RELION Benchmark - OpenBenchmarking.org

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.

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.

Performance Metrics

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)

Ampere Altra ARMv8 Neoverse-N1 160-Core

97th

332 ^{+/- 2}

2 x Intel Xeon Platinum 8280

89th

503 ^{+/- 1}

2 x AMD EPYC 7601 32-Core

84th

548

2 x Intel Xeon Gold 5220R

76th

650 ^{+/- 7}

Mid-Tier

75th

> 653

AMD EPYC 7F52 16-Core

71st

764

Intel Xeon Gold 6226R

64th

1247 ^{+/- 5}

AMD Ryzen Threadripper 3960X 24-Core

56th

1341 ^{+/- 5}

AMD Ryzen Threadripper 3970X 32-Core

52nd

1348 ^{+/- 2}

Median

50th

1350

AMD Ryzen 9 5900X 12-Core

47th

1530 ^{+/- 3}

Intel Core i9-10980XE

43rd

1601 ^{+/- 4}

AMD Ryzen Threadripper 3990X 64-Core

38th

1634

Intel Xeon Silver 4216

33rd

1806 ^{+/- 3}

AMD Ryzen 9 5950X 16-Core

26th

1872 ^{+/- 13}

Low-Tier

25th

> 1875

AMD Ryzen 7 5800X 8-Core

21st

2012 ^{+/- 6}

AMD Ryzen 5 5600X 6-Core

19th

2072 ^{+/- 8}

AMD Ryzen 9 3900XT 12-Core

12th

2213 ^{+/- 6}

AMD Ryzen 9 3900X 12-Core

11th

2216 ^{+/- 3}

Intel Core i3-10100

6th

4674 ^{+/- 6}

Intel Xeon E3-1235L v5

2nd

7530 ^{+/- 6}

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.

Xeon Gold Weekend 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
AMD EPYC 7F72 2P Linux 5.11 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
Core i3 10100 January 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
AMD EPYC 7601 2P 2021 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
Xeon E3 2021 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
5950X ASUS ROG CROSSHAIR VIII HERO WiFi BIOS 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
Xeon Gold 5220R 2P 2021 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
3900xt sun 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
5600X New 2021 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
7F72 2P Weekend 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
TR 3970X Fri 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
7F52 Fri 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

Xeon Gold 5220R 2P 2021 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
3900xt sun 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
Xeon E3 2021 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
AMD EPYC 7601 2P 2021 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
10980XE Thurs 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
5900X Running 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
plat thurs 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
5950X xx 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
7F52 Fri 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
Xeon Silver relion + more 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
5600X New 2021 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
altra-2p-q80-33 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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RELION 3.1.1

Test: Basic - Device: CPU

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