gromacs namd laptop

AMD Ryzen 7 7840U testing with a PHX Swift SFE16-43 Ray_PEU (V1.04 BIOS) and AMD Phoenix1 512MB 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 2402164-NE-GROMACSNA32
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February 16
  1 Hour, 8 Minutes
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February 16
  8 Minutes
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February 16
  7 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: performance) - CPU Microcode: 0xa704101
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: Vulnerable: Safe RET no microcode + 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

Processor: AMD Ryzen 7 7840U @ 5.29GHz (8 Cores / 16 Threads), Motherboard: PHX Swift SFE16-43 Ray_PEU (V1.04 BIOS), Chipset: AMD Device 14e8, Memory: 4 x 4GB DRAM-6400MT/s K3LKBKB0BM-MGCP, Disk: 1024GB Micron_3400_MTFDKBA1T0TFH, Graphics: AMD Phoenix1 512MB (2700/800MHz), Audio: AMD Rembrandt Radeon HD Audio, Network: MEDIATEK MT7922 802.11ax PCI

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~git2401230600.42fc83~oibaf~m (git-42fc83a 2024-01-23 mantic-oibaf-ppa) (LLVM 16.0.6 DRM 3.56), Compiler: GCC 13.2.0, File-System: ext4, Screen Resolution: 3200x2000

gromacs namd laptopOpenBenchmarking.orgPhoronix Test SuiteAMD Ryzen 7 7840U @ 5.29GHz (8 Cores / 16 Threads)PHX Swift SFE16-43 Ray_PEU (V1.04 BIOS)AMD Device 14e84 x 4GB DRAM-6400MT/s K3LKBKB0BM-MGCP1024GB Micron_3400_MTFDKBA1T0TFHAMD Phoenix1 512MB (2700/800MHz)AMD Rembrandt Radeon HD AudioMEDIATEK MT7922 802.11ax PCIUbuntu 23.106.7.0-060700-generic (x86_64)GNOME Shell 45.2X Server + Wayland4.6 Mesa 24.1~git2401230600.42fc83~oibaf~m (git-42fc83a 2024-01-23 mantic-oibaf-ppa) (LLVM 16.0.6 DRM 3.56)GCC 13.2.0ext43200x2000ProcessorMotherboardChipsetMemoryDiskGraphicsAudioNetworkOSKernelDesktopDisplay ServerOpenGLCompilerFile-SystemScreen ResolutionGromacs Namd Laptop BenchmarksSystem 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: performance) - CPU Microcode: 0xa704101- 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: Vulnerable: Safe RET no microcode + 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

abcResult OverviewPhoronix Test Suite100%107%114%121%NAMDNAMDGROMACSS.w.1.0.6.AA.w.3.5.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_barecba0.20.40.60.81SE +/- 0.007, N = 30.8890.8280.8081. (CXX) g++ options: -O3 -lm
OpenBenchmarking.orgNs Per Day, More Is BetterGROMACS 2024Implementation: MPI CPU - Input: water_GMX50_barecba246810Min: 0.8 / Avg: 0.81 / Max: 0.821. (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 Atomscba0.21460.42920.64380.85841.073SE +/- 0.01544, N = 120.953600.805670.82099
OpenBenchmarking.orgns/day, More Is BetterNAMD 3.0b6Input: ATPase with 327,506 Atomscba246810Min: 0.76 / Avg: 0.82 / Max: 0.93

OpenBenchmarking.orgns/day, More Is BetterNAMD 3.0b6Input: STMV with 1,066,628 Atomscba0.06040.12080.18120.24160.302SE +/- 0.00207, N = 120.268430.224130.20966
OpenBenchmarking.orgns/day, More Is BetterNAMD 3.0b6Input: STMV with 1,066,628 Atomscba12345Min: 0.2 / Avg: 0.21 / Max: 0.22

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: performance) - CPU Microcode: 0xa704101
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: Vulnerable: Safe RET no microcode + 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 20:45 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: performance) - CPU Microcode: 0xa704101
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: Vulnerable: Safe RET no microcode + 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 21:56 by user phoronix.

c

Processor: AMD Ryzen 7 7840U @ 5.29GHz (8 Cores / 16 Threads), Motherboard: PHX Swift SFE16-43 Ray_PEU (V1.04 BIOS), Chipset: AMD Device 14e8, Memory: 4 x 4GB DRAM-6400MT/s K3LKBKB0BM-MGCP, Disk: 1024GB Micron_3400_MTFDKBA1T0TFH, Graphics: AMD Phoenix1 512MB (2700/800MHz), Audio: AMD Rembrandt Radeon HD Audio, Network: MEDIATEK MT7922 802.11ax PCI

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~git2401230600.42fc83~oibaf~m (git-42fc83a 2024-01-23 mantic-oibaf-ppa) (LLVM 16.0.6 DRM 3.56), Compiler: GCC 13.2.0, File-System: ext4, Screen Resolution: 3200x2000

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: performance) - CPU Microcode: 0xa704101
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: Vulnerable: Safe RET no microcode + 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 22:32 by user phoronix.