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

11 December 2020

Test Maintainer

Andrew Schofield

Test Type

Processor

Average Install Time

20 Seconds

Average Run Time

31 Seconds

Test Dependencies

C/C++ Compiler Toolchain

Accolades

200k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms

* 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.
Data current as of Fri, 26 Feb 2021 05:59:12 GMT.

Revision History

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

Scientific Computing

Bioinformatics

HPC - High Performance Computing

Performance Metrics

Analyze Test Configuration:

Timed HMMer Search 3.3.1

Pfam Database Search

OpenBenchmarking.org metrics for this test profile configuration based on 1,055 public results since 27 September 2020 with the latest data as of 19 February 2021.

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

# Matching Public Results

Seconds (Average)

AMD Ryzen 5 5600X 6-Core

97th

87 ^{+/- 7}

AMD Ryzen 9 5900X 12-Core

97th

90 ^{+/- 8}

AMD Ryzen 9 5950X 16-Core

97th

92 ^{+/- 9}

AMD Ryzen 7 5800X 8-Core

96th

93 ^{+/- 5}

Intel Core i9-10900K

93rd

96 ^{+/- 1}

Intel Core i9-9900KS

93rd

AMD Ryzen 7 3800XT 8-Core

89th

100 ^{+/- 3}

Intel Xeon E-2288G

88th

101 ^{+/- 2}

Intel Core i7-7740K

88th

101

Intel Core i7-7700K

86th

102

AMD Ryzen 3 3300X 4-Core

83rd

103

Intel Core i9-9900K

83rd

103

Intel Core i5-10600K

83rd

103

AMD Ryzen 7 3700X 8-Core

81st

105 ^{+/- 6}

AMD Ryzen 5 3600XT 6-Core

80th

106 ^{+/- 1}

Intel Core i9-10885H

80th

106

AMD Ryzen 9 3900X 12-Core

80th

106 ^{+/- 7}

AMD Ryzen 9 3900XT 12-Core

79th

107 ^{+/- 5}

Intel Core i7-8700B

79th

107 ^{+/- 1}

AMD Ryzen 9 3950X 16-Core

77th

109 ^{+/- 10}

Intel Core i7-8086K

77th

109

Intel Core i7-8700K

77th

109

Intel Core i3-10100

76th

110

Mid-Tier

75th

> 110

Intel Core i5-7600K

74th

111

AMD Ryzen 3 3100 4-Core

74th

111

AMD Ryzen Threadripper 2950X 16-Core

72nd

113

AMD Ryzen 5 4500U

71st

114 ^{+/- 8}

Intel Xeon E3-1275 v6

71st

114

Intel Core i7-5775C

69th

115 ^{+/- 2}

Intel Core i7-8565U

69th

115 ^{+/- 3}

AMD Ryzen 7 2700X Eight-Core

69th

115 ^{+/- 2}

AMD EPYC 7F32 8-Core

68th

116 ^{+/- 4}

AMD Ryzen 5 3400G

68th

116 ^{+/- 2}

Intel Core i3-7100

68th

116 ^{+/- 1}

Intel Core i7-9750H

66th

117

Apple M1

66th

117

AMD Ryzen 3 1300X

63rd

118 ^{+/- 2}

Intel Xeon E3-1270 v5

63rd

118 ^{+/- 1}

Intel Core i5-9400F

63rd

118

Intel Core i7-1065G7

58th

120

Intel Core i5-8400

58th

120

Intel Xeon E3-1240 v5

56th

122 ^{+/- 1}

Intel Core i7-8550U

56th

122 ^{+/- 1}

Intel Xeon E3-1280 v5

55th

123 ^{+/- 1}

Intel Core i7-4790K

55th

123 ^{+/- 2}

Intel Xeon E3-1260L v5

54th

125 ^{+/- 1}

Intel Core i3-8100

53rd

126

Intel Xeon E3-1245 v5

53rd

126

AMD EPYC 7F52 16-Core

53rd

126 ^{+/- 9}

Median

50th

127

AMD Ryzen 3 3200U

49th

128 ^{+/- 4}

AMD Ryzen 7 1800X Eight-Core

49th

128 ^{+/- 4}

AMD Ryzen 3 2200G

49th

128 ^{+/- 1}

Intel Core i7-5600U

48th

129

AMD Ryzen 5 2400G

48th

129 ^{+/- 8}

Intel Core i9-10980XE

47th

130 ^{+/- 11}

AMD Ryzen Threadripper 3970X 32-Core

47th

130 ^{+/- 10}

Intel Core i7-9700TE

46th

131

Intel Core i7-6800K

46th

131

AMD Ryzen Threadripper 3960X 24-Core

46th

131

Intel Core i5-6500

46th

131

AMD Ryzen 7 2700 Eight-Core

42nd

132 ^{+/- 7}

Intel Core i9-7960X

41st

133

Intel Core i7-7900X

41st

133

AMD Ryzen 7 1700 Eight-Core

40th

134 ^{+/- 11}

AMD EPYC 7262 8-Core

39th

136

Intel Core i7-4770K

37th

138

AMD EPYC 7232P 8-Core

37th

139 ^{+/- 6}

Intel Core i5-4670

37th

140 ^{+/- 1}

Intel Xeon E3-1231 v3

35th

141

AMD EPYC 7F72 24-Core

35th

142

Intel Core i7-6700HQ

33rd

145 ^{+/- 3}

AMD EPYC 7272 12-Core

33rd

145 ^{+/- 10}

AMD EPYC 7252 8-Core

33rd

145

AMD EPYC 7302P 16-Core

32nd

146 ^{+/- 11}

Intel Core i7-4960X

32nd

146 ^{+/- 2}

Intel Core i7-3770K

31st

147

AMD Ryzen Threadripper 2970WX 24-Core

30th

150

AMD EPYC 7282 16-Core

30th

151 ^{+/- 9}

Intel Core i3-4130

29th

152

Intel Xeon Platinum 8280

28th

154

Intel Xeon E3-1235L v5

26th

157

AMD EPYC 7402P 24-Core

26th

159 ^{+/- 12}

Low-Tier

25th

> 162

AMD Ryzen Threadripper 2990WX 32-Core

25th

162 ^{+/- 1}

Intel Core i9-7980XE

25th

163 ^{+/- 3}

Intel Xeon E5-1680 v3

25th

163

Intel Core i5-3470

24th

165 ^{+/- 3}

Intel Xeon Silver 4215R

23rd

166

AMD EPYC 7542 32-Core

22nd

167 ^{+/- 15}

Intel Core i7-2700K

22nd

168 ^{+/- 1}

Intel Core i5-2500K

22nd

169 ^{+/- 19}

Intel Xeon E5-2687W v3

22nd

169 ^{+/- 2}

Intel Xeon Gold 6226R

21st

170 ^{+/- 7}

Intel Xeon Gold 5217

21st

170

AMD EPYC 7502P 32-Core

21st

171 ^{+/- 14}

Intel Core i7-5960X

21st

172

AMD EPYC 7352 24-Core

19th

173

AMD EPYC 7502 32-Core

17th

177

AMD EPYC 7452 32-Core

16th

178

AMD EPYC 7532 32-Core

16th

178 ^{+/- 16}

2 x AMD EPYC 7F72 24-Core

15th

182 ^{+/- 9}

AMD Ryzen Threadripper 3990X 64-Core

15th

183 ^{+/- 14}

AMD FX-8370 Eight-Core

13th

192

Intel Core i5-2520M

12th

196 ^{+/- 1}

AMD A10-7870K Radeon R7 12 Compute Cores 4C

11th

198

AMD EPYC 7601 32-Core

11th

200 ^{+/- 1}

AMD EPYC 7552 48-Core

10th

202 ^{+/- 18}

AMD EPYC 7642 48-Core

10th

203 ^{+/- 18}

Intel Xeon Gold 5218

10th

204

Intel Xeon Silver 4214R

10th

204

Intel Xeon Silver 4216

10th

206 ^{+/- 22}

AMD A10-7850K APU

9th

208

AMD EPYC 7702 64-Core

8th

213 ^{+/- 19}

AMD FX-8150 Eight-Core

8th

214 ^{+/- 3}

2 x Intel Xeon Platinum 8280

7th

222 ^{+/- 5}

2 x Intel Xeon Gold 5220R

6th

224

AMD EPYC 7662 64-Core

5th

228 ^{+/- 18}

AMD EPYC 7742 64-Core

5th

231

Intel Xeon E5-2609 v4

3rd

240

2 x AMD EPYC 7601 32-Core

2nd

291 ^{+/- 1}

2 x AMD EPYC 7742 64-Core

1st

433 ^{+/- 14}

Based on OpenBenchmarking.org data, the selected test / test configuration (Timed HMMer Search 3.3.1 - Pfam Database Search) has an average run-time of 7 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.

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 DIVSD ADDSD CVTSD2SS CVTSS2SD SUBSD MOVD PSHUFD MOVDQA CVTDQ2PS MOVAPD PMULUDQ PADDQ COMISD CVTTSD2SI MOVDQU XORPD PSUBQ PSRLDQ ANDPD ANDNPD CMPNLESD ORPD 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

The test / benchmark does honor compiler flag changes.

Last automated analysis: 30 January 2021

This test profile binary relies on the shared libraries libm.so.6, libpthread.so.0, libc.so.6.

Raspberry Pi 4 vs. Intel Comet Lake 5 Systems - 71 Benchmark Results	Intel Pentium Gold G6400 - Gigabyte B460M DS3H - Intel Device 9b73 Debian 10 - 4.19.0-9-amd64 - X Server 1.20.4
Xeon E 8 Systems - 84 Benchmark Results	Intel Xeon E-2288G - Compulab SBC-ATCFL v1.2 - Intel Cannon Lake PCH Ubuntu 20.10 - 5.8.0-41-generic - GNOME Shell 3.38.2
OnLogic Helix 500 Linux benchmarks 2 Systems - 151 Benchmark Results	Intel Xeon E-2278GEL - Logic Supply RXM-181 - Intel Cannon Lake PCH Ubuntu 20.10 - 5.8.0-41-generic - GNOME Shell 3.38.2
Y 2 Systems - 14 Benchmark Results	Intel Core 2 6300 - ASUS P5LD2-VM - Intel 82945G Peppermint 10 - 5.0.0-37-generic - LXDE
Ubuntu 20.04 Performance 1 System - 2 Benchmark Results	AMD EPYC 7542 32-Core - UpCloud Cloud Server - Intel 440FX 82441FX PMC Ubuntu 20.04 - 5.4.0-58-generic - bochs-drmdrmfb
Raspberry Pi 4 vs. Intel Comet Lake 7 Systems - 67 Benchmark Results	Intel Celeron G5900 - Gigabyte B460M DS3H - Intel Device 9b73 Debian 10 - 4.19.0-9-amd64 - X Server 1.20.4
FreeBSD 12.2 vs. FreeBSD 13 BETA AMD EPYC Benchmarks 2 Systems - 119 Benchmark Results	AMD EPYC 7F52 16-Core - Supermicro Super Server 0123456789 - AMD [AMD] Starship FreeBSD - 12.2-RELEASE - Clang 10.0.1
FreeBSD 12.2 vs. FreeBSD 13 BETA Benchmarks 5 Systems - 131 Benchmark Results	Intel Xeon E-2278GEL - Logic Supply RXM-181 TBD by OEM - Intel FreeBSD - 13.0-BETA1 - Clang 11.0.1
Raspberry Pi 4 vs. Intel Comet Lake 5 Systems - 67 Benchmark Results	ARMv7 Cortex-A72 - BCM2711 Raspberry Pi 4 Model B Rev 1.1 - 2048MB Raspbian 10 - 5.4.51-v7l+ - LXDE 0.10.0
FreeBSD 12.2 vs. FreeBSD 13 BETA Benchmarks 4 Systems - 131 Benchmark Results	Intel Core i7-10700T - Insyde CometLake TBD by OEM - Intel FreeBSD - 12.2-RELEASE - Clang 10.0.1
FreeBSD 12.2 vs. FreeBSD 13 Benchmarks 3 Systems - 156 Benchmark Results	Intel Core i7-10700T - Insyde CometLake TBD by OEM - Intel FreeBSD - 12.2-RELEASE - Clang 10.0.1
Xeon Platinum Ubuntu 19.04 1 System - 143 Benchmark Results	2 x Intel Xeon Platinum 8280 - GIGABYTE MD61-SC2-00 v01000100 - Intel Sky Lake-E DMI3 Registers Ubuntu 19.04 - 5.0.0-38-generic - GNOME Shell 3.32.2

Sandy 3 Systems - 268 Benchmark Results	Intel Core i5-2520M - HP 161C - Intel 2nd Generation Core DRAM Ubuntu 18.04 - 4.18.0-20-generic - GNOME Shell 3.28.3
Apple M1 vs. AMD Renoir vs. Intel Tiger Lake 4 Systems - 99 Benchmark Results	AMD Ryzen 5 4500U - LENOVO LNVNB161216 - AMD Renoir Root Complex Ubuntu 20.10 - 5.9.1-050901-generic - GNOME Shell 3.38.1
Xeon E 8 Systems - 84 Benchmark Results	Intel Xeon E-2288G - Compulab SBC-ATCFL v1.2 - Intel Cannon Lake PCH Ubuntu 20.10 - 5.8.0-41-generic - GNOME Shell 3.38.2
OnLogic Helix 500 Linux benchmarks 2 Systems - 151 Benchmark Results	Intel Xeon E-2278GEL - Logic Supply RXM-181 - Intel Cannon Lake PCH Ubuntu 20.10 - 5.8.0-41-generic - GNOME Shell 3.38.2
TR 3960X WK 3 Systems - 46 Benchmark Results	AMD Ryzen Threadripper 3960X 24-Core - MSI Creator TRX40 - AMD Starship Ubuntu 20.04 - 5.9.0-rc5-14sep-patch - GNOME Shell 3.36.4
Pre 10.0 Xeon 3 Systems - 40 Benchmark Results	2 x Intel Xeon Gold 5220R - TYAN S7106 - Intel Sky Lake-E DMI3 Registers Ubuntu 20.04 - 5.9.0-050900rc6-generic - GNOME Shell 3.36.4
Core i9 10900K - Ubuntu 20.04 LTS vs. Ubuntu 20.10 2 Systems - 403 Benchmark Results	Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH Ubuntu 20.04 - 5.4.0-48-generic - GNOME Shell 3.36.4
Ryzen 9 3900XT Ubuntu 20.04 LTS vs. Ubuntu 20.10 3 Systems - 406 Benchmark Results	Intel Core i9-10900K - Gigabyte Z490 AORUS MASTER - Intel Comet Lake PCH Ubuntu 20.04 - 5.4.0-48-generic - GNOME Shell 3.36.4
Core i5 10600K October 3 Systems - 131 Benchmark Results	Intel Core i5-10600K - ASUS PRIME Z490M-PLUS - Intel Comet Lake PCH Ubuntu 20.04 - 5.4.0-45-generic - GNOME Shell 3.36.4
Ryzen 5 3600X 10.0 L 3 Systems - 31 Benchmark Results	AMD Ryzen 5 3600XT 6-Core - MSI X470 GAMING M7 AC - AMD Starship Ubuntu 20.04 - 5.8.0-050800-generic - GNOME Shell 3.36.4
Apple M1 Mac Mini vs. AMD Renoir vs. Intel Tiger Lake 5 Systems - 99 Benchmark Results	AMD Ryzen 5 4500U - LENOVO LNVNB161216 - AMD Renoir Root Complex Ubuntu 20.10 - 5.9.1-050901-generic - GNOME Shell 3.38.1
7700K Intel 2020 3 Systems - 202 Benchmark Results	Intel Core i7-7700K - MSI Z270-A PRO - Intel Xeon E3-1200 v6 Ubuntu 20.04 - 5.8.14-050814-generic - GNOME Shell 3.36.4

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 3.3.1

Pfam Database Search

Does It Scale Well With Increasing Cores?

Notable Instruction Set Usage

Recent Test Results

Most Popular Test Results

User Comments