dell 0CN7X8 - Intel Xeon E7 v3

Ubuntu 22.04 - 5.15.0-82-generic - GNOME Shell 42.9

Most Popular Test Results

OpenBenchmarking.org Results Compare

3 Systems - 37 Benchmark Results

Intel Xeon E3-1235L v5 - ASRockRack C236M WS - Intel Xeon E3-1200 v5

Ubuntu 20.04 - 5.8.0-050800-generic - GNOME Shell 3.36.4

3 Systems - 78 Benchmark Results

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

Ubuntu 20.04 - 5.8.1-050801-generic - GNOME Shell 3.36.4

4 Systems - 11 Benchmark Results

AMD Ryzen Threadripper 2970WX 24-Core - Gigabyte X399 AORUS Gaming 7 - AMD 17h

Ubuntu 20.04 - 5.9.0-050900rc6daily20200926-generic - GNOME Shell 3.36.4

13 Systems - 333 Benchmark Results

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

Ubuntu 22.04 - 6.0.0-060000rc1daily20220820-generic - GNOME Shell 42.2

5 Systems - 94 Benchmark Results

ARMv8 Cortex-A72 - Amazon EC2 a1.4xlarge - Amazon Device 0200

Ubuntu 22.04 - 5.15.0-1004-aws - GCC 11.2.0

4 Systems - 82 Benchmark Results

Intel Core i5-6500 - Gigabyte Z170M-D3H-CF - Intel Xeon E3-1200 v5

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

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

3 Systems - 164 Benchmark Results

Intel Xeon E5-2609 v4 - MSI X99A RAIDER - Intel Xeon E7 v4

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

2 Systems - 38 Benchmark Results

Intel Xeon Gold 6226R - Supermicro X11SPL-F v1.02 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.10 - 5.11.0-rc4-max-boost-inv-patch - GNOME Shell 3.38.1

16 Systems - 333 Benchmark Results

AMD Ryzen 9 7900X 12-Core - ASUS ROG CROSSHAIR X670E HERO - AMD Device 14d8

Ubuntu 22.04 - 6.0.0-060000rc1daily20220820-generic - GNOME Shell 42.2

3 Systems - 117 Benchmark Results

Intel Core i3-7100 - Gigabyte B250M-DS3H-CF - Intel Xeon E3-1200 v6

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

6 Systems - 254 Benchmark Results

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

Find More Test Results