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.

Project Site

align.bmr.kyushu-u.ac.jp

Test Created

6 December 2010

Last Updated

11 December 2020

Test Maintainer

Andrew Schofield 

Test Type

Processor

Average Install Time

7 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/mafft2010.122011.052011.102012.032012.082013.012013.062013.112014.042014.092015.022015.072015.122016.052016.102017.032017.082018.012018.062018.112019.042019.092020.022020.072020.122021.052021.102022.032022.082023.012023.062023.1120K40K60K80K100K
* 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 updated weekly as of 4 December 2023.

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

HPC - High Performance Computing

CPU Massive

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 1,372 public results since 26 September 2020 with the latest data as of 2 December 2023.

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)
Intel Xeon W-2123
100th
3
4 +/- 1
Intel Core i7-9850H
100th
6
4
Intel Core i7-11700K
91st
3
8
Intel Core i9-12900K
91st
5
8
Intel Core i7-12700K
90th
6
8
AMD Ryzen Threadripper 3970X 32-Core
88th
8
8
AMD Ryzen Threadripper 3960X 24-Core
88th
6
8
Intel Core i5-12400
87th
3
8
Intel Core i5-12600K
86th
5
8
Intel Core i9-9900KS
85th
6
8
Intel Core i9-10900K
84th
21
9
AMD Ryzen 7 5800X 8-Core
84th
11
9
Intel Xeon E-2288G
81st
11
9
Intel Core i9-10980XE
81st
6
9
Intel Core i9-9900K
78th
6
9
AMD Ryzen Threadripper 3990X 64-Core
78th
8
9
AMD EPYC 7F52 16-Core
77th
10
9
AMD EPYC 7F32 8-Core
76th
10
9
Intel Core i5-10600K
76th
13
9
AMD Ryzen 9 3950X 16-Core
76th
10
9
AMD Ryzen 9 3900XT 12-Core
76th
11
9
Intel Core i5-11600K
76th
5
9 +/- 1
Mid-Tier
75th
> 9
AMD Ryzen 9 3900X 12-Core
74th
12
9
AMD EPYC 7313 16-Core
74th
6
9
Intel Core i9-7960X
74th
6
9
AMD EPYC 7F72 24-Core
71st
12
9
Intel Core i9-7980XE
71st
10
10
2 x AMD EPYC 7453 28-Core
69th
3
10 +/- 1
Intel Core i7-8700K
69th
3
10
AMD EPYC 7542 32-Core
69th
5
10
AMD EPYC 7402P 24-Core
69th
6
10
AMD EPYC 7262 8-Core
68th
3
10
Intel Core i7-1165G7
67th
17
10 +/- 1
AMD EPYC 7502P 32-Core
67th
6
10
Intel Core i7-10700T
66th
4
10
AMD EPYC 7302P 16-Core
66th
7
10
AMD EPYC 7502 32-Core
65th
6
10
AMD EPYC 7702 64-Core
65th
6
10
AMD EPYC 7532 32-Core
65th
6
10
AMD EPYC 7642 48-Core
65th
6
10
AMD EPYC 7552 48-Core
64th
6
10
AMD EPYC 7662 64-Core
63rd
6
10
Intel Xeon Gold 6226R
63rd
7
10
AMD EPYC 7452 32-Core
63rd
5
10
Intel Core i7-7700K
62nd
6
10
Intel Xeon Gold 5218
61st
4
10
Intel Core i7-7900X
60th
6
10
2 x AMD EPYC 7742 64-Core
60th
9
11
Intel Core i9-10885H
59th
4
11
AMD EPYC 7272 12-Core
59th
4
11
Intel Xeon Silver 4215R
58th
3
11
Intel Xeon Gold 5217
58th
4
11
AMD Ryzen 7 3700X 8-Core
58th
3
11 +/- 1
AMD EPYC 7352 24-Core
58th
5
11
AMD EPYC 7252 8-Core
57th
3
11
2 x Intel Xeon Gold 6254
57th
4
11
Intel Core i5-10210U
56th
12
11
AMD Ryzen Threadripper 2950X 16-Core
55th
6
11
Intel Xeon Silver 4214R
55th
3
11
Intel Core i7-9700TE
53rd
5
11
POWER9 44-Core
52nd
11
11
Intel Xeon E3-1275 v6
52nd
6
11
Intel Xeon E5-1680 v3
52nd
3
11
Intel Core i5-9400F
52nd
6
11
AMD EPYC 7232P 8-Core
52nd
6
11
Median
50th
11
AMD Ryzen 5 3600X 6-Core
50th
3
11
Intel Core i7-6800K
50th
6
11
AMD Ryzen 5 3600XT 6-Core
49th
6
12
2 x Intel Xeon Platinum 8280
47th
14
12 +/- 1
Intel Core i7-4790K
47th
6
12
2 x Intel Xeon Gold 5220R
46th
6
12
Intel Core i7-8850H
44th
12
12 +/- 1
Intel Core i3-8100
44th
6
12
Intel Core i7-5960X
43rd
4
12
Loongson-3A6000
43rd
8
12
AMD Ryzen Threadripper 2990WX 32-Core
42nd
6
12
Intel Xeon E3-1280 v5
42nd
6
12
AMD Ryzen 7 4800H
41st
10
12 +/- 1
Intel Xeon E3-1245 v5
40th
6
12
Intel Xeon Silver 4216
40th
7
12 +/- 1
Intel Xeon E5-2687W v3
39th
6
12
Intel Core i5-4670
39th
7
12
Intel Xeon E-2278GEL
39th
6
13
AMD Ryzen Threadripper 2970WX 24-Core
38th
6
13
Intel Xeon E3-1231 v3
37th
6
13
Intel Core i7-8565U
36th
6
13 +/- 1
AMD Ryzen 5 2600 Six-Core
35th
5
14
AMD Ryzen 3 1300X
35th
7
14
AMD Ryzen 7 1800X Eight-Core
34th
3
14
Intel Core i5-7600K
33rd
6
14
AMD Ryzen 7 2700X Eight-Core
33rd
5
14
POWER9 4-Core
32nd
4
14
Intel Core i7-8700
31st
22
14
2 x Intel Xeon E5-2680 v2
30th
3
14 +/- 1
AMD Ryzen 7 2700 Eight-Core
30th
7
14 +/- 1
Intel Xeon E3-1235L v5
28th
3
15
AMD Ryzen 7 1700 Eight-Core
27th
11
15
AMD EPYC 7601 32-Core
27th
9
15
2 x AMD EPYC 7601 32-Core
26th
4
15
Low-Tier
25th
> 15
AMD Ryzen 3 2200G
25th
10
15 +/- 1
AMD EPYC 7551 32-Core
25th
4
15
HUAWEI Kunpeng 920
24th
8
16 +/- 1
2 x Intel Xeon E5-2630 v4
24th
4
16
AMD Ryzen 5 4500U
23rd
5
16
Intel Core i7-5600U
20th
6
17
Intel Core i7-8700B
18th
11
19 +/- 1
Loongson-3A5000
16th
6
19
Intel Xeon E5-2609 v4
16th
7
20
AMD Athlon 3000G
14th
3
22 +/- 2
Phytium FT-2000
13th
4
22
AMD A10-7850K APU
11th
7
25
Intel Core i3-3110M
11th
11
25 +/- 2
Ampere eMAG ARMv8 32-Core
7th
11
36
Intel Celeron N3060
4th
3
89 +/- 7
ARMv8 Cortex-A72 4-Core
3rd
4
109 +/- 5
OpenBenchmarking.orgDistribution Of Public Results - Multiple Sequence Alignment - LSU RNA1372 Results Range From 2 To 1044 Seconds23466981301621942262582903223543864184504825145465786106426747067387708028348668989309629941026105830060090012001500

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: 1.47 / Max: 20

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.9%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsMultiple Sequence Alignment - LSU RNADeviation3691215Min: 0 / Avg: 0.87 / Max: 11

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.

IntelAMDOpenBenchmarking.orgRelative Core Scaling To BaseTimed MAFFT Alignment CPU Core ScalingMultiple Sequence Alignment - LSU RNA24681216202432640.70421.40842.11262.81683.521

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)
RISC-V 64-bit
riscv64
SiFive RISC-V, rv64imafdcvsu
IBM POWER (PowerPC) 64-bit
ppc64le
POWER9 4-Core, POWER9 44-Core
Loongson LoongArch 64-bit
loongarch64
Loongson-3A5000, Loongson-3A5000LL, Loongson-3A6000
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, ARMv8 Cortex-A72 4-Core, ARMv8 Neoverse-N1, 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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1 System - 3 Benchmark Results

Intel Xeon E5-2696 v3 - HUANANZHI X99-BD4 - 4 x 8192 MB 1866MHz

Microsoft Windows 10 Pro N Build 18363 - 10.0.18363.1198 - 31.0.101.4146

1 System - 3 Benchmark Results

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Loongnix 20 - 4.19.0-19-loongson-3 - X Server 1.20.4

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Loongson-3A6000 - Loongson Loongson-LS3A6000-7A2000-1w-EVB-V1.21 - Loongson LLC Hyper Transport Bridge

Loongnix 20 - 4.19.0-19-loongson-3 - X Server 1.20.4

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Loongnix 20 - 4.19.0-19-loongson-3 - X Server 1.20.4

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