Parallel Bioindormatic

Intel Core i7-3615QM testing with a Apple Mac-C3EC7CD22292981F (425.0.0.0.0 BIOS) and Intel HD 4000 981MB on Gentoo 2.8 via the Phoronix Test Suite.

HTML result view exported from: https://openbenchmarking.org/result/2201236-NE-2201234NE65.

Parallel BioindormaticProcessorMotherboardMemoryDiskGraphicsChipsetAudioMonitorNetworkOSKernelCompilerFile-SystemScreen ResolutionSystem LayerDesktopDisplay ServerDisplay DriverOpenGLOpenCLVulkanMusl Stable cmang 11.1.0Gentoo HDD GLIBC GCC 11.1Gentoo HDD GLIBC Clang 12.0Ubuntu 21.04 miti GCC 10.3Gentoo Glibc Clang 13 mold 1.01Gentoo Glibc GCC 11.2Intel Core i7-3615QM (8 Cores)Parallels Software Virtual (16.1.2 49151 BIOS)4096MB69GB Gentoo-Musl-0 SSvirtio_gpudrmfbGentoo/Linux5.10.27-gentoo-x86_64-gcc (x86_64)GCC 10.2.0ext41008x759Parallels VirtualizationIntel Core i7-3615QM @ 3.30GHz (4 Cores / 8 Threads)Apple Mac-C3EC7CD22292981F (421.0.0.0.0 BIOS)Intel 3rd Gen Core DRAM8GB251GB APPLE SSD SM256E + 500GB GenericNVIDIA GeForce GT 650M 1GBCirrus Logic CS4206Color LCDBroadcom NetXtreme BCM57786 PCIe + Broadcom BCM4331 802.11a/b/g/n5.12.4-gentoo-x86_64-v2 (x86_64)MATE 1.24.1X Server 1.20.11NVIDIA 465.274.6.0GCC 11.1.0 + Clang 12.0.0 + LLVM 12.0.0btrfs2880x1800Clang 12.0.0 + GCC 11.1.0 + LLVM 12.0.0251GB APPLE SSD SM256EBroadcom NetXtreme BCM57786 PCIe + Broadcom NetXtreme BCM57762 PCIe + Broadcom BCM4331 802.11a/b/g/nUbuntu 21.045.11.0-18-generic (x86_64)NVIDIA 460.80OpenCL 1.2 CUDA 11.2.1621.2.155GCC 10.3.0 + Clang 12.0.0-1ubuntu1 + LLVM 12.0.0zfsApple Mac-C3EC7CD22292981F (425.0.0.0.0 BIOS)Intel HD 4000 981MBBroadcom NetXtreme BCM57786 PCIe + Broadcom BCM4331 802.11a/b/g/nGentoo 2.85.16.2-gentoo (x86_64)KDE Plasma 5.23.5X Server 1.21.1.3 + WaylandNVIDIA4.2 Mesa 21.3.4Clang 13.0.0 + GCC 11.2.1 20220115 + LLVM 13.0.0btrfsGCC 11.2.1 20220115 + Clang 13.0.0 + LLVM 13.0.0OpenBenchmarking.orgKernel Details- Musl Stable cmang 11.1.0: Transparent Huge Pages: always- Gentoo HDD GLIBC GCC 11.1: i915.fastboot=1 - Transparent Huge Pages: always- Gentoo HDD GLIBC Clang 12.0: i915.fastboot=1 - Transparent Huge Pages: always- Ubuntu 21.04 miti GCC 10.3: Transparent Huge Pages: madvise- Gentoo Glibc Clang 13 mold 1.01: i915.enable_hd_vgaarb=1 - Transparent Huge Pages: always- Gentoo Glibc GCC 11.2: i915.enable_hd_vgaarb=1 - Transparent Huge Pages: alwaysCompiler Details- Musl Stable cmang 11.1.0: --bindir=/usr/x86_64-gentoo-linux-musl/gcc-bin/10.2.0 --build=x86_64-gentoo-linux-musl --datadir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/10.2.0 --disable-fixed-point --disable-libada --disable-libsanitizer --disable-libssp --disable-libstdcxx-pch --disable-libvtv --disable-multilib --disable-nls --disable-systemtap --disable-vtable-verify --disable-werror --enable-__cxa_atexit --enable-checking=release --enable-default-pie --enable-default-ssp --enable-esp --enable-languages=c,c++,fortran --enable-libgomp --enable-libstdcxx-time --enable-lto --enable-obsolete --enable-secureplt --enable-shared --enable-targets=all --enable-threads=posix --host=x86_64-gentoo-linux-musl --includedir=/usr/lib/gcc/x86_64-gentoo-linux-musl/10.2.0/include --mandir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/10.2.0/man --with-multilib-list=m64 --with-python-dir=/share/gcc-data/x86_64-gentoo-linux-musl/10.2.0/python --with-zstd --without-isl - Gentoo HDD GLIBC Clang 12.0: Optimized build; Default target: x86_64-pc-linux-gnu; Host CPU: ivybridge- Ubuntu 21.04 miti GCC 10.3: --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-gDeRY6/gcc-10-10.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-gDeRY6/gcc-10-10.3.0/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-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 - Gentoo Glibc Clang 13 mold 1.01: Optimized build; Default target: x86_64-pc-linux-gnu; Host CPU: ivybridgeProcessor Details- Musl Stable cmang 11.1.0: CPU Microcode: 0x21- Gentoo HDD GLIBC GCC 11.1: Scaling Governor: intel_cpufreq performance - CPU Microcode: 0x21- Gentoo HDD GLIBC Clang 12.0: Scaling Governor: intel_cpufreq performance - CPU Microcode: 0x21- Ubuntu 21.04 miti GCC 10.3: Scaling Governor: intel_cpufreq performance - CPU Microcode: 0x21 - Thermald 2.4.3- Gentoo Glibc Clang 13 mold 1.01: Scaling Governor: intel_cpufreq performance - CPU Microcode: 0x21- Gentoo Glibc GCC 11.2: Scaling Governor: intel_cpufreq performance - CPU Microcode: 0x21Security Details- Musl Stable cmang 11.1.0: itlb_multihit: KVM: Mitigation of VMX unsupported + l1tf: Mitigation of PTE Inversion + mds: Vulnerable: Clear buffers attempted no microcode; SMT Host state unknown + meltdown: Mitigation of PTI + spec_store_bypass: Vulnerable + spectre_v1: Mitigation of usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Full generic retpoline STIBP: disabled RSB filling + srbds: Unknown: Dependent on hypervisor status + tsx_async_abort: Not affected- Gentoo HDD GLIBC GCC 11.1: itlb_multihit: vulnerable + l1tf: Mitigation of PTE Inversion + mds: Mitigation of Clear buffers; SMT vulnerable + meltdown: Mitigation of PTI + 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 generic retpoline IBPB: conditional IBRS_FW STIBP: conditional RSB filling + srbds: Vulnerable: No microcode + tsx_async_abort: Not affected- Gentoo HDD GLIBC Clang 12.0: itlb_multihit: vulnerable + l1tf: Mitigation of PTE Inversion + mds: Mitigation of Clear buffers; SMT vulnerable + meltdown: Mitigation of PTI + 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 generic retpoline IBPB: conditional IBRS_FW STIBP: conditional RSB filling + srbds: Vulnerable: No microcode + tsx_async_abort: Not affected- Ubuntu 21.04 miti GCC 10.3: itlb_multihit: KVM: Mitigation of VMX disabled + l1tf: Mitigation of PTE Inversion; VMX: conditional cache flushes SMT vulnerable + mds: Mitigation of Clear buffers; SMT vulnerable + meltdown: Mitigation of PTI + 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 generic retpoline IBPB: conditional IBRS_FW STIBP: conditional RSB filling + srbds: Vulnerable: No microcode + tsx_async_abort: Not affected- Gentoo Glibc Clang 13 mold 1.01: itlb_multihit: vulnerable + l1tf: Mitigation of PTE Inversion + mds: Vulnerable; SMT vulnerable + meltdown: Vulnerable + spec_store_bypass: Vulnerable + spectre_v1: Vulnerable: __user pointer sanitization and usercopy barriers only; no swapgs barriers + spectre_v2: Vulnerable IBPB: disabled STIBP: disabled + srbds: Vulnerable: No microcode + tsx_async_abort: Not affected- Gentoo Glibc GCC 11.2: itlb_multihit: vulnerable + l1tf: Mitigation of PTE Inversion + mds: Vulnerable; SMT vulnerable + meltdown: Vulnerable + spec_store_bypass: Vulnerable + spectre_v1: Vulnerable: __user pointer sanitization and usercopy barriers only; no swapgs barriers + spectre_v2: Vulnerable IBPB: disabled STIBP: disabled + srbds: Vulnerable: No microcode + tsx_async_abort: Not affectedEnvironment Details- Gentoo Glibc Clang 13 mold 1.01: LDFLAGS=-fuse-ld=mold

Parallel Bioindormaticmafft: Multiple Sequence Alignment - LSU RNAhimeno: Poisson Pressure SolverMusl Stable cmang 11.1.0Gentoo HDD GLIBC GCC 11.1Gentoo HDD GLIBC Clang 12.0Ubuntu 21.04 miti GCC 10.3Gentoo Glibc Clang 13 mold 1.01Gentoo Glibc GCC 11.2317.0882205.42038320.3672549.61084622.1272167.7556702523.5097062401.9073112407.330765OpenBenchmarking.org

Timed MAFFT Alignment

Multiple Sequence Alignment - LSU RNA

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.471Multiple Sequence Alignment - LSU RNAMusl Stable cmang 11.1.0Gentoo HDD GLIBC GCC 11.1Gentoo HDD GLIBC Clang 12.070140210280350SE +/- 3.50, N = 5SE +/- 0.38, N = 2317.0920.3722.13gcc

Himeno Benchmark

Poisson Pressure Solver

OpenBenchmarking.orgMFLOPS, More Is BetterHimeno Benchmark 3.0Poisson Pressure SolverMusl Stable cmang 11.1.0Gentoo HDD GLIBC GCC 11.1Gentoo HDD GLIBC Clang 12.0Ubuntu 21.04 miti GCC 10.3Gentoo Glibc Clang 13 mold 1.01Gentoo Glibc GCC 11.25001000150020002500SE +/- 19.80, N = 3SE +/- 3.32, N = 3SE +/- 11.52, N = 3SE +/- 1.56, N = 3SE +/- 29.53, N = 3SE +/- 12.57, N = 32205.422549.612167.762523.512401.912407.33gccgccclanggccclanggcc

Phoronix Test Suite v10.8.4