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

Public Result Uploads *Reported Test Completions **Reported Installs **Test Profile Page Views ***OpenBenchmarking.orgEventsTimed HMMer Search Popularity Statisticspts/hmmer2010.122011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.042021.0816K32K48K64K80K
* 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 27 November 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 398 public results since 5 May 2021 with the latest data as of 17 November 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
3
91 +/- 1
AMD Ryzen 9 5900X 12-Core
96th
6
95 +/- 4
AMD Ryzen 9 5950X 16-Core
95th
22
97 +/- 4
Intel Core i9-12900K
92nd
4
99 +/- 1
AMD EPYC 7F52 16-Core
89th
4
100
Intel Core i7-7740K
87th
3
101
Intel Core i9-10900K
80th
5
107
AMD Ryzen Threadripper 3970X 32-Core
78th
3
110
AMD Ryzen 7 3700X 8-Core
76th
9
113 +/- 10
Intel Core i9-9900KS
76th
3
113
Mid-Tier
75th
> 117
Intel Core i3-7100
75th
7
117
AMD Ryzen 5 3600XT 6-Core
72nd
3
119
AMD Ryzen 9 3950X 16-Core
72nd
6
119
Intel Core i5-10600K
69th
3
121
Intel Core i7-7700K
69th
3
123
Intel Xeon E-2288G
69th
3
123
AMD Ryzen 5 3400G
66th
3
124
AMD Ryzen 3 1300X
66th
3
126
Intel Core i7-8700K
62nd
3
129
Intel Core i7-8086K
62nd
3
129
AMD Ryzen Threadripper 2950X 16-Core
61st
8
130 +/- 2
Intel Core i9-10980XE
61st
8
130 +/- 4
Intel Core i5-7600K
60th
3
131
Intel Core i5-1135G7
59th
4
134 +/- 1
Intel Core i5-9400F
57th
3
136
Intel Core i3-10100
57th
3
136
AMD Ryzen 5 4500U
55th
3
137
Intel Core i5-8400
55th
3
138
Intel Xeon Gold 6226R
54th
4
140
Intel Xeon E3-1275 v6
52nd
4
141
2 x Intel Xeon Gold 6254
52nd
4
141 +/- 1
Intel Xeon E3-1231 v3
51st
3
142
Intel Core i3-8100
51st
4
143
Intel Xeon E3-1270 v5
51st
6
143
Median
50th
143
AMD Ryzen 5 2400G
47th
5
144 +/- 1
Intel Xeon E3-1260L v5
46th
3
147
AMD Ryzen 3 3200U
43rd
3
149
Intel Core i7-1165G7
43rd
6
149 +/- 15
Intel Core i9-7980XE
43rd
3
149
AMD EPYC 7742 64-Core
42nd
9
150 +/- 1
Intel Core i7-6800K
41st
3
151
Intel Core i3-4130
41st
3
151
Intel Core i7-4770K
38th
7
153 +/- 1
Intel Xeon E3-1280 v5
38th
6
153
Intel Core i7-9750H
35th
3
154
AMD Ryzen Threadripper 2990WX 32-Core
35th
3
154 +/- 5
Intel Core i5-6500
33rd
4
155
AMD Ryzen 7 2700 Eight-Core
33rd
3
155
AMD Ryzen 3 2200G
29th
4
156
Intel Xeon E3-1245 v5
28th
6
157
AMD Ryzen 7 4700U
28th
3
157 +/- 1
Low-Tier
25th
> 160
AMD Ryzen Threadripper 2970WX 24-Core
25th
3
161
Intel Core i7-4960X
24th
3
166
Intel Core i7-3770K
23rd
4
169
Intel Core i7-8550U
22nd
3
170 +/- 2
2 x Intel Xeon Gold 5220R
20th
3
176
Intel Core i7-8565U
20th
4
176 +/- 2
Intel Xeon Silver 4216
17th
3
182
AMD Ryzen 7 1700 Eight-Core
16th
3
183 +/- 21
Intel Core i7-10700T
16th
4
185 +/- 1
Intel Xeon E3-1235L v5
15th
3
187
Intel Xeon E5-2687W v3
13th
3
188
2 x AMD EPYC 7601 32-Core
12th
4
192 +/- 13
Intel Core i7-1065G7
12th
3
197 +/- 7
Intel Core i3-3110M
6th
20
237 +/- 21
Intel Xeon E5-2609 v4
5th
3
261
AMD FX-8150 Eight-Core
3rd
3
270 +/- 3
OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search398 Results Range From 85 To 1201 Seconds851181511842172502833163493824154484815145475806136466797127457788118448779109439761009104210751108114111741207306090120150

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.

OpenBenchmarking.orgMinutesTime Required To Complete BenchmarkPfam Database SearchRun-Time510152025Min: 2 / Avg: 5.44 / Max: 22

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.1%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsPfam Database SearchDeviation246810Min: 0 / Avg: 0.06 / Max: 2

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 Search2468160.44790.89581.34371.79162.2395

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 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)
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 Bulldozer (2011).
 
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.

Recent Test Results

OpenBenchmarking.org Results Compare

2 Systems - 267 Benchmark Results

Intel Core i9-12900K - ASUS ROG STRIX Z690-E GAMING WIFI - Intel Device 7aa7

Ubuntu 21.10 - 5.16.0-051600rc1daily20211116-generic - GNOME Shell 40.5

1 System - 23 Benchmark Results

AMD Ryzen 7 5700G - MSI MAG B550 TORPEDO - AMD Renoir Root Complex

ManjaroLinux 21.1.6 - 5.13.19-2-MANJARO - Xfce 4.16

1 System - 336 Benchmark Results

2 x Intel Xeon Gold 6254 - HPE ProLiant DL380 Gen10 - Intel Sky Lake-E DMI3 Registers

Ubuntu 18.04 - 5.4.0-89-generic - GNOME Shell 3.28.4

1 System - 24 Benchmark Results

AMD Ryzen 7 5700G - MSI MAG B550 TORPEDO - AMD Renoir Root Complex

ManjaroLinux 21.1.6 - 5.13.19-2-MANJARO - Xfce 4.16

1 System - 5 Benchmark Results

AMD Ryzen 9 5950X 16-Core - ASRock B550 Taichi - AMD Starship

Ubuntu 21.10 - 5.13.0-20-generic - GNOME Shell 40.5

1 System - 338 Benchmark Results

2 x Intel Xeon Gold 6254 - HPE ProLiant DL380 Gen10 - Intel Sky Lake-E DMI3 Registers

Ubuntu 18.04 - 5.4.0-89-generic - GNOME Shell 3.28.4

1 System - 338 Benchmark Results

2 x Intel Xeon Gold 6254 - HPE ProLiant DL380 Gen10 - Intel Sky Lake-E DMI3 Registers

Ubuntu 18.04 - 5.4.0-89-generic - GNOME Shell 3.28.4

1 System - 1 Benchmark Result

AMD Ryzen 7 3800X 8-Core - ASUS CROSSHAIR VI HERO - AMD Starship

ManjaroLinux 21.1.6 - 5.14.10-1-MANJARO - KDE Plasma 5.22.5

1 System - 2 Benchmark Results

2 x Intel Xeon E5-2697 v2 - Intel 440BX - Intel 440BX

Ubuntu 20.04 - 5.4.0-89-generic - 1.0.2

1 System - 2 Benchmark Results

2 x Intel Xeon E5-2667 v2 - Intel 440BX - Intel 440BX

Ubuntu 20.04 - 5.4.0-89-generic - 1.0.2

1 System - 1 Benchmark Result

Intel Core i7-4770K - Gigabyte Z97X-Gaming GT - Intel 4th Gen Core DRAM

ManjaroLinux 21.1.6 - 5.14.10-1-MANJARO - KDE Plasma 5.22.5

1 System - 1 Benchmark Result

AMD Ryzen 9 5900X 12-Core - MSI X570-A PRO - AMD Starship

Artix rolling - 5.14.14-artix1-1 - X Server 1.20.13

1 System - 1 Benchmark Result

Intel Core - Yandex xeon-e5-2660 - Intel 82G33

Ubuntu 20.04 - 5.4.0-42-generic - 1.0.2

1 System - 338 Benchmark Results

2 x Intel Xeon Gold 6254 - HPE ProLiant DL380 Gen10 - Intel Sky Lake-E DMI3 Registers

Ubuntu 18.04 - 5.4.0-89-generic - GNOME Shell 3.28.4

1 System - 1 Benchmark Result

Intel Core i5-6300U - TOSHIBA PORTEGE Z30-C - Intel Xeon E3-1200 v5

Linuxmint 20.2 - 5.4.0-74-generic - MATE 1.24.0

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

9 Systems - 16 Benchmark Results

Intel Core i3-3110M - LENOVO - Intel 3rd Gen Core DRAM

Gentoo - 5.12.8-gentoo-dist - MATE 1.24.0

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

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

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

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

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

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

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

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

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

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

3 Systems - 26 Benchmark Results

AMD Ryzen Threadripper 3970X 32-Core - ASUS ROG ZENITH II EXTREME - AMD Starship

Ubuntu 20.10 - 5.11.0-rc6-phx - GNOME Shell 3.38.1
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