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.

Source Repository

github.com

Test Created

13 January 2021

Last Updated

19 June 2023

Test Maintainer

Michael Larabel 

Test Type

Processor

Average Install Time

7 Minutes, 50 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

Supported Platforms


Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsRELION Popularity Statisticspts/relion2021.012021.022021.032021.042021.052021.062021.072021.082021.092021.102021.112021.122022.012022.022022.032022.042022.052022.062022.072022.082022.092022.102022.112022.122023.012023.022023.032023.042023.052023.062023.072023.082023.092023.102023.112023.122024.012024.022024.032024.042024.052024.062K4K6K8K10K
* 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 16 June 2024.

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 164 public results since 19 June 2023 with the latest data as of 22 May 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)
Mid-Tier
75th
> 169
59th
11
216 +/- 26
Median
50th
253
27th
4
390 +/- 6
Low-Tier
25th
> 404
23rd
4
408 +/- 5
3rd
6
1428 +/- 57
OpenBenchmarking.orgDistribution Of Public Results - Test: Basic - Device: CPU164 Results Range From 79 To 1471 Seconds7911615319022726430133837541244948652356059763467170874578281985689393096710041041107811151152118912261263130013371374141114481485612182430

Based on OpenBenchmarking.org data, the selected test / test configuration (RELION 4.0.1 - Test: Basic - Device: CPU) has an average run-time of 38 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.

OpenBenchmarking.orgMinutesTime Required To Complete BenchmarkTest: Basic - Device: CPURun-Time20406080100Min: 6 / Avg: 37.48 / Max: 106

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 2.3%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsTest: Basic - Device: CPUDeviation3691215Min: 0 / Avg: 2.25 / Max: 8

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
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
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)
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 Bulldozer (2011).

 
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

OpenBenchmarking.org Results Compare

22 Systems - 263 Benchmark Results

2 x AMD EPYC 9754 128-Core - AMD Titanite_4G - AMD Device 14a4

Ubuntu 24.04 - 6.9.0-060900rc3-generic - GCC 13.2.0

2 Systems - 3 Benchmark Results

ARMv8 Neoverse-V2 - Quanta Cloud QuantaGrid S74G-2U 1S7GZ9Z0000 S7G MB - 1 x 480GB DRAM-6400MT

Ubuntu 23.10 - 6.8.0-060800rc3daily20240208-generic-64k - GCC 13.2.0

1 System - 3 Benchmark Results

ARMv8 Neoverse-V2 - Quanta Cloud QuantaGrid S74G-2U 1S7GZ9Z0000 S7G MB - 1 x 480GB DRAM-6400MT

Ubuntu 23.10 - 6.8.0-060800rc3daily20240208-generic-64k - GCC 13.2.0

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