gromacs + mafft update

AMD Ryzen 7 1700 Eight-Core testing with a MSI B350 TOMAHAWK (MS-7A34) v1.0 (1.H0 BIOS) and AMD Radeon RX 470/480/570/570X/580/580X/590 8GB on Ubuntu 19.10 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 2009262-FI-GROMACSMA31
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1
September 26 2020
  46 Minutes
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1

Processor: AMD Ryzen 7 1700 Eight-Core @ 3.00GHz (8 Cores / 16 Threads), Motherboard: MSI B350 TOMAHAWK (MS-7A34) v1.0 (1.H0 BIOS), Chipset: AMD 17h, Memory: 16GB, Disk: 120GB Samsung SSD 840, Graphics: AMD Radeon RX 470/480/570/570X/580/580X/590 8GB (1266/2000MHz), Audio: AMD Ellesmere HDMI Audio, Monitor: VA2431, Network: Realtek RTL8111/8168/8411

OS: Ubuntu 19.10, Kernel: 5.9.0-050900rc2-generic (x86_64) 20200823, Desktop: GNOME Shell 3.34.1, Display Server: X Server 1.20.5, Display Driver: amdgpu 19.0.1, OpenGL: 4.5 Mesa 19.2.8 (LLVM 9.0.0), Vulkan: 1.1.107, Compiler: GCC 9.2.1 20191008, File-System: ext4, Screen Resolution: 1920x1080

Compiler Notes: --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --enable-bootstrap --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-offload-targets=nvptx-none,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
Processor Notes: Scaling Governor: acpi-cpufreq ondemand - CPU Microcode: 0x8001137
Security Notes: 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: disabled RSB filling + srbds: Not affected + tsx_async_abort: Not affected

gromacs + mafft updateOpenBenchmarking.orgPhoronix Test SuiteAMD Ryzen 7 1700 Eight-Core @ 3.00GHz (8 Cores / 16 Threads)MSI B350 TOMAHAWK (MS-7A34) v1.0 (1.H0 BIOS)AMD 17h16GB120GB Samsung SSD 840AMD Radeon RX 470/480/570/570X/580/580X/590 8GB (1266/2000MHz)AMD Ellesmere HDMI AudioVA2431Realtek RTL8111/8168/8411Ubuntu 19.105.9.0-050900rc2-generic (x86_64) 20200823GNOME Shell 3.34.1X Server 1.20.5amdgpu 19.0.14.5 Mesa 19.2.8 (LLVM 9.0.0)1.1.107GCC 9.2.1 20191008ext41920x1080ProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenGLVulkanCompilerFile-SystemScreen ResolutionGromacs + Mafft Update BenchmarksSystem Logs- --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --enable-bootstrap --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-offload-targets=nvptx-none,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 - CPU Microcode: 0x8001137- 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: disabled RSB filling + srbds: Not affected + tsx_async_abort: Not affected

Timed MAFFT Alignment

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.471Multiple Sequence Alignment - LSU RNA1306090120150SE +/- 8.94, N = 12145.881. (CC) gcc options: -std=c99 -O3 -lm -lpthread

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 2020.3Water Benchmark10.11970.23940.35910.47880.5985SE +/- 0.003, N = 30.5321. (CXX) g++ options: -O3 -pthread -lrt -lpthread -lm

1

Processor: AMD Ryzen 7 1700 Eight-Core @ 3.00GHz (8 Cores / 16 Threads), Motherboard: MSI B350 TOMAHAWK (MS-7A34) v1.0 (1.H0 BIOS), Chipset: AMD 17h, Memory: 16GB, Disk: 120GB Samsung SSD 840, Graphics: AMD Radeon RX 470/480/570/570X/580/580X/590 8GB (1266/2000MHz), Audio: AMD Ellesmere HDMI Audio, Monitor: VA2431, Network: Realtek RTL8111/8168/8411

OS: Ubuntu 19.10, Kernel: 5.9.0-050900rc2-generic (x86_64) 20200823, Desktop: GNOME Shell 3.34.1, Display Server: X Server 1.20.5, Display Driver: amdgpu 19.0.1, OpenGL: 4.5 Mesa 19.2.8 (LLVM 9.0.0), Vulkan: 1.1.107, Compiler: GCC 9.2.1 20191008, File-System: ext4, Screen Resolution: 1920x1080

Compiler Notes: --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --enable-bootstrap --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-offload-targets=nvptx-none,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
Processor Notes: Scaling Governor: acpi-cpufreq ondemand - CPU Microcode: 0x8001137
Security Notes: 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: disabled RSB filling + srbds: Not affected + tsx_async_abort: Not affected

Testing initiated at 26 September 2020 15:28 by user phoronix.