RELION

RELION - REgularised LIkelihood OptimisatioN - is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy (cryo-EM). It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology.

To run this test with the Phoronix Test Suite, the basic command is: phoronix-test-suite benchmark relion.

Test Created

13 January 2021

Last Updated

13 January 2021

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

7 Minutes, 58 Seconds

Average Run Time

1 Hour, 16 Minutes, 9 Seconds

Test Dependencies

OpenMPI + Fast Fourier Transform 3 + Git + CMake + TIFF Image + C/C++ Compiler Toolchain

Accolades

Recently Created Test Profile

Supported Platforms


Revision History

pts/relion-1.0.1   [View Source]   Wed, 13 Jan 2021 16:14:18 GMT
Build without the GUI to avoid fltk dependency and since GUI isn't used anyway...

pts/relion-1.0.0   [View Source]   Wed, 13 Jan 2021 10:31:35 GMT
Initial commit of RELION Cryo-EM benchmarks.

Suites Using This Test

HPC - High Performance Computing


Performance Metrics

Analyze Test Configuration:

RELION 3.1.1

Test: Basic - Device: CPU

OpenBenchmarking.org metrics for this test profile configuration based on 77 public results since 13 January 2021 with the latest data as of 24 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)
Mid-Tier
75th
> 653
64th
7
1247 +/- 5
Median
50th
1350
43rd
3
1601 +/- 4
33rd
4
1806 +/- 3
Low-Tier
25th
> 1875
6th
3
4674 +/- 6
OpenBenchmarking.orgDistribution Of Public Results - Test: Basic - Device: CPU74 Results Range From 330 To 7536 Seconds33047562076591010551200134514901635178019252070221523602505265027952940308532303375352036653810395541004245439045354680482549705115526054055550569558405985613062756420656567106855700071457290743575803691215

Based on OpenBenchmarking.org data, the selected test / test configuration (RELION 3.1.1 - Test: Basic - Device: CPU) has an average run-time of 1 hour, 13 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 BenchmarkTest: Basic - Device: CPURun-Time4080120160200Min: 17 / Avg: 72.72 / Max: 234

Recent Test Results

OpenBenchmarking.org Results Compare

3 Systems - 58 Benchmark Results

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

Ubuntu 20.04 - 5.9.0-050900rc6daily20200921-generic - GNOME Shell 3.36.4

1 System - 466 Benchmark Results

2 x AMD EPYC 7F72 24-Core - Supermicro H11DSi-NT v2.00 - AMD Starship

Ubuntu 20.10 - 5.10.9-051009-generic - GNOME Shell 3.38.1

3 Systems - 44 Benchmark Results

Intel Core i3-10100 - Gigabyte B460M DS3H - Intel Device 9b63

Ubuntu 20.04 - 5.9.0-050900rc7daily20201002-generic - GNOME Shell 3.36.3

3 Systems - 74 Benchmark Results

2 x AMD EPYC 7601 32-Core - Dell 02MJ3T - AMD 17h

Ubuntu 19.10 - 5.9.0-050900rc6daily20200922-generic - GNOME Shell 3.34.1

3 Systems - 34 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

2 Systems - 129 Benchmark Results

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

Ubuntu 20.10 - 5.11.0-051100rc2daily20210108-generic - GNOME Shell 3.38.1

3 Systems - 32 Benchmark Results

2 x Intel Xeon Gold 5220R - TYAN S7106 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.9.0-050900rc6-generic - GNOME Shell 3.36.4

4 Systems - 9 Benchmark Results

AMD Ryzen 9 3900XT 12-Core - MSI MEG X570 GODLIKE - AMD Starship

Ubuntu 20.10 - 5.11.0-rc1-phx - GNOME Shell 3.38.1

4 Systems - 91 Benchmark Results

AMD Ryzen 5 5600X 6-Core - ASUS TUF GAMING B550M-PLUS - AMD Starship

Ubuntu 20.10 - 5.10.4-051004-generic - GNOME Shell 3.38.1

4 Systems - 19 Benchmark Results

2 x AMD EPYC 7F72 24-Core - Supermicro H11DSi-NT v2.00 - AMD Starship

Ubuntu 20.10 - 5.11.0-rc2-phx - GNOME Shell 3.38.1

3 Systems - 14 Benchmark Results

AMD Ryzen Threadripper 3960X 24-Core - MSI Creator TRX40 - AMD Starship

Ubuntu 20.04 - 5.9.0-rc5-14sep-patch - GNOME Shell 3.36.4

3 Systems - 14 Benchmark Results

AMD EPYC 7F52 16-Core - Supermicro H11DSi-NT v2.00 - AMD Starship

Ubuntu 20.04 - 5.10.3-051003-generic - GNOME Shell 3.36.1

Most Popular Test Results

OpenBenchmarking.org Results Compare

3 Systems - 32 Benchmark Results

2 x Intel Xeon Gold 5220R - TYAN S7106 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.9.0-050900rc6-generic - GNOME Shell 3.36.4

4 Systems - 9 Benchmark Results

AMD Ryzen 9 3900XT 12-Core - MSI MEG X570 GODLIKE - AMD Starship

Ubuntu 20.10 - 5.11.0-rc1-phx - GNOME Shell 3.38.1

3 Systems - 34 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 - 74 Benchmark Results

2 x AMD EPYC 7601 32-Core - Dell 02MJ3T - AMD 17h

Ubuntu 19.10 - 5.9.0-050900rc6daily20200922-generic - GNOME Shell 3.34.1

3 Systems - 18 Benchmark Results

Intel Core i9-10980XE - ASRock X299 Steel Legend - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.11.0-rc2-phx - GNOME Shell 3.36.4

4 Systems - 12 Benchmark Results

AMD Ryzen 9 5900X 12-Core - ASUS ROG CROSSHAIR VIII HERO - AMD Starship

Ubuntu 20.10 - 5.11.0-rc2-phx - GNOME Shell 3.38.1

2 Systems - 8 Benchmark Results

2 x Intel Xeon Platinum 8280 - GIGABYTE MD61-SC2-00 v01000100 - Intel Sky Lake-E DMI3 Registers

Ubuntu 20.04 - 5.4.0-18-generic - GNOME Shell 3.36.0

3 Systems - 16 Benchmark Results

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

Ubuntu 20.10 - 5.11.0-051100rc2daily20210108-generic - GNOME Shell 3.38.1

3 Systems - 14 Benchmark Results

AMD EPYC 7F52 16-Core - Supermicro H11DSi-NT v2.00 - AMD Starship

Ubuntu 20.04 - 5.10.3-051003-generic - GNOME Shell 3.36.1

2 Systems - 11 Benchmark Results

Intel Xeon Silver 4216 - TYAN S7100AG2NR - Intel Sky Lake-E DMI3 Registers

Debian 10 - 4.19.0-9-amd64 - GNOME Shell 3.30.2

4 Systems - 91 Benchmark Results

AMD Ryzen 5 5600X 6-Core - ASUS TUF GAMING B550M-PLUS - AMD Starship

Ubuntu 20.10 - 5.10.4-051004-generic - GNOME Shell 3.38.1

5 Systems - 9 Benchmark Results

Ampere Altra ARMv8 Neoverse-N1 - WIWYNN Mt.Jade - Ampere Computing LLC Device e100

Ubuntu 20.04 - 5.4.0-60-generic - GCC 9.3.0

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