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

* 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)

AMD Ryzen 5 7600X 6-Core

98th

AMD Ryzen 9 7900X 12-Core

97th

69 ^{+/- 1}

AMD Ryzen 9 7950X3D 16-Core

96th

Intel Core i7-12700K

95th

73 ^{+/- 1}

AMD Ryzen 9 7900 12-Core

95th

74 ^{+/- 2}

AMD Ryzen 7 5800X3D 8-Core

91st

84 ^{+/- 1}

AMD Ryzen 5 5600G

91st

84 ^{+/- 2}

AMD Ryzen 7 5800X 8-Core

91st

84 ^{+/- 3}

AMD EPYC 72F3 8-Core

87th

89 ^{+/- 4}

AMD Ryzen 7 5700G

86th

91 ^{+/- 3}

Intel Core i9-10900K

82nd

AMD EPYC 7373X 16-Core

81st

2 x AMD EPYC 7373X 16-Core

80th

101 ^{+/- 1}

AMD Ryzen 9 3950X 16-Core

78th

104 ^{+/- 2}

AMD EPYC 75F3 32-Core

78th

104

AMD EPYC 7F52 16-Core

78th

104

AMD Ryzen 5 3600XT 6-Core

76th

105

Intel Core i5-10600K

76th

105 ^{+/- 1}

2 x AMD EPYC 75F3 32-Core

76th

105

Mid-Tier

75th

> 105

AMD Ryzen 7 3700X 8-Core

75th

106

AMD Ryzen 9 3900X 12-Core

74th

107 ^{+/- 5}

AMD Ryzen 9 3900XT 12-Core

74th

107 ^{+/- 1}

AMD EPYC 7F32 8-Core

74th

107

AMD Ryzen Threadripper 3970X 32-Core

73rd

109

Intel Core i5-13600K

71st

112 ^{+/- 3}

Intel Core i9-9900KS

71st

112 ^{+/- 1}

Intel Core i7-7700K

70th

115 ^{+/- 1}

2 x AMD EPYC 7453 28-Core

68th

117 ^{+/- 2}

Intel Core i7-8086K

66th

120

Intel Core i7-8700K

65th

121

Intel Core i5-13400

65th

125 ^{+/- 1}

Intel Xeon Gold 6346

63rd

128 ^{+/- 1}

2 x Intel Xeon Gold 6346

63rd

128 ^{+/- 1}

Intel Core i5-7600K

61st

130

Intel Xeon E3-1275 v6

61st

130

Intel Core i7-7740K

61st

131

Intel Core i7-10750H

60th

133 ^{+/- 8}

AMD Ryzen 5 4500U

59th

136 ^{+/- 5}

Intel Core i5-8400

59th

137

Intel Core i3-7100

59th

137 ^{+/- 6}

Intel Xeon Gold 6342

57th

139

AMD EPYC 7763 64-Core

56th

140 ^{+/- 3}

Intel Xeon E3-1280 v5

54th

141 ^{+/- 1}

2 x Intel Xeon Gold 6342

54th

141

2 x AMD EPYC 7763 64-Core

54th

142 ^{+/- 1}

AMD Ryzen 5 2400G

53rd

143 ^{+/- 8}

AMD EPYC 7713 64-Core

53rd

143 ^{+/- 5}

AMD Ryzen 3 1300X

52nd

144 ^{+/- 2}

Intel Xeon E-2288G

52nd

144

Intel Core i3-8100

52nd

144

Intel Xeon E3-1245 v5

51st

145

Median

50th

145

Intel Core i7-1165G7

49th

148 ^{+/- 12}

2 x Intel Xeon Platinum 8362

49th

149 ^{+/- 2}

2 x AMD EPYC 7773X 64-Core

49th

149 ^{+/- 17}

AMD Ryzen 7 4700U

48th

151 ^{+/- 2}

AMD EPYC 7742 64-Core

45th

154

Intel Xeon E3-1270 v5

44th

156 ^{+/- 1}

AMD Ryzen 7 2700 Eight-Core

43rd

157 ^{+/- 4}

2 x AMD EPYC 7742 64-Core

42nd

158 ^{+/- 1}

AMD Ryzen 7 1700 Eight-Core

41st

159 ^{+/- 13}

Intel Core i5-4570

39th

165 ^{+/- 4}

Intel Xeon E3-1260L v5

39th

167 ^{+/- 1}

Intel Xeon Platinum 8380

38th

168 ^{+/- 1}

2 x Intel Xeon Platinum 8380

36th

171 ^{+/- 11}

AMD Ryzen Threadripper 2970WX 24-Core

35th

172 ^{+/- 1}

Intel Core i3-4130

35th

173 ^{+/- 1}

Intel Core i7-6800K

33rd

176 ^{+/- 4}

Intel Core i9-7980XE

32nd

178 ^{+/- 1}

AMD Ryzen 3 3200U

31st

179 ^{+/- 1}

Intel Core i7-9750H

31st

179 ^{+/- 3}

AMD Ryzen Threadripper 2950X 16-Core

30th

182 ^{+/- 13}

Intel Core i7-4770K

30th

184 ^{+/- 2}

Intel Xeon E5-2687W v3

29th

186 ^{+/- 2}

Intel Core i7-10700T

27th

192

2 x Intel Xeon Platinum 8280

27th

192 ^{+/- 2}

Intel Xeon E3-1235L v5

27th

192 ^{+/- 1}

Intel Core i7-5960X

27th

192 ^{+/- 2}

Low-Tier

25th

> 194

Intel Xeon E3-1231 v3

25th

194

Intel Xeon Gold 6226R

25th

196 ^{+/- 6}

Apple M2

25th

196 ^{+/- 22}

Intel Core i7-8565U

24th

202 ^{+/- 10}

2 x Intel Xeon E5-2680 v3

23rd

204 ^{+/- 2}

2 x AMD EPYC 7601 32-Core

23rd

209 ^{+/- 4}

Intel Core i7-4960X

21st

217 ^{+/- 4}

Intel Core i7-3770K

21st

218 ^{+/- 2}

2 x Intel Xeon Gold 5220R

21st

219 ^{+/- 8}

Apple M1

18th

242 ^{+/- 2}

Ampere Altra ARMv8 Neoverse-N1 160-Core

16th

296 ^{+/- 2}

Intel Xeon E5-2609 v4

15th

302 ^{+/- 1}

ARMv8 Neoverse-N1 160-Core

14th

315 ^{+/- 16}

Intel Core i7-2700K

13th

328 ^{+/- 3}

Intel Xeon Silver 4216

12th

368 ^{+/- 2}

Intel Core i7-9850H

8th

495 ^{+/- 7}

Intel Xeon W-3235

8th

537 ^{+/- 6}

Intel Xeon W-2123

7th

572 ^{+/- 7}

4 x AMD Opteron 8378

6th

599 ^{+/- 2}

Ampere eMAG ARMv8 32-Core

2nd

1221

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.

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

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.

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

Advanced Vector Extensions (AVX)

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

Advanced Vector Extensions 2 (AVX2)

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

test2 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
2023-11-01-0307 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
cpu-massive-test-results 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
intel-4690k 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
Xeon & EPYC Tests 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
2023-10-26-1352 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
mrbayes-O2 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
mrbayes-base 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
2023-10-14-1025 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
2023-10-10-1533 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
6.5.5-1-MANJARO + ManjaroLinux 23.0.4 Tests 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
Intel Core i5-4570 On ManjaroLinux 23.0.4 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
Intel Core i5-4570 On ManjaroLinux 23.0.4 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
Ryzen 9 7950X LONG 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
mrbayes-O2 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

1235 may 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
3700X Mayt 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
tr 2970wx may 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
AMD Ryzen 7900 Series Linux CPU Benchmarks 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
Amazon EC2 Graviton3 Benchmark Comparison 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
6500 May 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
Ryzen 9 5950X Clang 12 vs. GCC 11 Benchmarks Featured Compiler Comparison	AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Fedora 34 - 5.11.20-300.fc34.x86_64 - GNOME Shell 40.1
Linux Servers AlmaLinux vs. RHEL 9.0 Featured OS Comparison	2 x AMD EPYC 7773X 64-Core - AMD DAYTONA_X - AMD Starship Red Hat Enterprise Linux 9.0 - 5.14.0-70.13.1.el9_0.x86_64 - GNOME Shell 40.9
3950x may 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
xeon broadwell may 2021 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
gold may 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
12700k HPC+OpenCL AVX512 performance profiling Featured Disk Comparison	Intel Core i7-12700K - MSI PRO Z690-A DDR4 - Intel Device 7aa7 Pop 21.04 - 5.15.5-76051505-generic - GNOME Shell 3.38.4
Intel Core i9 13900K Linux CPU Benchmarks 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
7100 june 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
clearlinux-ryzen3-4350 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

Timed MrBayes Analysis

Project Site

Test Created

Last Updated

Test Maintainer

Test Type

Average Install Time

Average Run Time

Test Dependencies

Accolades

Supported Platforms

Revision History

Suites Using This Test

Performance Metrics

Timed MrBayes Analysis 3.2.7

Primate Phylogeny Analysis

Does It Scale Well With Increasing Cores?

Notable Instruction Set Usage

Tested CPU Architectures

Recent Test Results

Most Popular Test Results