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

21 Seconds

Average Run Time

31 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

200k+ Downloads + 10k+ Public Benchmark Results + Recently Updated Test Profile

Supported Platforms


Public Result UploadsTest Completions*Reported Installs*OpenBenchmarking.orgEventsTimed HMMer Search Popularity Statisticspts/hmmer2011.052011.092012.012012.052012.092013.012013.052013.092014.012014.052014.092015.012015.052015.092016.012016.052016.092017.012017.052017.092018.012018.052018.092019.012019.052019.092020.012020.052020.092021.012021.0512K24K36K48K60K
* 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, 08 May 2021 18:51:05 GMT.

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

Scientific Computing

HPC - High Performance 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 114 public results since 5 May 2021 with the latest data as of 8 May 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.

OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search114 Results Range From 90 To 221 Seconds90101112123134145156167178189200211222510152025

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 5 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-Time48121620Min: 2 / Avg: 4.89 / Max: 15

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: 0.11 / Max: 4

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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