lubu20-wk1_scientific_12aug2020

lubu20-wk1_scientific_12aug2020

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lubu20-wk1_scientific_12aug2020
August 12 2020
  2 Days, 15 Hours, 32 Minutes
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lubu20-wk1_scientific_12aug2020OpenBenchmarking.orgPhoronix Test SuiteAMD Ryzen Threadripper 3960X 24-Core (2 Cores)Intel 440BX (6.00 BIOS)Intel 440BX/ZX/DX4096MB54GB VMware Virtual SSVGA3D; buildEnsoniq ES1371/ES1373Intel 82545EM + 4 x AMD 79c970Ubuntu 16.044.15.0-112-generic (x86_64)LXDE 0.8.2X Server 1.19.6modesetting 1.19.62.1 Mesa 18.0.5GCC 5.5.0 20171010ext41280x1024VMwareProcessorMotherboardChipsetMemoryDiskGraphicsAudioNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenGLCompilerFile-SystemScreen ResolutionSystem LayerLubu20-wk1_scientific_12aug2020 BenchmarksSystem Logs- --build=x86_64-linux-gnu --disable-browser-plugin --disable-vtable-verify --disable-werror --enable-checking=release --enable-clocale=gnu --enable-gnu-unique-object --enable-gtk-cairo --enable-java-awt=gtk --enable-java-home --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --enable-libmpx --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc --enable-plugin --enable-shared --enable-threads=posix --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-abi=m64 --with-arch-32=i686 --with-arch-directory=amd64 --with-default-libstdcxx-abi=new --with-multilib-list=m32,m64,mx32 --with-tune=generic -v - CPU Microcode: 0x8301039- itlb_multihit: Not affected + l1tf: Not affected + mds: Not affected + meltdown: Not affected + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1: Mitigation of usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full generic retpoline IBPB: conditional STIBP: disabled RSB filling + srbds: Not affected + tsx_async_abort: Not affected

lubu20-wk1_scientific_12aug2020hpcc: G-HPLminife: Smallcloverleaf: Lagrangian-Eulerian Hydrodynamicscp2k: Fayalite-FIST Datanamd: ATPase Simulation - 327,506 Atomsamg: ffte: N=256, 1D Complex FFT Routinefftw: Stock - 1D FFT Size 32fftw: Stock - 2D FFT Size 32fftw: Stock - 1D FFT Size 4096fftw: Stock - 2D FFT Size 4096fftw: Float + SSE - 1D FFT Size 32fftw: Float + SSE - 2D FFT Size 32fftw: Float + SSE - 1D FFT Size 4096fftw: Float + SSE - 2D FFT Size 4096pennant: sedovbigpennant: leblancbigmrbayes: Primate Phylogeny Analysishmmer: Pfam Database Searchmafft: Multiple Sequence Alignmentlulesh: arrayfire: BLAS CPUmt-dgemm: Sustained Floating-Point Ratehimeno: Poisson Pressure Solverrbenchmark: lubu20-wk1_scientific_12aug202035.946773.231994.55751.9619.90469612321338988.059953.3112698843.06540.412736377985423219207200.7415142.8697138.65919.0727.7891251.547862.98880.4210174589.0916830.3273OpenBenchmarking.org

HPC Challenge

HPC Challenge (HPCC) is a cluster-focused benchmark consisting of the HPL Linpack TPP benchmark, DGEMM, STREAM, PTRANS, RandomAccess, FFT, and communication bandwidth and latency. This HPC Challenge test profile attempts to ship with standard yet versatile configuration/input files though they can be modified. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgGFLOPS, More Is BetterHPC Challenge 1.5.0Test / Class: G-HPLlubu20-wk1_scientific_12aug2020816243240SE +/- 0.55, N = 335.951. (CC) gcc options: -lblas -lm -pthread -lmpi -fomit-frame-pointer -funroll-loops2. BLAS + Open MPI 1.10.2

miniFE

MiniFE Finite Element is an application for unstructured implicit finite element codes. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgCG Mflops, More Is BetterminiFE 2.2Problem Size: Smalllubu20-wk1_scientific_12aug20200.72721.45442.18162.90883.636SE +/- 0.08081, N = 33.231991. (CXX) g++ options: -O3 -fopenmp -pthread -lmpi_cxx -lmpi

CloverLeaf

CloverLeaf is a Lagrangian-Eulerian hydrodynamics benchmark. This test profile currently makes use of CloverLeaf's OpenMP version and benchmarked with the clover_bm8192.in input file. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterCloverLeafLagrangian-Eulerian Hydrodynamicslubu20-wk1_scientific_12aug20201.02382.04763.07144.09525.119SE +/- 0.06, N = 34.551. (F9X) gfortran options: -O3 -march=native -funroll-loops -fopenmp

CP2K Molecular Dynamics

CP2K is an open-source molecular dynamics software package focused on quantum chemistry and solid-state physics. This test profile currently makes use of the OpenMP implementation and using the Fayalite-FIST molecular dynamics run and measures the total time to complete. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterCP2K Molecular Dynamics 6.1Fayalite-FIST Datalubu20-wk1_scientific_12aug2020160320480640800751.96

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgdays/ns, Fewer Is BetterNAMD 2.13ATPase Simulation - 327,506 Atomslubu20-wk1_scientific_12aug20203691215SE +/- 0.03442, N = 39.90469

Algebraic Multi-Grid Benchmark

AMG is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. The driver provided with AMG builds linear systems for various 3-dimensional problems. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgFigure Of Merit, More Is BetterAlgebraic Multi-Grid Benchmarklubu20-wk1_scientific_12aug202013M26M39M52M65MSE +/- 911503.92, N = 3612321331. (CC) gcc options: -lparcsr_ls -lparcsr_mv -lseq_mv -lIJ_mv -lkrylov -lHYPRE_utilities -lm -fopenmp -pthread -lmpi

FFTE

FFTE is a package by Daisuke Takahashi to compute Discrete Fourier Transforms of 1-, 2- and 3- dimensional sequences of length (2^p)*(3^q)*(5^r). Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgMFLOPS, More Is BetterFFTE 6.0Test: N=256, 1D Complex FFT Routinelubu20-wk1_scientific_12aug20202K4K6K8K10KSE +/- 38.44, N = 38988.051. (F9X) gfortran options: -O3 -fomit-frame-pointer -fopenmp -pthread -lmpi_usempif08 -lmpi_mpifh -lmpi

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Stock - Size: 1D FFT Size 32lubu20-wk1_scientific_12aug20202K4K6K8K10KSE +/- 8.06, N = 39953.31. (CC) gcc options: -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Stock - Size: 2D FFT Size 32lubu20-wk1_scientific_12aug20202K4K6K8K10KSE +/- 11.17, N = 3112691. (CC) gcc options: -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Stock - Size: 1D FFT Size 4096lubu20-wk1_scientific_12aug20202K4K6K8K10KSE +/- 8.32, N = 38843.01. (CC) gcc options: -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Stock - Size: 2D FFT Size 4096lubu20-wk1_scientific_12aug202014002800420056007000SE +/- 26.79, N = 36540.41. (CC) gcc options: -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Float + SSE - Size: 1D FFT Size 32lubu20-wk1_scientific_12aug20203K6K9K12K15KSE +/- 27.33, N = 3127361. (CC) gcc options: -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Float + SSE - Size: 2D FFT Size 32lubu20-wk1_scientific_12aug20208K16K24K32K40KSE +/- 21.79, N = 3377981. (CC) gcc options: -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Float + SSE - Size: 1D FFT Size 4096lubu20-wk1_scientific_12aug202012K24K36K48K60KSE +/- 241.66, N = 3542321. (CC) gcc options: -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Float + SSE - Size: 2D FFT Size 4096lubu20-wk1_scientific_12aug20204K8K12K16K20KSE +/- 161.28, N = 3192071. (CC) gcc options: -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

Pennant

Pennant is an application focused on hydrodynamics on general unstructured meshes in 2D. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgHydro Cycle Time - Seconds, Fewer Is BetterPennant 1.0.1Test: sedovbiglubu20-wk1_scientific_12aug20204080120160200SE +/- 0.34, N = 3200.741. (CXX) g++ options: -fopenmp -pthread -lmpi_cxx -lmpi

OpenBenchmarking.orgHydro Cycle Time - Seconds, Fewer Is BetterPennant 1.0.1Test: leblancbiglubu20-wk1_scientific_12aug2020306090120150SE +/- 0.70, N = 3142.871. (CXX) g++ options: -fopenmp -pthread -lmpi_cxx -lmpi

Timed MrBayes Analysis

This test performs a bayesian analysis of a set of primate genome sequences in order to estimate their phylogeny. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny Analysislubu20-wk1_scientific_12aug2020306090120150SE +/- 0.58, N = 3138.661. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -std=c99 -pedantic -lm -lreadline

Timed HMMer Search

This test searches through the Pfam database of profile hidden markov models. The search finds the domain structure of Drosophila Sevenless protein. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 2.3.2Pfam Database Searchlubu20-wk1_scientific_12aug2020510152025SE +/- 0.09, N = 319.071. (CC) gcc options: -O2 -pthread -lhmmer -lsquid -lm

Timed MAFFT Alignment

This test performs an alignment of 100 pyruvate decarboxylase sequences. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.392Multiple Sequence Alignmentlubu20-wk1_scientific_12aug2020246810SE +/- 0.014, N = 37.7891. (CC) gcc options: -std=c99 -O3 -lm -lpthread

LULESH

LULESH is the Livermore Unstructured Lagrangian Explicit Shock Hydrodynamics. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgz/s, More Is BetterLULESH 2.0.3lubu20-wk1_scientific_12aug202030060090012001500SE +/- 9.98, N = 131251.551. (CXX) g++ options: -O3 -fopenmp -lm -pthread -lmpi_cxx -lmpi

ArrayFire

ArrayFire is an GPU and CPU numeric processing library, this test uses the built-in CPU and OpenCL ArrayFire benchmarks. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgGFLOPS, More Is BetterArrayFire 3.7Test: BLAS CPUlubu20-wk1_scientific_12aug20201428425670SE +/- 0.07, N = 362.991. (CXX) g++ options: -rdynamic

ACES DGEMM

This is a multi-threaded DGEMM benchmark. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgGFLOP/s, More Is BetterACES DGEMM 1.0Sustained Floating-Point Ratelubu20-wk1_scientific_12aug20200.09470.18940.28410.37880.4735SE +/- 0.002511, N = 30.4210171. (CC) gcc options: -O3 -march=native -fopenmp

Himeno Benchmark

The Himeno benchmark is a linear solver of pressure Poisson using a point-Jacobi method. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgMFLOPS, More Is BetterHimeno Benchmark 3.0Poisson Pressure Solverlubu20-wk1_scientific_12aug202010002000300040005000SE +/- 28.81, N = 34589.091. (CC) gcc options: -O3 -mavx2

R Benchmark

This test is a quick-running survey of general R performance Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterR Benchmarklubu20-wk1_scientific_12aug20200.07360.14720.22080.29440.368SE +/- 0.0024, N = 30.32731. R scripting front-end version 3.2.3 (2015-12-10)