bioinformatics-zeus

AMD Ryzen 7 7800X3D 8-Core testing with a ASUS ROG STRIX B650E-I GAMING WIFI (2214 BIOS) and amdgpudrmfb on Pop 22.04 via the Phoronix Test Suite.

HTML result view exported from: https://openbenchmarking.org/result/2401172-NE-BIOINFORM05&grs.

bioinformatics-zeusProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerOpenGLVulkanCompilerFile-SystemScreen ResolutionAMD Ryzen 7 7800X3D 8-CoreAMD Ryzen 7 7800X3D 8-Core @ 5.05GHz (8 Cores / 16 Threads)ASUS ROG STRIX B650E-I GAMING WIFI (2214 BIOS)AMD Device 14d832GB4001GB Samsung SSD 990 PRO 4TBamdgpudrmfb (2304/1249MHz)AMD Device ab3024E3Intel I225-V + MEDIATEK Device 0616Pop 22.046.6.6-76060606-generic (x86_64)GNOME Shell 42.5X Server 1.21.1.34.6 Mesa 23.3.2-1pop0~1704238321~22.04~36f1d0e (LLVM 15.0.7 DRM 3.54)1.3.267GCC 11.4.0ext41920x1080OpenBenchmarking.org- 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: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xa601206 - Python 3.10.12- gather_data_sampling: Not affected + itlb_multihit: Not affected + l1tf: Not affected + mds: Not affected + meltdown: Not affected + mmio_stale_data: Not affected + retbleed: Not affected + spec_rstack_overflow: Mitigation of Safe RET + 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 + srbds: Not affected + tsx_async_abort: Not affected

bioinformatics-zeusmafft: Multiple Sequence Alignment - LSU RNAhmmer: Pfam Database Searchqmcpack: FeCO6_b3lyp_gmsqmcpack: O_ae_pyscf_UHFqmcpack: simple-H2Oqmcpack: LiH_ae_MSDqmcpack: Li2_STO_aeqmcpack: H4_aemrbayes: Primate Phylogeny Analysishimeno: Poisson Pressure SolverAMD Ryzen 7 7800X3D 8-Core6.85191.199125.70129.9218.40774.207225.1524.4569.9994452.140427OpenBenchmarking.org

Timed MAFFT Alignment

Multiple Sequence Alignment - LSU RNA

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.471Multiple Sequence Alignment - LSU RNAAMD Ryzen 7 7800X3D 8-Core246810SE +/- 0.024, N = 36.8511. (CC) gcc options: -std=c99 -O3 -lm -lpthread

Timed HMMer Search

Pfam Database Search

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 3.3.2Pfam Database SearchAMD Ryzen 7 7800X3D 8-Core20406080100SE +/- 0.11, N = 391.201. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm -lmpi

QMCPACK

Input: FeCO6_b3lyp_gms

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: FeCO6_b3lyp_gmsAMD Ryzen 7 7800X3D 8-Core306090120150SE +/- 0.12, N = 3125.701. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: O_ae_pyscf_UHF

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: O_ae_pyscf_UHFAMD Ryzen 7 7800X3D 8-Core306090120150SE +/- 0.16, N = 3129.921. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: simple-H2O

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: simple-H2OAMD Ryzen 7 7800X3D 8-Core510152025SE +/- 0.06, N = 318.411. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: LiH_ae_MSD

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: LiH_ae_MSDAMD Ryzen 7 7800X3D 8-Core1632486480SE +/- 0.17, N = 374.211. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: Li2_STO_ae

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: Li2_STO_aeAMD Ryzen 7 7800X3D 8-Core50100150200250SE +/- 1.52, N = 3225.151. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

QMCPACK

Input: H4_ae

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: H4_aeAMD Ryzen 7 7800X3D 8-Core612182430SE +/- 0.31, N = 1224.451. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

Timed MrBayes Analysis

Primate Phylogeny Analysis

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny AnalysisAMD Ryzen 7 7800X3D 8-Core1632486480SE +/- 0.20, N = 370.001. (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

Himeno Benchmark

Poisson Pressure Solver

OpenBenchmarking.orgMFLOPS, More Is BetterHimeno Benchmark 3.0Poisson Pressure SolverAMD Ryzen 7 7800X3D 8-Core10002000300040005000SE +/- 74.40, N = 154452.141. (CC) gcc options: -O3 -mavx2

Phoronix Test Suite v10.8.4