20210117 bioinformatics

AMD Ryzen 7 3700X 8-Core testing with a ASRock X570 Phantom Gaming-ITX/TB3 (P2.80 BIOS) and Zotac NVIDIA GeForce RTX 2060 SUPER 8GB on Ubuntu 20.10 via the Phoronix Test Suite.

HTML result view exported from: https://openbenchmarking.org/result/2101188-HA-20210117B63&grs.

20210117 bioinformaticsProcessorMotherboardChipsetMemoryDiskGraphicsAudioNetworkOSKernelDisplay ServerDisplay DriverOpenCLVulkanCompilerFile-SystemScreen ResolutionAMD Ryzen 7 3700X 8-CoreAMD Ryzen 7 3700X 8-Core @ 3.60GHz (8 Cores / 16 Threads)ASRock X570 Phantom Gaming-ITX/TB3 (P2.80 BIOS)AMD Starship/Matisse32GB500GB Western Digital WDS500G3X0C-00SJG0 + 4 x 2000GB Seagate ST2000LM015-2E81Zotac NVIDIA GeForce RTX 2060 SUPER 8GBNVIDIA TU106 HD AudioIntel I211 + Intel Wi-Fi 6 AX200Ubuntu 20.105.8.0-38-lowlatency (x86_64)X Server 1.20.9modesetting 1.20.9OpenCL 1.2 CUDA 11.2.1091.2.155GCC 10.2.0 + CUDA 11.0btrfs640x480OpenBenchmarking.org- --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --enable-checking=release --enable-clocale=gnu --enable-default-pie --enable-gnu-unique-object --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,hsa --enable-plugin --enable-shared --enable-threads=posix --host=x86_64-linux-gnu --program-prefix=x86_64-linux-gnu- --target=x86_64-linux-gnu --with-abi=m64 --with-arch-32=i686 --with-default-libstdcxx-abi=new --with-gcc-major-version-only --with-multilib-list=m32,m64,mx32 --with-target-system-zlib=auto --with-tune=generic --without-cuda-driver -v - Scaling Governor: acpi-cpufreq performance (Boost: Enabled) - CPU Microcode: 0x8701021- 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 AMD retpoline IBPB: conditional STIBP: conditional RSB filling + srbds: Not affected + tsx_async_abort: Not affected

20210117 bioinformaticshimeno: Poisson Pressure Solvermafft: Multiple Sequence Alignment - LSU RNAhmmer: Pfam Database Searchqmcpack: mrbayes: Primate Phylogeny AnalysisAMD Ryzen 7 3700X 8-Core4911.10588810.36292.883580.4183.327OpenBenchmarking.org

Himeno Benchmark

Poisson Pressure Solver

OpenBenchmarking.orgMFLOPS, More Is BetterHimeno Benchmark 3.0Poisson Pressure SolverAMD Ryzen 7 3700X 8-Core11002200330044005500SE +/- 62.25, N = 34911.111. (CC) gcc options: -O3 -mavx2

Timed MAFFT Alignment

Multiple Sequence Alignment - LSU RNA

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.471Multiple Sequence Alignment - LSU RNAAMD Ryzen 7 3700X 8-Core3691215SE +/- 0.06, N = 310.361. (CC) gcc options: -std=c99 -O3 -lm -lpthread

Timed HMMer Search

Pfam Database Search

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 3.3.1Pfam Database SearchAMD Ryzen 7 3700X 8-Core20406080100SE +/- 0.15, N = 392.881. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm

QMCPACK

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.8AMD Ryzen 7 3700X 8-Core130260390520650580.411. (CXX) g++ options: -fopenmp -fomit-frame-pointer -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -march=native -O3 -ffast-math -lm

Timed MrBayes Analysis

Primate Phylogeny Analysis

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny AnalysisAMD Ryzen 7 3700X 8-Core20406080100SE +/- 2.47, N = 1586.421. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -std=c99 -pedantic -lm

Phoronix Test Suite v10.8.4