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.

Test Created

13 January 2021

Test Maintainer

Michael Larabel 

Test Type

Processor

Average Install Time

9 Minutes, 6 Seconds

Average Run Time

1 Hour, 16 Minutes, 9 Seconds

Test Dependencies

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

Accolades

5k+ Downloads

Supported Platforms


Public Result Uploads *Reported Installs **Reported Test Completions **Test Profile Page Views ***OpenBenchmarking.orgEventsRELION Popularity Statisticspts/relion2021.012021.022021.032021.042021.052021.062021.072021.082021.092021.102021.112021.122022.012022.022022.032022.042022.052022.062022.072022.082022.097001400210028003500
* 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 24 September 2022.

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 358 public results since 13 January 2021 with the latest data as of 27 September 2022.

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)
84th
12
284 +/- 4
Mid-Tier
75th
> 299
52nd
8
464 +/- 7
Median
50th
488
47th
3
517 +/- 5
45th
3
530 +/- 3
45th
11
537 +/- 72
40th
15
562 +/- 3
36th
8
568 +/- 8
36th
8
569 +/- 5
27th
6
758 +/- 4
Low-Tier
25th
> 764
21st
7
1247 +/- 5
16th
3
1601 +/- 4
14th
4
1691 +/- 1
11th
4
1806 +/- 3
7th
4
2212 +/- 279
5th
6
2441 +/- 14
3rd
3
3054 +/- 58
2nd
3
4674 +/- 6
OpenBenchmarking.orgDistribution Of Public Results - Test: Basic - Device: CPU346 Results Range From 147 To 7536 Seconds14729544359173988710351183133114791627177519232071221923672515266328112959310732553403355136993847399541434291443945874735488350315179532754755623577159196067621563636511665968076955710372517399754720406080100

Based on OpenBenchmarking.org data, the selected test / test configuration (RELION 3.1.1 - Test: Basic - Device: CPU) has an average run-time of 45 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-Time4080120160200Min: 11 / Avg: 44.26 / Max: 218

Based on public OpenBenchmarking.org results, the selected test / test configuration has an average standard deviation of 0.5%.

OpenBenchmarking.orgPercent, Fewer Is BetterAverage Deviation Between RunsTest: Basic - Device: CPUDeviation3691215Min: 0 / Avg: 0.53 / Max: 7

Does It Scale Well With Increasing Cores?

Yes, based on the automated analysis of the collected public benchmark data, this test / test settings does generally scale well with increasing CPU core counts. Data based on publicly available results for this test / test settings, separated by vendor, result divided by the reference CPU clock speed, grouped by matching physical CPU core count, and normalized against the smallest core count tested from each vendor for each CPU having a sufficient number of test samples and statistically significant data.

OpenBenchmarking.orgRelative Core Scaling To BaseRELION CPU Core ScalingTest: Basic - Device: CPU1216324864128510152025

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 PMULUDQ PSRLDQ CMPLESD SUBPD MOVHPD PSUBQ PADDQ MINSD MOVLPD CMPLEPD CVTPD2PS CVTSD2SS MAXSD DIVPD CMPNLTSD CMPLTSD CVTDQ2PS
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
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 VPBROADCASTD VPBROADCASTQ 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 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: 18 January 2022

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.6, 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
Ampere ARMv8 Neoverse-N1 128-Core, Ampere ARMv8 Neoverse-N1 256-Core, Ampere Altra ARMv8 Neoverse-N1 160-Core, Ampere Altra ARMv8 Neoverse-N1 80-Core

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