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/mafft2011.052011.092012.012012.052012.092013.012013.052013.092014.012014.052014.092015.012015.052015.092016.012016.052016.092017.012017.052017.092018.012018.052018.092019.012019.052019.092020.012020.052020.092021.012021.0520K40K60K80K100K
* 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, 08 May 2021 11:19:12 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

HPC - High Performance Computing

Bioinformatics


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 906 public results since 26 September 2020 with the latest data as of 7 May 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)
Mid-Tier
75th
> 9
63rd
16
10 +/- 1
Median
50th
11
Low-Tier
25th
> 13
25th
6
13 +/- 1
16th
9
15 +/- 2
10th
11
19 +/- 1
OpenBenchmarking.orgDistribution Of Public Results - Multiple Sequence Alignment - LSU RNA906 Results Range From 3 To 1044 Seconds3356799131163195227259291323355387419451483515547579611643675707739771803835867899931963995102710592004006008001000

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-Time510152025Min: 1 / Avg: 1.24 / Max: 18

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: 0.72 / Max: 7

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

Recent Test Results

OpenBenchmarking.org Results Compare

2 Systems - 1 Benchmark Result

Unknown - Huawei BC82AMDDA - Huawei HiSilicon

CentOS Linux 7 - 4.18.0-80.7.2.el7.aarch64 - GNOME Shell 3.28.3

2 Systems - 1 Benchmark Result

Unknown - Huawei BC82AMDDA - 4 x 32 GB DDR4-2666MHz Hynix HMA84GR7AFR4N-VK

Linx 9.6 - 4.19.0-0.bpo.1-linx-security-arm64 - X Server 1.19.2

2 Systems - 1 Benchmark Result

Unknown - Huawei BC82AMDDA - Huawei HiSilicon

Linx 10 - 4.19.0-11-linx-generic-arm64 - X Server 1.20.4

1 System - 1 Benchmark Result

Unknown - Huawei BC82AMDDA - Huawei HiSilicon

Linx 10 - 4.19.0-11-linx-generic-arm64 - X Server 1.20.4

1 System - 2 Benchmark Results

Intel Core i7-3615QM - Parallels Software Virtual - 4096MB

Gentoo - 5.10.27-gentoo-x86_64-gcc - GCC 10.2.0

1 System - 732 Benchmark Results

2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998

Ubuntu 20.04 - 5.11.6-051106-generic - GNOME Shell 3.36.4

1 System - 71 Benchmark Results

Intel Pentium G3220 - ASUS H81M-K - Intel 4th Gen Core DRAM

Arch Linux - 5.10.29-1-bcachefs-git-307472-g6a3927a96b2f - Openbox 3.6.1

10 Systems - 454 Benchmark Results

AMD Ryzen 5 5600X 6-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 21.04 - 5.12.0-051200rc3daily20210315-generic - GNOME Shell 3.38.3

1 System - 42 Benchmark Results

AMD Ryzen 9 5950X 16-Core - ASRock X570M Pro4 - 64GB

Ubuntu 20.04.1 LTS - 5.11.14-200.fc33.x86_64 - NVIDIA

1 System - 11 Benchmark Results

Intel Celeron J1900 - Type2- Board - Intel Atom Z36xxx

Ubuntu 18.04 - 4.15.0-117-generic - TCC 0.9.27

1 System - 24 Benchmark Results

Intel Core i5-7200U - HP 8314 v32.25 - Intel Xeon E3-1200 v6

Mageia 8 - 5.10.27-desktop-1.mga8 - GNOME Shell 3.38.3

3 Systems - 95 Benchmark Results

2 x AMD EPYC 7551 32-Core - Microsoft Virtual Machine - 226GB

CentOS Linux 8 - 4.18.0-147.8.1.el8_1.x86_64 - GCC 8.3.1 20190507

Most Popular Test Results

OpenBenchmarking.org Results Compare

11 Systems - 217 Benchmark Results

AMD Ryzen 9 3900XT 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 20.04 - 5.9.0-050900-generic - GNOME Shell 3.36.4

4 Systems - 99 Benchmark Results

AMD Ryzen 5 4500U - LENOVO LNVNB161216 - AMD Renoir Root Complex

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

6 Systems - 143 Benchmark Results

AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 20.10 - 5.10.7-051007-generic - GNOME Shell 3.38.1

3 Systems - 174 Benchmark Results

Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH

Fedora 32 - 5.8.11-200.fc32.x86_64 - GNOME Shell 3.36.6

3 Systems - 46 Benchmark Results

AMD Ryzen Threadripper 3960X 24-Core - MSI Creator TRX40 - AMD Starship

Ubuntu 20.04 - 5.9.0-rc5-14sep-patch - GNOME Shell 3.36.4

5 Systems - 42 Benchmark Results

ARMv8 Cortex-A72 - SolidRun CEX7 - 32GB

Fedora 33 - 5.10.10-00042-gbfa806f5daa5-dirty - X Server 1.20.10

2 Systems - 403 Benchmark Results

Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH

Ubuntu 20.04 - 5.4.0-48-generic - GNOME Shell 3.36.4

12 Systems - 229 Benchmark Results

AMD Ryzen 5 3600X 6-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 20.04 - 5.9.0-050900-generic - GNOME Shell 3.36.4

3 Systems - 40 Benchmark Results

2 x Intel Xeon Gold 5220R - TYAN S7106 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.9.0-050900rc6-generic - GNOME Shell 3.36.4

3 Systems - 406 Benchmark Results

AMD Ryzen 9 3900XT 12-Core - MSI MEG X570 GODLIKE - AMD Starship

Ubuntu 20.10 - 5.8.0-20-generic - GNOME Shell 3.38.0

5 Systems - 99 Benchmark Results

Apple M1 - Apple Mac mini - 8GB

macOS 11.0 - 20.1.0 - OpenCL 1.2

8 Systems - 439 Benchmark Results

Intel Core i5-10600K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH

Ubuntu 21.04 - 5.12.0-051200rc3daily20210315-generic - GNOME Shell 3.38.3

Find More Test Results