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

Accolades

200k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms


Public Result UploadsTest Completions*Reported Installs*OpenBenchmarking.orgEventsTimed MAFFT Alignment Popularity Statisticspts/mafft2011.012011.052011.092012.012012.052012.092013.012013.052013.092014.012014.052014.092015.012015.052015.092016.012016.052016.092017.012017.052017.092018.012018.052018.092019.012019.052019.092020.012020.052020.092021.0120K40K60K80K100K
* 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 Mon, 18 Jan 2021 17:36:58 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 764 public results since 26 September 2020 with the latest data as of 17 January 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
37
7.4 +/- 0.4
93rd
30
7.5 +/- 0.5
86th
16
8.6 +/- 0.1
84th
6
8.6 +/- 0.1
84th
11
8.7 +/- 0.1
83rd
6
8.7 +/- 0.5
81st
10
8.8 +/- 0.4
79th
9
8.9 +/- 0.1
77th
10
8.9 +/- 0.3
76th
9
8.9 +/- 0.1
76th
10
9.0 +/- 0.2
Mid-Tier
75th
> 9.0
73rd
6
9.2 +/- 0.1
71st
12
9.4 +/- 0.1
70th
10
9.6 +/- 0.2
68th
3
9.9 +/- 0.1
65th
15
10.1 +/- 0.6
63rd
4
10.2 +/- 0.1
63rd
6
10.2 +/- 0.1
62nd
6
10.2 +/- 0.1
60th
7
10.3 +/- 0.3
57th
6
10.3 +/- 0.1
55th
7
10.5 +/- 0.2
55th
6
10.5 +/- 0.1
53rd
3
10.6 +/- 0.1
53rd
7
10.6 +/- 0.2
Median
50th
10.8
45th
5
11.3 +/- 0.1
44th
11
11.3 +/- 0.1
44th
6
11.3 +/- 0.1
44th
3
11.3 +/- 0.1
44th
6
11.3 +/- 0.1
44th
12
11.3 +/- 0.2
41st
6
11.5 +/- 0.1
40th
6
11.5 +/- 0.2
39th
6
11.6 +/- 0.1
37th
6
11.8 +/- 0.2
37th
3
11.8 +/- 0.1
37th
6
11.8 +/- 0.1
34th
6
12.0 +/- 0.1
32nd
6
12.1 +/- 0.1
29th
7
12.4 +/- 0.6
28th
6
12.4 +/- 0.2
28th
7
12.5 +/- 0.1
27th
4
12.5 +/- 0.1
Low-Tier
25th
> 12.8
25th
6
12.8 +/- 0.1
25th
6
12.9 +/- 0.1
23rd
6
13.4 +/- 1.5
23rd
4
13.6 +/- 0.5
20th
6
13.9 +/- 0.2
19th
4
14.2 +/- 0.1
18th
6
14.3 +/- 0.4
18th
4
14.5 +/- 0.1
15th
11
14.8 +/- 0.3
14th
9
15.0 +/- 0.1
14th
4
15.0 +/- 0.1
13th
9
15.1 +/- 2.2
12th
4
15.4 +/- 0.4
12th
5
15.9 +/- 0.1
10th
6
17.3 +/- 0.2
9th
11
19.0 +/- 0.7
8th
7
19.6 +/- 0.1
7th
12
22.1
6th
7
24.9 +/- 0.3
OpenBenchmarking.orgDistribution Of Public Results - Multiple Sequence Alignment - LSU RNA764 Results Range From 3 To 220 Seconds3183348637893108123138153168183198213228150300450600750

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: 1.15 / 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 RNADeviation3691215Min: 0 / Avg: 0.74 / Max: 7

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4 Systems - 210 Benchmark Results

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Most Popular Test Results

OpenBenchmarking.org Results Compare

11 Systems - 217 Benchmark Results

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4 Systems - 99 Benchmark Results

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Ubuntu 20.10 - 5.9.1-050901-generic - GNOME Shell 3.38.1

3 Systems - 174 Benchmark Results

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5 Systems - 99 Benchmark Results

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Find More Test Results

OpenBenchmarking.org Community User Comments

Internal Server Error 500

http://fire-salamander.co.uk/pts-tests/pyruvate_decarboxylase.fasta.bz2 returns Error 500 Internal server error

Post by honiix on 25 September 2017, 11.05.

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