bioinf

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 24.04 via the Phoronix Test Suite.

HTML result view exported from: https://openbenchmarking.org/result/2410315-NE-BIOINF94961&grs.

bioinfProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenGLOpenCLCompilerFile-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/Matisse2 x 16GB DDR4-3200MT/s TEAMGROUP-UD4-32001000GB Western Digital WDS100T3X0C-00SJG0 + 1000GB Western Digital WD Blue SN580 1TB + 2000GB Seagate ST2000DX001-1CM1MSI NVIDIA GeForce RTX 3080 12GBNVIDIA GA102 HD AudioDELL S2721QSIntel I211 + Intel Dual Band-AC 3168NGWUbuntu 24.046.8.0-47-generic (x86_64)GNOME Shell 46.0X Server 1.21.1.11NVIDIA 560.35.034.6.0OpenCL 3.0 CUDA 12.6.65GCC 13.2.0 + CUDA 12.6ext45120x2880OpenBenchmarking.org- Transparent Huge Pages: madvise- --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --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-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-uJ7kn6/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-uJ7kn6/gcc-13-13.2.0/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-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 schedutil (Boost: Enabled) - CPU Microcode: 0xa20102b- 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: 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

bioinfmafft: Multiple Sequence Alignment - LSU RNAhmmer: Pfam Database Searchqmcpack: FeCO6_b3lyp_gmsqmcpack: O_ae_pyscf_UHFqmcpack: simple-H2Oqmcpack: LiH_ae_MSDqmcpack: Li2_STO_aemrbayes: Primate Phylogeny Analysishimeno: Poisson Pressure Solverqmcpack: H4_aeAMD Ryzen 9 5900X 12-Core8.13296.946137.64154.8622.91891.075196.0988.2145115.48634418.34OpenBenchmarking.org

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 +/- 0.005, N = 38.1321. (CC) gcc options: -std=c99 -O3 -lm -lpthread

Timed HMMer Search

Pfam Database Search

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 3.3.2Pfam Database SearchAMD Ryzen 9 5900X 12-Core20406080100SE +/- 0.09, N = 396.951. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm -lmpi

QMCPACK

Input: FeCO6_b3lyp_gms

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: FeCO6_b3lyp_gmsAMD Ryzen 9 5900X 12-Core306090120150SE +/- 0.51, N = 3137.641. (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 +/- 0.58, N = 3154.861. (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 +/- 0.08, N = 322.921. (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 +/- 0.48, N = 391.081. (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 +/- 2.14, N = 4196.091. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

Timed MrBayes Analysis

Primate Phylogeny Analysis

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny AnalysisAMD Ryzen 9 5900X 12-Core20406080100SE +/- 0.33, N = 388.211. (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

Himeno Benchmark

Poisson Pressure Solver

OpenBenchmarking.orgMFLOPS, More Is BetterHimeno Benchmark 3.0Poisson Pressure SolverAMD Ryzen 9 5900X 12-Core11002200330044005500SE +/- 86.98, N = 155115.491. (CC) gcc options: -O3 -mavx2

QMCPACK

Input: H4_ae

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: H4_aeAMD Ryzen 9 5900X 12-Core510152025SE +/- 0.33, N = 1218.341. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

Phoronix Test Suite v10.8.5