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.

Learn more about this test at the upstream project site: http://hmmer.org/.

This scientific test profile is maintained by Andrew Schofield. This OpenBenchmarking.org test profile was created on 6 December 2010 and last updated on 27 September 2020. To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark hmmer.

This test has an average install time of 10 seconds and an average run-time of 33 seconds.

200k+ Downloads + 5k+ Public Benchmark Results

Installation StatsTest Completion StatsOpenBenchmarking.orgEventsTimed HMMer Search Popularitypts/hmmer2015.102015.122016.022016.042016.062016.082016.102016.122017.022017.042017.062017.082017.102017.122018.022018.042018.062018.082018.102018.122019.022019.042019.062019.082019.102019.122020.022020.042020.062020.0815003000450060007500

* Data based on those opting to upload their test results to OpenBenchmarking.org and users enabling the opt-in anonymous statistics reporting.

Revision History

pts/hmmer-1.2.0   [View Source]   27 Sep 2020 13:46 EDT
Update against HMMer 3.3.1 upstream, other install/build improvements.

pts/hmmer-1.1.2   [View Source]   09 Sep 2017 11:45 EDT
Update download links

pts/hmmer-1.1.1   [View Source]   25 Aug 2016 14:16 EDT
Update download links

pts/hmmer-1.1.0   [View Source]   06 Dec 2010 14:53 EST
Initial import into OpenBenchmarking.org

Suites Using This Test

C/C++ Compiler Tests

CPU Massive

Scientific Computing

Bioinformatics

Performance Metrics

Analyze Test Configuration:

Timed HMMer Search 3.3.1

Pfam Database Search

OpenBenchmarking.org metrics for this test profile configuration based on 267 public samples since 27 September 2020 with the latest data as of 29 October 2020.

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
Seconds (Average)
Mid-Tier
75th
> 114
Median
50th
127
Low-Tier
25th
> 154
OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search267 Results Range From 93 To 867 Seconds9312114917720523326128931734537340142945748551354156959762565368170973776579382184987720406080100

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 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-Time510152025Min: 5 / Avg: 7.27 / Max: 22

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