epyc_bioinformatics

AMD EPYC 7232P 8-Core testing with a ASRockRack ROMED6U-2L2T (L0.08 BIOS) and llvmpipe 94GB on Fedora 32 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 2007312-NE-EPYCBIOIN21
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epyv_rome_bio
July 31 2020
  20 Minutes
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epyc_bioinformaticsOpenBenchmarking.orgPhoronix Test SuiteAMD EPYC 7232P 8-Core @ 3.10GHz (8 Cores / 16 Threads)ASRockRack ROMED6U-2L2T (L0.08 BIOS)AMD Starship/Matisse96GB512GB KXG60ZNV512G TOSHIBAllvmpipe 94GBDELL 1908WFP2 x Intel X710 for 10GBASE-T + 2 x Intel I210Fedora 325.7.10-201.fc32.x86_64 (x86_64)GNOME Shell 3.36.4X Server + Wayland3.3 Mesa 20.1.4 (LLVM 10.0.0 256 bits)GCC 10.2.1 20200723 + Clang 10.0.0ext41440x900ProcessorMotherboardChipsetMemoryDiskGraphicsMonitorNetworkOSKernelDesktopDisplay ServerOpenGLCompilerFile-SystemScreen ResolutionEpyc_bioinformatics PerformanceSystem Logs- --build=x86_64-redhat-linux --disable-libunwind-exceptions --enable-__cxa_atexit --enable-bootstrap --enable-cet --enable-checking=release --enable-gnu-indirect-function --enable-gnu-unique-object --enable-initfini-array --enable-languages=c,c++,fortran,objc,obj-c++,ada,go,d,lto --enable-multilib --enable-offload-targets=nvptx-none --enable-plugin --enable-shared --enable-threads=posix --mandir=/usr/share/man --with-arch_32=i686 --with-gcc-major-version-only --with-isl --with-linker-hash-style=gnu --with-tune=generic --without-cuda-driver - Scaling Governor: acpi-cpufreq ondemand - CPU Microcode: 0x8301034- SELinux + itlb_multihit: Not affected + l1tf: Not affected + mds: Not affected + meltdown: Not affected + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1: Mitigation of usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full AMD retpoline IBPB: conditional IBRS_FW STIBP: conditional RSB filling + srbds: Not affected + tsx_async_abort: Not affected

epyc_bioinformaticsmrbayes: Primate Phylogeny Analysisqmcpack: hmmer: Pfam Database Searchhimeno: Poisson Pressure Solverepyv_rome_bio87.191728.385.7743526.754563OpenBenchmarking.org

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 Analysisepyv_rome_bio20406080100SE +/- 0.04, N = 387.191. (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

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. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.8epyv_rome_bio160320480640800728.381. (CXX) g++ options: -fopenmp -fomit-frame-pointer -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -march=native -O2 -ffast-math

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 2.3.2Pfam Database Searchepyv_rome_bio1.29922.59843.89765.19686.496SE +/- 0.047, N = 35.7741. (CC) gcc options: -O2 -pthread -lhmmer -lsquid -lm

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 Solverepyv_rome_bio8001600240032004000SE +/- 46.01, N = 33526.751. (CC) gcc options: -O3 -mavx2