bioinfo

AMD Ryzen 9 5900X 12-Core testing with a ASRock X570 Steel Legend (P5.63 BIOS) and MSI NVIDIA GeForce RTX 3080 12GB on Ubuntu 22.04 via the Phoronix Test Suite.

HTML result view exported from: https://openbenchmarking.org/result/2501174-NE-BIOINFO1916.

bioinfoProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverVulkanCompilerFile-SystemScreen ResolutionAMD Ryzen 9 5900X 12-CoreAMD Ryzen 9 5900X 12-Core @ 3.70GHz (12 Cores / 24 Threads)ASRock X570 Steel Legend (P5.63 BIOS)AMD Starship/Matisse4 x 16GB DDR4-3600MT/s TEAMGROUP-UD4-32001000GB Western Digital WDS100T3X0C-00SJG0 + 1000GB Western Digital WD Blue SN580 1TB + 2000GB Seagate ST2000DX001-1CM1 + 250GB Samsung SSD 840MSI NVIDIA GeForce RTX 3080 12GBNVIDIA GA102 HD AudioDELL S2721QSIntel I211 + Intel Dual Band-AC 3168NGWUbuntu 22.046.8.0-51-generic (x86_64)GNOME Shell 42.9X Server 1.21.1.4NVIDIA 565.57.011.3.289GCC 11.4.0 + CUDA 12.6ext41600x1200OpenBenchmarking.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,brig,d,fortran,objc,obj-c++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-link-serialization=2 --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: acpi-cpufreq performance (Boost: Enabled) - CPU Microcode: 0xa20102b- Python 3.10.12- 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: Mitigation of Safe RET + spec_store_bypass: Mitigation of SSB disabled via prctl + spectre_v1: Mitigation of usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Retpolines; IBPB: conditional; IBRS_FW; STIBP: always-on; RSB filling; PBRSB-eIBRS: Not affected; BHI: Not affected + srbds: Not affected + tsx_async_abort: Not affected

bioinfomrbayes: Primate Phylogeny Analysisqmcpack: H4_aeqmcpack: Li2_STO_aeqmcpack: LiH_ae_MSDqmcpack: simple-H2Oqmcpack: O_ae_pyscf_UHFqmcpack: FeCO6_b3lyp_gmshmmer: Pfam Database Searchmafft: Multiple Sequence Alignment - LSU RNAhimeno: Poisson Pressure SolverAMD Ryzen 9 5900X 12-Core86.05718.93192.5694.00822.013155.76145.9696.0498.0605384.577700OpenBenchmarking.org

Timed MrBayes Analysis

Primate Phylogeny Analysis

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny AnalysisAMD Ryzen 9 5900X 12-Core20406080100SE +/- 0.38, N = 386.061. (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

QMCPACK

Input: H4_ae

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: H4_aeAMD Ryzen 9 5900X 12-Core510152025SE +/- 0.18, N = 1518.931. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: Li2_STO_ae

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: Li2_STO_aeAMD Ryzen 9 5900X 12-Core4080120160200SE +/- 1.69, N = 3192.561. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: LiH_ae_MSD

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: LiH_ae_MSDAMD Ryzen 9 5900X 12-Core20406080100SE +/- 0.43, N = 394.011. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: simple-H2O

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: simple-H2OAMD Ryzen 9 5900X 12-Core510152025SE +/- 0.04, N = 322.011. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: O_ae_pyscf_UHF

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: O_ae_pyscf_UHFAMD Ryzen 9 5900X 12-Core306090120150SE +/- 1.25, N = 3155.761. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: FeCO6_b3lyp_gms

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: FeCO6_b3lyp_gmsAMD Ryzen 9 5900X 12-Core306090120150SE +/- 0.23, N = 3145.961. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

Timed HMMer Search

Pfam Database Search

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 3.3.2Pfam Database SearchAMD Ryzen 9 5900X 12-Core20406080100SE +/- 0.25, N = 396.051. (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 RNAAMD Ryzen 9 5900X 12-Core246810SE +/- 0.031, N = 38.0601. (CC) gcc options: -std=c99 -O3 -lm -lpthread

Himeno Benchmark

Poisson Pressure Solver

OpenBenchmarking.orgMFLOPS, More Is BetterHimeno Benchmark 3.0Poisson Pressure SolverAMD Ryzen 9 5900X 12-Core12002400360048006000SE +/- 81.21, N = 125384.581. (CC) gcc options: -O3 -mavx2

Phoronix Test Suite v10.8.5