gromacs + mafft

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 2009263-FI-GROMACSMA76
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September 26 2020
  18 Minutes
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September 26 2020
  18 Minutes
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September 26 2020
  18 Minutes
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1

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

2

3

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

gromacs + mafftProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenGLVulkanCompilerFile-SystemScreen Resolution123AMD 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 20191008ext41920x1080OpenBenchmarking.orgCompiler Details- --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 Details- Scaling Governor: acpi-cpufreq ondemand - CPU Microcode: 0x8001137Security Details- 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

This test performs an alignment of 100 pyruvate decarboxylase sequences. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.471Multiple Sequence Alignment - LSU RNA12348121620SE +/- 0.04, N = 3SE +/- 0.03, N = 3SE +/- 0.04, N = 314.7414.6914.701. (CC) gcc options: -std=c99 -O3 -lm -lpthread
OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.471Multiple Sequence Alignment - LSU RNA12348121620Min: 14.66 / Avg: 14.74 / Max: 14.79Min: 14.63 / Avg: 14.69 / Max: 14.72Min: 14.64 / Avg: 14.7 / Max: 14.781. (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 Benchmark1230.12020.24040.36060.48080.601SE +/- 0.000, N = 3SE +/- 0.000, N = 3SE +/- 0.000, N = 30.5330.5340.5341. (CXX) g++ options: -O3 -pthread -lrt -lpthread -lm
OpenBenchmarking.orgNs Per Day, More Is BetterGROMACS 2020.3Water Benchmark123246810Min: 0.53 / Avg: 0.53 / Max: 0.53Min: 0.53 / Avg: 0.53 / Max: 0.53Min: 0.53 / Avg: 0.53 / Max: 0.531. (CXX) g++ options: -O3 -pthread -lrt -lpthread -lm

1

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 16:39 by user phoronix.

2

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 17:13 by user phoronix.

3

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 17:43 by user phoronix.