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, 16 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/mrbayes2010.122011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.042021.082021.122022.042022.086K12K18K24K30K
* 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 27 September 2022.

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

HPC - High Performance Computing

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 726 public results since 5 May 2021 with the latest data as of 27 September 2022.

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)
97th
46
82 +/- 10
87th
4
91 +/- 3
76th
3
105 +/- 1
Mid-Tier
75th
> 105
71st
3
112 +/- 1
70th
3
115 +/- 1
64th
3
131 +/- 3
63rd
17
133 +/- 8
62nd
4
136 +/- 5
62nd
7
137 +/- 6
57th
6
141 +/- 1
55th
5
143 +/- 8
55th
3
143 +/- 5
54th
3
144 +/- 2
Median
50th
151
50th
3
151 +/- 2
48th
6
154 +/- 2
46th
6
156 +/- 1
44th
4
158 +/- 1
36th
3
173 +/- 1
35th
3
176 +/- 4
33rd
3
178 +/- 1
32nd
3
179 +/- 1
32nd
4
179 +/- 3
30th
6
184 +/- 2
26th
3
192 +/- 2
Low-Tier
25th
> 192
24th
6
196 +/- 22
24th
4
196 +/- 6
22nd
5
202 +/- 10
22nd
4
205 +/- 6
20th
3
217 +/- 4
20th
4
218 +/- 2
14th
3
302 +/- 1
13th
3
328 +/- 3
9th
6
495 +/- 7
8th
5
537 +/- 6
7th
3
572 +/- 7
OpenBenchmarking.orgDistribution Of Public Results - Primate Phylogeny Analysis698 Results Range From 46 To 4868 Seconds461432403374345316287258229191016111312101307140415011598169517921889198620832180227723742471256826652762285929563053315032473344344135383635373238293926402341204217431444114508460547024799489670140210280350

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 14 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: 2 / Avg: 13.15 / Max: 99

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.4%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsPrimate Phylogeny AnalysisDeviation246810Min: 0 / Avg: 0.41 / Max: 6

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 Analysis468121632641280.4750.951.4251.92.375

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 Pro
DEC Alpha
alpha
Alpha
ARMv8 64-bit
aarch64
ARMv8 Cortex-A72, ARMv8 Cortex-A72 4-Core, ARMv8 Neoverse-N1, 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

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