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 120 public results since 13 January 2021 with the latest data as of 10 April 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)

2 x AMD EPYC 7763 64-Core

97th

319

Ampere Altra ARMv8 Neoverse-N1 160-Core

92nd

332 ^{+/- 2}

2 x Intel Xeon Platinum 8280

76th

503 ^{+/- 1}

Mid-Tier

75th

> 503

2 x AMD EPYC 7601 32-Core

71st

548

2 x Intel Xeon Gold 5220R

65th

650 ^{+/- 7}

AMD EPYC 7F52 16-Core

60th

764

Intel Xeon Gold 6226R

56th

1247 ^{+/- 5}

AMD Ryzen Threadripper 3960X 24-Core

51st

1341 ^{+/- 5}

Median

50th

1346

AMD Ryzen Threadripper 3970X 32-Core

48th

1348 ^{+/- 2}

AMD Ryzen 9 5900X 12-Core

45th

1530 ^{+/- 3}

Intel Core i9-10980XE

42nd

1601 ^{+/- 4}

AMD Ryzen Threadripper 3990X 64-Core

39th

1634

AMD Ryzen Threadripper 2990WX 32-Core

36th

1793 ^{+/- 21}

Intel Xeon Silver 4216

32nd

1806 ^{+/- 3}

AMD Ryzen 9 5950X 16-Core

27th

1872 ^{+/- 13}

Low-Tier

25th

> 2007

AMD Ryzen 7 5800X 8-Core

24th

2012 ^{+/- 6}

AMD Ryzen 5 5600X 6-Core

19th

2212 ^{+/- 279}

AMD Ryzen 9 3900XT 12-Core

18th

2213 ^{+/- 6}

AMD Ryzen 9 3900X 12-Core

17th

2216 ^{+/- 3}

Intel Core i9-11900K

13th

2441 ^{+/- 14}

Intel Core i5-10600K

8th

3054 ^{+/- 58}

Intel Core i3-10100

4th

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 1 hour, 9 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 0.2%.

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.

i5 11600k 4 Systems - 179 Benchmark Results	AMD Ryzen 5 5600X 6-Core - ASRock X570 Taichi - AMD Starship Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4
i5 11600k 3 Systems - 179 Benchmark Results	AMD Ryzen 5 5600X 6-Core - ASRock X570 Taichi - AMD Starship Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4
i5 11600k 3 Systems - 179 Benchmark Results	AMD Ryzen 5 5600X 6-Core - ASRock X570 Taichi - AMD Starship Ubuntu 20.04 - 5.10.13-051013-lowlatency - GNOME Shell 3.36.4
i5 11600k 1 System - 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
onerun EPYC data 2 Systems - 255 Benchmark Results	2 x AMD EPYC 7763 64-Core - AMD DAYTONA_X - AMD Starship Ubuntu 20.04 - 5.11.6-051106-generic - GNOME Shell 3.36.4
onerun data 1 System - 255 Benchmark Results	2 x AMD EPYC 7763 64-Core - AMD DAYTONA_X - AMD Starship Ubuntu 20.04 - 5.11.6-051106-generic - GNOME Shell 3.36.4
epyc-march 4 Systems - 290 Benchmark Results	2 x AMD EPYC 7742 64-Core - Supermicro H11DSi-NT v2.00 - AMD Starship Ubuntu 20.04 - 5.8.0-44-generic - X Server 1.20.8
Core i5 10600K January Linux 3 Systems - 74 Benchmark Results	Intel Core i5-10600K - ASUS PRIME Z490M-PLUS - Intel Comet Lake PCH Ubuntu 20.04 - 5.9.0-050900daily20201012-generic - GNOME Shell 3.36.4
AMD EPYC 7F72 2P Linux 5.11 - Perf Governor Featured Monitor Comparison	VE228
2990wx-2021-amd 6 Systems - 78 Benchmark Results	AMD Ryzen Threadripper 2990WX 32-Core - ASUS ROG ZENITH EXTREME - AMD 17h Ubuntu 20.10 - 5.8.0-34-generic - GNOME Shell 3.38.1
AMD EPYC 7F72 2P Linux 5.11 Perf Governor 3 Systems - 376 Benchmark Results	2 x AMD EPYC 7F72 24-Core - Supermicro H11DSi-NT v2.00 - AMD Starship Ubuntu 20.10 - 5.11.0-rc4-max-boost-inv-patch - GNOME Shell 3.38.1
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 - 5.11.0-051100rc4daily20210122-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
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
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
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
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
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
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
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
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
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

RELION

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RELION 3.1.1

Test: Basic - Device: CPU

Notable Instruction Set Usage

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