bioinformatics-ncasem1

Intel Xeon E5-2699 v4 testing with a ASRock X99E-ITX/ac (P3.80 BIOS) and NVIDIA TITAN X 12GB on Pop 22.04 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 2401149-NE-BIOINFORM85
Jump To Table - Results

Statistics

Remove Outliers Before Calculating Averages

Graph Settings

Prefer Vertical Bar Graphs

Multi-Way Comparison

Condense Multi-Option Tests Into Single Result Graphs

Table

Show Detailed System Result Table

Run Management

Result
Identifier
View Logs
Performance Per
Dollar
Date
Run
  Test
  Duration
bioinformatics
January 14
  1 Hour, 29 Minutes
Only show results matching title/arguments (delimit multiple options with a comma):
Do not show results matching title/arguments (delimit multiple options with a comma):


bioinformatics-ncasem1OpenBenchmarking.orgPhoronix Test SuiteIntel Xeon E5-2699 v4 @ 3.60GHz (22 Cores / 44 Threads)ASRock X99E-ITX/ac (P3.80 BIOS)Intel Xeon E7 v4/Xeon64GBSamsung SSD 950 PRO 512GBNVIDIA TITAN X 12GBRealtek ALC1150DELL S2721QSIntel I218-V + Intel I211Pop 22.046.6.6-76060606-generic (x86_64)GNOME Shell 42.5X Server 1.21.1.4NVIDIA 470.199.024.6.0OpenCL 3.0 CUDA 11.4.4021.2.175GCC 11.4.0ext43840x2160ProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenGLOpenCLVulkanCompilerFile-SystemScreen ResolutionBioinformatics-ncasem1 BenchmarksSystem 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,brig,d,fortran,objc,obj-c++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-link-serialization=2 --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: intel_cpufreq performance - CPU Microcode: 0xb000040- Python 3.10.12- gather_data_sampling: Not affected + itlb_multihit: KVM: Mitigation of VMX disabled + l1tf: Mitigation of PTE Inversion; VMX: conditional cache flushes SMT vulnerable + mds: Mitigation of Clear buffers; SMT vulnerable + meltdown: Mitigation of PTI + mmio_stale_data: Mitigation of Clear buffers; SMT vulnerable + 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 Retpolines IBPB: conditional IBRS_FW STIBP: conditional RSB filling PBRSB-eIBRS: Not affected + srbds: Not affected + tsx_async_abort: Mitigation of Clear buffers; SMT vulnerable

bioinformatics-ncasem1himeno: 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_gmsbioinformatics3569.511115200.908171.03211.96731.83322.75229.5554.900352.12346.35OpenBenchmarking.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 Solverbioinformatics8001600240032004000SE +/- 40.93, N = 33569.511. (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 Analysisbioinformatics4080120160200SE +/- 0.73, N = 3200.911. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -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 Searchbioinformatics4080120160200SE +/- 0.47, N = 3171.031. (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 RNAbioinformatics3691215SE +/- 0.01, N = 311.971. (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_aebioinformatics714212835SE +/- 0.22, N = 331.831. (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_aebioinformatics70140210280350SE +/- 2.60, N = 3322.751. (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_MSDbioinformatics50100150200250SE +/- 0.88, N = 3229.551. (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-H2Obioinformatics1224364860SE +/- 0.15, N = 354.901. (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_UHFbioinformatics80160240320400SE +/- 2.70, N = 3352.121. (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_gmsbioinformatics80160240320400SE +/- 0.83, N = 3346.351. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl