bioinformatics-40c-shared

Bioinformatics 40c Shared

Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2106037-IB-BIOINFORM58
Jump To Table - Results

Statistics

Remove Outliers Before Calculating Averages

Graph Settings

Prefer Vertical Bar Graphs

Table

Show Detailed System Result Table
Only show results matching title/arguments (delimit multiple options with a comma):


bioinformatics-40c-sharedOpenBenchmarking.orgPhoronix Test Suite 10.4.02 x Intel Xeon (Skylake IBRS) (40 Cores)OpenStack Foundation Nova v21.0.0 (1.13.0-1ubuntu1.1 BIOS)Intel 440FX 82441FX PMC16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 8192 MB RAM50GBCirrus Logic GD 5446Red Hat Virtio deviceUbuntu 20.045.4.0-74-generic (x86_64)GCC 9.3.0ext41024x768KVMProcessorMotherboardChipsetMemoryDiskGraphicsNetworkOSKernelCompilerFile-SystemScreen ResolutionSystem LayerBioinformatics-40c-shared BenchmarksSystem Logs- Transparent Huge Pages: madvise- --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --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++,gm2 --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-9-HskZEa/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --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 - CPU Microcode: 0x1- itlb_multihit: Not affected + l1tf: Mitigation of PTE Inversion; VMX: flush not necessary SMT disabled + mds: Mitigation of Clear buffers; SMT Host state unknown + meltdown: Mitigation of PTI + 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 generic retpoline IBPB: conditional IBRS_FW STIBP: disabled RSB filling + srbds: Not affected + tsx_async_abort: Mitigation of Clear buffers; SMT Host state unknown

bioinformatics-40c-sharedmrbayes: Primate Phylogeny Analysisqmcpack: simple-H2Ohmmer: Pfam Database Searchmafft: Multiple Sequence Alignment - LSU RNAhimeno: Poisson Pressure Solverbioinformatics-40c-shared261.60956.685186.49214.2923154.140783OpenBenchmarking.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 Analysisbioinformatics-40c-shared60120180240300SE +/- 0.61, N = 3261.611. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -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. 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 3.11Input: simple-H2Obioinformatics-40c-shared1326395265SE +/- 0.17, N = 356.691. (CXX) g++ options: -fopenmp -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -march=native -O3 -fomit-frame-pointer -ffast-math -pthread -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 Searchbioinformatics-40c-shared4080120160200SE +/- 2.38, N = 3186.491. (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 RNAbioinformatics-40c-shared48121620SE +/- 0.10, N = 314.291. (CC) gcc options: -std=c99 -O3 -lm -lpthread

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 Solverbioinformatics-40c-shared7001400210028003500SE +/- 12.04, N = 33154.141. (CC) gcc options: -O3 -mavx2