Timed HMMer Search

This test searches through the Pfam database of profile hidden markov models. The search finds the domain structure of Drosophila Sevenless protein.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark hmmer.

Project Site

hmmer.org

Test Created

6 December 2010

Last Updated

5 May 2021

Test Maintainer

Andrew Schofield 

Test Type

Processor

Average Install Time

23 Seconds

Average Run Time

28 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

200k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms

Public Result Uploads *Reported Test Completions **Reported Installs **Test Profile Page Views ***OpenBenchmarking.orgEventsTimed HMMer Search Popularity Statisticspts/hmmer2010.122011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.042021.082021.122022.042022.082022.1216K32K48K64K80K
* 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 17 March 2023.

Revision History

pts/hmmer-1.3.0   [View Source]   Wed, 05 May 2021 17:11:53 GMT
Update against HMMER 3.3.2 upstream, switch to MPI version rather than the threads.

pts/hmmer-1.2.2   [View Source]   Fri, 11 Dec 2020 16:35:20 GMT
BSD fix.

pts/hmmer-1.2.1   [View Source]   Fri, 13 Nov 2020 10:22:20 GMT
Add macOS support.

pts/hmmer-1.2.0   [View Source]   Sun, 27 Sep 2020 13:46:44 GMT
Update against HMMer 3.3.1 upstream, other install/build improvements.

pts/hmmer-1.1.2   [View Source]   Sat, 09 Sep 2017 11:45:43 GMT
Update download links

pts/hmmer-1.1.1   [View Source]   Thu, 25 Aug 2016 14:16:23 GMT
Update download links

pts/hmmer-1.1.0   [View Source]   Mon, 06 Dec 2010 14:53:06 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 HMMer Search 3.3.2

Pfam Database Search

OpenBenchmarking.org metrics for this test profile configuration based on 654 public results since 5 May 2021 with the latest data as of 16 March 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)
AMD Ryzen 7 7700X 8-Core
100th
9
77
AMD Ryzen 9 7950X 16-Core
97th
9
79 +/- 2
AMD Ryzen 5 7600X 6-Core
97th
6
79
AMD Ryzen 9 7900X 12-Core
96th
7
80
Intel Core i9-13900K
94th
10
86 +/- 1
AMD EPYC 72F3 8-Core
93rd
4
87
AMD Ryzen 5 5600X 6-Core
92nd
3
89
AMD Ryzen 7 5800X 8-Core
91st
7
90 +/- 1
Intel Core i5-13600K
89th
9
91 +/- 1
AMD Ryzen 7 5800X3D 8-Core
87th
4
92
Intel Core i9-12900K
84th
13
94 +/- 4
AMD Ryzen 9 5900X 12-Core
84th
9
94 +/- 4
Intel Core i5-12600K
84th
4
94 +/- 3
AMD Ryzen 9 5950X 16-Core
83rd
33
96 +/- 4
AMD Ryzen 7 5700G
82nd
4
98 +/- 3
AMD EPYC 7F32 8-Core
77th
5
100
AMD EPYC 7F52 16-Core
77th
4
100
Intel Core i7-7740K
76th
3
101
Mid-Tier
75th
> 101
Intel Core i5-13400
73rd
4
103 +/- 1
Intel Core i9-10900K
70th
5
107
AMD Ryzen Threadripper 3970X 32-Core
68th
3
110
AMD Ryzen 9 3950X 16-Core
66th
9
113 +/- 9
Intel Core i9-9900KS
66th
3
113
AMD Ryzen 7 3700X 8-Core
66th
11
114 +/- 10
Intel Core i3-7100
65th
7
117
AMD Ryzen 5 3600XT 6-Core
63rd
3
119
Intel Core i5-10600K
61st
3
121
Intel Core i7-7700K
60th
4
123
Intel Xeon E-2288G
60th
3
123
AMD Ryzen 5 3400G
59th
3
124
AMD Ryzen 3 1300X
58th
3
126
Intel Core i7-8700B
56th
5
127 +/- 15
Intel Core i7-8700K
54th
3
129
Intel Core i9-10980XE
54th
9
129 +/- 4
Intel Core i7-8086K
54th
3
129
AMD Ryzen Threadripper 2950X 16-Core
53rd
8
130 +/- 2
Intel Core i5-7600K
52nd
3
131
Intel Core i5-1135G7
51st
4
134 +/- 1
Median
50th
134
Intel Core i5-9400F
48th
3
136
Intel Core i3-10100
48th
3
136
AMD Ryzen 5 4500U
47th
4
137 +/- 1
AMD Ryzen 7 PRO 5850U
47th
25
137 +/- 6
Intel Core i5-8400
47th
3
138
Intel Xeon Gold 6226R
45th
4
140
2 x Intel Xeon Gold 6254
44th
4
141 +/- 1
Intel Xeon E3-1275 v6
44th
4
141
Intel Xeon E3-1231 v3
42nd
3
142
AMD Ryzen 3 2200G
42nd
8
142 +/- 15
Intel Core i3-8100
41st
4
143
Intel Xeon E3-1270 v5
41st
6
143
AMD Ryzen 5 2400G
39th
5
144 +/- 1
Intel Xeon E3-1260L v5
37th
3
147
Intel Core i9-7980XE
36th
3
149
Intel Core i7-1165G7
36th
6
149 +/- 15
AMD Ryzen 3 3200U
36th
3
149
AMD EPYC 7742 64-Core
35th
9
150 +/- 1
Intel Core i7-6800K
34th
3
151
Intel Core i3-4130
34th
3
151
Intel Xeon E3-1280 v5
32nd
6
153
Intel Core i7-4770K
32nd
7
153 +/- 1
AMD Ryzen Threadripper 2990WX 32-Core
30th
3
154 +/- 5
Intel Core i7-9750H
30th
3
154
AMD Ryzen 7 2700 Eight-Core
29th
3
155
Intel Core i5-6500
29th
4
155
Intel Xeon E3-1245 v5
26th
7
156 +/- 4
AMD Ryzen 7 4700U
26th
3
157 +/- 1
Low-Tier
25th
> 157
AMD Ryzen Threadripper 2970WX 24-Core
23rd
3
161
Intel Core i7-4960X
22nd
3
166
Intel Core i7-5960X
21st
3
168
Intel Core i7-3770K
21st
4
169
AMD Ryzen 7 1700 Eight-Core
20th
10
170 +/- 14
Intel Core i7-8550U
19th
5
174 +/- 6
Intel Core i7-8565U
19th
4
176 +/- 2
2 x Intel Xeon Gold 5220R
19th
3
176
Intel Xeon Silver 4216
16th
3
182
Intel Core i7-10700T
16th
4
185 +/- 1
Intel Xeon E3-1235L v5
15th
3
187
2 x Intel Xeon E5-2680 v2
14th
3
188 +/- 9
Intel Xeon E5-2687W v3
14th
3
188
2 x AMD EPYC 7601 32-Core
13th
4
192 +/- 13
Intel Core i7-1065G7
13th
3
197 +/- 7
Intel Core i3-3110M
8th
20
237 +/- 21
Intel Xeon E5-2609 v4
6th
3
261
AMD FX-8150 Eight-Core
5th
3
270 +/- 3
4 x AMD Opteron 8378
4th
5
291
OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search654 Results Range From 77 To 36780 Seconds7781215472282301737524487522259576692742781628897963210367111021183712572133071404214777155121624716982177171845219187199222065721392221272286223597243322506725802265372727228007287422947730212309473168232417331523388734622353573609236827140280420560700

Based on OpenBenchmarking.org data, the selected test / test configuration (Timed HMMer Search 3.3.2 - Pfam Database Search) has an average run-time of 9 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 BenchmarkPfam Database SearchRun-Time20406080100Min: 4 / Avg: 8.88 / Max: 101

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.3%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsPfam Database SearchDeviation510152025Min: 0 / Avg: 0.28 / Max: 21

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 HMMer Search CPU Core ScalingPfam Database Search246810160.44790.89581.34371.79162.2395

Notable Instruction Set Usage

Notable instruction set extensions supported by this test, based on an automatic analysis by the Phoronix Test Suite / OpenBenchmarking.org analytics engine.

Instruction Set
Support
Instructions Detected
SSE2 (SSE2)
Used by default on supported hardware.
 
UCOMISD CVTSI2SD MULSD PUNPCKLQDQ MOVDQU DIVSD ADDSD CVTSD2SS CVTSS2SD SUBSD MOVD PSHUFD MOVDQA CVTDQ2PS MOVAPD PMULUDQ PADDQ COMISD CVTTSD2SI XORPD PSUBQ PSRLDQ ANDPD ANDNPD ORPD CMPNLESD PSLLDQ PSHUFLW UNPCKLPD CVTPD2PS CVTPS2PD MULPD ADDPD MAXSD MINSD MOVUPD SUBPD UNPCKHPD SQRTSD CMPLTSD DIVPD SHUFPD CVTDQ2PD CVTTPS2DQ
SSE 4.2 (SSE4_2)
Requires passing a supported compiler/build flag (verified with targets: sandybridge, skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since at least 2010.
Found on AMD processors since Bulldozer (2011).
 
POPCNT
Advanced Vector Extensions (AVX)
Requires passing a supported compiler/build flag (verified with targets: sandybridge, skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Sandy Bridge (2011).
Found on AMD processors since Bulldozer (2011).
 
VZEROUPPER VEXTRACTF128 VINSERTF128 VBROADCASTSS VPERMILPS VBROADCASTSD VPERM2F128 VPERMILPD
Advanced Vector Extensions 2 (AVX2)
Requires passing a supported compiler/build flag (verified with targets: skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).
 
VPBROADCASTD VPBROADCASTQ VPERMQ VEXTRACTI128 VPBROADCASTB VPBROADCASTW VINSERTI128 VPERM2I128 VPERMD VPSLLVD VPGATHERDD VPERMPD VPGATHERDQ VPSRLVQ
FMA (FMA)
Requires passing a supported compiler/build flag (verified with targets: skylake, tigerlake, cascadelake, sapphirerapids, alderlake, znver2, znver3).
Found on Intel processors since Haswell (2013).
Found on AMD processors since Bulldozer (2011).
 
VFMADD231SS VFMADD132SD VFMADD213SS VFMADD231SD VFNMADD231SD VFNMADD132SD VFMADD132SS VFMADD231PS VFMADD132PS VFMSUB132SD VFMADD132PD VFMADD213SD VFMSUB231SD VFNMADD213SD VFNMADD231PD VFNMADD132PD VFMADD213PD VFMADD213PS VFNMADD231SS VFNMADD132PS VFNMADD231PS
Advanced Vector Extensions 512 (AVX512)
Requires passing a supported compiler/build flag (verified with targets: cascadelake, sapphirerapids).
 
(ZMM REGISTER USE)
The test / benchmark does honor compiler flag changes.
Last automated analysis: 17 January 2022

This test profile binary relies on the shared libraries libm.so.6, libmpi.so.40, libc.so.6, libopen-rte.so.40, libopen-pal.so.40, libhwloc.so.15, libz.so.1, libudev.so.1.

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)
Intel / AMD x86 32-bit
i686
(Many Processors)

Recent Test Results

OpenBenchmarking.org Results Compare

1 System - 1 Benchmark Result

AMD Ryzen 3 2200G - Oracle VirtualBox v1.2 - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 5.19.0-35-generic - GNOME Shell 42.5

1 System - 1 Benchmark Result

Intel Core i5-8250U - HP 832B v23.47 - Intel Xeon E3-1200 v6

Ubuntu 22.04 - 5.15.0-60-generic - X Server 1.21.1.3

1 System - 1 Benchmark Result

Common KVM - Red Hat KVM - Intel 440FX 82441FX PMC

Ubuntu 20.04 - 5.4.0-144-generic - 1.1.182

1 System - 1 Benchmark Result

Intel Xeon Gold 6348 - QEMU Standard PC - Intel 440FX 82441FX PMC

Ubuntu 20.04 - 5.4.0-144-generic - 1.1.182

3 Systems - 345 Benchmark Results

Intel Core i5-13600K - ASUS ROG STRIX B760-A GAMING WIFI D4 - Intel Device 7a27

ManjaroLinux 22.0.4 - 6.1.12-1-MANJARO - KDE Plasma 5.26.5

3 Systems - 345 Benchmark Results

2 Systems - 345 Benchmark Results

Intel Core i5-13600K - ASUS ROG STRIX B760-F GAMING WIFI - Intel Device 7a27

ManjaroLinux 22.0.4 - 6.1.12-1-MANJARO - KDE Plasma 5.26.5

1 System - 1 Benchmark Result

2 x Intel Xeon L5640 - Oracle ASSY X4170 - Intel 5520 I

Ubuntu 20.04 - 5.13.0-48-generic - GNOME Shell 3.36.9

29 Systems - 11 Benchmark Results

AMD Ryzen 7 PRO 5850U - LENOVO 20X7003WFR - AMD Renoir

Gentoo 2.8 - 5.17.5-gentoo-clang - KDE Plasma 5.24.4

1 System - 342 Benchmark Results

AMD Ryzen 9 7950X 16-Core - ASUS TUF GAMING X670E-PLUS WIFI - AMD Device 14d8

EndeavourOS rolling - 6.1.12-arch1-1 - Cinnamon 5.6.7

1 System - 345 Benchmark Results

AMD Ryzen 9 6900HX - Shenzhen Meigao Electronic Equipment F7BFC - AMD 17h-19h PCIe Root Complex

ManjaroLinux 22.0.3 - 6.2.0-2-MANJARO - KDE Plasma 5.26.5

8 Systems - 45 Benchmark Results

AMD Ryzen 7 1700 Eight-Core - Gigabyte AB350M-Gaming 3-CF - AMD 17h

Ubuntu 20.04 - 5.15.30-hdr - 1.1.182

7 Systems - 45 Benchmark Results

AMD Ryzen 7 1700 Eight-Core - Gigabyte AB350M-Gaming 3-CF - AMD 17h

Ubuntu 20.04 - 5.15.30-hdr - 1.1.182

2 Systems - 21 Benchmark Results

2 x AMD EPYC 7H12 64-Core - Dell PowerEdge R7525 [0590KW] - AMD Starship

CentOS 7.9.2009 - 5.4.230-1.el7.elrepo.x86_64 - X Server

6 Systems - 45 Benchmark Results

AMD Ryzen 7 1700 Eight-Core - Gigabyte AB350M-Gaming 3-CF - AMD 17h

Ubuntu 20.04 - 5.15.30-hdr - 1.1.182

Most Popular Test Results

OpenBenchmarking.org Results Compare

3 Systems - 37 Benchmark Results

Intel Xeon E3-1235L v5 - ASRockRack C236M WS - Intel Xeon E3-1200 v5

Ubuntu 20.04 - 5.8.0-050800-generic - GNOME Shell 3.36.4

3 Systems - 78 Benchmark Results

AMD Ryzen 7 3700X 8-Core - Gigabyte A320M-S2H-CF - AMD Starship

Ubuntu 20.04 - 5.8.1-050801-generic - GNOME Shell 3.36.4

4 Systems - 11 Benchmark Results

AMD Ryzen Threadripper 2970WX 24-Core - Gigabyte X399 AORUS Gaming 7 - AMD 17h

Ubuntu 20.04 - 5.9.0-050900rc6daily20200926-generic - GNOME Shell 3.36.4

4 Systems - 82 Benchmark Results

Intel Core i5-6500 - Gigabyte Z170M-D3H-CF - Intel Xeon E3-1200 v5

Ubuntu 20.04 - 5.9.0-050900rc7daily20200929-generic - GNOME Shell 3.36.4

3 Systems - 107 Benchmark Results

AMD FX-8150 Eight-Core - ASUS M5A78L-M LX PLUS - AMD RS780 + SB7x0

Ubuntu 20.10 - 5.8.0-33-generic - GNOME Shell 3.38.1

13 Systems - 333 Benchmark Results

AMD Ryzen 9 7950X 16-Core - ASUS ROG CROSSHAIR X670E HERO - AMD Device 14d8

Ubuntu 22.04 - 6.0.0-060000rc1daily20220820-generic - GNOME Shell 42.2

6 Systems - 36 Benchmark Results

AMD Ryzen 9 3950X 16-Core - ASUS ROG CROSSHAIR VII HERO - AMD Starship

Ubuntu 20.04 - 5.9.0-050900rc6daily20200922-generic - GNOME Shell 3.36.4

2 Systems - 38 Benchmark Results

Intel Xeon Gold 6226R - Supermicro X11SPL-F v1.02 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.10 - 5.11.0-rc4-max-boost-inv-patch - GNOME Shell 3.38.1

6 Systems - 254 Benchmark Results

AMD Ryzen 3 PRO 4350G - ASRock B450M Pro4 - AMD Renoir Root Complex

Clear Linux OS 34550 - 5.10.32-1035.native - GNOME Shell 40.0

3 Systems - 164 Benchmark Results

Intel Xeon E5-2609 v4 - MSI X99A RAIDER - Intel Xeon E7 v4

Ubuntu 20.04 - 5.9.0-050900rc6daily20200926-generic - GNOME Shell 3.36.2

2 Systems - 222 Benchmark Results

Intel Core i9-10980XE - ASRock X299 Steel Legend - Intel Sky Lake-E DMI3 Registers

Clear Linux OS 35320 - 5.15.4-1100.native - GNOME Shell 41.1

4 Systems - 193 Benchmark Results

AMD Ryzen 3 2200G - ASUS PRIME B350M-E - AMD Raven

Ubuntu 20.10 - 5.8.0-38-generic - GNOME Shell 3.38.1

3 Systems - 117 Benchmark Results

Intel Core i3-7100 - Gigabyte B250M-DS3H-CF - Intel Xeon E3-1200 v6

Ubuntu 20.10 - 5.8.0-48-generic - GNOME Shell 3.38.1
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