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

20 Seconds

Average Run Time

1 Minute, 10 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

250k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms

* 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 28 November 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

HPC - High Performance Computing

CPU Massive

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 728 public results since 5 May 2021 with the latest data as of 3 November 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

AMD Ryzen 5 7600X 6-Core

97th

AMD Ryzen 9 7950X 16-Core

97th

79 ^{+/- 2}

AMD Ryzen 9 7900X 12-Core

97th

AMD EPYC 72F3 8-Core

94th

Intel Core i9-13900K

93rd

88 ^{+/- 3}

AMD Ryzen 7 5800X 8-Core

92nd

90 ^{+/- 1}

Intel Core i5-13600K

90th

91 ^{+/- 1}

AMD Ryzen 7 5800X3D 8-Core

88th

AMD Ryzen 5 5600X 6-Core

88th

92 ^{+/- 5}

Intel Core i9-12900K

85th

94 ^{+/- 4}

AMD Ryzen 9 5900X 12-Core

85th

94 ^{+/- 4}

Intel Core i5-12600K

85th

94 ^{+/- 3}

AMD Ryzen 7 5700G

82nd

98 ^{+/- 3}

AMD Ryzen 9 5950X 16-Core

81st

99 ^{+/- 6}

AMD Ryzen 5 5600G

81st

99 ^{+/- 3}

AMD EPYC 7F32 8-Core

78th

100

AMD EPYC 7F52 16-Core

78th

100

Intel Core i7-7740K

76th

101

Mid-Tier

75th

> 101

Intel Core i5-13400

73rd

103 ^{+/- 1}

Intel Core i9-10900K

70th

107

AMD Ryzen Threadripper 3970X 32-Core

68th

110

Intel Core i9-9900KS

66th

113

AMD Ryzen 9 3950X 16-Core

66th

113 ^{+/- 9}

AMD Ryzen 7 3700X 8-Core

66th

114 ^{+/- 10}

Intel Core i3-7100

65th

117

AMD Ryzen 5 3600XT 6-Core

63rd

119

Intel Core i5-10600K

61st

121

Intel Xeon E-2288G

60th

123

Intel Core i7-7700K

60th

123

AMD Ryzen 5 3400G

58th

124

AMD Ryzen 3 1300X

58th

126

Intel Core i7-8700B

56th

127 ^{+/- 15}

Intel Core i7-8086K

54th

129

Intel Core i7-8700K

54th

129

Intel Core i9-10980XE

54th

129 ^{+/- 4}

AMD Ryzen Threadripper 2950X 16-Core

53rd

130 ^{+/- 2}

Intel Core i5-9400F

52nd

131 ^{+/- 9}

Intel Core i5-7600K

52nd

131

Median

50th

135

Intel Core i3-10100

49th

136

AMD Ryzen 5 4500U

48th

137 ^{+/- 1}

AMD Ryzen 7 PRO 5850U

48th

137 ^{+/- 6}

Intel Core i5-8400

48th

138

Intel Xeon Gold 6226R

46th

140

2 x Intel Xeon Gold 6254

45th

141 ^{+/- 1}

Intel Xeon E3-1275 v6

45th

141

AMD Ryzen 3 2200G

43rd

142 ^{+/- 15}

Intel Xeon E3-1231 v3

43rd

142

Intel Core i3-8100

42nd

143

Intel Xeon E3-1270 v5

42nd

143

AMD Ryzen 5 2400G

40th

144 ^{+/- 1}

Intel Xeon E3-1260L v5

39th

147

Intel Core i9-7980XE

37th

149

Intel Core i7-1165G7

37th

149 ^{+/- 15}

AMD Ryzen 3 3200U

37th

149

AMD EPYC 7742 64-Core

36th

150 ^{+/- 1}

Intel Core i7-6800K

36th

151

Intel Core i3-4130

36th

151

Intel Core i7-4770K

33rd

153 ^{+/- 1}

Intel Xeon E3-1280 v5

33rd

153

Intel Core i7-9750H

31st

154

AMD Ryzen 7 2700 Eight-Core

31st

154 ^{+/- 2}

AMD Ryzen Threadripper 2990WX 32-Core

31st

154 ^{+/- 5}

Intel Core i5-6500

30th

155

Intel Xeon E3-1245 v5

28th

156 ^{+/- 4}

AMD Ryzen 7 4700U

27th

157 ^{+/- 1}

Low-Tier

25th

> 160

AMD Ryzen Threadripper 2970WX 24-Core

25th

161

Intel Core i7-4960X

23rd

166

Intel Core i7-5960X

23rd

168

Intel Core i7-3770K

22nd

169

AMD Ryzen 7 1700 Eight-Core

22nd

170 ^{+/- 14}

Intel Core i7-8550U

20th

174 ^{+/- 6}

Intel Core i7-8565U

20th

176 ^{+/- 2}

2 x Intel Xeon Gold 5220R

20th

176

Intel Xeon Silver 4216

18th

182

Intel Core i7-10700T

17th

185 ^{+/- 1}

Intel Xeon E3-1235L v5

16th

187

Intel Xeon E5-2687W v3

15th

188

2 x Intel Xeon E5-2680 v2

14th

192 ^{+/- 10}

2 x AMD EPYC 7601 32-Core

14th

192 ^{+/- 13}

Intel Core i7-1065G7

14th

197 ^{+/- 7}

Intel Core i3-3110M

8th

237 ^{+/- 21}

Intel Xeon E5-2609 v4

7th

261

AMD FX-8150 Eight-Core

6th

270 ^{+/- 3}

4 x AMD Opteron 8378

5th

291

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 11 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.

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.4%.

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.

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)

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)

World bench 30 Systems - 11 Benchmark Results	AMD Ryzen 7 PRO 5850U - LENOVO 20X7003WFR - AMD Renoir Fedora Linux 36 - 5.18.16-200.fc36.x86_64 - KDE Plasma 5.25.4
intel-4690k 13 Systems - 102 Benchmark Results	AMD Ryzen 7 1700 Eight-Core - ASUS CROSSHAIR VI HERO - AMD Family 17h ManjaroLinux 18.0.2 - 4.19.13-1-MANJARO - Xfce 4.13
phoronix 2 Systems - 21 Benchmark Results	Intel Xeon E5-1650 v2 - Apple Mac-F60DEB81FF30ACF6 - Intel Xeon E7 v2 Ubuntu 20.04 - 5.15.0-88-generic - GNOME Shell 3.36.9
Intel Core i7-12700H Benchmarks 1 System - 4 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
Intel Core i7-12700H + Intel ADL GT2 4GB + HP 89C0 (U97 Ver. 01.08.00 BIOS) 1 System - 6 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
Intel Core i7-12700H Benchmarks 1 System - 4 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
HP 89C0 (U97 Ver. 01.08.00 BIOS) On Fedora Linux 39 1 System - 10 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
Fedora Linux 39 Performance 1 System - 4 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
Intel Core i7-12700H On Fedora Linux 39 1 System - 4 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
Fedora Linux 39 Performance 1 System - 18 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
Fedora Linux 39 Performance 1 System - 3 Benchmark Results	Intel Core i7-12700H - HP 89C0 - Intel Alder Lake PCH Fedora Linux 39 - 6.5.11-300.fc39.x86_64 - KDE Plasma 5.27.9
phoronix 2 Systems - 21 Benchmark Results	AMD Phenom II X4 945 - Gigabyte GA-MA78GM-S2H - 6144MB Calculate Linux Desktop 11.15 GNOME - 3.3.3-calculate - GNOME Shell 3.2.2.1
GCC Clang Intel Skylake Compiler Perf Featured Compiler Comparison	GCC 4.9.3 - GCC 5.2.0 - GCC 6.0.0 20150830 - Clang 3.8.0
Intel Core i5 6600K Skylake CPU Tests 8 Systems - 11 Benchmark Results	AMD FX-8370 Eight-Core - ASRock 990FX Killer - AMD RD890 bridge Fedora 22 - 4.2.0-0.rc6.git0.1.fc24.x86_64 - GNOME Shell 3.16.3
result1 1 System - 1 Benchmark Result	Intel Core i5-7400 - ASUS H110M-R - Intel Xeon E3-1200 v6 Debian 11 - 5.10.0-26-amd64 - GNOME Shell 3.38.6

1235 may 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
3700X Mayt 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
tr 2970wx may 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
Ryzen 9 5950X Clang 12 vs. GCC 11 Benchmarks Featured Compiler Comparison	AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Fedora 34 - 5.11.20-300.fc34.x86_64 - GNOME Shell 40.1
AMD Ryzen 7900 Series Linux CPU Benchmarks 13 Systems - 333 Benchmark Results	Intel Core i5-12600K - ASUS ROG STRIX Z690-E GAMING WIFI - Intel Device 7aa7 Ubuntu 22.04 - 6.0.0-060000rc1daily20220820-generic - GNOME Shell 42.2
6500 May 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
3950x may 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
fx 8150 2021 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
xeon broadwell may 2021 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
12700k HPC+OpenCL AVX512 performance profiling Featured Disk Comparison	Intel Core i7-12700K - MSI PRO Z690-A DDR4 - Intel Device 7aa7 Pop 21.04 - 5.15.5-76051505-generic - GNOME Shell 3.38.4
gold may 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
7100 june 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
clearlinux-ryzen3-4350 6 Systems - 254 Benchmark Results	AMD Ryzen 3 PRO 4350G - ASRock B450M Pro4 - AMD Renoir Root Complex Clear Linux OS 35000 - 5.13.13-1070.native - GNOME Shell 40.4
Clear Compare BSD 2 Systems - 222 Benchmark Results	Intel Core i9-10980XE - Intel Sky Lake-E DMI3 Registers - 32GB FreeBSD - 13.0-RELEASE - Clang 11.0.1
2200G May 2021 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

Timed HMMer Search

Project Site

Test Created

Last Updated

Test Maintainer

Test Type

Average Install Time

Average Run Time

Test Dependencies

Accolades

Supported Platforms

Revision History

Suites Using This Test

Performance Metrics

Timed HMMer Search 3.3.2

Pfam Database Search

Does It Scale Well With Increasing Cores?

Notable Instruction Set Usage

Tested CPU Architectures

Recent Test Results

Most Popular Test Results