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, 6 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 26 March 2024.

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 1,033 public results since 11 October 2019 with the latest data as of 30 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)
94th
14
59 +/- 3
89th
25
64 +/- 1
Mid-Tier
75th
> 72
70th
4
79 +/- 1
61st
3
90 +/- 13
Median
50th
102
48th
21
104 +/- 1
45th
4
107 +/- 1
43rd
20
109 +/- 5
38th
14
112 +/- 6
37th
13
113 +/- 4
35th
8
116 +/- 1
34th
5
118 +/- 16
33rd
7
121 +/- 11
Low-Tier
25th
> 139
21st
4
149 +/- 16
21st
3
149 +/- 20
21st
4
150 +/- 6
13th
4
243 +/- 35
OpenBenchmarking.orgDistribution Of Public Results - Primate Phylogeny Analysis1033 Results Range From 44 To 18923 Seconds444228001178155619342312269030683446382442024580495853365714609264706848722676047982836087389116949498721025010628110061138411762121401251812896132741365214030144081478615164155421592016298166761705417432178101818818566189442004006008001000

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-Time306090120150Min: 2 / Avg: 9.09 / Max: 136

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.6%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsPrimate Phylogeny AnalysisDeviation48121620Min: 0 / Avg: 0.56 / Max: 13

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 Analysis4812162432640.40830.81661.22491.63322.0415

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)
SPARC64
sparc64
(Many Processors)
IBM Z
s390x
(Many Processors)
IBM POWER (PowerPC) 64-bit
ppc64le
POWER9 4-Core, POWER9 44-Core
Intel / AMD x86 32-bit
i686
(Many Processors)
ARMv7 32-bit
armv7l
ARMv7 Cortex-A7 4-Core, ARMv7 Cortex-A72 4-Core
DEC Alpha
alpha
(Many Processors)
ARMv8 64-bit
aarch64
ARMv8 Cortex-A53 4-Core, ARMv8 Cortex-A72 16-Core, ARMv8 Neoverse-N1 64-Core, ARMv8 rev 0 8-Core

Recent Test Results

OpenBenchmarking.org Results Compare

20 Systems - 119 Benchmark Results

Intel Xeon Platinum 8259L - ASRockRack EP2C621D16-4LP - Intel Sky Lake-E DMI3 Registers

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

19 Systems - 119 Benchmark Results

AMD EPYC 7K83 64-Core - Supermicro H12SSL-i v1.01 - AMD Starship

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

18 Systems - 119 Benchmark Results

2 x Intel Xeon Platinum 8272CL - ASRockRack EP2C621D16-4LP - Intel Sky Lake-E DMI3 Registers

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

17 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

17 Systems - 119 Benchmark Results

AMD EPYC 7K83 64-Core - Supermicro H12SSL-i v1.01 - AMD Starship

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

Find More Test Results