Timed MAFFT Alignment

This test performs an alignment of 100 pyruvate decarboxylase sequences.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark mafft.

Test Created

6 December 2010

Last Updated

11 December 2020

Test Maintainer

Andrew Schofield 

Test Type

Processor

Average Install Time

10 Seconds

Average Run Time

2 Minutes, 27 Seconds

Test Dependencies

C/C++ Compiler Toolchain

Accolades

200k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms


Public Result UploadsTest Completions*Reported Installs*OpenBenchmarking.orgEventsTimed MAFFT Alignment Popularity Statisticspts/mafft2011.032011.072011.112012.032012.072012.112013.032013.072013.112014.032014.072014.112015.032015.072015.112016.032016.072016.112017.032017.072017.112018.032018.072018.112019.032019.072019.112020.032020.072020.112021.0320K40K60K80K100K
* 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.
Data current as of Sat, 06 Mar 2021 15:31:39 GMT.

Revision History

pts/mafft-1.6.2   [View Source]   Fri, 11 Dec 2020 14:03:01 GMT
MAFFT fixes for BSD based on https://github.com/apurvanandan1997/pts-test-profiles-dev/tree/master/mafft-1.5.0

pts/mafft-1.6.1   [View Source]   Sat, 26 Sep 2020 16:35:16 GMT
Tighten arguments of update over noise.

pts/mafft-1.6.0   [View Source]   Sat, 26 Sep 2020 15:16:36 GMT
Update to newest MAFFT upstream 7.471 to address build issues with newer distros. Also use larger dataset input so it takes longer to run on modern hardware.

pts/mafft-1.5.0   [View Source]   Sun, 04 Mar 2018 12:47:04 GMT
Update against MAFFT 7.392, add Windows support.

pts/mafft-1.4.2   [View Source]   Tue, 06 Feb 2018 19:40:04 GMT
Minor cleanup to the install.sh

pts/mafft-1.4.1   [View Source]   Tue, 06 Feb 2018 17:59:13 GMT
Update download mirrors

pts/mafft-1.4.0   [View Source]   Tue, 21 Feb 2012 10:36:03 GMT
Support multi-threaded MAFFT build.

pts/mafft-1.3.0   [View Source]   Wed, 07 Dec 2011 12:40:18 GMT
Update against MAFFT upstream 6.864.

pts/mafft-1.2.0   [View Source]   Mon, 06 Dec 2010 14:55:19 GMT
Initial import into OpenBenchmarking.org

Suites Using This Test

C/C++ Compiler Tests

CPU Massive

Scientific Computing

Bioinformatics

HPC - High Performance Computing


Performance Metrics

Analyze Test Configuration:

Timed MAFFT Alignment 7.471

Multiple Sequence Alignment - LSU RNA

OpenBenchmarking.org metrics for this test profile configuration based on 816 public results since 26 September 2020 with the latest data as of 3 March 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
# Matching Public Results
Seconds (Average)
94th
41
7.5 +/- 0.4
93rd
32
7.5 +/- 0.5
88th
7
8.5 +/- 0.3
87th
16
8.6 +/- 0.1
84th
11
8.7 +/- 0.1
84th
6
8.7 +/- 0.5
81st
10
8.8 +/- 0.4
79th
10
8.9 +/- 0.1
78th
10
8.9 +/- 0.1
78th
10
8.9 +/- 0.3
76th
10
9.0 +/- 0.2
Mid-Tier
75th
> 9.1
74th
6
9.2 +/- 0.1
72nd
12
9.4 +/- 0.1
71st
10
9.6 +/- 0.2
69th
3
9.9 +/- 0.1
68th
5
9.9 +/- 0.2
68th
6
10.0 +/- 0.1
65th
6
10.1 +/- 0.2
65th
16
10.2 +/- 0.6
63rd
7
10.2 +/- 0.2
63rd
4
10.2 +/- 0.1
63rd
6
10.2 +/- 0.1
63rd
6
10.2 +/- 0.1
63rd
6
10.2 +/- 0.1
63rd
6
10.2 +/- 0.1
61st
6
10.3 +/- 0.2
60th
6
10.3 +/- 0.1
60th
7
10.3 +/- 0.3
57th
6
10.3 +/- 0.1
57th
6
10.3 +/- 0.1
55th
6
10.5 +/- 0.1
54th
4
10.5 +/- 0.1
54th
7
10.6 +/- 0.2
53rd
4
10.6 +/- 0.2
Median
50th
10.8
48th
11
11.0 +/- 0.1
44th
5
11.3 +/- 0.1
44th
11
11.3 +/- 0.1
44th
6
11.3 +/- 0.1
44th
3
11.3 +/- 0.1
43rd
6
11.3 +/- 0.1
43rd
6
11.3 +/- 0.1
43rd
12
11.3 +/- 0.2
40th
6
11.5 +/- 0.1
39th
6
11.5 +/- 0.2
39th
6
11.6 +/- 0.1
36th
6
11.8 +/- 0.2
36th
3
11.8 +/- 0.1
36th
6
11.8 +/- 0.1
33rd
6
12.0 +/- 0.1
31st
6
12.1 +/- 0.1
28th
7
12.4 +/- 0.6
28th
6
12.4 +/- 0.2
27th
7
12.5 +/- 0.1
27th
4
12.5 +/- 0.1
27th
6
12.5 +/- 0.1
Low-Tier
25th
> 12.6
25th
6
12.8 +/- 0.1
24th
6
12.9 +/- 0.1
23rd
6
13.4 +/- 1.5
23rd
4
13.6 +/- 0.5
19th
6
13.9 +/- 0.2
18th
4
14.2 +/- 0.1
18th
6
14.3 +/- 0.4
16th
7
14.7 +/- 0.3
15th
11
14.8 +/- 0.3
14th
9
15.0 +/- 0.1
13th
4
15.0 +/- 0.1
13th
9
15.1 +/- 2.2
12th
4
15.4 +/- 0.4
11th
5
15.9 +/- 0.1
10th
6
17.3 +/- 0.2
9th
11
19.0 +/- 0.7
8th
7
19.6 +/- 0.1
6th
7
24.9 +/- 0.3
OpenBenchmarking.orgDistribution Of Public Results - Multiple Sequence Alignment - LSU RNA816 Results Range From 3 To 220 Seconds3183348637893108123138153168183198213228160320480640800

Based on OpenBenchmarking.org data, the selected test / test configuration (Timed MAFFT Alignment 7.471 - Multiple Sequence Alignment - LSU RNA) has an average run-time of 2 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 BenchmarkMultiple Sequence Alignment - LSU RNARun-Time3691215Min: 1 / Avg: 1.14 / Max: 10

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.7%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsMultiple Sequence Alignment - LSU RNADeviation246810Min: 0 / Avg: 0.71 / 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 MAFFT Alignment CPU Core ScalingMultiple Sequence Alignment - LSU RNA46812162432640.78131.56262.34393.12523.9065

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