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

9 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/mafft2010.122011.052011.102012.032012.082013.012013.062013.112014.042014.092015.022015.072015.122016.052016.102017.032017.082018.012018.062018.112019.042019.092020.022020.072020.122021.052021.102022.032022.082023.012023.062023.112024.042024.0920K40K60K80K100K
* 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 3 October 2024.

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 1,601 public results since 26 September 2020 with the latest data as of 30 September 2024.

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
99th
6
4
AMD Ryzen 9 9950X 16-Core
99th
4
5
AMD Ryzen 9 7950X 16-Core
98th
21
7
AMD Ryzen 9 5950X 16-Core
92nd
54
7
AMD Ryzen 9 5900X 12-Core
92nd
36
7
Intel Core i7-11700K
92nd
3
8
Intel Core i9-12900K
92nd
5
8
Intel Core i7-12700K
91st
6
8
Intel Core i9-11900K
91st
10
8
AMD Ryzen Threadripper 3970X 32-Core
89th
8
8
AMD Ryzen Threadripper 3960X 24-Core
88th
6
8
Intel Core i5-12400
88th
3
8
Apple M2 Pro
87th
3
8
Intel Core i5-12600K
87th
5
8
Intel Core i9-9900KS
86th
6
8
Intel Core i9-10900K
85th
20
9
AMD Ryzen 7 5800X 8-Core
85th
11
9
AMD Ryzen 5 5600X 6-Core
83rd
17
9 +/- 1
Intel Xeon E-2288G
83rd
11
9
Intel Core i9-10980XE
82nd
6
9
Intel Core i9-9900K
80th
6
9
AMD Ryzen Threadripper 3990X 64-Core
80th
8
9
AMD EPYC 7F52 16-Core
79th
10
9
AMD EPYC 7F32 8-Core
78th
10
9
AMD Ryzen 9 3950X 16-Core
78th
10
9
Intel Core i5-10600K
78th
12
9
Intel Core i5-11600K
78th
5
9 +/- 1
AMD Ryzen 9 3900XT 12-Core
77th
12
9
AMD Ryzen 9 3900X 12-Core
77th
12
9
AMD EPYC 7313 16-Core
76th
6
9
Intel Core i9-7960X
76th
6
9
Mid-Tier
75th
> 9
AMD EPYC 7F72 24-Core
74th
12
9
Intel Core i9-7980XE
73rd
10
10
2 x AMD EPYC 7453 28-Core
72nd
3
10 +/- 1
Intel Core i7-8700K
72nd
3
10
AMD EPYC 9554P 64-Core
72nd
4
10
AMD EPYC 7542 32-Core
72nd
5
10
AMD EPYC 7402P 24-Core
71st
6
10
AMD EPYC 7262 8-Core
71st
3
10
Intel Core i7-1165G7
70th
17
10 +/- 1
AMD EPYC 7502P 32-Core
70th
6
10
Intel Core i7-10700T
69th
4
10
AMD EPYC 7302P 16-Core
69th
7
10
AMD EPYC 7502 32-Core
68th
6
10
AMD EPYC 7702 64-Core
68th
6
10
AMD EPYC 7532 32-Core
68th
6
10
AMD EPYC 7642 48-Core
68th
6
10
AMD EPYC 7552 48-Core
67th
6
10
AMD EPYC 7662 64-Core
67th
6
10
Intel Xeon Gold 6226R
67th
7
10
AMD EPYC 7452 32-Core
67th
5
10
AMD EPYC 7282 16-Core
65th
6
10
Intel Core i7-7700K
65th
6
10
Intel Core i7-7900X
64th
6
10
Intel Core i9-10885H
63rd
4
11
AMD EPYC 7272 12-Core
63rd
4
11
2 x AMD EPYC 7742 64-Core
63rd
8
11
Intel Xeon Silver 4215R
63rd
3
11
Intel Xeon Gold 5217
62nd
4
11
AMD Ryzen 7 3700X 8-Core
62nd
3
11 +/- 1
AMD EPYC 7352 24-Core
62nd
5
11
AMD EPYC 7252 8-Core
61st
3
11
2 x Intel Xeon Gold 6254
61st
4
11
Intel Core i5-10210U
60th
12
11
AMD Ryzen Threadripper 2950X 16-Core
60th
6
11
Intel Xeon Silver 4214R
60th
3
11
Intel Core i7-9700TE
58th
5
11
POWER9 44-Core
57th
11
11
Intel Xeon E3-1275 v6
57th
6
11
Intel Xeon E5-1680 v3
57th
3
11
Intel Core i5-9400F
57th
6
11
AMD EPYC 7232P 8-Core
57th
6
11
AMD Ryzen 7 3800XT 8-Core
56th
11
11
Intel Core i7-6800K
55th
6
11
AMD Ryzen 5 3600XT 6-Core
55th
6
12
Intel Core i3-10100
54th
6
12
Intel Core i7-4790K
53rd
6
12
2 x Intel Xeon Gold 5220R
53rd
6
12
2 x Intel Xeon Platinum 8280
52nd
13
12
Median
50th
12
Intel Core i7-8850H
50th
12
12 +/- 1
Intel Core i3-8100
50th
6
12
Intel Core i7-5960X
50th
4
12
Loongson-3A6000
49th
8
12
AMD Ryzen Threadripper 2990WX 32-Core
49th
6
12
Intel Xeon E3-1280 v5
49th
6
12
AMD Ryzen 7 4800H
48th
10
12 +/- 1
Intel Xeon E3-1245 v5
47th
6
12
Intel Xeon Silver 4216
47th
7
12 +/- 1
Intel Xeon E5-2687W v3
46th
6
12
Intel Core i5-4670
46th
7
12
Intel Xeon E-2278GEL
46th
6
13
AMD Ryzen Threadripper 2970WX 24-Core
45th
6
13
Intel Core i5-6500
45th
6
13
Intel Xeon E3-1231 v3
44th
6
13
Intel Core i7-8565U
43rd
6
13 +/- 1
AMD Ryzen 3 1300X
43rd
7
14
AMD Ryzen 5 2600 Six-Core
42nd
4
14
AMD Ryzen 7 1800X Eight-Core
42nd
3
14
Intel Core i5-7600K
41st
6
14
AMD Ryzen 7 2700X Eight-Core
40th
5
14
POWER9 4-Core
40th
4
14
Intel Core i7-8700
39th
22
14
2 x Intel Xeon E5-2680 v2
38th
3
14 +/- 1
AMD Ryzen 7 2700 Eight-Core
38th
7
14 +/- 1
Intel Xeon E3-1235L v5
36th
3
15
AMD Ryzen 7 1700 Eight-Core
36th
11
15
AMD EPYC 7601 32-Core
35th
9
15
2 x AMD EPYC 7601 32-Core
35th
4
15
AMD Ryzen 5 3400G
34th
9
15 +/- 2
AMD Ryzen 3 2200G
34th
10
15 +/- 1
AMD EPYC 7551 32-Core
34th
4
15
HUAWEI Kunpeng 920
33rd
8
16 +/- 1
2 x Intel Xeon E5-2630 v4
33rd
4
16
AMD Ryzen 5 4500U
32nd
5
16
Intel Core i7-5600U
29th
6
17
Intel Core i7-8700B
26th
9
19
Low-Tier
25th
> 19
Loongson-3A5000
25th
6
19
Intel Xeon E5-2609 v4
24th
7
20
AMD Athlon 3000G
23rd
3
22 +/- 2
Phytium FT-2000
22nd
4
22
AMD A10-7850K APU
18th
7
25
Intel Core i3-3110M
17th
11
25 +/- 2
Intel Core i5-10500
15th
19
27 +/- 1
Ampere eMAG ARMv8 32-Core
10th
11
36
2 x Intel Xeon E5-2620 v2
7th
45
39
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 RNA1600 Results Range From 2 To 1162 Seconds2367010413817220624027430834237641044447851254658061464868271675078481885288692095498810221056109011241158119230060090012001500

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-Time612182430Min: 1 / Avg: 1.96 / Max: 27

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 1.1%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsMultiple Sequence Alignment - LSU RNADeviation3691215Min: 0 / Avg: 1.1 / 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 RNA24681216202432640.76671.53342.30013.06683.8335

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, Apple M2 Pro, Apple M3 Pro
DEC Alpha
alpha
Alpha
ARMv8 64-bit
aarch64
ARMv8 8-Core, ARMv8 Cortex-A72 16-Core, ARMv8 Cortex-A72 4-Core, ARMv8 Cortex-A76 4-Core, ARMv8 Neoverse-N1, ARMv8 Neoverse-N1 160-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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