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.

Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2410315-NE-BIOINF94961
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Result
Identifier
Performance Per
Dollar
Date
Run
  Test
  Duration
AMD Ryzen 9 5900X 12-Core
October 31
  1 Hour, 3 Minutes
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bioinfOpenBenchmarking.orgPhoronix Test SuiteAMD 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 12.6ext45120x2880ProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenGLOpenCLCompilerFile-SystemScreen ResolutionBioinf BenchmarksSystem Logs- 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

bioinfhimeno: Poisson Pressure Solvermrbayes: Primate Phylogeny Analysishmmer: Pfam Database Searchmafft: Multiple Sequence Alignment - LSU RNAqmcpack: H4_aeqmcpack: Li2_STO_aeqmcpack: LiH_ae_MSDqmcpack: simple-H2Oqmcpack: O_ae_pyscf_UHFqmcpack: FeCO6_b3lyp_gmsAMD Ryzen 9 5900X 12-Core5115.48634488.21496.9468.13218.34196.0991.07522.918154.86137.64OpenBenchmarking.org

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 SolverAMD Ryzen 9 5900X 12-Core11002200330044005500SE +/- 86.98, N = 155115.491. (CC) gcc options: -O3 -mavx2

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 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

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

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 7.471Multiple Sequence Alignment - LSU RNAAMD Ryzen 9 5900X 12-Core246810SE +/- 0.005, N = 38.1321. (CC) gcc options: -std=c99 -O3 -lm -lpthread

QMCPACK

QMCPACK is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code making use of MPI for this benchmark of the H20 example code. QMCPACK is an open-source production level many-body ab initio Quantum Monte Carlo code for computing the electronic structure of atoms, molecules, and solids. QMCPACK is supported by the U.S. Department of Energy. Learn more via the OpenBenchmarking.org test page.

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

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

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

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

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

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