scipbs-vm-01

Sci testing on scipbs-vm-01

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Bioinformatics 2 Tests
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scipbs-vm-01-24-02-2020
February 24 2020
  2 Minutes
odin-procesor
February 24 2020
  2 Minutes
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scipbs-vm-01-24-02-2020

Processor: Intel Xeon X5690 (6 Cores), Motherboard: oVirt Node (1.11.0-2.el7 BIOS), Memory: 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 3616 MB RAM, Disk: 64GB QEMU HDD

OS: CentOS Linux 7, Kernel: 3.10.0-1062.12.1.el7.x86_64 (x86_64), Compiler: GCC 4.8.5 20150623, File-System: xfs, System Layer: KVM

Compiler Notes: --build=x86_64-redhat-linux --disable-libgcj --disable-libunwind-exceptions --enable-__cxa_atexit --enable-bootstrap --enable-checking=release --enable-gnu-indirect-function --enable-gnu-unique-object --enable-initfini-array --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-shared --enable-threads=posix --mandir=/usr/share/man --with-arch_32=x86-64 --with-linker-hash-style=gnu --with-tune=generic
Processor Notes: CPU Microcode: 0x1
Security Notes: SELinux + itlb_multihit: vulnerable + l1tf: Mitigation of PTE Inversion + mds: Vulnerable: Clear buffers attempted no microcode; SMT Host state unknown + meltdown: Mitigation of PTI + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1: Mitigation of Load fences usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full retpoline IBPB + tsx_async_abort: Not affected

odin-procesor

Processor: 2 x Intel Xeon X5690 @ 3.47GHz (12 Cores), Motherboard: Supermicro X8DTN v2.0 (2.1c BIOS), Chipset: Intel 5520 I/O + ICH10R, Memory: 16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB DDR3-800MT/s, Disk: 120GB Samsung SSD 840, Graphics: AMD ES1000, Audio: NVIDIA GK208 HDMI/DP, Network: Aquantia AQC107 NBase-T/IEEE + 2 x Broadcom NetXtreme II BCM57711 10-Gigabit PCIe + 2 x Intel 82576

OS: CentOS Linux 7, Kernel: 3.10.0-1062.12.1.el7.x86_64 (x86_64), Compiler: GCC 4.8.5 20150623, File-System: xfs, Screen Resolution: 1024x768

Compiler Notes: --build=x86_64-redhat-linux --disable-libgcj --disable-libunwind-exceptions --enable-__cxa_atexit --enable-bootstrap --enable-checking=release --enable-gnu-indirect-function --enable-gnu-unique-object --enable-initfini-array --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-shared --enable-threads=posix --mandir=/usr/share/man --with-arch_32=x86-64 --with-linker-hash-style=gnu --with-tune=generic
Processor Notes: Scaling Governor: acpi-cpufreq performance - CPU Microcode: 0x1f
Security Notes: SELinux + itlb_multihit: KVM: Mitigation of Split huge pages + l1tf: Mitigation of PTE Inversion; VMX: conditional cache flushes SMT disabled + mds: Vulnerable: Clear buffers attempted no microcode; SMT disabled + meltdown: Mitigation of PTI + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1: Mitigation of Load fences usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full retpoline IBPB + tsx_async_abort: Not affected

scipbs-vm-01ProcessorMotherboardMemoryDiskChipsetGraphicsAudioNetworkOSKernelCompilerFile-SystemSystem LayerScreen Resolutionscipbs-vm-01-24-02-2020odin-procesorIntel Xeon X5690 (6 Cores)oVirt Node (1.11.0-2.el7 BIOS)16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 3616 MB RAM64GB QEMU HDDCentOS Linux 73.10.0-1062.12.1.el7.x86_64 (x86_64)GCC 4.8.5 20150623xfsKVM2 x Intel Xeon X5690 @ 3.47GHz (12 Cores)Supermicro X8DTN v2.0 (2.1c BIOS)Intel 5520 I/O + ICH10R16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB DDR3-800MT/s120GB Samsung SSD 840AMD ES1000NVIDIA GK208 HDMI/DPAquantia AQC107 NBase-T/IEEE + 2 x Broadcom NetXtreme II BCM57711 10-Gigabit PCIe + 2 x Intel 825761024x768OpenBenchmarking.orgCompiler Details- --build=x86_64-redhat-linux --disable-libgcj --disable-libunwind-exceptions --enable-__cxa_atexit --enable-bootstrap --enable-checking=release --enable-gnu-indirect-function --enable-gnu-unique-object --enable-initfini-array --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-shared --enable-threads=posix --mandir=/usr/share/man --with-arch_32=x86-64 --with-linker-hash-style=gnu --with-tune=genericProcessor Details- scipbs-vm-01-24-02-2020: CPU Microcode: 0x1- odin-procesor: Scaling Governor: acpi-cpufreq performance - CPU Microcode: 0x1fSecurity Details- scipbs-vm-01-24-02-2020: SELinux + itlb_multihit: vulnerable + l1tf: Mitigation of PTE Inversion + mds: Vulnerable: Clear buffers attempted no microcode; SMT Host state unknown + meltdown: Mitigation of PTI + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1: Mitigation of Load fences usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full retpoline IBPB + tsx_async_abort: Not affected - odin-procesor: SELinux + itlb_multihit: KVM: Mitigation of Split huge pages + l1tf: Mitigation of PTE Inversion; VMX: conditional cache flushes SMT disabled + mds: Vulnerable: Clear buffers attempted no microcode; SMT disabled + meltdown: Mitigation of PTI + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1: Mitigation of Load fences usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full retpoline IBPB + tsx_async_abort: Not affected

scipbs-vm-01ffte: N=256, 1D Complex FFT Routinefftw: Stock - 1D FFT Size 4096fftw: Float + SSE - 1D FFT Size 4096hmmer: Pfam Database Searchmafft: Multiple Sequence Alignmentscipbs-vm-01-24-02-2020odin-procesor5126.784717.81597212.1695.6464760.5162717.9253.765OpenBenchmarking.org

FFTE

FFTE is a package by Daisuke Takahashi to compute Discrete Fourier Transforms of 1-, 2- and 3- dimensional sequences of length (2^p)*(3^q)*(5^r). Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgMFLOPS, More Is BetterFFTE 6.0Test: N=256, 1D Complex FFT Routinescipbs-vm-01-24-02-202011002200330044005500SE +/- 6.42, N = 35126.781. (F9X) gfortran options: -O3 -fomit-frame-pointer -fopenmp

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions. Learn more via the OpenBenchmarking.org test page.

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Stock - Size: 1D FFT Size 4096scipbs-vm-01-24-02-2020odin-procesor10002000300040005000SE +/- 7.45, N = 3SE +/- 12.70, N = 34717.84760.51. (CC) gcc options: -std=gnu99 -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm
OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Stock - Size: 1D FFT Size 4096scipbs-vm-01-24-02-2020odin-procesor8001600240032004000Min: 4704.6 / Avg: 4717.8 / Max: 4730.4Min: 4740.4 / Avg: 4760.53 / Max: 47841. (CC) gcc options: -std=gnu99 -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm

OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Float + SSE - Size: 1D FFT Size 4096scipbs-vm-01-24-02-2020odin-procesor3K6K9K12K15KSE +/- 55.05, N = 3SE +/- 64.49, N = 315972162711. (CC) gcc options: -std=gnu99 -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -lm
OpenBenchmarking.orgMflops, More Is BetterFFTW 3.3.6Build: Float + SSE - Size: 1D FFT Size 4096scipbs-vm-01-24-02-2020odin-procesor3K6K9K12K15KMin: 15904 / Avg: 15972 / Max: 16081Min: 16156 / Avg: 16271.33 / Max: 163791. (CC) gcc options: -std=gnu99 -pthread -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -ffast-math -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 2.3.2Pfam Database Searchscipbs-vm-01-24-02-2020odin-procesor3691215SE +/- 0.027, N = 3SE +/- 0.030, N = 312.1697.9251. (CC) gcc options: -O2 -pthread -lhmmer -lsquid -lm
OpenBenchmarking.orgSeconds, Fewer Is BetterTimed HMMer Search 2.3.2Pfam Database Searchscipbs-vm-01-24-02-2020odin-procesor48121620Min: 12.14 / Avg: 12.17 / Max: 12.22Min: 7.87 / Avg: 7.93 / Max: 7.971. (CC) gcc options: -O2 -pthread -lhmmer -lsquid -lm

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 7.392Multiple Sequence Alignmentscipbs-vm-01-24-02-2020odin-procesor1.27042.54083.81125.08166.352SE +/- 0.011, N = 3SE +/- 0.129, N = 125.6463.7651. (CC) gcc options: -std=c99 -O3 -lm -lpthread
OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.392Multiple Sequence Alignmentscipbs-vm-01-24-02-2020odin-procesor246810Min: 5.63 / Avg: 5.65 / Max: 5.66Min: 3.39 / Avg: 3.76 / Max: 5.071. (CC) gcc options: -std=c99 -O3 -lm -lpthread

scipbs-vm-01-24-02-2020

Processor: Intel Xeon X5690 (6 Cores), Motherboard: oVirt Node (1.11.0-2.el7 BIOS), Memory: 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 3616 MB RAM, Disk: 64GB QEMU HDD

OS: CentOS Linux 7, Kernel: 3.10.0-1062.12.1.el7.x86_64 (x86_64), Compiler: GCC 4.8.5 20150623, File-System: xfs, System Layer: KVM

Compiler Notes: --build=x86_64-redhat-linux --disable-libgcj --disable-libunwind-exceptions --enable-__cxa_atexit --enable-bootstrap --enable-checking=release --enable-gnu-indirect-function --enable-gnu-unique-object --enable-initfini-array --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-shared --enable-threads=posix --mandir=/usr/share/man --with-arch_32=x86-64 --with-linker-hash-style=gnu --with-tune=generic
Processor Notes: CPU Microcode: 0x1
Security Notes: SELinux + itlb_multihit: vulnerable + l1tf: Mitigation of PTE Inversion + mds: Vulnerable: Clear buffers attempted no microcode; SMT Host state unknown + meltdown: Mitigation of PTI + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1: Mitigation of Load fences usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full retpoline IBPB + tsx_async_abort: Not affected

Testing initiated at 24 February 2020 10:09 by user .

odin-procesor

Processor: 2 x Intel Xeon X5690 @ 3.47GHz (12 Cores), Motherboard: Supermicro X8DTN v2.0 (2.1c BIOS), Chipset: Intel 5520 I/O + ICH10R, Memory: 16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 8192 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB + 16384 MB DDR3-800MT/s, Disk: 120GB Samsung SSD 840, Graphics: AMD ES1000, Audio: NVIDIA GK208 HDMI/DP, Network: Aquantia AQC107 NBase-T/IEEE + 2 x Broadcom NetXtreme II BCM57711 10-Gigabit PCIe + 2 x Intel 82576

OS: CentOS Linux 7, Kernel: 3.10.0-1062.12.1.el7.x86_64 (x86_64), Compiler: GCC 4.8.5 20150623, File-System: xfs, Screen Resolution: 1024x768

Compiler Notes: --build=x86_64-redhat-linux --disable-libgcj --disable-libunwind-exceptions --enable-__cxa_atexit --enable-bootstrap --enable-checking=release --enable-gnu-indirect-function --enable-gnu-unique-object --enable-initfini-array --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-shared --enable-threads=posix --mandir=/usr/share/man --with-arch_32=x86-64 --with-linker-hash-style=gnu --with-tune=generic
Processor Notes: Scaling Governor: acpi-cpufreq performance - CPU Microcode: 0x1f
Security Notes: SELinux + itlb_multihit: KVM: Mitigation of Split huge pages + l1tf: Mitigation of PTE Inversion; VMX: conditional cache flushes SMT disabled + mds: Vulnerable: Clear buffers attempted no microcode; SMT disabled + meltdown: Mitigation of PTI + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1: Mitigation of Load fences usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full retpoline IBPB + tsx_async_abort: Not affected

Testing initiated at 24 February 2020 10:20 by user .