moldyn-no-miniFE

AMD Ryzen Threadripper PRO 3945WX 12-Cores testing with a LENOVO 1046 (S07KT17A BIOS) and NVIDIA Quadro P2200 5GB on Ubuntu 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 2104146-LKM-MOLDYNNO55
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moldyn-no-miniFEOpenBenchmarking.orgPhoronix Test Suite 10.4.0m1AMD Ryzen Threadripper PRO 3945WX 12-Cores @ 4.00GHz (12 Cores / 24 Threads)LENOVO 1046 (S07KT17A BIOS)AMD Starship/Matisse126GB512GB SAMSUNG MZVL2512HCJQ-00BL7NVIDIA Quadro P2200 5GBNVIDIA GP106 HD AudioDELL U2719DAquantia AQC107 NBase-T/IEEE + Intel-AC 9260Ubuntu 20.045.8.0-49-generic (x86_64)MATE 1.24.0X Server 1.20.9NVIDIA 460.394.6.0OpenCL 1.2 CUDA 11.2.1361.2.155GCC 9.3.0 + Clang 12.0.0ext42560x1440ProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenGLOpenCLVulkanCompilerFile-SystemScreen ResolutionMoldyn-no-miniFE BenchmarksSystem Logs- Transparent Huge Pages: madvise- WM_LDFLAGS=-m64 WM_CFLAGS="-m64 -fPIC" WM_CXXFLAGS="-m64 -fPIC -std=c++0x"- --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 performance (Boost: Enabled) - CPU Microcode: 0x830104d- 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

moldyn-no-miniFEcloverleaf: Lagrangian-Eulerian Hydrodynamicscp2k: Fayalite-FISTnamd: ATPase Simulation - 327,506 Atomsdolfyn: Computational Fluid Dynamicspennant: sedovbigpennant: leblancbignwchem: C240 Buckyballincompact3d: X3D-benchmarking input.i3dincompact3d: input.i3d 129 Cells Per Directionincompact3d: input.i3d 193 Cells Per Directionopenfoam: Motorbike 30Mopenfoam: Motorbike 60Mlammps: 20k Atomslammps: Rhodopsin Proteinlulesh: gromacs: water_GMX50_bareAMD Ryzen Threadripper PRO 3945WX 12-Cores42.96923.5931.4172116.51739.9694627.744456811.91231.6119812.955280655.911665655.16461.789.9409.9668888.03561.780OpenBenchmarking.org

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 HydrodynamicsAMD Ryzen Threadripper PRO 3945WX 12-Cores1020304050SE +/- 0.12, N = 342.961. (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-FISTAMD Ryzen Threadripper PRO 3945WX 12-Cores2004006008001000923.59

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 AtomsAMD Ryzen Threadripper PRO 3945WX 12-Cores0.31890.63780.95671.27561.5945SE +/- 0.00082, N = 31.41721

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 DynamicsAMD Ryzen Threadripper PRO 3945WX 12-Cores48121620SE +/- 0.16, N = 1516.52

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: sedovbigAMD Ryzen Threadripper PRO 3945WX 12-Cores918273645SE +/- 0.08, N = 339.971. (CXX) g++ options: -fopenmp -pthread -lmpi_cxx -lmpi

OpenBenchmarking.orgHydro Cycle Time - Seconds, Fewer Is BetterPennant 1.0.1Test: leblancbigAMD Ryzen Threadripper PRO 3945WX 12-Cores714212835SE +/- 0.04, N = 327.741. (CXX) g++ options: -fopenmp -pthread -lmpi_cxx -lmpi

NWChem

NWChem is an open-source high performance computational chemistry package. Per NWChem's documentation, "NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters." Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterNWChem 7.0.2Input: C240 BuckyballAMD Ryzen Threadripper PRO 3945WX 12-Cores150030004500600075006811.91. (F9X) gfortran options: -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm -lga -larmci -lpeigs -l64to32 -lopenblas -lpthread -lrt -llapack -lnwcblas -lmpi_usempif08 -lmpi_mpifh -lmpi -lcomex -lm -m64 -ffast-math -std=legacy -fdefault-integer-8 -finline-functions -O2

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: X3D-benchmarking input.i3dAMD Ryzen Threadripper PRO 3945WX 12-Cores30060090012001500SE +/- 1.70, N = 31231.611. (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 129 Cells Per DirectionAMD Ryzen Threadripper PRO 3945WX 12-Cores3691215SE +/- 0.10, N = 312.961. (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 DirectionAMD Ryzen Threadripper PRO 3945WX 12-Cores1326395265SE +/- 0.45, N = 355.911. (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 30MAMD Ryzen Threadripper PRO 3945WX 12-Cores1224364860SE +/- 0.05, N = 355.161. (CXX) g++ options: -std=c++11 -m64 -O3 -ftemplate-depth-100 -fPIC -fuse-ld=bfd -Xlinker --add-needed --no-as-needed -ldynamicMesh -lgenericPatchFields -lOpenFOAM -ldl -lm

OpenBenchmarking.orgSeconds, Fewer Is BetterOpenFOAM 8Input: Motorbike 60MAMD Ryzen Threadripper PRO 3945WX 12-Cores100200300400500SE +/- 0.50, N = 3461.781. (CXX) g++ options: -std=c++11 -m64 -O3 -ftemplate-depth-100 -fPIC -fuse-ld=bfd -Xlinker --add-needed --no-as-needed -ldynamicMesh -lgenericPatchFields -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 AtomsAMD Ryzen Threadripper PRO 3945WX 12-Cores3691215SE +/- 0.019, N = 39.9401. (CXX) g++ options: -O3 -pthread -lm

OpenBenchmarking.orgns/day, More Is BetterLAMMPS Molecular Dynamics Simulator 29Oct2020Model: Rhodopsin ProteinAMD Ryzen Threadripper PRO 3945WX 12-Cores3691215SE +/- 0.004, N = 39.9661. (CXX) g++ options: -O3 -pthread -lm

LULESH

LULESH is the Livermore Unstructured Lagrangian Explicit Shock Hydrodynamics. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgz/s, More Is BetterLULESH 2.0.3AMD Ryzen Threadripper PRO 3945WX 12-Cores2K4K6K8K10KSE +/- 32.14, N = 38888.041. (CXX) g++ options: -O3 -fopenmp -lm -pthread -lmpi_cxx -lmpi

GROMACS

The GROMACS (GROningen MAchine for Chemical Simulations) molecular dynamics package testing on the CPU with the water_GMX50 data. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgNs Per Day, More Is BetterGROMACS 2021Input: water_GMX50_bareAMD Ryzen Threadripper PRO 3945WX 12-Cores0.40050.8011.20151.6022.0025SE +/- 0.002, N = 31.7801. (CXX) g++ options: -O3 -pthread