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

23 Seconds

Average Run Time

29 Seconds

Test Dependencies

C/C++ Compiler Toolchain + OpenMPI

Accolades

200k+ 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/hmmer2010.122011.042011.082011.122012.042012.082012.122013.042013.082013.122014.042014.082014.122015.042015.082015.122016.042016.082016.122017.042017.082017.122018.042018.082018.122019.042019.082019.122020.042020.082020.122021.042021.082021.122022.042022.0816K32K48K64K80K
* 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 current as of 29 November 2022.

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

HPC - High Performance Computing

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 593 public results since 5 May 2021 with the latest data as of 24 November 2022.

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)
86th
12
94 +/- 4
83rd
4
98 +/- 3
Mid-Tier
75th
> 102
68th
10
114 +/- 10
58th
5
127 +/- 15
56th
9
129 +/- 4
53rd
4
134 +/- 1
Median
50th
136
49th
4
137 +/- 1
49th
24
137 +/- 6
43rd
8
142 +/- 15
40th
5
144 +/- 1
36th
6
149 +/- 15
36th
9
150 +/- 1
32nd
7
153 +/- 1
26th
7
156 +/- 4
Low-Tier
25th
> 157
25th
3
157 +/- 1
19th
5
174 +/- 6
19th
4
176 +/- 2
16th
4
185 +/- 1
13th
3
197 +/- 7
8th
20
237 +/- 21
OpenBenchmarking.orgDistribution Of Public Results - Pfam Database Search593 Results Range From 77 To 1201 Seconds7711114517921324728131534938341745148551955358762165568972375779182585989392796199510291063109711311165119912334080120160200

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 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-Time714212835Min: 4 / Avg: 8.06 / Max: 34

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: 0.06 / Max: 3

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 Search2468160.44790.89581.34371.79162.2395

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)

Recent Test Results

OpenBenchmarking.org Results Compare

1 System - 1 Benchmark Result

Intel Xeon E5450 - Intel 440BX - Intel 440BX

CentOS Linux 7 - 3.10.0-1160.62.1.el7.x86_64 - GCC 4.8.5 20150623

1 System - 1 Benchmark Result

Common KVM - QEMU Standard PC - 1 x 2048 MB RAM QEMU

CentOS Linux 7 - 3.10.0-1160.el7.x86_64 - GCC 4.8.5 20150623

1 System - 1 Benchmark Result

Intel Atom D2500 - 3Q TD2500G-SM v1.3 - Intel Atom D2xxx

Debian 11 - 5.10.0-19-686-pae - 1.0.2

1 System - 1 Benchmark Result

2 x Intel Xeon E5-2680 0 - Dell PowerEdge R620 [0PXXHP] - 4 x 8192 MB DDR3-1333MT

CentOS Linux 7 - 3.10.0-1160.80.1.el7.x86_64 - GCC 4.8.5 20150623

1 System - 5 Benchmark Results

8 x Intel Xeon Gold 6240R - Intel 440BX - Intel 440BX

Ubuntu 22.04 - 5.15.0-43-generic - 1.2.204

1 System - 5 Benchmark Results

8 x Intel Xeon - RDO OpenStack Compute - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 5.15.0-46-generic - 1.2.204

1 System - 5 Benchmark Results

8 x Intel Xeon E3-12xx v2 - OpenStack Foundation Nova v24.1.1 - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 5.15.0-30-generic - 1.2.204

1 System - 5 Benchmark Results

56 x Intel Xeon Gold 6348 - Intel 440BX - Intel 440BX

Ubuntu 22.04 - 5.15.0-43-generic - 1.2.204

1 System - 5 Benchmark Results

8 x AMD EPYC - RDO OpenStack Compute - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 5.15.0-30-generic - 1.2.204

1 System - 5 Benchmark Results

8 x Intel Xeon Gold 6348 - Intel 440BX - Intel 440BX

Ubuntu 22.04 - 5.15.0-48-generic - 1.2.204

1 System - 5 Benchmark Results

8 x AMD EPYC - RDO OpenStack Compute - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 5.15.0-30-generic - 1.2.204

1 System - 5 Benchmark Results

8 x Intel Xeon - RDO OpenStack Compute - Intel 440FX 82441FX PMC

Ubuntu 22.04 - 5.15.0-46-generic - 1.2.204

27 Systems - 11 Benchmark Results

AMD Ryzen 7 PRO 5850U - LENOVO 20X7003WFR - AMD Renoir

Gentoo - 5.15.26-gentoo-x86_64 - X Server 1.21.1.3

1 System - 1 Benchmark Result

Intel Pentium E6600 - Gigabyte EG41MFT-US2H - Intel 4 DRAM + ICH7

Fedora Linux 36 - 5.19.15-201.fc36.x86_64 - GNOME Shell 42.5

Most Popular Test Results

OpenBenchmarking.org Results Compare

3 Systems - 37 Benchmark Results

Intel Xeon E3-1235L v5 - ASRockRack C236M WS - Intel Xeon E3-1200 v5

Ubuntu 20.04 - 5.8.0-050800-generic - GNOME Shell 3.36.4

3 Systems - 78 Benchmark Results

AMD Ryzen 7 3700X 8-Core - Gigabyte A320M-S2H-CF - AMD Starship

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

4 Systems - 82 Benchmark Results

Intel Core i5-6500 - Gigabyte Z170M-D3H-CF - Intel Xeon E3-1200 v5

Ubuntu 20.04 - 5.9.0-050900rc7daily20200929-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

3 Systems - 107 Benchmark Results

AMD FX-8150 Eight-Core - ASUS M5A78L-M LX PLUS - AMD RS780 + SB7x0

Ubuntu 20.10 - 5.8.0-33-generic - GNOME Shell 3.38.1

6 Systems - 36 Benchmark Results

AMD Ryzen 9 3950X 16-Core - ASUS ROG CROSSHAIR VII HERO - AMD Starship

Ubuntu 20.04 - 5.9.0-050900rc6daily20200922-generic - GNOME Shell 3.36.4

13 Systems - 333 Benchmark Results

Intel Core i9-11900K - ASUS ROG MAXIMUS XIII HERO - Intel Tiger Lake-H

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

2 Systems - 38 Benchmark Results

Intel Xeon Gold 6226R - Supermicro X11SPL-F v1.02 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.10 - 5.11.0-rc4-max-boost-inv-patch - GNOME Shell 3.38.1

3 Systems - 164 Benchmark Results

Intel Xeon E5-2609 v4 - MSI X99A RAIDER - Intel Xeon E7 v4

Ubuntu 20.04 - 5.9.0-050900rc6daily20200926-generic - GNOME Shell 3.36.2

9 Systems - 16 Benchmark Results

Intel Core i3-3110M - LENOVO - Intel 3rd Gen Core DRAM

OpenMandrivaLinux 4.2 - 5.11.12-desktop-1omv4002 - KDE Plasma 5.20.5

3 Systems - 37 Benchmark Results

Intel Core i5-10600K - ASUS PRIME Z490M-PLUS - Intel Comet Lake PCH

Ubuntu 20.10 - 5.11.0-051100rc2daily20210106-generic - GNOME Shell 3.38.1

4 Systems - 193 Benchmark Results

AMD Ryzen 3 2200G - ASUS PRIME B350M-E - AMD Raven

Ubuntu 20.10 - 5.8.0-38-generic - GNOME Shell 3.38.1

3 Systems - 117 Benchmark Results

Intel Core i3-7100 - Gigabyte B250M-DS3H-CF - Intel Xeon E3-1200 v6

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

6 Systems - 254 Benchmark Results

AMD Ryzen 3 PRO 4350G - ASRock B450M Pro4 - AMD Renoir Root Complex

Clear Linux OS 34550 - 5.10.32-1035.native - GNOME Shell 40.0

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