molecular-dynamics_230521

AMD Ryzen 7 5800X 8-Core testing with a MSI MAG X570 TOMAHAWK WIFI (MS-7C84) v1.0 (1.50 BIOS) and ASUS NVIDIA GeForce GTX 1050 Ti 4GB on Neon 20.04 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 2105238-IB-MOLECULAR64
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molecular-dynamics_230521
May 23
  3 Hours, 32 Minutes
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molecular-dynamics_230521OpenBenchmarking.orgPhoronix Test Suite 10.4.0AMD Ryzen 7 5800X 8-Core @ 4.20GHz (8 Cores / 16 Threads)MSI MAG X570 TOMAHAWK WIFI (MS-7C84) v1.0 (1.50 BIOS)AMD Starship/Matisse16GB1000GB Corsair MP400 + 3001GB My Book 1140 + 4001GB My Book 25EEASUS NVIDIA GeForce GTX 1050 Ti 4GBNVIDIA GP107GL HD AudioDELL S2721QSRealtek RTL8125 2.5GbE + Intel Wi-Fi 6 AX200Neon 20.045.4.0-73-generic (x86_64)KDE Plasma 5.21.5X Server 1.20.9NVIDIA 460.73.014.6.0OpenCL 1.2 CUDA 11.2.1621.2.155GCC 9.3.0ext43840x2160ProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenGLOpenCLVulkanCompilerFile-SystemScreen ResolutionMolecular-dynamics_230521 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 - Scaling Governor: acpi-cpufreq ondemand (Boost: Enabled) - CPU Microcode: 0xa201009- 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 IBRS_FW STIBP: always-on RSB filling + srbds: Not affected + tsx_async_abort: Not affected

molecular-dynamics_230521minife: Smallcloverleaf: Lagrangian-Eulerian Hydrodynamicscp2k: Fayalite-FISTnamd: ATPase Simulation - 327,506 Atomsdolfyn: Computational Fluid Dynamicspennant: sedovbigpennant: leblancbigincompact3d: input.i3d 129 Cells Per Directionincompact3d: input.i3d 193 Cells Per Directionopenfoam: Motorbike 30Mopenfoam: Motorbike 60Mlammps: 20k Atomslammps: Rhodopsin Proteingromacs: MPI CPU - water_GMX50_baremolecular-dynamics_2305214084.14215.23689.9091.7561614.27995.7741368.5603537.3442869147.010854186.801224.167.6887.5050.893OpenBenchmarking.org

miniFE

MiniFE Finite Element is an application for unstructured implicit finite element codes. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgCG Mflops, More Is BetterminiFE 2.2Problem Size: Smallmolecular-dynamics_2305219001800270036004500SE +/- 14.86, N = 34084.141. (CXX) g++ options: -O3 -fopenmp -pthread -lmpi_cxx -lmpi

CloverLeaf

CloverLeaf is a Lagrangian-Eulerian hydrodynamics benchmark. This test profile currently makes use of CloverLeaf's OpenMP version and benchmarked with the clover_bm.in input file (Problem 5). Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterCloverLeafLagrangian-Eulerian Hydrodynamicsmolecular-dynamics_23052150100150200250SE +/- 0.51, N = 3215.231. (F9X) gfortran options: -O3 -march=native -funroll-loops -fopenmp

CP2K Molecular Dynamics

CP2K is an open-source molecular dynamics software package focused on quantum chemistry and solid-state physics. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterCP2K Molecular Dynamics 8.1Input: Fayalite-FISTmolecular-dynamics_230521150300450600750689.91

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgdays/ns, Fewer Is BetterNAMD 2.14ATPase Simulation - 327,506 Atomsmolecular-dynamics_2305210.39510.79021.18531.58041.9755SE +/- 0.00693, N = 31.75616

Dolfyn

Dolfyn is a Computational Fluid Dynamics (CFD) code of modern numerical simulation techniques. The Dolfyn test profile measures the execution time of the bundled computational fluid dynamics demos that are bundled with Dolfyn. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterDolfyn 0.527Computational Fluid Dynamicsmolecular-dynamics_23052148121620SE +/- 0.42, N = 1514.28

Pennant

Pennant is an application focused on hydrodynamics on general unstructured meshes in 2D. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgHydro Cycle Time - Seconds, Fewer Is BetterPennant 1.0.1Test: sedovbigmolecular-dynamics_23052120406080100SE +/- 0.97, N = 595.771. (CXX) g++ options: -fopenmp -pthread -lmpi_cxx -lmpi

OpenBenchmarking.orgHydro Cycle Time - Seconds, Fewer Is BetterPennant 1.0.1Test: leblancbigmolecular-dynamics_2305211530456075SE +/- 0.11, N = 368.561. (CXX) g++ options: -fopenmp -pthread -lmpi_cxx -lmpi

Xcompact3d Incompact3d

Xcompact3d Incompact3d is a Fortran-MPI based, finite difference high-performance code for solving the incompressible Navier-Stokes equation and as many as you need scalar transport equations. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterXcompact3d Incompact3d 2021-03-11Input: input.i3d 129 Cells Per Directionmolecular-dynamics_230521918273645SE +/- 0.44, N = 437.341. (F9X) gfortran options: -cpp -O2 -funroll-loops -floop-optimize -fcray-pointer -fbacktrace -pthread -lmpi_usempif08 -lmpi_mpifh -lmpi

OpenBenchmarking.orgSeconds, Fewer Is BetterXcompact3d Incompact3d 2021-03-11Input: input.i3d 193 Cells Per Directionmolecular-dynamics_230521306090120150SE +/- 1.19, N = 3147.011. (F9X) gfortran options: -cpp -O2 -funroll-loops -floop-optimize -fcray-pointer -fbacktrace -pthread -lmpi_usempif08 -lmpi_mpifh -lmpi

OpenFOAM

OpenFOAM is the leading free, open source software for computational fluid dynamics (CFD). Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterOpenFOAM 8Input: Motorbike 30Mmolecular-dynamics_2305214080120160200SE +/- 1.70, N = 3186.801. (CXX) g++ options: -std=c++11 -m64 -O3 -ftemplate-depth-100 -fPIC -fuse-ld=bfd -Xlinker --add-needed --no-as-needed -lfoamToVTK -ldynamicMesh -llagrangian -lgenericPatchFields -lfileFormats -lOpenFOAM -ldl -lm

OpenBenchmarking.orgSeconds, Fewer Is BetterOpenFOAM 8Input: Motorbike 60Mmolecular-dynamics_23052130060090012001500SE +/- 2.39, N = 31224.161. (CXX) g++ options: -std=c++11 -m64 -O3 -ftemplate-depth-100 -fPIC -fuse-ld=bfd -Xlinker --add-needed --no-as-needed -lfoamToVTK -ldynamicMesh -llagrangian -lgenericPatchFields -lfileFormats -lOpenFOAM -ldl -lm

LAMMPS Molecular Dynamics Simulator

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgns/day, More Is BetterLAMMPS Molecular Dynamics Simulator 29Oct2020Model: 20k Atomsmolecular-dynamics_230521246810SE +/- 0.015, N = 37.6881. (CXX) g++ options: -O3 -pthread -lm

OpenBenchmarking.orgns/day, More Is BetterLAMMPS Molecular Dynamics Simulator 29Oct2020Model: Rhodopsin Proteinmolecular-dynamics_230521246810SE +/- 0.067, N = 37.5051. (CXX) g++ options: -O3 -pthread -lm

GROMACS

The GROMACS (GROningen MAchine for Chemical Simulations) molecular dynamics package testing with the water_GMX50 data. This test profile allows selecting between CPU and GPU-based GROMACS builds. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgNs Per Day, More Is BetterGROMACS 2021.2Implementation: MPI CPU - Input: water_GMX50_baremolecular-dynamics_2305210.20090.40180.60270.80361.0045SE +/- 0.008, N = 30.8931. (CXX) g++ options: -O3 -pthread