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

21 Seconds

Average Run Time

31 Seconds

Test Dependencies

C/C++ Compiler Toolchain

Accolades

200k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms

Public Result UploadsTest Completions*Reported Installs*OpenBenchmarking.orgEventsTimed HMMer Search Popularity Statisticspts/hmmer2011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.0412K24K36K48K60K
* 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 Sat, 10 Apr 2021 12:39:36 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 1,124 public results since 27 September 2020 with the latest data as of 9 April 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
96th
14
84 +/- 7
AMD Ryzen 9 5900X 12-Core
95th
45
87 +/- 8
AMD Ryzen 7 5800X 8-Core
95th
17
88 +/- 8
AMD Ryzen 9 5950X 16-Core
95th
43
91 +/- 9
Intel Core i9-10900K
91st
14
96 +/- 1
Intel Core i5-11600K
91st
5
96 +/- 1
Intel Core i9-11900K
91st
7
96
Intel Core i9-9900KS
89th
6
97
AMD Ryzen 7 3800XT 8-Core
85th
10
100 +/- 3
Intel Core i7-7740K
84th
3
101
Intel Xeon E-2288G
84th
18
101 +/- 2
Intel Core i7-7700K
83rd
6
102
AMD Ryzen 3 3300X 4-Core
80th
9
103
Intel Core i5-10600K
80th
13
103
Intel Core i9-9900K
80th
9
103
AMD Ryzen 7 3700X 8-Core
77th
12
105 +/- 6
Intel Core i9-10885H
77th
3
106
AMD Ryzen 5 3600XT 6-Core
77th
6
106 +/- 1
AMD Ryzen 9 3900X 12-Core
77th
16
106 +/- 7
AMD Ryzen 9 3900XT 12-Core
76th
11
107 +/- 5
Intel Core i7-8700B
76th
8
107 +/- 1
Mid-Tier
75th
> 107
Intel Core i7-8086K
74th
6
109
AMD Ryzen 9 3950X 16-Core
74th
9
109 +/- 10
Intel Core i7-8700K
74th
6
109
Intel Core i3-10100
73rd
9
110
Intel Core i5-7600K
71st
9
111
AMD Ryzen 3 3100 4-Core
71st
6
111
Intel Core i7-5775C
69th
6
113 +/- 3
AMD Ryzen Threadripper 2950X 16-Core
69th
6
113
AMD Ryzen 5 4500U
69th
12
113 +/- 9
Intel Xeon E3-1275 v6
68th
9
114
AMD Ryzen 7 2700X Eight-Core
66th
4
115 +/- 2
Intel Core i7-8565U
66th
9
115 +/- 3
AMD Ryzen 5 3400G
65th
6
116 +/- 2
AMD EPYC 7F32 8-Core
65th
10
116 +/- 4
Intel Core i3-7100
65th
9
116 +/- 1
Apple M1
63rd
6
117
Intel Core i7-9750H
63rd
10
117
AMD Ryzen 3 1300X
60th
10
118 +/- 2
Intel Core i5-9400F
60th
9
118
Intel Xeon E3-1270 v5
60th
24
118 +/- 1
Intel Core i7-1065G7
56th
6
120
Intel Core i5-8400
56th
9
120
Intel Xeon E3-1240 v5
54th
3
122 +/- 1
Intel Core i7-8550U
54th
9
122 +/- 1
Intel Core i7-4790K
53rd
6
123 +/- 2
Intel Xeon E3-1280 v5
53rd
9
123 +/- 1
Intel Xeon E3-1260L v5
51st
6
125 +/- 1
Median
50th
126
Intel Core i3-8100
50th
9
126
AMD EPYC 7F52 16-Core
50th
12
126 +/- 9
Intel Xeon E3-1245 v5
50th
9
126
AMD Ryzen 7 1800X Eight-Core
47th
13
128 +/- 4
AMD Ryzen 3 3200U
47th
9
128 +/- 4
AMD Ryzen 3 2200G
47th
7
128 +/- 1
Intel Core i7-5600U
46th
6
129
AMD Ryzen 5 2400G
46th
8
129 +/- 8
AMD Ryzen Threadripper 3970X 32-Core
46th
13
129 +/- 10
Intel Core i9-10980XE
45th
15
130 +/- 11
Intel Core i7-6800K
44th
6
131
Intel Core i5-6500
44th
6
131
AMD Ryzen Threadripper 3960X 24-Core
44th
9
131
Intel Core i7-9700TE
44th
5
131
AMD Ryzen 7 2700 Eight-Core
41st
9
132 +/- 7
Intel Core i7-7900X
40th
9
133
Intel Core i9-7960X
40th
6
133
AMD Ryzen 7 1700 Eight-Core
38th
8
134 +/- 11
AMD EPYC 7262 8-Core
38th
3
136
Intel Core i7-4770K
36th
9
138
AMD EPYC 7232P 8-Core
36th
6
139 +/- 6
Intel Core i5-4670
36th
10
140 +/- 1
Intel Xeon E3-1231 v3
34th
6
141
AMD EPYC 7F72 24-Core
34th
15
142
AMD EPYC 7272 12-Core
32nd
4
145 +/- 10
AMD EPYC 7252 8-Core
32nd
3
145
Intel Core i7-6700HQ
32nd
9
145 +/- 3
Intel Core i7-4960X
31st
9
146 +/- 2
AMD EPYC 7302P 16-Core
31st
7
146 +/- 11
Intel Core i7-3770K
30th
3
147
AMD Ryzen Threadripper 2970WX 24-Core
29th
9
150
AMD EPYC 7282 16-Core
28th
6
151 +/- 9
Intel Core i3-4130
28th
10
152
Intel Xeon Platinum 8280
27th
3
154
Intel Xeon E3-1235L v5
26th
3
157
Low-Tier
25th
> 157
AMD EPYC 7402P 24-Core
25th
6
159 +/- 12
AMD Ryzen Threadripper 2990WX 32-Core
24th
6
162 +/- 1
Intel Xeon E5-1680 v3
24th
3
163
Intel Core i9-7980XE
24th
10
163 +/- 3
Intel Core i5-3470
23rd
6
165 +/- 3
Intel Xeon Silver 4215R
22nd
3
166
AMD EPYC 7542 32-Core
22nd
5
167 +/- 15
Intel Core i7-2700K
21st
6
168 +/- 1
Intel Core i5-2500K
21st
9
169 +/- 19
Intel Xeon E5-2687W v3
21st
6
169 +/- 2
Intel Xeon Gold 6226R
21st
13
170 +/- 7
Intel Xeon Gold 5217
21st
4
170
AMD EPYC 7502P 32-Core
20th
6
171 +/- 14
Intel Core i7-5960X
20th
4
172
AMD EPYC 7352 24-Core
19th
5
173
AMD EPYC 7502 32-Core
17th
12
177
AMD EPYC 7532 32-Core
16th
6
178 +/- 16
AMD EPYC 7452 32-Core
16th
5
178
2 x AMD EPYC 7F72 24-Core
15th
5
182 +/- 9
AMD Ryzen Threadripper 3990X 64-Core
15th
11
183 +/- 14
AMD FX-8370 Eight-Core
13th
4
192
Intel Core i5-2520M
12th
3
196 +/- 1
AMD A10-7870K Radeon R7 12 Compute Cores 4C
11th
3
198
AMD EPYC 7601 32-Core
11th
9
200 +/- 1
AMD EPYC 7552 48-Core
10th
6
202 +/- 18
AMD EPYC 7642 48-Core
10th
6
203 +/- 18
Intel Xeon Gold 5218
10th
4
204
Intel Xeon Silver 4214R
10th
3
204
Intel Xeon Silver 4216
9th
10
206 +/- 22
AMD A10-7850K APU
9th
3
208
AMD EPYC 7702 64-Core
8th
12
213 +/- 19
AMD FX-8150 Eight-Core
8th
4
214 +/- 3
2 x Intel Xeon Platinum 8280
7th
17
222 +/- 5
2 x Intel Xeon Gold 5220R
6th
10
224
AMD EPYC 7662 64-Core
5th
6
228 +/- 18
AMD EPYC 7742 64-Core
5th
3
231
Intel Xeon E5-2609 v4
3rd
8
240
2 x AMD EPYC 7601 32-Core
2nd
7
291 +/- 1
2 x AMD EPYC 7742 64-Core
1st
10
423 +/- 20
OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search1123 Results Range From 76 To 867 Seconds7610413216018821624427230032835638441244046849652455258060863666469272074877680483286088890180270360450

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.

OpenBenchmarking.orgMinutesTime Required To Complete BenchmarkPfam Database SearchRun-Time510152025Min: 2 / Avg: 7.1 / Max: 22

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.

AMDIntelOpenBenchmarking.orgRelative Core Scaling To BaseTimed HMMer Search CPU Core ScalingPfam Database Search4681216243248640.46880.93761.40641.87522.344

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)
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
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.

Recent Test Results

OpenBenchmarking.org Results Compare

1 System - 4 Benchmark Results

AMD Ryzen Threadripper 3970X 32-Core - ASRock TRX40 Creator - AMD Starship

Debian 10 - 4.19.0-16-amd64 - GNOME Shell 3.30.2

1 System - 1 Benchmark Result

AMD Ryzen 5 4500U - RO Kona_RN - AMD Renoir Root Complex

ManjaroLinux 21.0.1 - 5.11.6-1-MANJARO - Xfce 4.16

1 System - 105 Benchmark Results

Intel Core - Red Hat RHEL-AV - Intel 82G33

Debian 9.12 - 4.9.0-12-amd64 - GCC 6.3.0 20170516

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

3 Systems - 21 Benchmark Results

AMD Ryzen 9 5900X 12-Core - MSI B550M PRO-VDH WIFI - AMD Device 1480

Ubuntu 18.04 - 5.4.0-70-generic - LXDE 0.9.3

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

9 Systems - 442 Benchmark Results

AMD Ryzen 5 5600X 6-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 21.04 - 5.12.0-051200rc3daily20210315-generic - GNOME Shell 3.38.3

1 System - 272 Benchmark Results

1 System - 272 Benchmark Results

1 System - 1 Benchmark Result

2 x Intel Xeon Gold 6330 - Supermicro X12DPi-N6 v1.00 - Intel Device 0998

CentOS Linux 8 - 4.18.0-80.el8.x86_64 - GCC 8.3.1 20191121

1 System - 1 Benchmark Result

Intel Core i7-10750H - Dell 0MDFDR - Intel Comet Lake PCH

Arch rolling - 5.11.11-arch1-1 - X Server 1.20.10

Most Popular Test Results

OpenBenchmarking.org Results Compare

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

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

8 Systems - 84 Benchmark Results

Intel Xeon E-2288G - Compulab SBC-ATCFL v1.2 - Intel Cannon Lake PCH

Ubuntu 20.10 - 5.8.0-26-generic - GNOME Shell 3.38.1

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

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

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

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

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

5 Systems - 99 Benchmark Results

Intel Core i7-1165G7 - Dell 0GG9PT - Intel Tiger Lake-LP

Ubuntu 20.10 - 5.9.2-050902-generic - GNOME Shell 3.38.1

3 Systems - 131 Benchmark Results

Intel Core i5-10600K - ASUS PRIME Z490M-PLUS - Intel Comet Lake PCH

Ubuntu 20.04 - 5.9.0-050900daily20201012-generic - GNOME Shell 3.36.4

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
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