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

17 Seconds

Average Run Time

1 Minute, 17 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

250k+ Downloads + 10k+ Public Benchmark Results

Supported Platforms


Public Result Uploads *Reported Test Completions **Reported Installs **Test Profile Page Views ***OpenBenchmarking.orgEventsTimed HMMer Search Popularity Statisticspts/hmmer2010.122011.052011.102012.032012.082013.012013.062013.112014.042014.092015.022015.072015.122016.052016.102017.032017.082018.012018.062018.112019.042019.092020.022020.072020.122021.052021.102022.032022.082023.012023.062023.1116K32K48K64K80K
* Uploading of benchmark result data to OpenBenchmarking.org is always optional (opt-in) via the Phoronix Test Suite for users wishing to share their results publicly.
** 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.
*** Test profile page view reporting began March 2021.
Data updated weekly as of 18 March 2024.

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

HPC - High Performance Computing

CPU Massive

Scientific 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 758 public results since 5 May 2021 with the latest data as of 15 February 2024.

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
# Compatible Public Results
Seconds (Average)
94th
16
88 +/- 3
85th
13
94 +/- 4
82nd
4
98 +/- 3
81st
4
99 +/- 3
Mid-Tier
75th
> 101
74th
4
103 +/- 1
67th
11
114 +/- 10
57th
5
127 +/- 15
55th
9
129 +/- 4
54th
4
131 +/- 9
Median
50th
136
50th
28
136 +/- 6
49th
4
137 +/- 1
44th
8
142 +/- 15
42nd
5
144 +/- 1
38th
6
149 +/- 15
38th
9
150 +/- 1
35th
7
153 +/- 1
30th
7
156 +/- 4
29th
3
157 +/- 1
Low-Tier
25th
> 165
22nd
5
174 +/- 6
22nd
4
176 +/- 2
19th
4
185 +/- 1
15th
3
197 +/- 7
9th
20
237 +/- 21
OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search758 Results Range From 77 To 36780 Seconds7781215472282301737524487522259576692742781628897963210367111021183712572133071404214777155121624716982177171845219187199222065721392221272286223597243322506725802265372727228007287422947730212309473168232417331523388734622353573609236827160320480640800

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 11 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-Time80160240320400Min: 4 / Avg: 10.67 / Max: 429

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.6%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsPfam Database SearchDeviation714212835Min: 0 / Avg: 0.56 / Max: 31

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.

IntelAMDOpenBenchmarking.orgRelative Core Scaling To BaseTimed HMMer Search CPU Core ScalingPfam Database Search246810160.44790.89581.34371.79162.2395

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 MOVDQU DIVSD ADDSD CVTSD2SS CVTSS2SD SUBSD MOVD PSHUFD MOVDQA CVTDQ2PS MOVAPD PMULUDQ PADDQ COMISD CVTTSD2SI XORPD PSUBQ PSRLDQ ANDPD ANDNPD ORPD CMPNLESD 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
Advanced Vector Extensions 512 (AVX512)
Requires passing a supported compiler/build flag (verified with targets: cascadelake, sapphirerapids).
 
(ZMM REGISTER USE)
The test / benchmark does honor compiler flag changes.
Last automated analysis: 17 January 2022

This test profile binary relies on the shared libraries libm.so.6, libmpi.so.40, libc.so.6, libopen-rte.so.40, libopen-pal.so.40, libhwloc.so.15, libz.so.1, libudev.so.1.

Tested CPU Architectures

This benchmark has been successfully tested on the below mentioned architectures. The CPU architectures listed is where successful OpenBenchmarking.org result uploads occurred, namely for helping to determine if a given test is compatible with various alternative CPU architectures.

CPU Architecture
Kernel Identifier
Verified On
Intel / AMD x86 64-bit
x86_64
(Many Processors)
Intel / AMD x86 32-bit
i686
(Many Processors)

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Ubuntu 22.04 - 5.15.0-92-generic - GCC 11.4.0

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8 x Intel Xeon E5-2620 v4 - Xen HVM domU v4.13 - Intel 440FX 82441FX PMC

Debian 11 - 5.10.0-28-amd64 - GNOME Shell 3.38.6

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Debian 11 - 5.10.0-28-amd64 - GNOME Shell 3.38.6

3 Systems - 4 Benchmark Results

Intel Core i7-12700H - Intel Alder Lake-H PCH - Intel Alder Lake PCH

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3 Systems - 21 Benchmark Results

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2 Systems - 1 Benchmark Result

AMD Ryzen 7 6800H - ASUS M3402RA v1.0 - AMD 17h-19h PCIe Root Complex

Fedora Linux 39 - 6.6.13-200.fc39.x86_64 - KDE Plasma 5.27.10

2 Systems - 1 Benchmark Result

AMD Ryzen 7 6800H - ASUS M3402RA v1.0 - AMD 17h-19h PCIe Root Complex

Fedora Linux 39 - 6.6.13-200.fc39.x86_64 - KDE Plasma 5.27.10

1 System - 1 Benchmark Result

AMD Ryzen 7 6800H - ASUS M3402RA v1.0 - AMD 17h-19h PCIe Root Complex

Fedora Linux 39 - 6.6.13-200.fc39.x86_64 - KDE Plasma 5.27.10

1 System - 1 Benchmark Result

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Ubuntu 20.04 - 5.8.1-050801-generic - GNOME Shell 3.36.4

4 Systems - 11 Benchmark Results

AMD Ryzen Threadripper 2970WX 24-Core - Gigabyte X399 AORUS Gaming 7 - AMD 17h

Ubuntu 20.04 - 5.9.0-050900rc6daily20200926-generic - GNOME Shell 3.36.4

4 Systems - 82 Benchmark Results

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13 Systems - 333 Benchmark Results

AMD Ryzen 9 5950X 16-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 22.04 - 6.0.0-060000rc1daily20220820-generic - GNOME Shell 42.2

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Ubuntu 21.10 - 5.13.0-19-generic - GNOME Shell 40.5

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Ubuntu 20.10 - 5.8.0-48-generic - GNOME Shell 3.38.1

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