some3600

AMD Ryzen 9 9950X 16-Core testing with a ASUS ProArt B650-CREATOR (2401 BIOS) and ASUS AMD Radeon 2GB on Ubuntu 24.04 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 2409301-NE-2409237NE77
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Bioinformatics 5 Tests
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  Test
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3600
September 23
  55 Minutes
5200xmp
September 23
  1 Hour, 3 Minutes
3600redux
September 24
  56 Minutes
4000xmp
September 30
  53 Minutes
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  57 Minutes

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some3600ProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerOpenGLCompilerFile-SystemScreen Resolution36005200xmp3600redux4000xmpAMD Ryzen 9 9950X 16-Core @ 8.18GHz (16 Cores / 32 Threads)ASRock X670E PG Lightning (3.08 BIOS)AMD Device 14d84 x 48GB DDR5-3600MT/s CMK192GX5M4B5200C384001GB Samsung SSD 990 PRO 4TBAMD Radeon 2GBAMD Rembrandt Radeon HD AudioASUS PB258Realtek RTL8125 2.5GbE + Intel Wi-Fi 6EUbuntu 24.046.8.0-45-generic (x86_64)KDE Plasma 5.27.11X Server 1.21.1.114.6 Mesa 24.0.9-0ubuntu0.1 (LLVM 17.0.6 DRM 3.57)GCC 13.2.0ext42560x14402 x 48GB DDR5-5200MT/s CMK192GX5M4B5200C384 x 48GB DDR5-3600MT/s CMK192GX5M4B5200C38ASUS ProArt B650-CREATOR (2401 BIOS)4 x 48GB DDR5-4000MT/s Corsair CMK192GX5M4B5200C38ASUS AMD Radeon 2GBRealtek RTL8111/8168/8211/8411 + Realtek RTL8125 2.5GbE + Intel Wi-Fi 6EOpenBenchmarking.orgKernel Details- Transparent Huge Pages: madviseCompiler Details- --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --enable-cet --enable-checking=release --enable-clocale=gnu --enable-default-pie --enable-gnu-unique-object --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --enable-libphobos-checking=release --enable-libstdcxx-backtrace --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-uJ7kn6/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-uJ7kn6/gcc-13-13.2.0/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-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 Details- 3600: Scaling Governor: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xb404022- 5200xmp: Scaling Governor: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xb404022- 3600redux: Scaling Governor: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xb404022- 4000xmp: Scaling Governor: amd-pstate-epp performance (EPP: performance) - CPU Microcode: 0xb404022Python Details- Python 3.12.5Security Details- gather_data_sampling: Not affected + itlb_multihit: Not affected + l1tf: Not affected + mds: Not affected + meltdown: Not affected + mmio_stale_data: Not affected + reg_file_data_sampling: Not affected + 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 Enhanced / Automatic IBRS; IBPB: conditional; STIBP: always-on; RSB filling; PBRSB-eIBRS: Not affected; BHI: Not affected + srbds: Not affected + tsx_async_abort: Not affected

36005200xmp3600redux4000xmpResult OverviewPhoronix Test Suite100%108%115%123%Algebraic Multi-Grid BenchmarkQMCPACKTimed MAFFT AlignmentR BenchmarkTimed MrBayes AnalysisHimeno BenchmarkNumpy BenchmarkTimed HMMer SearchACES DGEMM

some3600amg: qmcpack: Li2_STO_aeqmcpack: O_ae_pyscf_UHFqmcpack: FeCO6_b3lyp_gmsqmcpack: LiH_ae_MSDmafft: Multiple Sequence Alignment - LSU RNAqmcpack: simple-H2Orbenchmark: mrbayes: Primate Phylogeny Analysishimeno: Poisson Pressure Solvernumpy: hmmer: Pfam Database Searchmt-dgemm: Sustained Floating-Point Rateqmcpack: H4_ae36005200xmp3600redux4000xmp277673467126.05124.9256.14945.1365.23016.7440.092655.6839367.142922831.3280.020150.47941211.26362123267124.66125.7758.55345.4124.83917.0410.091654.8299013.576565838.4380.949149.80336711.57286895033127.84124.8357.61744.9865.04916.5690.093254.3879360.551153860.9479.821150.62714611.43299118367112.37111.7253.33941.7364.91115.7750.088453.0479444.912166857.1479.005150.96091910.259OpenBenchmarking.org

Algebraic Multi-Grid Benchmark

AMG is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. The driver provided with AMG builds linear systems for various 3-dimensional problems. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgFigure Of Merit, More Is BetterAlgebraic Multi-Grid Benchmark 1.24000xmp3600redux5200xmp360080M160M240M320M400MSE +/- 1093951.86, N = 3SE +/- 295457.27, N = 3SE +/- 2120343.38, N = 3SE +/- 791182.93, N = 32991183672868950333621232672776734671. (CC) gcc options: -lparcsr_ls -lparcsr_mv -lseq_mv -lIJ_mv -lkrylov -lHYPRE_utilities -lm -fopenmp -lmpi

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: Li2_STO_ae4000xmp3600redux5200xmp3600306090120150SE +/- 0.18, N = 3SE +/- 0.69, N = 3SE +/- 1.41, N = 3SE +/- 0.82, N = 3112.37127.84124.66126.051. (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_UHF4000xmp3600redux5200xmp3600306090120150SE +/- 0.26, N = 3SE +/- 1.74, N = 3SE +/- 0.39, N = 3SE +/- 0.76, N = 3111.72124.83125.77124.921. (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_gms4000xmp3600redux5200xmp36001326395265SE +/- 0.06, N = 3SE +/- 0.37, N = 3SE +/- 0.42, N = 12SE +/- 0.18, N = 353.3457.6258.5556.151. (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_MSD4000xmp3600redux5200xmp36001020304050SE +/- 0.05, N = 3SE +/- 0.53, N = 3SE +/- 0.32, N = 3SE +/- 0.58, N = 341.7444.9945.4145.141. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

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 RNA4000xmp3600redux5200xmp36001.17682.35363.53044.70725.884SE +/- 0.015, N = 3SE +/- 0.014, N = 3SE +/- 0.006, N = 3SE +/- 0.008, N = 34.9115.0494.8395.2301. (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: simple-H2O4000xmp3600redux5200xmp360048121620SE +/- 0.08, N = 3SE +/- 0.20, N = 3SE +/- 0.09, N = 3SE +/- 0.12, N = 315.7816.5717.0416.741. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

R Benchmark

This test is a quick-running survey of general R performance Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterR Benchmark4000xmp3600redux5200xmp36000.0210.0420.0630.0840.105SE +/- 0.0008, N = 3SE +/- 0.0010, N = 3SE +/- 0.0012, N = 3SE +/- 0.0005, N = 30.08840.09320.09160.0926

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 Analysis4000xmp3600redux5200xmp36001326395265SE +/- 0.42, N = 3SE +/- 0.26, N = 3SE +/- 0.39, N = 3SE +/- 0.33, N = 353.0554.3954.8355.681. (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

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 Solver4000xmp3600redux5200xmp36002K4K6K8K10KSE +/- 103.79, N = 3SE +/- 111.41, N = 4SE +/- 122.76, N = 3SE +/- 28.37, N = 39444.919360.559013.589367.141. (CC) gcc options: -O3 -mavx2

Numpy Benchmark

This is a test to obtain the general Numpy performance. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgScore, More Is BetterNumpy Benchmark4000xmp3600redux5200xmp36002004006008001000SE +/- 1.07, N = 3SE +/- 11.30, N = 3SE +/- 7.18, N = 3SE +/- 4.49, N = 3857.14860.94838.43831.32

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 Search4000xmp3600redux5200xmp360020406080100SE +/- 0.03, N = 3SE +/- 0.06, N = 3SE +/- 0.10, N = 3SE +/- 0.13, N = 379.0179.8280.9580.021. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm -lmpi

ACES DGEMM

OpenBenchmarking.orgGFLOP/s, More Is BetterACES DGEMM 1.0Sustained Floating-Point Rate4000xmp3600redux5200xmp3600306090120150SE +/- 0.08, N = 3SE +/- 0.25, N = 3SE +/- 0.25, N = 3SE +/- 0.15, N = 3150.96150.63149.80150.481. (CC) gcc options: -ffast-math -mavx2 -O3 -fopenmp -lopenblas

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_ae4000xmp3600redux5200xmp36003691215SE +/- 0.09, N = 15SE +/- 0.13, N = 15SE +/- 0.26, N = 12SE +/- 0.10, N = 1510.2611.4311.5711.261. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl