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.

Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2501316-NE-NIELSENBI27
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Date
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  Duration
NielsenBioinformatics
January 31
  11 Minutes
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NielsenBioinformaticsOpenBenchmarking.orgPhoronix Test SuiteAMD 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 12.4ext41920x1080ProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenCLCompilerFile-SystemScreen ResolutionNielsenBioinformatics PerformanceSystem Logs- 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

NielsenBioinformaticshmmer: Pfam Database Searchmafft: Multiple Sequence Alignment - LSU RNAmrbayes: Primate Phylogeny Analysishimeno: Poisson Pressure Solverqmcpack: FeCO6_b3lyp_gmsNielsenBioinformatics75.8765.07555.8189282.233840OpenBenchmarking.org

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 SearchNielsenBioinformatics20406080100SE +/- 0.18, N = 375.881. (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 RNANielsenBioinformatics1.14192.28383.42574.56765.7095SE +/- 0.019, N = 35.0751. (CC) gcc options: -std=c99 -O3 -lm -lpthread

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 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

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 SolverNielsenBioinformatics2K4K6K8K10KSE +/- 97.77, N = 59282.231. (CC) gcc options: -O3 -mavx2

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.

Input: H4_ae

NielsenBioinformatics: The test quit with a non-zero exit status. E: mpirun was unable to launch the specified application as it could not access

Input: Li2_STO_ae

NielsenBioinformatics: The test quit with a non-zero exit status. E: mpirun was unable to launch the specified application as it could not access

Input: LiH_ae_MSD

NielsenBioinformatics: The test quit with a non-zero exit status. E: mpirun was unable to launch the specified application as it could not access

Input: simple-H2O

NielsenBioinformatics: The test quit with a non-zero exit status. E: mpirun was unable to launch the specified application as it could not access

Input: O_ae_pyscf_UHF

NielsenBioinformatics: The test quit with a non-zero exit status. E: mpirun was unable to launch the specified application as it could not access

Input: FeCO6_b3lyp_gms

NielsenBioinformatics: The test quit with a non-zero exit status. E: mpirun was unable to launch the specified application as it could not access