xeon 5 may

Intel Xeon E-2288G testing with a Compulab SBC-ATCFL v1.2 (ATOP3.PRD.0.29.2 BIOS) and NVIDIA Quadro RTX 4000 8GB on Ubuntu 20.10 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 2105052-IB-XEON5MAY293
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Bioinformatics 3 Tests
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May 05 2021
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May 05 2021
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May 05 2021
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1

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --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-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,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: intel_pstate powersave - CPU Microcode: 0xde - Thermald 2.3
Security Notes: itlb_multihit: KVM: Mitigation of VMX disabled + 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 Enhanced IBRS IBPB: conditional RSB filling + srbds: Mitigation of TSX disabled + tsx_async_abort: Mitigation of TSX disabled

2

3

Processor: Intel Xeon E-2288G @ 5.00GHz (8 Cores / 16 Threads), Motherboard: Compulab SBC-ATCFL v1.2 (ATOP3.PRD.0.29.2 BIOS), Chipset: Intel Cannon Lake PCH, Memory: 2 x 32 GB DDR4-2667MT/s Samsung M378A4G43MB1-CTD, Disk: Samsung SSD 970 EVO Plus 250GB, Graphics: NVIDIA Quadro RTX 4000 8GB, Audio: Intel Cannon Lake PCH cAVS, Network: Intel I219-LM + Intel I210

OS: Ubuntu 20.10, Kernel: 5.8.0-41-generic (x86_64), Desktop: GNOME Shell 3.38.2, Display Server: X Server 1.20.9, Display Driver: NVIDIA, OpenCL: OpenCL 1.2 CUDA 11.2.109, Vulkan: 1.2.155, Compiler: GCC 10.2.0, File-System: ext4, Screen Resolution: 1920x1080

xeon 5 mayProcessorMotherboardChipsetMemoryDiskGraphicsAudioNetworkOSKernelDesktopDisplay ServerDisplay DriverOpenCLVulkanCompilerFile-SystemScreen Resolution123Intel Xeon E-2288G @ 5.00GHz (8 Cores / 16 Threads)Compulab SBC-ATCFL v1.2 (ATOP3.PRD.0.29.2 BIOS)Intel Cannon Lake PCH2 x 32 GB DDR4-2667MT/s Samsung M378A4G43MB1-CTDSamsung SSD 970 EVO Plus 250GBNVIDIA Quadro RTX 4000 8GBIntel Cannon Lake PCH cAVSIntel I219-LM + Intel I210Ubuntu 20.105.8.0-41-generic (x86_64)GNOME Shell 3.38.2X Server 1.20.9NVIDIAOpenCL 1.2 CUDA 11.2.1091.2.155GCC 10.2.0ext41920x1080OpenBenchmarking.orgKernel Details- Transparent Huge Pages: madviseCompiler Details- --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --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-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,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: intel_pstate powersave - CPU Microcode: 0xde - Thermald 2.3 Security Details- itlb_multihit: KVM: Mitigation of VMX disabled + 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 Enhanced IBRS IBPB: conditional RSB filling + srbds: Mitigation of TSX disabled + tsx_async_abort: Mitigation of TSX disabled

123Result OverviewPhoronix Test Suite100%100%100%101%QMCPACKNebular Empirical Analysis ToolTimed HMMer SearchTimed MrBayes Analysissimple-H2OP.D.SP.P.A

xeon 5 mayneat: mrbayes: Primate Phylogeny Analysisqmcpack: simple-H2Ohmmer: Pfam Database Search12341.375144.70228.850122.61341.644144.39228.722123.17241.673144.13628.971123.415OpenBenchmarking.org

Nebular Empirical Analysis Tool

NEAT is the Nebular Empirical Analysis Tool for empirical analysis of ionised nebulae, with uncertainty propagation. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterNebular Empirical Analysis Tool 2.31231020304050SE +/- 0.44, N = 3SE +/- 0.44, N = 3SE +/- 0.30, N = 341.3841.6441.671. (F9X) gfortran options: -O3 -cpp -ffree-line-length-0 -Jsource/ -fopenmp -fno-backtrace -lcfitsio
OpenBenchmarking.orgSeconds, Fewer Is BetterNebular Empirical Analysis Tool 2.3123918273645Min: 40.49 / Avg: 41.38 / Max: 41.89Min: 40.81 / Avg: 41.64 / Max: 42.27Min: 41.12 / Avg: 41.67 / Max: 42.151. (F9X) gfortran options: -O3 -cpp -ffree-line-length-0 -Jsource/ -fopenmp -fno-backtrace -lcfitsio

Timed MrBayes Analysis

This test performs a bayesian analysis of a set of primate genome sequences in order to estimate their phylogeny. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny Analysis123306090120150SE +/- 1.14, N = 3SE +/- 0.69, N = 3SE +/- 0.59, N = 3144.70144.39144.141. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -O3 -std=c99 -pedantic -lm
OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MrBayes Analysis 3.2.7Primate Phylogeny Analysis123306090120150Min: 142.45 / Avg: 144.7 / Max: 146.1Min: 143.07 / Avg: 144.39 / Max: 145.38Min: 142.98 / Avg: 144.14 / Max: 144.881. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -O3 -std=c99 -pedantic -lm

QMCPACK

QMCPACK is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code making use of MPI for this benchmark of the H20 example code. QMCPACK is an open-source production level many-body ab initio Quantum Monte Carlo code for computing the electronic structure of atoms, molecules, and solids. QMCPACK is supported by the U.S. Department of Energy. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.11Input: simple-H2O123714212835SE +/- 0.28, N = 3SE +/- 0.21, N = 3SE +/- 0.21, N = 328.8528.7228.971. (CXX) g++ options: -fopenmp -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -march=native -O3 -fomit-frame-pointer -ffast-math -pthread -lm
OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.11Input: simple-H2O123612182430Min: 28.34 / Avg: 28.85 / Max: 29.3Min: 28.48 / Avg: 28.72 / Max: 29.14Min: 28.61 / Avg: 28.97 / Max: 29.351. (CXX) g++ options: -fopenmp -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -march=native -O3 -fomit-frame-pointer -ffast-math -pthread -lm

Timed HMMer Search

This test searches through the Pfam database of profile hidden markov models. The search finds the domain structure of Drosophila Sevenless protein. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 3.3.2Pfam Database Search123306090120150SE +/- 0.21, N = 3SE +/- 0.15, N = 3SE +/- 0.11, N = 3122.61123.17123.421. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm -lmpi
OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 3.3.2Pfam Database Search12320406080100Min: 122.23 / Avg: 122.61 / Max: 122.96Min: 122.92 / Avg: 123.17 / Max: 123.45Min: 123.25 / Avg: 123.42 / Max: 123.611. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm -lmpi

1

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --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-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,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: intel_pstate powersave - CPU Microcode: 0xde - Thermald 2.3
Security Notes: itlb_multihit: KVM: Mitigation of VMX disabled + 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 Enhanced IBRS IBPB: conditional RSB filling + srbds: Mitigation of TSX disabled + tsx_async_abort: Mitigation of TSX disabled

Testing initiated at 5 May 2021 17:13 by user root.

2

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --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-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,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: intel_pstate powersave - CPU Microcode: 0xde - Thermald 2.3
Security Notes: itlb_multihit: KVM: Mitigation of VMX disabled + 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 Enhanced IBRS IBPB: conditional RSB filling + srbds: Mitigation of TSX disabled + tsx_async_abort: Mitigation of TSX disabled

Testing initiated at 5 May 2021 17:39 by user root.

3

Processor: Intel Xeon E-2288G @ 5.00GHz (8 Cores / 16 Threads), Motherboard: Compulab SBC-ATCFL v1.2 (ATOP3.PRD.0.29.2 BIOS), Chipset: Intel Cannon Lake PCH, Memory: 2 x 32 GB DDR4-2667MT/s Samsung M378A4G43MB1-CTD, Disk: Samsung SSD 970 EVO Plus 250GB, Graphics: NVIDIA Quadro RTX 4000 8GB, Audio: Intel Cannon Lake PCH cAVS, Network: Intel I219-LM + Intel I210

OS: Ubuntu 20.10, Kernel: 5.8.0-41-generic (x86_64), Desktop: GNOME Shell 3.38.2, Display Server: X Server 1.20.9, Display Driver: NVIDIA, OpenCL: OpenCL 1.2 CUDA 11.2.109, Vulkan: 1.2.155, Compiler: GCC 10.2.0, File-System: ext4, Screen Resolution: 1920x1080

Kernel Notes: Transparent Huge Pages: madvise
Compiler Notes: --build=x86_64-linux-gnu --disable-vtable-verify --disable-werror --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-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,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: intel_pstate powersave - CPU Microcode: 0xde - Thermald 2.3
Security Notes: itlb_multihit: KVM: Mitigation of VMX disabled + 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 Enhanced IBRS IBPB: conditional RSB filling + srbds: Mitigation of TSX disabled + tsx_async_abort: Mitigation of TSX disabled

Testing initiated at 5 May 2021 18:02 by user root.