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.

Project Site

www3.mrc-lmb.cam.ac.uk

Test Created

13 January 2021

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

8 Minutes, 32 Seconds

Average Run Time

1 Hour, 16 Minutes, 9 Seconds

Test Dependencies

OpenMPI + FFTW + Git + CMake + TIFF Image + C/C++ Compiler Toolchain

Supported Platforms

* 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 15 June 2021.

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 217 public results since 13 January 2021 with the latest data as of 5 June 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

# Compatible Public Results

Seconds (Average)

2 x AMD EPYC 75F3 32-Core

100th

242 ^{+/- 6}

2 x AMD EPYC 7543 32-Core

97th

259 ^{+/- 6}

2 x AMD EPYC 7643 48-Core

94th

273 ^{+/- 13}

2 x AMD EPYC 7663 56-Core

93rd

286 ^{+/- 18}

2 x AMD EPYC 7763 64-Core

90th

315 ^{+/- 11}

Ampere Altra ARMv8 Neoverse-N1 160-Core

86th

332 ^{+/- 2}

2 x AMD EPYC 7513 32-Core

85th

342 ^{+/- 3}

2 x AMD EPYC 7443 24-Core

85th

343 ^{+/- 7}

Mid-Tier

75th

> 350

2 x Intel Xeon Platinum 8380

73rd

351 ^{+/- 4}

2 x AMD EPYC 73F3 16-Core

70th

384 ^{+/- 4}

2 x AMD EPYC 7453 28-Core

67th

409 ^{+/- 16}

AMD EPYC 75F3 32-Core

64th

467 ^{+/- 6}

AMD EPYC 7543 32-Core

61st

497 ^{+/- 4}

2 x Intel Xeon Platinum 8280

59th

503 ^{+/- 1}

AMD EPYC 7643 48-Core

57th

517 ^{+/- 5}

2 x AMD EPYC 7601 32-Core

53rd

548

Median

50th

567

AMD EPYC 74F3 24-Core

50th

571 ^{+/- 3}

2 x Intel Xeon Gold 5220R

47th

650 ^{+/- 7}

Intel Xeon Platinum 8380

43rd

687

AMD EPYC 73F3 16-Core

40th

758 ^{+/- 4}

AMD EPYC 7F52 16-Core

37th

764

AMD EPYC 7453 28-Core

36th

772

Intel Xeon Gold 6226R

32nd

1247 ^{+/- 5}

AMD Ryzen Threadripper 3960X 24-Core

30th

1341 ^{+/- 5}

AMD Ryzen Threadripper 3970X 32-Core

28th

1348 ^{+/- 2}

Low-Tier

25th

> 1528

AMD Ryzen 9 5900X 12-Core

25th

1530 ^{+/- 3}

Intel Core i9-10980XE

24th

1601 ^{+/- 4}

AMD Ryzen Threadripper 3990X 64-Core

22nd

1634

AMD Ryzen Threadripper 2990WX 32-Core

20th

1793 ^{+/- 21}

Intel Xeon Silver 4216

18th

1806 ^{+/- 3}

AMD Ryzen 9 5950X 16-Core

16th

1872 ^{+/- 13}

AMD Ryzen 7 5800X 8-Core

14th

2012 ^{+/- 6}

AMD Ryzen 5 5600X 6-Core

11th

2212 ^{+/- 279}

AMD Ryzen 9 3900XT 12-Core

11th

2213 ^{+/- 6}

AMD Ryzen 9 3900X 12-Core

10th

2216 ^{+/- 3}

Intel Core i9-11900K

8th

2441 ^{+/- 14}

Intel Core i5-10600K

5th

3054 ^{+/- 58}

Intel Core i3-10100

3rd

4674 ^{+/- 6}

Intel Xeon E3-1235L v5

1st

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 47 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.

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.4%.

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.

MOVDQU COMISD MOVAPD XORPD MULSD ANDPD CVTSI2SD DIVSD ADDSD SUBSD MOVDQA PUNPCKLQDQ MOVD PSHUFD MOVUPD SHUFPD UNPCKHPD UNPCKLPD MULPD UCOMISD CVTTSD2SI CVTSS2SD SQRTSD ANDNPD CMPNLESD ORPD CVTPS2PD CVTDQ2PD CMPLTPD ADDPD PMULUDQ PSRLDQ CMPLESD SUBPD MOVHPD PSUBQ PADDQ MINSD MOVLPD CMPLEPD CVTPD2PS CVTSD2SS MAXSD DIVPD CMPNLTSD CMPLTSD CVTDQ2PS

Advanced Vector Extensions (AVX)

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 VPERM2F128 VPERMILPD VBROADCASTSD VBROADCASTSS

Advanced Vector Extensions 2 (AVX2)

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).

VEXTRACTI128 VPERMQ VPERMPD VINSERTI128 VPBROADCASTD VPBROADCASTQ VPERM2I128 VPMASKMOVD VPBROADCASTW VPBROADCASTB

FMA (FMA)

VFMADD231SD VFMADD132SD VFNMADD132SD VFMSUB132PD VFMADD132PD VFNMADD231SD VFMADD231PD VFMSUB231SD VFMSUB132SD VFMADD213SD VFNMADD213SD VFNMSUB132SD VFMSUB213SD VFMADD213PD VFMSUB231PD VFNMSUB231SD VFNMADD213PD VFNMADD132PD VFMADD132SS VFNMADD132SS VFMADD231SS

The test / benchmark does honor compiler flag changes.

Last automated analysis: 31 January 2021

This test profile binary relies on the shared libraries libmpi.so.40, libdl.so.2, libtiff.so.5, libfftw3f.so.3, libfftw3.so.3, libpng16.so.16, libm.so.6, libgomp.so.1, libpthread.so.0, libc.so.6, libopen-rte.so.40, libopen-pal.so.40, libhwloc.so.15, libwebp.so.6, libzstd.so.1, liblzma.so.5, libjbig.so.0, libjpeg.so.8, libz.so.1, libevent-2.1.so.7, libutil.so.1, libudev.so.1.

single 12 Systems - 214 Benchmark Results	Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4
server-cpus-june-2021 1 System - 369 Benchmark Results	2 x AMD EPYC 7713 64-Core - AMD DAYTONA_X - AMD Starship Ubuntu 21.04 - 5.13.0-051300rc4-generic - X Server 1.20.11
single 4 Systems - 214 Benchmark Results	Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4
server-cpus-june-2021 3 Systems - 214 Benchmark Results	Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4
Server CPUs June 2021 1 System - 485 Benchmark Results	2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4
Server CPUs June 2021 1 System - 206 Benchmark Results	2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 21.04 - 5.13.0-051300rc4-generic - GNOME Shell 3.38.4
Xeon E-2278GEL Linux Kernel Benchmarks 1 System - 105 Benchmark Results	Intel Xeon E-2278GEL - Logic Supply RXM-181 - Intel Cannon Lake PCH Ubuntu 21.04 - 5.11.19-051119-generic - GNOME Shell 3.38.4
Ice Lake Ubuntu 20.04.2 / 20.10 / 21.04 Linux Benchmarks 4 Systems - 126 Benchmark Results	2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Clear Linux OS 34630 - 5.10.19-1032.native - GNOME Shell 40.0
ice-lake-ubuntu 2 Systems - 204 Benchmark Results	2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 21.04 - 5.11.0-17-generic - GNOME Shell 3.38.4
ice-lake-ubuntu 2 Systems - 215 Benchmark Results	2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 21.04 - 5.11.0-17-generic - GNOME Shell 3.38.4
ice-lake-ubuntu 2 Systems - 212 Benchmark Results	2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 21.04 - 5.11.0-17-generic - GNOME Shell 3.38.4
Xeon Platinum 8380 2P 1 System - 732 Benchmark Results	2 x Intel Xeon Platinum 8380 - Intel M50CYP2SB2U - Intel Device 0998 Ubuntu 20.04 - 5.11.6-051106-generic - GNOME Shell 3.36.4

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
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
i5 11600k 4 Systems - 179 Benchmark Results	Intel Core i5-11600K - ASUS ROG MAXIMUS XIII HERO - Intel Device 43ef Ubuntu 20.04 - 5.10.13-051013-lowlatency - 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
AMD EPYC 7F72 2P Linux 5.11 3 Systems - 376 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
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
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
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
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