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

20 Seconds

Average Run Time

32 Seconds

Accolades

200k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms


Public Result UploadsTest Completions*Reported Installs*OpenBenchmarking.orgEventsTimed HMMer Search Popularity Statisticspts/hmmer2011.012011.052011.092012.012012.052012.092013.012013.052013.092014.012014.052014.092015.012015.052015.092016.012016.052016.092017.012017.052017.092018.012018.052018.092019.012019.052019.092020.012020.052020.092021.0112K24K36K48K60K
* 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 Mon, 18 Jan 2021 21:40:53 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 999 public results since 27 September 2020 with the latest data as of 18 January 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)
88th
15
101 +/- 2
80th
8
107 +/- 1
Mid-Tier
75th
> 110
71st
11
114 +/- 8
69th
9
115 +/- 3
69th
4
115 +/- 2
69th
19
115 +/- 34
68th
9
116 +/- 1
68th
6
116 +/- 2
66th
6
117
66th
9
117 +/- 1
63rd
24
118 +/- 1
63rd
10
118 +/- 2
56th
9
122 +/- 1
56th
3
122 +/- 1
55th
6
123 +/- 2
55th
9
123 +/- 1
Median
50th
127
49th
9
128 +/- 7
49th
9
128 +/- 4
48th
8
129 +/- 8
47th
15
130 +/- 11
37th
10
140 +/- 1
33rd
9
145 +/- 3
33rd
9
146 +/- 2
Low-Tier
25th
> 162
25th
10
163 +/- 3
24th
6
165 +/- 3
22nd
6
168 +/- 1
22nd
9
169 +/- 19
21st
13
170 +/- 7
12th
3
196 +/- 1
11th
9
200 +/- 1
9th
10
206 +/- 22
8th
11
215 +/- 19
OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search999 Results Range From 76 To 867 Seconds7610413216018821624427230032835638441244046849652455258060863666469272074877680483286088880160240320400

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: 4 / Avg: 7.19 / Max: 21

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