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

12 Seconds

Average Run Time

2 Minutes, 27 Seconds

Test Dependencies

C/C++ Compiler Toolchain

Accolades

250k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms


Public Result Uploads *Reported Test Completions **Reported Installs **Test Profile Page Views ***OpenBenchmarking.orgEventsTimed MAFFT Alignment Popularity Statisticspts/mafft2010.122011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.042021.082021.122022.042022.0820K40K60K80K100K
* 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 28 November 2022.

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

HPC - High Performance Computing

Scientific 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 1,212 public results since 26 September 2020 with the latest data as of 1 December 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)
100th
3
4 +/- 1
Mid-Tier
75th
> 9
66th
17
10 +/- 1
Median
50th
11
40th
12
12 +/- 1
33rd
6
13 +/- 1
Low-Tier
25th
> 15
24th
9
15 +/- 2
23rd
10
15 +/- 1
22nd
8
16 +/- 1
15th
11
19 +/- 1
10th
11
25 +/- 2
OpenBenchmarking.orgDistribution Of Public Results - Multiple Sequence Alignment - LSU RNA1209 Results Range From 2 To 1044 Seconds2346698130162194226258290322354386418450482514546578610642674706738770802834866898930962994102610582004006008001000

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: 1.38 / Max: 20

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.8%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsMultiple Sequence Alignment - LSU RNADeviation3691215Min: 0 / Avg: 0.82 / Max: 10

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 RNA4681216202432640.78751.5752.36253.153.9375

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)
IBM Z
s390x
(Many Processors)
IBM POWER (PowerPC) 64-bit
ppc64le
POWER9 4-Core, POWER9 44-Core
Loongson LoongArch 64-bit
loongarch64
Loongson-3A5000LL
Itanium 64-bit
ia64
2 x Madison
Intel / AMD x86 32-bit
i686
(Many Processors)
ARMv8 64-bit
arm64
Apple, Apple M1, Apple M1 Max, Apple M2
DEC Alpha
alpha
Alpha
ARMv8 64-bit
aarch64
ARMv8 Cortex-A72 16-Core, Ampere Altra ARMv8 Neoverse-N1 160-Core, Ampere eMAG ARMv8 32-Core, HUAWEI Kunpeng 920, HUAWEI Kunpeng 920 5221K, Phytium FT-2000, Phytium S2500

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