20210117 bioinformatics

AMD Ryzen 7 3700X 8-Core testing with a ASRock X570 Phantom Gaming-ITX/TB3 (P2.80 BIOS) and Zotac NVIDIA GeForce RTX 2060 SUPER 8GB on Ubuntu 20.10 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 2101188-HA-20210117B63
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AMD Ryzen 7 3700X 8-Core
January 17 2021
  39 Minutes
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AMD Ryzen 7 3700X 8-Core

Processor: AMD Ryzen 7 3700X 8-Core @ 3.60GHz (8 Cores / 16 Threads), Motherboard: ASRock X570 Phantom Gaming-ITX/TB3 (P2.80 BIOS), Chipset: AMD Starship/Matisse, Memory: 32GB, Disk: 500GB Western Digital WDS500G3X0C-00SJG0 + 4 x 2000GB Seagate ST2000LM015-2E81, Graphics: Zotac NVIDIA GeForce RTX 2060 SUPER 8GB, Audio: NVIDIA TU106 HD Audio, Network: Intel I211 + Intel Wi-Fi 6 AX200

OS: Ubuntu 20.10, Kernel: 5.8.0-38-lowlatency (x86_64), Display Server: X Server 1.20.9, Display Driver: modesetting 1.20.9, OpenCL: OpenCL 1.2 CUDA 11.2.109, Vulkan: 1.2.155, Compiler: GCC 10.2.0 + CUDA 11.0, File-System: btrfs, Screen Resolution: 640x480

Compiler Notes: --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++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/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
Processor Notes: Scaling Governor: acpi-cpufreq performance (Boost: Enabled) - CPU Microcode: 0x8701021
Security Notes: 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 STIBP: conditional RSB filling + srbds: Not affected + tsx_async_abort: Not affected

20210117 bioinformaticsOpenBenchmarking.orgPhoronix Test SuiteAMD Ryzen 7 3700X 8-Core @ 3.60GHz (8 Cores / 16 Threads)ASRock X570 Phantom Gaming-ITX/TB3 (P2.80 BIOS)AMD Starship/Matisse32GB500GB Western Digital WDS500G3X0C-00SJG0 + 4 x 2000GB Seagate ST2000LM015-2E81Zotac NVIDIA GeForce RTX 2060 SUPER 8GBNVIDIA TU106 HD AudioIntel I211 + Intel Wi-Fi 6 AX200Ubuntu 20.105.8.0-38-lowlatency (x86_64)X Server 1.20.9modesetting 1.20.9OpenCL 1.2 CUDA 11.2.1091.2.155GCC 10.2.0 + CUDA 11.0btrfs640x480ProcessorMotherboardChipsetMemoryDiskGraphicsAudioNetworkOSKernelDisplay ServerDisplay DriverOpenCLVulkanCompilerFile-SystemScreen Resolution20210117 Bioinformatics PerformanceSystem Logs- --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++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/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 - Scaling Governor: acpi-cpufreq performance (Boost: Enabled) - CPU Microcode: 0x8701021- 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 STIBP: conditional RSB filling + srbds: Not affected + tsx_async_abort: Not affected

20210117 bioinformaticsmrbayes: Primate Phylogeny Analysisqmcpack: hmmer: Pfam Database Searchmafft: Multiple Sequence Alignment - LSU RNAhimeno: Poisson Pressure SolverAMD Ryzen 7 3700X 8-Core83.327580.4192.88310.3624911.105888OpenBenchmarking.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 AnalysisAMD Ryzen 7 3700X 8-Core20406080100SE +/- 2.47, N = 1586.421. (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
OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny AnalysisAMD Ryzen 7 3700X 8-Core1632486480Min: 71.46 / Avg: 86.42 / Max: 96.241. (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 3.8AMD Ryzen 7 3700X 8-Core130260390520650580.411. (CXX) g++ options: -fopenmp -fomit-frame-pointer -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -march=native -O3 -ffast-math -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 3.3.1Pfam Database SearchAMD Ryzen 7 3700X 8-Core20406080100SE +/- 0.15, N = 392.881. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm

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 7 3700X 8-Core3691215SE +/- 0.06, N = 310.361. (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 SolverAMD Ryzen 7 3700X 8-Core11002200330044005500SE +/- 62.25, N = 34911.111. (CC) gcc options: -O3 -mavx2

AMD Ryzen 7 3700X 8-Core

Processor: AMD Ryzen 7 3700X 8-Core @ 3.60GHz (8 Cores / 16 Threads), Motherboard: ASRock X570 Phantom Gaming-ITX/TB3 (P2.80 BIOS), Chipset: AMD Starship/Matisse, Memory: 32GB, Disk: 500GB Western Digital WDS500G3X0C-00SJG0 + 4 x 2000GB Seagate ST2000LM015-2E81, Graphics: Zotac NVIDIA GeForce RTX 2060 SUPER 8GB, Audio: NVIDIA TU106 HD Audio, Network: Intel I211 + Intel Wi-Fi 6 AX200

OS: Ubuntu 20.10, Kernel: 5.8.0-38-lowlatency (x86_64), Display Server: X Server 1.20.9, Display Driver: modesetting 1.20.9, OpenCL: OpenCL 1.2 CUDA 11.2.109, Vulkan: 1.2.155, Compiler: GCC 10.2.0 + CUDA 11.0, File-System: btrfs, Screen Resolution: 640x480

Compiler Notes: --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++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/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
Processor Notes: Scaling Governor: acpi-cpufreq performance (Boost: Enabled) - CPU Microcode: 0x8701021
Security Notes: 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 STIBP: conditional RSB filling + srbds: Not affected + tsx_async_abort: Not affected

Testing initiated at 17 January 2021 18:17 by user joukyuuk.