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

24 Seconds

Average Run Time

31 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

200k+ 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 current as of 16 September 2021.

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

Scientific Computing

HPC - High Performance 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 351 public results since 5 May 2021 with the latest data as of 1 September 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

# Compatible Public Results

Seconds (Average)

AMD Ryzen 7 5800X 8-Core

99th

91 ^{+/- 1}

AMD Ryzen 9 5950X 16-Core

96th

95 ^{+/- 2}

AMD Ryzen 9 5900X 12-Core

96th

96 ^{+/- 4}

Intel Core i7-7740K

90th

101

Intel Core i9-10900K

84th

107

AMD Ryzen Threadripper 3970X 32-Core

81st

110

Intel Core i9-9900KS

80th

113

AMD Ryzen 7 3700X 8-Core

80th

113 ^{+/- 10}

Intel Core i3-7100

79th

117

Mid-Tier

75th

> 118

AMD Ryzen 9 3950X 16-Core

75th

119

AMD Ryzen 5 3600XT 6-Core

75th

119

Intel Core i5-10600K

72nd

121

Intel Core i7-7700K

71st

123

Intel Xeon E-2288G

71st

123

AMD Ryzen 5 3400G

68th

124

AMD Ryzen 3 1300X

68th

126

Intel Core i7-8700K

64th

129

Intel Core i7-8086K

64th

129

Intel Core i9-10980XE

63rd

130 ^{+/- 4}

AMD Ryzen Threadripper 2950X 16-Core

63rd

130 ^{+/- 1}

Intel Core i5-7600K

62nd

131

Intel Core i5-1135G7

61st

134 ^{+/- 1}

Intel Core i3-10100

59th

136

Intel Core i5-9400F

59th

136

AMD Ryzen 5 4500U

57th

137

Intel Core i5-8400

57th

138

Intel Xeon Gold 6226R

55th

140

Intel Xeon E3-1275 v6

54th

141

Intel Xeon E3-1231 v3

53rd

142

Intel Xeon E3-1270 v5

53rd

143

Intel Core i3-8100

53rd

143

Median

50th

144

AMD Ryzen 5 2400G

49th

144 ^{+/- 1}

Intel Xeon E3-1260L v5

48th

147

AMD Ryzen 3 3200U

46th

149

Intel Core i9-7980XE

46th

149

Intel Core i7-1165G7

46th

149 ^{+/- 15}

Intel Core i7-6800K

45th

151

Intel Core i3-4130

45th

151

Intel Xeon E3-1280 v5

42nd

153

AMD Ryzen Threadripper 2990WX 32-Core

38th

154 ^{+/- 5}

Intel Core i7-4770K

38th

154

Intel Core i7-9750H

38th

154

Intel Core i5-6500

36th

155

AMD Ryzen 7 2700 Eight-Core

36th

155

AMD Ryzen 3 2200G

32nd

156

Intel Xeon E3-1245 v5

30th

157

AMD Ryzen 7 4700U

30th

157 ^{+/- 1}

AMD Ryzen Threadripper 2970WX 24-Core

27th

161

Intel Core i7-4960X

26th

166

Low-Tier

25th

> 166

Intel Core i7-3770K

24th

169

Intel Core i7-8550U

23rd

170 ^{+/- 2}

Intel Core i7-8565U

22nd

176 ^{+/- 2}

2 x Intel Xeon Gold 5220R

22nd

176

Intel Xeon Silver 4216

18th

182

AMD Ryzen 7 1700 Eight-Core

18th

183 ^{+/- 21}

Intel Core i7-10700T

17th

185 ^{+/- 1}

Intel Xeon E3-1235L v5

16th

187

Intel Xeon E5-2687W v3

14th

188

2 x AMD EPYC 7601 32-Core

13th

192 ^{+/- 13}

Intel Core i7-1065G7

13th

197 ^{+/- 7}

Intel Core i3-3110M

6th

237 ^{+/- 21}

Intel Xeon E5-2609 v4

5th

261

AMD FX-8150 Eight-Core

3rd

270 ^{+/- 3}

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 6 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 0.1%.

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 COMISD CVTSI2SD MULSD PUNPCKLQDQ MOVDQU DIVSD ADDSD CVTSD2SS CVTSS2SD SUBSD MOVD PSHUFD MOVDQA CVTDQ2PS MOVAPD PMULUDQ PADDQ CVTTSD2SI XORPD PSUBQ PSRLDQ ANDPD ANDNPD ORPD CMPNLESD PSLLDQ PSHUFLW UNPCKLPD CVTPS2PD MULPD ADDPD CVTPD2PS 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, 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, 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, znver2, znver3).
Found on Intel processors since Haswell (2013).
Found on AMD processors since Excavator (2016).

VPBROADCASTD VPBROADCASTQ VPERMQ VEXTRACTI128 VPBROADCASTB VPBROADCASTW VPERM2I128 VPERMD VPSLLVD VPGATHERDD VINSERTI128 VPERMPD VPGATHERDQ VPSRLVQ

FMA (FMA)

VFMADD231SS VFMADD132SD VFMADD213SS VFMADD231SD VFNMADD231SD VFNMADD132SD VFMADD132SS VFMADD231PS VFMADD132PS VFMSUB132SD VFMADD132PD VFMADD213SD VFMSUB231SD VFNMADD213SD VFNMADD231PD VFNMADD132PD VFMADD213PD VFMADD213PS VFNMADD231SS VFNMADD231PS VFNMADD132PS

The test / benchmark does honor compiler flag changes.

Last automated analysis: 10 May 2021

This test profile binary relies on the shared libraries libm.so.6, libmpi.so.40, libpthread.so.0, libc.so.6, libopen-rte.so.40, libopen-pal.so.40, libhwloc.so.15, libz.so.1, libdl.so.2, libutil.so.1, libudev.so.1.

Ubuntu Linux 4.18 Intel / AMD High-End Desktop Benchmarks 12 Systems - 121 Benchmark Results	AMD Ryzen 7 1700 Eight-Core - ASUS GL702ZC v1.0 - AMD 17h ManjaroLinux 19.0.2 - 5.5.8-1-MANJARO - X Server 1.20.7
Core i9 10900K/9900KS vs. AMD Ryzen 9 3950X/3900X - BENCHMARK 6 Systems - 133 Benchmark Results	AMD Ryzen 9 3900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 20.04 - 5.4.0-9-generic - GNOME Shell 3.34.3
Raspberry Pi 4 vs. Intel Comet Lake 5 Systems - 74 Benchmark Results	Intel Celeron G5900 - Gigabyte B460M DS3H - Intel Device 9b73 Debian 10 - 4.19.0-9-amd64 - X Server 1.20.4
Raspberry Pi 4 vs. Intel Comet Lake 5 Systems - 71 Benchmark Results	AMD Ryzen 7 2700X Eight-Core - ASUS PRIME B450M-A - AMD 17h Ubuntu 20.04 - 5.4.0-81-generic - KDE Frameworks 5.68.0
Raspberry Pi 4 vs. Intel Comet Lake 5 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
Raspberry Pi 4 vs. Intel Comet Lake 5 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
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
5950X GCC 11 PGO 2 Systems - 106 Benchmark Results	AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship Ubuntu 21.10 - 5.13.0-14-generic - GNOME Shell 40.2
phoronix 2 Systems - 21 Benchmark Results	AMD Ryzen Threadripper 1920X 12-Core - ASRock X399M Taichi - AMD 17h Fedora 33 - 5.13.12-100.fc33.x86_64 - GNOME Shell 3.38.5
2021aug25-cacule-2 1 System - 28 Benchmark Results	Intel Core i5-1135G7 - Intel NUC11PABi5 - Intel Device a0ef Ubuntu 20.04 - 5.11.18 - GNOME Shell 3.36.9
2021aug25-cacule 1 System - 28 Benchmark Results	Intel Core i5-1135G7 - Intel NUC11PABi5 - Intel Device a0ef Ubuntu 20.04 - 5.11.18 - GNOME Shell 3.36.9
2021aug24-2 1 System - 28 Benchmark Results	Intel Core i5-1135G7 - Intel NUC11PABi5 - Intel Device a0ef Ubuntu 20.04 - 5.11.0-27-generic - GNOME Shell 3.36.9
2021Aug24 1 System - 28 Benchmark Results	Intel Core i5-1135G7 - Intel NUC11PABi5 - Intel Device a0ef Ubuntu 20.04 - 5.11.0-27-generic - GNOME Shell 3.36.9
2X-E5-2609v2-MC0 5 Systems - 20 Benchmark Results	UltraSparc T2 - PLX PEX 8533 32-lane 6-port - 32768MB Debian 7.8 - 3.2.0-4-sparc64-smp - GCC 4.6.3
7452-hmmer 1 System - 1 Benchmark Result	AMD EPYC 7452 32-Core - Supermicro H12SSL-i v1.01 - AMD Starship Ubuntu 20.04 - 5.11.0-25-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
Lenovo rebuild world part 4 9 Systems - 16 Benchmark Results	Intel Core i3-3110M - LENOVO - Intel 3rd Gen Core DRAM OpenMandrivaLinux 4.2 - 5.11.12-desktop-1omv4002 - KDE Plasma 5.20.5
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
1-0600k mat 3 Systems - 37 Benchmark Results	Intel Core i5-10600K - ASUS PRIME Z490M-PLUS - Intel Comet Lake PCH Ubuntu 20.10 - 5.11.0-051100rc2daily20210106-generic - GNOME Shell 3.38.1
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
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
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
1275 june 4 Systems - 172 Benchmark Results	Intel Xeon E3-1275 v6 - ASUS P10S-M WS - Intel Xeon E3-1200 v6 Ubuntu 20.04 - 5.9.0-050900rc8daily20201007-generic - X Server 1.20.8
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
4770k haswell 2021 may 3 Systems - 178 Benchmark Results	Intel Core i7-4770K - Gigabyte Z97-HD3 - Intel 4th Gen Core DRAM Ubuntu 20.10 - 5.8.0-43-generic - GNOME Shell 3.38.1
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
1280 june 3 Systems - 136 Benchmark Results	Intel Xeon E3-1280 v5 - MSI Z170A SLI PLUS - Intel Xeon E3-1200 v5 Ubuntu 20.04 - 5.9.0-050900rc2daily20200826-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
Lenovo Rebuild World part 1 13 Systems - 10 Benchmark Results	Intel Core i3-3110M - LENOVO - Intel 3rd Gen Core DRAM Calculate - 5.10.32-calculate - MATE 1.24.1
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

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

Recent Test Results

Most Popular Test Results