bioinfo-HDS-Inserm-ubuntu-8

VMware testing on Ubuntu 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 2211087-DSAL-BIOINFO98
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Identifier
Performance Per
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Date
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  Test
  Duration
HDS-Inserm-ubuntu-8
October 21 2022
  19 Minutes
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HDS-Inserm-ubuntu-8

Processor: 8 x Intel Xeon Gold 6348 (15 Cores), Motherboard: Intel 440BX (6.00 BIOS), Chipset: Intel 440BX/ZX/DX, Memory: 32GB, Disk: 215GB Virtual disk, Graphics: VMware SVGA II, Network: VMware VMXNET3

OS: Ubuntu 22.04, Kernel: 5.15.0-48-generic (x86_64), Vulkan: 1.2.204, Compiler: GCC 11.2.0, File-System: ext4, Screen Resolution: 800x600, System Layer: VMware

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-gBFGDP/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-gBFGDP/gcc-11-11.2.0/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: CPU Microcode: 0xd0002b1
Python Notes: Python 3.10.6
Security Notes: itlb_multihit: KVM: Mitigation of VMX unsupported + l1tf: Mitigation of PTE Inversion + mds: Mitigation of Clear buffers; SMT Host state unknown + meltdown: Mitigation of PTI + mmio_stale_data: Mitigation of Clear buffers; SMT Host state unknown + retbleed: Mitigation of IBRS + 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 IBRS IBPB: conditional RSB filling + srbds: Not affected + tsx_async_abort: Not affected

bioinfo-HDS-Inserm-ubuntu-8OpenBenchmarking.orgPhoronix Test Suite8 x Intel Xeon Gold 6348 (15 Cores)Intel 440BX (6.00 BIOS)Intel 440BX/ZX/DX32GB215GB Virtual diskVMware SVGA IIVMware VMXNET3Ubuntu 22.045.15.0-48-generic (x86_64)1.2.204GCC 11.2.0ext4800x600VMwareProcessorMotherboardChipsetMemoryDiskGraphicsNetworkOSKernelVulkanCompilerFile-SystemScreen ResolutionSystem LayerBioinfo-HDS-Inserm-ubuntu-8 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-gBFGDP/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-gBFGDP/gcc-11-11.2.0/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 - CPU Microcode: 0xd0002b1- Python 3.10.6- itlb_multihit: KVM: Mitigation of VMX unsupported + l1tf: Mitigation of PTE Inversion + mds: Mitigation of Clear buffers; SMT Host state unknown + meltdown: Mitigation of PTI + mmio_stale_data: Mitigation of Clear buffers; SMT Host state unknown + retbleed: Mitigation of IBRS + 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 IBRS IBPB: conditional RSB filling + srbds: Not affected + tsx_async_abort: Not affected

bioinfo-HDS-Inserm-ubuntu-8himeno: Poisson Pressure Solvermafft: Multiple Sequence Alignment - LSU RNAhmmer: Pfam Database Searchqmcpack: simple-H2Omrbayes: Primate Phylogeny AnalysisHDS-Inserm-ubuntu-83906.14459510.156142.19229.792120.330OpenBenchmarking.org

Himeno Benchmark

The Himeno benchmark is a linear solver of pressure Poisson using a point-Jacobi method. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgMFLOPS, More Is BetterHimeno Benchmark 3.0Poisson Pressure SolverHDS-Inserm-ubuntu-88001600240032004000SE +/- 10.29, N = 33906.141. (CC) gcc options: -O3 -mavx2

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 RNAHDS-Inserm-ubuntu-83691215SE +/- 0.04, N = 310.161. (CC) gcc options: -std=c99 -O3 -lm -lpthread

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 SearchHDS-Inserm-ubuntu-8306090120150SE +/- 0.05, N = 3142.191. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm -lmpi

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 3.13Input: simple-H2OHDS-Inserm-ubuntu-8714212835SE +/- 0.07, N = 329.791. (CXX) g++ options: -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -lm -ldl

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 AnalysisHDS-Inserm-ubuntu-8306090120150SE +/- 0.07, N = 3120.331. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -mabm -O3 -std=c99 -pedantic -lm

HDS-Inserm-ubuntu-8

Processor: 8 x Intel Xeon Gold 6348 (15 Cores), Motherboard: Intel 440BX (6.00 BIOS), Chipset: Intel 440BX/ZX/DX, Memory: 32GB, Disk: 215GB Virtual disk, Graphics: VMware SVGA II, Network: VMware VMXNET3

OS: Ubuntu 22.04, Kernel: 5.15.0-48-generic (x86_64), Vulkan: 1.2.204, Compiler: GCC 11.2.0, File-System: ext4, Screen Resolution: 800x600, System Layer: VMware

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-gBFGDP/gcc-11-11.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-gBFGDP/gcc-11-11.2.0/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: CPU Microcode: 0xd0002b1
Python Notes: Python 3.10.6
Security Notes: itlb_multihit: KVM: Mitigation of VMX unsupported + l1tf: Mitigation of PTE Inversion + mds: Mitigation of Clear buffers; SMT Host state unknown + meltdown: Mitigation of PTI + mmio_stale_data: Mitigation of Clear buffers; SMT Host state unknown + retbleed: Mitigation of IBRS + 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 IBRS IBPB: conditional RSB filling + srbds: Not affected + tsx_async_abort: Not affected

Testing initiated at 21 October 2022 14:54 by user usr_paage.