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

Source Repository

github.com

Test Created

13 January 2021

Last Updated

19 June 2023

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

9 Minutes, 41 Seconds

Average Run Time

1 Hour, 16 Minutes, 9 Seconds

Test Dependencies

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

Accolades

10k+ Downloads

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 updated weekly as of 27 September 2023.

Revision History

pts/relion-1.1.0 [View Source] Mon, 19 Jun 2023 13:12:40 GMT
Update against Relion 4.0.1 upstream.

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 4.0.1

Test: Basic - Device: CPU

OpenBenchmarking.org metrics for this test profile configuration based on 78 public results since 19 June 2023 with the latest data as of 18 July 2023.

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 9684X 96-Core

95th

92 ^{+/- 7}

2 x AMD EPYC 9654 96-Core

89th

130 ^{+/- 8}

2 x AMD EPYC 9554 64-Core

76th

141 ^{+/- 2}

Mid-Tier

75th

> 141

2 x AMD EPYC 7773X 64-Core

67th

158 ^{+/- 11}

2 x AMD EPYC 9754 128-Core

67th

160 ^{+/- 14}

2 x Intel Xeon Platinum 8490H

51st

195 ^{+/- 9}

Median

50th

204

2 x Intel Xeon Max 9480

44th

227 ^{+/- 28}

2 x Intel Xeon Max 9468

40th

248 ^{+/- 21}

2 x Intel Xeon Platinum 8462Y

34th

262 ^{+/- 5}

2 x Intel Xeon Platinum 8380

27th

352 ^{+/- 3}

Low-Tier

25th

> 356

2 x Intel Xeon Gold 6444Y

21st

379 ^{+/- 12}

AMD Ryzen 9 7950X 16-Core

16th

920 ^{+/- 14}

AMD Ryzen Threadripper 3990X 64-Core

11th

1018 ^{+/- 20}

Intel Core i9-10980XE

6th

1428 ^{+/- 57}

Based on OpenBenchmarking.org data, the selected test / test configuration (RELION 4.0.1 - Test: Basic - Device: CPU) has an average run-time of 35 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 1.1%.

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 ADDSD DIVSD SUBSD MOVDQA PUNPCKLQDQ MOVD PSHUFD MOVUPD SHUFPD UNPCKHPD UNPCKLPD MULPD UCOMISD CVTTSD2SI CVTSS2SD SQRTSD ANDNPD CMPNLESD ORPD CVTPS2PD CVTDQ2PD CMPLTPD ADDPD PADDQ PMULUDQ PSRLDQ CMPLESD SUBPD MOVHPD PSUBQ MINSD MOVLPD CMPLEPD CVTTPD2DQ CVTSD2SS CVTPD2PS CVTDQ2PS MAXSD DIVPD CMPNLTSD CMPLTSD

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 VINSERTF128 VPERM2F128 VEXTRACTF128 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).

VPERMQ VEXTRACTI128 VPERMPD VINSERTI128 VPBROADCASTQ VPBROADCASTD VPERM2I128 VPMASKMOVD VPBROADCASTW VPBROADCASTB VGATHERQPD

FMA (FMA)

VFMADD231SD VFMADD132SD VFNMADD132SD VFMSUB132PD VFMADD132PD VFNMADD231SD VFMADD231PD VFMSUB132SD VFMSUB231SD VFMADD213SD VFNMADD213SD VFNMSUB132SD VFMSUB213SD VFMADD213PD VFMSUB231PD VFNMADD231PD VFNMSUB231SD VFNMADD213PD VFNMADD132PD VFMADD132SS VFNMADD132SS VFMADD231SS

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: 25 June 2023

This test profile binary relies on the shared libraries libmpi.so.40, libtiff.so.5, libfftw3.so.3, libm.so.6, libgomp.so.1, libc.so.6, libopen-pal.so.40, libopen-rte.so.40, libhwloc.so.15, libwebp.so.7, libzstd.so.1, liblzma.so.5, libjbig.so.0, libjpeg.so.8, libdeflate.so.0, 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)

Recent Test Results

Compare

epyc 1 System - 88 Benchmark Results	2 x AMD EPYC 9654 96-Core - AMD Titanite_4G - AMD Device 14a4 Ubuntu 23.04 - 6.2.0-23-generic - GNOME Shell 44.0
june 3 Systems - 143 Benchmark Results	Intel Core i9-10980XE - ASRock X299 Steel Legend - Intel Sky Lake-E DMI3 Registers Ubuntu 22.04 - 5.19.0-051900rc7-generic - GNOME Shell 42.2
new wed 2 Systems - 115 Benchmark Results	2 x Intel Xeon Platinum 8490H - Quanta Cloud S6Q-MB-MPS - Intel Device 1bce Ubuntu 22.04 - 5.15.0-47-generic - GNOME Shell 42.4
rep 2 Systems - 7 Benchmark Results	AMD Ryzen Threadripper 3990X 64-Core - Gigabyte TRX40 AORUS PRO WIFI - AMD Starship Ubuntu 23.04 - 6.2.0-20-generic - GNOME Shell 44.0
rep 2 Systems - 7 Benchmark Results	AMD Ryzen Threadripper 3990X 64-Core - Gigabyte TRX40 AORUS PRO WIFI - AMD Starship Ubuntu 23.04 - 6.2.0-20-generic - GNOME Shell 44.0
osppr 3 Systems - 15 Benchmark Results	AMD Ryzen 9 7950X 16-Core - ASUS ROG STRIX X670E-E GAMING WIFI - AMD Device 14d8 Ubuntu 23.04 - 6.2.0-20-generic - GNOME Shell 44.1
osppr 3 Systems - 15 Benchmark Results