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)
91st
14
96 +/- 1
84th
18
101 +/- 2
76th
8
107 +/- 1
Mid-Tier
75th
> 107
69th
6
113 +/- 3
69th
12
113 +/- 9
66th
9
115 +/- 3
65th
6
116 +/- 2
65th
10
116 +/- 4
65th
9
116 +/- 1
63rd
6
117
60th
10
118 +/- 2
60th
24
118 +/- 1
54th
3
122 +/- 1
54th
9
122 +/- 1
53rd
6
123 +/- 2
53rd
9
123 +/- 1
Median
50th
126
50th
12
126 +/- 9
47th
9
128 +/- 4
47th
7
128 +/- 1
46th
8
129 +/- 8
45th
15
130 +/- 11
36th
6
139 +/- 6
36th
10
140 +/- 1
32nd
4
145 +/- 10
32nd
9
145 +/- 3
31st
9
146 +/- 2
31st
7
146 +/- 11
28th
6
151 +/- 9
Low-Tier
25th
> 157
25th
6
159 +/- 12
24th
10
163 +/- 3
23rd
6
165 +/- 3
22nd
5
167 +/- 15
21st
6
168 +/- 1
21st
9
169 +/- 19
21st
13
170 +/- 7
20th
6
171 +/- 14
16th
6
178 +/- 16
12th
3
196 +/- 1
11th
9
200 +/- 1
10th
6
202 +/- 18
10th
6
203 +/- 18
9th
10
206 +/- 22
8th
12
213 +/- 19
5th
6
228 +/- 18
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
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
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.

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