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

4 December 2024

Test Maintainer

Michael Larabel

Test Type

Processor

Average Install Time

6 Minutes, 45 Seconds

Average Run Time

1 Hour, 16 Minutes, 9 Seconds

Test Dependencies

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

Accolades

20k+ Downloads + Recently Updated Test Profile

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 23 December 2024.

Revision History

pts/relion-1.2.0 [View Source] Wed, 04 Dec 2024 17:05:26 GMT
Update against RELION 5.0.

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 5.0

Test: Basic - Device: CPU

OpenBenchmarking.org metrics for this test profile configuration based on 65 public results since 4 December 2024 with the latest data as of 20 December 2024.

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)

AMD EPYC 9655P 96-Core

97th

147 ^{+/- 7}

AMD EPYC 9575F 64-Core

90th

176 ^{+/- 4}

ARMv8 Neoverse-V2 72-Core

85th

300 ^{+/- 11}

AMD Ryzen Threadripper 7980X 64-Cores

79th

400 ^{+/- 23}

Mid-Tier

75th

> 418

AMD EPYC 4584PX 16-Core

68th

553 ^{+/- 3}

AMD Ryzen 9 9950X 16-Core

57th

725 ^{+/- 11}

AMD Ryzen 7 9800X3D 8-Core

57th

725 ^{+/- 12}

Median

50th

730

AMD EPYC 4484PX 12-Core

41st

737 ^{+/- 16}

AMD EPYC 4564P 16-Core

31st

921 ^{+/- 34}

AMD EPYC 4464P 12-Core

31st

928 ^{+/- 32}

Low-Tier

25th

> 940

AMD EPYC 4364P 8-Core

11th

1377 ^{+/- 14}

AMD EPYC 4124P 4-Core

5th

2913 ^{+/- 138}

Detailed Performance Overview

Based on OpenBenchmarking.org data, the selected test / test configuration (RELION 5.0 - Test: Basic - Device: CPU) has an average run-time of 1 hour, 16 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 0.9%.

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)

ARMv8 64-bit

aarch64

ARMv8 Neoverse-V2 72-Core

Recent Test Results

Compare

9950X EOY 2024 3 Systems - 127 Benchmark Results	AMD Ryzen 9 9950X 16-Core - ASRock X870E Taichi - AMD Device 14d8 Ubuntu 24.04 - 6.8.0-50-generic - GNOME Shell 46.0
new tests 9655 Dec 3 Systems - 19 Benchmark Results	AMD EPYC 9655P 96-Core - Supermicro Super Server H13SSL-N v1.01 - AMD 1Ah Ubuntu 24.10 - 6.13.0-rc1-phx - GNOME Shell 47.0
newaa 4 Systems - 25 Benchmark Results	AMD Ryzen Threadripper 7980X 64-Cores - System76 Thelio Major - AMD Device 14a4 Ubuntu 24.04 - 6.8.0-49-generic - GNOME Shell 46.0
eoy2024 3 Systems - 218 Benchmark Results
rel 4 Systems - 1 Benchmark Result	ARMv8 Neoverse-V2 - Pegatron JIMBO P4352 - 1 x 480GB LPDDR5-6400MT Ubuntu 24.04 - 6.8.0-49-generic-64k - NVIDIA
re;l 4 Systems - 1 Benchmark Result	AMD Ryzen 7 9800X3D 8-Core - ASRock X870E Taichi - AMD Device 14d8 Ubuntu 24.04 - 6.8.0-49-generic - GNOME Shell 46.0
2024-10-08-0736 1 System - 461 Benchmark Results	AMD Ryzen 7 5800X 8-Core - GIGABYTE MC12-LE0-00 v01000100 - AMD Starship Ubuntu 24.04 - 6.11.0-061100-generic - GNOME Shell 46.0
AMD 5th Gen EPYC Turin CPUs vs. Intel Xeon 6980P Benchmarks 10 Systems - 145 Benchmark Results	Intel Xeon 6980P - Intel AvenueCity v0.01 - Intel Ice Lake IEH Ubuntu 24.04 - 6.10.0-phx - GCC 13.2.0
wrf relion 4 Systems - 2 Benchmark Results	AMD Ryzen 9 9950X 16-Core - ASUS ROG STRIX X670E-E GAMING WIFI - AMD Device 14d8 Ubuntu 24.04 - 6.10.0-phx - GNOME Shell 46.0