NielsenBioinformatics

AMD Ryzen 9 9950X 16-Core testing with a ASUS PRIME B650M-A II (3201 BIOS) and Gigabyte NVIDIA GeForce RTX 2070 SUPER 8GB on Ubuntu 24.04 via the Phoronix Test Suite.

HTML result view exported from: https://openbenchmarking.org/result/2501316-NE-NIELSENBI27.

NielsenBioinformaticsProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenCLCompilerFile-SystemScreen ResolutionNielsenBioinformaticsAMD Ryzen 9 9950X 16-Core @ 5.75GHz (16 Cores / 32 Threads)ASUS PRIME B650M-A II (3201 BIOS)AMD Device 14d84 x 48GB DDR5-3600MT/s G Skill F5-6800J3446F48G2000GB Samsung SSD 980 PRO 2TBGigabyte NVIDIA GeForce RTX 2070 SUPER 8GBNVIDIA TU104 HD AudioVS2447 100Hz2 x Intel 10-Gigabit X540-AT2 + Realtek RTL8125 2.5GbEUbuntu 24.046.8.0-51-generic (x86_64)GNOME Shell 46.0X Server 1.21.1.11NVIDIAOpenCL 3.0 CUDA 12.4.131GCC 13.3.0 + CUDA 12.4ext41920x1080OpenBenchmarking.org- Transparent Huge Pages: madvise- --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --enable-bootstrap --enable-cet --enable-checking=release --enable-clocale=gnu --enable-default-pie --enable-gnu-unique-object --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --enable-libphobos-checking=release --enable-libstdcxx-backtrace --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-link-serialization=2 --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-fG75Ri/gcc-13-13.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-fG75Ri/gcc-13-13.3.0/debian/tmp-gcn/usr --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-build-config=bootstrap-lto-lean --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: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xb404023 - Python 3.12.3- gather_data_sampling: Not affected + itlb_multihit: Not affected + l1tf: Not affected + mds: Not affected + meltdown: Not affected + mmio_stale_data: Not affected + reg_file_data_sampling: Not affected + retbleed: Not affected + spec_rstack_overflow: Not affected + spec_store_bypass: Mitigation of SSB disabled via prctl + spectre_v1: Mitigation of usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Enhanced / Automatic IBRS; IBPB: conditional; STIBP: always-on; RSB filling; PBRSB-eIBRS: Not affected; BHI: Not affected + srbds: Not affected + tsx_async_abort: Not affected

NielsenBioinformaticsmrbayes: Primate Phylogeny Analysishmmer: Pfam Database Searchmafft: Multiple Sequence Alignment - LSU RNAhimeno: Poisson Pressure SolverNielsenBioinformatics55.81875.8765.0759282.233840OpenBenchmarking.org

Timed MrBayes Analysis

Primate Phylogeny Analysis

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny AnalysisNielsenBioinformatics1326395265SE +/- 0.21, N = 355.821. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4a -msha -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512ifma -mavx512vbmi -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -std=c99 -pedantic -lm -lreadline

Timed HMMer Search

Pfam Database Search

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 3.3.2Pfam Database SearchNielsenBioinformatics20406080100SE +/- 0.18, N = 375.881. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm -lmpi

Timed MAFFT Alignment

Multiple Sequence Alignment - LSU RNA

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.471Multiple Sequence Alignment - LSU RNANielsenBioinformatics1.14192.28383.42574.56765.7095SE +/- 0.019, N = 35.0751. (CC) gcc options: -std=c99 -O3 -lm -lpthread

Himeno Benchmark

Poisson Pressure Solver

OpenBenchmarking.orgMFLOPS, More Is BetterHimeno Benchmark 3.0Poisson Pressure SolverNielsenBioinformatics2K4K6K8K10KSE +/- 97.77, N = 59282.231. (CC) gcc options: -O3 -mavx2

Phoronix Test Suite v10.8.5