testebioinformaticsdebian1

KVM testing on Debian 11 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 2402098-NE-TESTEBIOI18
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Result
Identifier
Performance Per
Dollar
Date
Run
  Test
  Duration
8 x Intel Xeon E5-2620 v4
February 09
  4 Hours, 59 Minutes
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8 x Intel Xeon E5-2620 v4

Processor: 8 x Intel Xeon E5-2620 v4 (8 Cores), Motherboard: QEMU Standard PC (Q35 + ICH9 2009) (1.15.0-1 BIOS), Chipset: Intel 82G33/G31/P35/P31 + ICH9, Memory: 3584MB, Disk: 57GB, Graphics: llvmpipe, Audio: QEMU Generic, Monitor: QEMU Monitor, Network: Red Hat Virtio device

OS: Debian 11, Kernel: 5.10.0-27-amd64 (x86_64), Desktop: GNOME Shell 3.38.6, Display Server: X Server + Wayland, OpenGL: 4.5 Mesa 20.3.5 (LLVM 11.0.1 256 bits), Compiler: GCC 10.2.1 20210110, File-System: ext4, Screen Resolution: 1024x768, System Layer: KVM

Kernel Notes: Transparent Huge Pages: always
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++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-link-mutex --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/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-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: 0xb000040
Python Notes: Python 3.9.2
Security Notes: gather_data_sampling: Not affected + itlb_multihit: Not affected + l1tf: Mitigation of PTE Inversion; VMX: flush not necessary SMT disabled + mds: Mitigation of Clear buffers; SMT Host state unknown + meltdown: Mitigation of PTI + mmio_stale_data: Vulnerable: Clear buffers attempted no microcode; SMT Host state unknown + retbleed: Not affected + spec_rstack_overflow: 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 Retpolines IBPB: conditional IBRS_FW STIBP: disabled RSB filling PBRSB-eIBRS: Not affected + srbds: Not affected + tsx_async_abort: Mitigation of Clear buffers; SMT Host state unknown

testebioinformaticsdebian1OpenBenchmarking.orgPhoronix Test Suite8 x Intel Xeon E5-2620 v4 (8 Cores)QEMU Standard PC (Q35 + ICH9 2009) (1.15.0-1 BIOS)Intel 82G33/G31/P35/P31 + ICH93584MB57GBllvmpipeQEMU GenericQEMU MonitorRed Hat Virtio deviceDebian 115.10.0-27-amd64 (x86_64)GNOME Shell 3.38.6X Server + Wayland4.5 Mesa 20.3.5 (LLVM 11.0.1 256 bits)GCC 10.2.1 20210110ext41024x768KVMProcessorMotherboardChipsetMemoryDiskGraphicsAudioMonitorNetworkOSKernelDesktopDisplay ServerOpenGLCompilerFile-SystemScreen ResolutionSystem LayerTestebioinformaticsdebian1 BenchmarksSystem Logs- Transparent Huge Pages: always- --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++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-link-mutex --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/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-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: 0xb000040- Python 3.9.2- gather_data_sampling: Not affected + itlb_multihit: Not affected + l1tf: Mitigation of PTE Inversion; VMX: flush not necessary SMT disabled + mds: Mitigation of Clear buffers; SMT Host state unknown + meltdown: Mitigation of PTI + mmio_stale_data: Vulnerable: Clear buffers attempted no microcode; SMT Host state unknown + retbleed: Not affected + spec_rstack_overflow: 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 Retpolines IBPB: conditional IBRS_FW STIBP: disabled RSB filling PBRSB-eIBRS: Not affected + srbds: Not affected + tsx_async_abort: Mitigation of Clear buffers; SMT Host state unknown

testebioinformaticsdebian1mrbayes: Primate Phylogeny Analysisqmcpack: H4_aeqmcpack: Li2_STO_aeqmcpack: LiH_ae_MSDqmcpack: simple-H2Oqmcpack: O_ae_pyscf_UHFqmcpack: FeCO6_b3lyp_gmshmmer: Pfam Database Searchhimeno: Poisson Pressure Solver8 x Intel Xeon E5-2620 v4236.934108.861051.6367.8287.690600.19461.88243.3941509.637854OpenBenchmarking.org

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 Analysis8 x Intel Xeon E5-2620 v450100150200250SE +/- 5.65, N = 9236.931. (CC) gcc options: -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -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 3.17.1Input: H4_ae8 x Intel Xeon E5-2620 v420406080100SE +/- 3.44, N = 15108.861. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -pthread -lm -ldl

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: Li2_STO_ae8 x Intel Xeon E5-2620 v42004006008001000SE +/- 12.74, N = 31051.61. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -pthread -lm -ldl

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: LiH_ae_MSD8 x Intel Xeon E5-2620 v480160240320400SE +/- 0.78, N = 3367.821. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -pthread -lm -ldl

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: simple-H2O8 x Intel Xeon E5-2620 v420406080100SE +/- 0.78, N = 387.691. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -pthread -lm -ldl

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: O_ae_pyscf_UHF8 x Intel Xeon E5-2620 v4130260390520650SE +/- 14.56, N = 9600.191. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -pthread -lm -ldl

OpenBenchmarking.orgTotal Execution Time - Seconds, Fewer Is BetterQMCPACK 3.17.1Input: FeCO6_b3lyp_gms8 x Intel Xeon E5-2620 v4100200300400500SE +/- 1.42, N = 3461.881. (CXX) g++ options: -fopenmp -foffload=disable -finline-limit=1000 -fstrict-aliasing -funroll-all-loops -ffast-math -march=native -O3 -pthread -lm -ldl

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 Search8 x Intel Xeon E5-2620 v450100150200250SE +/- 11.82, N = 8243.391. (CC) gcc options: -O3 -pthread -lhmmer -leasel -lm -lmpi

Timed MAFFT Alignment

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

8 x Intel Xeon E5-2620 v4: The test quit with a non-zero exit status. The test quit with a non-zero exit status. The test quit with a non-zero exit status.

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 Solver8 x Intel Xeon E5-2620 v430060090012001500SE +/- 149.39, N = 151509.641. (CC) gcc options: -O3 -mavx2

8 x Intel Xeon E5-2620 v4

Processor: 8 x Intel Xeon E5-2620 v4 (8 Cores), Motherboard: QEMU Standard PC (Q35 + ICH9 2009) (1.15.0-1 BIOS), Chipset: Intel 82G33/G31/P35/P31 + ICH9, Memory: 3584MB, Disk: 57GB, Graphics: llvmpipe, Audio: QEMU Generic, Monitor: QEMU Monitor, Network: Red Hat Virtio device

OS: Debian 11, Kernel: 5.10.0-27-amd64 (x86_64), Desktop: GNOME Shell 3.38.6, Display Server: X Server + Wayland, OpenGL: 4.5 Mesa 20.3.5 (LLVM 11.0.1 256 bits), Compiler: GCC 10.2.1 20210110, File-System: ext4, Screen Resolution: 1024x768, System Layer: KVM

Kernel Notes: Transparent Huge Pages: always
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++,m2 --enable-libphobos-checking=release --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-link-mutex --enable-multiarch --enable-multilib --enable-nls --enable-objc-gc=auto --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/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-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: 0xb000040
Python Notes: Python 3.9.2
Security Notes: gather_data_sampling: Not affected + itlb_multihit: Not affected + l1tf: Mitigation of PTE Inversion; VMX: flush not necessary SMT disabled + mds: Mitigation of Clear buffers; SMT Host state unknown + meltdown: Mitigation of PTI + mmio_stale_data: Vulnerable: Clear buffers attempted no microcode; SMT Host state unknown + retbleed: Not affected + spec_rstack_overflow: 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 Retpolines IBPB: conditional IBRS_FW STIBP: disabled RSB filling PBRSB-eIBRS: Not affected + srbds: Not affected + tsx_async_abort: Mitigation of Clear buffers; SMT Host state unknown

Testing initiated at 9 February 2024 20:54 by user xenserver.