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

29 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/hmmer2010.122011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.042021.082021.122022.042022.0816K32K48K64K80K
* 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 29 November 2022.

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 593 public results since 5 May 2021 with the latest data as of 24 November 2022.

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
8
77
AMD Ryzen 9 7950X 16-Core
98th
6
78 +/- 1
AMD Ryzen 5 7600X 6-Core
97th
5
79
AMD Ryzen 9 7900X 12-Core
97th
6
80
Intel Core i9-13900K
95th
9
86 +/- 1
AMD EPYC 72F3 8-Core
94th
4
87
Intel Core i5-13600K
92nd
6
90 +/- 1
AMD Ryzen 7 5800X 8-Core
92nd
6
90 +/- 1
AMD Ryzen 7 5800X3D 8-Core
89th
4
92
Intel Core i9-12900K
86th
12
94 +/- 4
AMD Ryzen 9 5900X 12-Core
86th
8
94 +/- 4
Intel Core i5-12600K
85th
3
95 +/- 4
AMD Ryzen 9 5950X 16-Core
84th
32
96 +/- 4
AMD Ryzen 7 5700G
83rd
4
98 +/- 3
AMD EPYC 7F32 8-Core
79th
5
100
AMD EPYC 7F52 16-Core
79th
4
100
Intel Core i7-7740K
77th
3
101
Mid-Tier
75th
> 102
Intel Core i9-10900K
71st
5
107
AMD Ryzen Threadripper 3970X 32-Core
70th
3
110
Intel Core i9-9900KS
68th
3
113
AMD Ryzen 9 3950X 16-Core
68th
8
114 +/- 8
AMD Ryzen 7 3700X 8-Core
68th
10
114 +/- 10
Intel Core i3-7100
67th
7
117
AMD Ryzen 5 3600XT 6-Core
65th
3
119
Intel Core i5-10600K
63rd
3
121
Intel Xeon E-2288G
63rd
3
123
Intel Core i7-7700K
63rd
4
123
AMD Ryzen 5 3400G
61st
3
124
AMD Ryzen 3 1300X
60th
3
126
Intel Core i7-8700B
58th
5
127 +/- 15
Intel Core i7-8700K
56th
3
129
Intel Core i7-8086K
56th
3
129
Intel Core i9-10980XE
56th
9
129 +/- 4
AMD Ryzen Threadripper 2950X 16-Core
55th
8
130 +/- 2
Intel Core i5-7600K
54th
3
131
Intel Core i5-1135G7
53rd
4
134 +/- 1
Median
50th
136
Intel Core i5-9400F
50th
3
136
Intel Core i3-10100
50th
3
136
AMD Ryzen 5 4500U
49th
4
137 +/- 1
AMD Ryzen 7 PRO 5850U
49th
24
137 +/- 6
Intel Core i5-8400
48th
3
138
Intel Xeon Gold 6226R
47th
4
140
2 x Intel Xeon Gold 6254
45th
4
141 +/- 1
Intel Xeon E3-1275 v6
45th
4
141
AMD Ryzen 3 2200G
43rd
8
142 +/- 15
Intel Xeon E3-1231 v3
43rd
3
142
Intel Xeon E3-1270 v5
42nd
6
143
Intel Core i3-8100
42nd
4
143
AMD Ryzen 5 2400G
40th
5
144 +/- 1
Intel Xeon E3-1260L v5
38th
3
147
AMD Ryzen 3 3200U
36th
3
149
Intel Core i7-1165G7
36th
6
149 +/- 15
Intel Core i9-7980XE
36th
3
149
AMD EPYC 7742 64-Core
36th
9
150 +/- 1
Intel Core i3-4130
35th
3
151
Intel Core i7-6800K
35th
3
151
Intel Core i7-4770K
32nd
7
153 +/- 1
Intel Xeon E3-1280 v5
32nd
6
153
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
Low-Tier
25th
> 157
AMD Ryzen 7 4700U
25th
3
157 +/- 1
AMD Ryzen Threadripper 2970WX 24-Core
23rd
3
161
Intel Core i7-4960X
23rd
3
166
Intel Core i7-5960X
22nd
3
168
Intel Core i7-3770K
21st
4
169
Intel Core i7-8550U
19th
5
174 +/- 6
2 x Intel Xeon Gold 5220R
19th
3
176
Intel Core i7-8565U
19th
4
176 +/- 2
Intel Xeon Silver 4216
16th
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
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
7th
3
261
AMD FX-8150 Eight-Core
6th
3
270 +/- 3
4 x AMD Opteron 8378
4th
5
291
OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search593 Results Range From 77 To 1201 Seconds7711114517921324728131534938341745148551955358762165568972375779182585989392796199510291063109711311165119912334080120160200

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 8 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-Time714212835Min: 4 / Avg: 8.06 / Max: 34

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: 3

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 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

2 Systems - 21 Benchmark Results

AMD Ryzen Threadripper 3970X 32-Core - ASUS PRIME TRX40-PRO S - AMD Starship

Ubuntu 22.04 - 5.15.0-53-generic - GNOME Shell 42.5

2 Systems - 21 Benchmark Results

AMD Ryzen Threadripper 1950X 16-Core - ASUS PRIME X399-A - AMD 17h

Ubuntu 22.04 - 5.15.0-53-generic - GNOME Shell 42.5

2 Systems - 21 Benchmark Results

AMD Ryzen Threadripper 1950X 16-Core - ASUS PRIME X399-A - AMD 17h

Ubuntu 22.04 - 5.15.0-53-generic - GNOME Shell 42.5

1 System - 1 Benchmark Result

Intel Xeon E5450 - Intel 440BX - Intel 440BX

CentOS Linux 7 - 3.10.0-1160.62.1.el7.x86_64 - GCC 4.8.5 20150623

1 System - 1 Benchmark Result

Common KVM - QEMU Standard PC - 1 x 2048 MB RAM QEMU

CentOS Linux 7 - 3.10.0-1160.el7.x86_64 - GCC 4.8.5 20150623

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

1 System - 1 Benchmark Result

Intel Atom D2500 - 3Q TD2500G-SM v1.3 - Intel Atom D2xxx

Debian 11 - 5.10.0-19-686-pae - 1.0.2

1 System - 1 Benchmark Result

2 x Intel Xeon E5-2680 0 - Dell PowerEdge R620 [0PXXHP] - 4 x 8192 MB DDR3-1333MT

CentOS Linux 7 - 3.10.0-1160.80.1.el7.x86_64 - GCC 4.8.5 20150623

1 System - 5 Benchmark Results

8 x Intel Xeon Gold 6240R - Intel 440BX - Intel 440BX

Ubuntu 22.04 - 5.15.0-43-generic - 1.2.204

1 System - 5 Benchmark Results

8 x Intel Xeon Gold 6240R - Intel 440BX - Intel 440BX

Ubuntu 22.04 - 5.15.0-43-generic - 1.2.204

1 System - 162 Benchmark Results

Intel Celeron J1800 - LENOVO Aptio CRB - 4096MB

Alpine Linux v3.17 3.17.0_rc1 - 5.15.78-0-lts - ext4

10 Systems - 105 Benchmark Results

VirtualApple - Apple Mac mini - 8GB

macOS 11.0 - 20.1.0 - OpenCL 1.2

5 Systems - 67 Benchmark Results

Intel Core i3-10100 - Gigabyte B460M DS3H - Intel Device 9b63

Debian 10 - 4.19.0-9-amd64 - X Server 1.20.4

1 System - 5 Benchmark Results

8 x Intel Xeon - RDO OpenStack Compute - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 5.15.0-46-generic - 1.2.204

1 System - 5 Benchmark Results

8 x Intel Xeon E3-12xx v2 - OpenStack Foundation Nova v24.1.1 - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 5.15.0-30-generic - 1.2.204

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 - 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

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 - 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

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

13 Systems - 333 Benchmark Results

AMD Ryzen 7 5700G - ASUS ROG CROSSHAIR VIII HERO - AMD Renoir

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

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 - 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

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

9 Systems - 16 Benchmark Results

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

EndeavourOS rolling - 5.12.3-arch1-1 - MATE 1.24.1

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

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
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