namd gromacs

AMD Ryzen 7 7840HS testing with a NB05 TUXEDO Pulse 14 Gen3 R14FA1 (8.06 BIOS) and AMD Phoenix1 4GB on Ubuntu 23.10 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 2402166-NE-NAMDGROMA40
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a
February 16
  17 Minutes
b
February 16
  15 Minutes
c
February 16
  15 Minutes
d
February 16
  15 Minutes
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a

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --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,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-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/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-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
Processor Notes: Scaling Governor: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xa704104
Security Notes: 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

b

c

d

Processor: AMD Ryzen 7 7840HS @ 5.29GHz (8 Cores / 16 Threads), Motherboard: NB05 TUXEDO Pulse 14 Gen3 R14FA1 (8.06 BIOS), Chipset: AMD Device 14e8, Memory: 4 x 8GB DRAM-6400MT/s Micron MT62F2G32D4DS-026 WT, Disk: 2000GB Samsung SSD 980 PRO 2TB, Graphics: AMD Phoenix1 4GB (2700/800MHz), Audio: AMD Rembrandt Radeon HD Audio, Network: MEDIATEK MT7921K

OS: Ubuntu 23.10, Kernel: 6.7.0-060700-generic (x86_64), Desktop: GNOME Shell 45.2, Display Server: X Server + Wayland, OpenGL: 4.6 Mesa 24.1~git2401200600.ebcab1~oibaf~m (git-ebcab14 2024-01-20 mantic-oibaf-ppa) (LLVM 16.0.6 DRM 3.56), Compiler: GCC 13.2.0, File-System: ext4, Screen Resolution: 2880x1800

namd gromacsOpenBenchmarking.orgPhoronix Test SuiteAMD Ryzen 7 7840HS @ 5.29GHz (8 Cores / 16 Threads)NB05 TUXEDO Pulse 14 Gen3 R14FA1 (8.06 BIOS)AMD Device 14e84 x 8GB DRAM-6400MT/s Micron MT62F2G32D4DS-026 WT2000GB Samsung SSD 980 PRO 2TBAMD Phoenix1 4GB (2700/800MHz)AMD Rembrandt Radeon HD AudioMEDIATEK MT7921KUbuntu 23.106.7.0-060700-generic (x86_64)GNOME Shell 45.2X Server + Wayland4.6 Mesa 24.1~git2401200600.ebcab1~oibaf~m (git-ebcab14 2024-01-20 mantic-oibaf-ppa) (LLVM 16.0.6 DRM 3.56)GCC 13.2.0ext42880x1800ProcessorMotherboardChipsetMemoryDiskGraphicsAudioNetworkOSKernelDesktopDisplay ServerOpenGLCompilerFile-SystemScreen ResolutionNamd Gromacs PerformanceSystem Logs- 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,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-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/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-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: 0xa704104- 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

abcdResult OverviewPhoronix Test Suite100%101%103%104%105%NAMDNAMDGROMACSA.w.3.5.AS.w.1.0.6.AMPI CPU - water_GMX50_bare

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 2024Implementation: MPI CPU - Input: water_GMX50_barecbda0.29090.58180.87271.16361.4545SE +/- 0.002, N = 3SE +/- 0.002, N = 3SE +/- 0.002, N = 3SE +/- 0.001, N = 31.2931.2911.2901.2901. (CXX) g++ options: -O3 -lm
OpenBenchmarking.orgNs Per Day, More Is BetterGROMACS 2024Implementation: MPI CPU - Input: water_GMX50_barecbda246810Min: 1.29 / Avg: 1.29 / Max: 1.3Min: 1.29 / Avg: 1.29 / Max: 1.29Min: 1.29 / Avg: 1.29 / Max: 1.29Min: 1.29 / Avg: 1.29 / Max: 1.291. (CXX) g++ options: -O3 -lm

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.orgns/day, More Is BetterNAMD 3.0b6Input: ATPase with 327,506 Atomscdba0.29570.59140.88711.18281.4785SE +/- 0.01714, N = 3SE +/- 0.00813, N = 3SE +/- 0.01434, N = 3SE +/- 0.01062, N = 31.314261.286421.279801.25116
OpenBenchmarking.orgns/day, More Is BetterNAMD 3.0b6Input: ATPase with 327,506 Atomscdba246810Min: 1.28 / Avg: 1.31 / Max: 1.34Min: 1.27 / Avg: 1.29 / Max: 1.3Min: 1.26 / Avg: 1.28 / Max: 1.31Min: 1.23 / Avg: 1.25 / Max: 1.27

OpenBenchmarking.orgns/day, More Is BetterNAMD 3.0b6Input: STMV with 1,066,628 Atomsdacb0.08720.17440.26160.34880.436SE +/- 0.00095, N = 3SE +/- 0.00098, N = 3SE +/- 0.00076, N = 3SE +/- 0.00029, N = 30.387500.387400.387170.38420
OpenBenchmarking.orgns/day, More Is BetterNAMD 3.0b6Input: STMV with 1,066,628 Atomsdacb12345Min: 0.39 / Avg: 0.39 / Max: 0.39Min: 0.39 / Avg: 0.39 / Max: 0.39Min: 0.39 / Avg: 0.39 / Max: 0.39Min: 0.38 / Avg: 0.38 / Max: 0.38

a

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --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,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-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/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-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
Processor Notes: Scaling Governor: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xa704104
Security Notes: 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

Testing initiated at 16 February 2024 19:36 by user phoronix.

b

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --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,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-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/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-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
Processor Notes: Scaling Governor: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xa704104
Security Notes: 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

Testing initiated at 16 February 2024 19:54 by user phoronix.

c

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --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,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-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/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-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
Processor Notes: Scaling Governor: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xa704104
Security Notes: 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

Testing initiated at 16 February 2024 20:38 by user phoronix.

d

Processor: AMD Ryzen 7 7840HS @ 5.29GHz (8 Cores / 16 Threads), Motherboard: NB05 TUXEDO Pulse 14 Gen3 R14FA1 (8.06 BIOS), Chipset: AMD Device 14e8, Memory: 4 x 8GB DRAM-6400MT/s Micron MT62F2G32D4DS-026 WT, Disk: 2000GB Samsung SSD 980 PRO 2TB, Graphics: AMD Phoenix1 4GB (2700/800MHz), Audio: AMD Rembrandt Radeon HD Audio, Network: MEDIATEK MT7921K

OS: Ubuntu 23.10, Kernel: 6.7.0-060700-generic (x86_64), Desktop: GNOME Shell 45.2, Display Server: X Server + Wayland, OpenGL: 4.6 Mesa 24.1~git2401200600.ebcab1~oibaf~m (git-ebcab14 2024-01-20 mantic-oibaf-ppa) (LLVM 16.0.6 DRM 3.56), Compiler: GCC 13.2.0, File-System: ext4, Screen Resolution: 2880x1800

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --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,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-defaulted --enable-offload-targets=nvptx-none=/build/gcc-13-XYspKM/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-XYspKM/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-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
Processor Notes: Scaling Governor: amd-pstate-epp powersave (EPP: balance_performance) - CPU Microcode: 0xa704104
Security Notes: 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

Testing initiated at 16 February 2024 20:55 by user phoronix.