namd gromacs oidn

AMD Ryzen Threadripper 3990X 64-Core testing with a Gigabyte TRX40 AORUS PRO WIFI (F6 BIOS) and AMD Radeon RX 5600 OEM/5600 XT / 5700/5700 on Pop 22.04 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 2402162-NE-NAMDGROMA57
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a
February 16
  14 Minutes
b
February 16
  13 Minutes
c
February 16
  13 Minutes
d
February 16
  13 Minutes
e
February 16
  13 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,brig,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-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: acpi-cpufreq schedutil (Boost: Enabled) - CPU Microcode: 0x830107a
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: Mitigation of untrained return thunk; SMT enabled with STIBP protection + 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 Retpolines IBPB: conditional STIBP: always-on RSB filling PBRSB-eIBRS: Not affected + srbds: Not affected + tsx_async_abort: Not affected

b

c

d

e

Processor: AMD Ryzen Threadripper 3990X 64-Core @ 2.90GHz (64 Cores / 128 Threads), Motherboard: Gigabyte TRX40 AORUS PRO WIFI (F6 BIOS), Chipset: AMD Starship/Matisse, Memory: 4 x 32GB DDR4-3000MT/s CMK64GX4M2D3000C16, Disk: Samsung SSD 970 EVO Plus 500GB, Graphics: AMD Radeon RX 5600 OEM/5600 XT / 5700/5700 (1750/875MHz), Audio: AMD Navi 10 HDMI Audio, Monitor: DELL P2415Q, Network: Intel I211 + Intel Wi-Fi 6 AX200

OS: Pop 22.04, Kernel: 6.6.6-76060606-generic (x86_64), Desktop: GNOME Shell 42.5, Display Server: X Server 1.21.1.4, Vulkan: 1.3.267, Compiler: GCC 11.4.0, File-System: ext4, Screen Resolution: 3840x2160

namd gromacs oidnOpenBenchmarking.orgPhoronix Test SuiteAMD Ryzen Threadripper 3990X 64-Core @ 2.90GHz (64 Cores / 128 Threads)Gigabyte TRX40 AORUS PRO WIFI (F6 BIOS)AMD Starship/Matisse4 x 32GB DDR4-3000MT/s CMK64GX4M2D3000C16Samsung SSD 970 EVO Plus 500GBAMD Radeon RX 5600 OEM/5600 XT / 5700/5700 (1750/875MHz)AMD Navi 10 HDMI AudioDELL P2415QIntel I211 + Intel Wi-Fi 6 AX200Pop 22.046.6.6-76060606-generic (x86_64)GNOME Shell 42.5X Server 1.21.1.41.3.267GCC 11.4.0ext43840x2160ProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerVulkanCompilerFile-SystemScreen ResolutionNamd Gromacs Oidn 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,brig,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-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: acpi-cpufreq schedutil (Boost: Enabled) - CPU Microcode: 0x830107a- gather_data_sampling: Not affected + itlb_multihit: Not affected + l1tf: Not affected + mds: Not affected + meltdown: Not affected + mmio_stale_data: Not affected + retbleed: Mitigation of untrained return thunk; SMT enabled with STIBP protection + 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 Retpolines IBPB: conditional STIBP: always-on RSB filling PBRSB-eIBRS: Not affected + srbds: Not affected + tsx_async_abort: Not affected

abcdeResult OverviewPhoronix Test Suite100%101%101%102%102%Intel Open Image DenoiseNAMDIntel Open Image DenoiseIntel Open Image DenoiseNAMDGROMACSRT.hdr_alb_nrm.3840x2160 - CPU-OnlyA.w.3.5.ART.ldr_alb_nrm.3840x2160 - CPU-OnlyRTLightmap.hdr.4096x4096 - CPU-OnlyS.w.1.0.6.AMPI CPU - water_GMX50_bare

namd gromacs oidnnamd: ATPase with 327,506 Atomsnamd: STMV with 1,066,628 Atomsoidn: RT.hdr_alb_nrm.3840x2160 - CPU-Onlyoidn: RT.ldr_alb_nrm.3840x2160 - CPU-Onlyoidn: RTLightmap.hdr.4096x4096 - CPU-Onlygromacs: MPI CPU - water_GMX50_bareabcde2.693190.674151.361.330.673.7062.690780.670971.341.330.663.7102.676020.672141.331.320.663.7132.645960.669671.331.310.663.7122.670160.668281.331.310.663.709OpenBenchmarking.org

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 Atomsabced0.6061.2121.8182.4243.03SE +/- 0.00287, N = 3SE +/- 0.01095, N = 3SE +/- 0.01722, N = 3SE +/- 0.00122, N = 3SE +/- 0.00176, N = 32.693192.690782.676022.670162.64596

OpenBenchmarking.orgns/day, More Is BetterNAMD 3.0b6Input: STMV with 1,066,628 Atomsacbde0.15170.30340.45510.60680.7585SE +/- 0.00046, N = 3SE +/- 0.00077, N = 3SE +/- 0.00031, N = 3SE +/- 0.00047, N = 3SE +/- 0.00078, N = 30.674150.672140.670970.669670.66828

Intel Open Image Denoise

Open Image Denoise is a denoising library for ray-tracing and part of the Intel oneAPI rendering toolkit. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgImages / Sec, More Is BetterIntel Open Image Denoise 2.2Run: RT.hdr_alb_nrm.3840x2160 - Device: CPU-Onlyabedc0.3060.6120.9181.2241.53SE +/- 0.00, N = 3SE +/- 0.01, N = 3SE +/- 0.01, N = 3SE +/- 0.01, N = 3SE +/- 0.01, N = 31.361.341.331.331.33

OpenBenchmarking.orgImages / Sec, More Is BetterIntel Open Image Denoise 2.2Run: RT.ldr_alb_nrm.3840x2160 - Device: CPU-Onlybaced0.29930.59860.89791.19721.4965SE +/- 0.01, N = 3SE +/- 0.01, N = 3SE +/- 0.01, N = 3SE +/- 0.00, N = 3SE +/- 0.00, N = 31.331.331.321.311.31

OpenBenchmarking.orgImages / Sec, More Is BetterIntel Open Image Denoise 2.2Run: RTLightmap.hdr.4096x4096 - Device: CPU-Onlyaedcb0.15080.30160.45240.60320.754SE +/- 0.00, N = 3SE +/- 0.00, N = 3SE +/- 0.00, N = 3SE +/- 0.01, N = 3SE +/- 0.01, N = 30.670.660.660.660.66

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_barecdbea0.83541.67082.50623.34164.177SE +/- 0.002, N = 3SE +/- 0.006, N = 3SE +/- 0.001, N = 3SE +/- 0.002, N = 3SE +/- 0.003, N = 33.7133.7123.7103.7093.7061. (CXX) g++ options: -O3 -lm

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,brig,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-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: acpi-cpufreq schedutil (Boost: Enabled) - CPU Microcode: 0x830107a
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: Mitigation of untrained return thunk; SMT enabled with STIBP protection + 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 Retpolines 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 13:29 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,brig,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-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: acpi-cpufreq schedutil (Boost: Enabled) - CPU Microcode: 0x830107a
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: Mitigation of untrained return thunk; SMT enabled with STIBP protection + 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 Retpolines 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 13:54 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,brig,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-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: acpi-cpufreq schedutil (Boost: Enabled) - CPU Microcode: 0x830107a
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: Mitigation of untrained return thunk; SMT enabled with STIBP protection + 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 Retpolines 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 14:39 by user phoronix.

d

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,brig,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-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: acpi-cpufreq schedutil (Boost: Enabled) - CPU Microcode: 0x830107a
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: Mitigation of untrained return thunk; SMT enabled with STIBP protection + 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 Retpolines 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 14:54 by user phoronix.

e

Processor: AMD Ryzen Threadripper 3990X 64-Core @ 2.90GHz (64 Cores / 128 Threads), Motherboard: Gigabyte TRX40 AORUS PRO WIFI (F6 BIOS), Chipset: AMD Starship/Matisse, Memory: 4 x 32GB DDR4-3000MT/s CMK64GX4M2D3000C16, Disk: Samsung SSD 970 EVO Plus 500GB, Graphics: AMD Radeon RX 5600 OEM/5600 XT / 5700/5700 (1750/875MHz), Audio: AMD Navi 10 HDMI Audio, Monitor: DELL P2415Q, Network: Intel I211 + Intel Wi-Fi 6 AX200

OS: Pop 22.04, Kernel: 6.6.6-76060606-generic (x86_64), Desktop: GNOME Shell 42.5, Display Server: X Server 1.21.1.4, Vulkan: 1.3.267, Compiler: GCC 11.4.0, File-System: ext4, Screen Resolution: 3840x2160

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,brig,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-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/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: acpi-cpufreq schedutil (Boost: Enabled) - CPU Microcode: 0x830107a
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: Mitigation of untrained return thunk; SMT enabled with STIBP protection + 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 Retpolines 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 15:10 by user phoronix.