mafft-1.6.2run

2 x Intel Xeon E5-2620 v2 testing with a ASUS Z9PE-D8 WS (5503 BIOS) and ASPEED on CentOS Stream 9 via the Phoronix Test Suite.

HTML result view exported from: https://openbenchmarking.org/result/2409050-NE-MAFFT162R21&rdt.

mafft-1.6.2runProcessorMotherboardChipsetMemoryDiskGraphicsAudioNetworkMonitorOSKernelDisplay ServerDisplay DriverCompilerFile-SystemScreen ResolutiondebugNoGVNO2NoGVNO3OptNoSimplO2OptNoSimplO3OptSimplO2OptSimplO3OptRedO2OptRedO32 x Intel Xeon E5-2620 v2OptPREO2GVNO2NewGVNO2OptPREO3NewGVNO333GVNO3PessimisticO3PessimisticO22 x Intel Xeon E5-2620 v2 @ 2.60GHz (12 Cores / 24 Threads)ASUS Z9PE-D8 WS (5503 BIOS)Intel Xeon E7 v2/Xeon32GB256GB Samsung SSD 850 + 2000GB Western Digital WD20EARX-00PASPEEDRealtek ALC8982 x Intel 82574LCentOS Stream 95.14.0-467.el9.x86_64 (x86_64)X ServerNVIDIAGCC 11.4.1 20231218 + PGI Compiler 16.10-0 + LLVM 3.1 + CUDA 11.2ext41024x7682000GB Western Digital WD20EARX-00P + 256GB Samsung SSD 850ASUS VW1905.14.0-474.el9.x86_64 (x86_64)5.14.0-480.el9.x86_64 (x86_64)256GB Samsung SSD 850 + 2000GB Western Digital WD20EARX-00P5.14.0-496.el9.x86_64 (x86_64)GCC 11.5.0 20240719 + PGI Compiler 16.10-0 + LLVM 3.1 + CUDA 11.25.14.0-503.el9.x86_64 (x86_64)OpenBenchmarking.orgKernel Details- Transparent Huge Pages: alwaysEnvironment Details- debug: CXXFLAGS=-O2 CFLAGS=-O2- NoGVNO2: CXXFLAGS="-O2 -mllvm -enable-newgvn -mllvm -disable-gvn=true" CFLAGS="-O2 -mllvm -enable-newgvn -mllvm -disable-gvn=true"- NoGVNO3: CXXFLAGS="-O3 -mllvm -enable-newgvn -mllvm -disable-gvn=true" CFLAGS="-O3 -mllvm -enable-newgvn -mllvm -disable-gvn=true"- OptNoSimplO2: CXXFLAGS="-O2 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=false -mllvm -enable-newgvn-pre=false -mllvm -enable-newgvn-simpl=false" CFLAGS="-O2 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=false -mllvm -enable-newgvn-pre=false -mllvm -enable-newgvn-simpl=false"- OptNoSimplO3: CXXFLAGS="-O3 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=false -mllvm -enable-newgvn-pre=false -mllvm -enable-newgvn-simpl=false" CFLAGS="-O3 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=false -mllvm -enable-newgvn-pre=false -mllvm -enable-newgvn-simpl=false"- OptSimplO2: CXXFLAGS="-O2 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=false -mllvm -enable-newgvn-pre=false -mllvm -enable-newgvn-simpl=true" CFLAGS="-O2 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=false -mllvm -enable-newgvn-pre=false -mllvm -enable-newgvn-simpl=true"- OptSimplO3: CXXFLAGS="-O3 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=false -mllvm -enable-newgvn-pre=false -mllvm -enable-newgvn-simpl=true" CFLAGS="-O3 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=false -mllvm -enable-newgvn-pre=false -mllvm -enable-newgvn-simpl=true"- OptRedO2: CXXFLAGS="-O2 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=true -mllvm -enable-newgvn-simpl=true -mllvm -enable-newgvn-pre=false" CFLAGS="-O2 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=true -mllvm -enable-newgvn-simpl=true -mllvm -enable-newgvn-pre=false"- OptRedO3: CXXFLAGS="-O3 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=true -mllvm -enable-newgvn-simpl=true -mllvm -enable-newgvn-pre=false" CFLAGS="-O3 -mllvm -enable-newgvn -mllvm -enable-phi-of-ops=true -mllvm -enable-newgvn-simpl=true -mllvm -enable-newgvn-pre=false"- 2 x Intel Xeon E5-2620 v2: CXXFLAGS="-O2 -mllvm -enable-newgvn -mllvm -enable-newgvn-pre=false" CFLAGS="-O2 -mllvm -enable-newgvn -mllvm -enable-newgvn-pre=false"- OptPREO2: CXXFLAGS="-O2 -mllvm -enable-newgvn" CFLAGS="-O2 -mllvm -enable-newgvn"- GVNO2: CXXFLAGS=-O2 CFLAGS=-O2- NewGVNO2: CXXFLAGS="-O2 -mllvm -enable-newgvn" CFLAGS="-O2 -mllvm -enable-newgvn"- OptPREO3: CXXFLAGS="-O3 -mllvm -enable-newgvn" CFLAGS="-O3 -mllvm -enable-newgvn"- NewGVNO333: CXXFLAGS="-O3 -mllvm -enable-newgvn" CFLAGS="-O3 -mllvm -enable-newgvn"- GVNO3: CXXFLAGS=-O3 CFLAGS=-O3- PessimisticO3: CXXFLAGS=-O3 CFLAGS=-O3- PessimisticO2: CXXFLAGS=-O2 CFLAGS=-O2Compiler Details- Optimized build with assertions; Built Apr 11 2013 (07:43:48); Default target: i386-pc-linux-gnu; Host CPU: i686Processor Details- Scaling Governor: intel_cpufreq conservative - CPU Microcode: 0x42eSecurity Details- gather_data_sampling: Not affected + 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 + mmio_stale_data: Unknown: No mitigations + reg_file_data_sampling: Not affected + retbleed: Not affected + spec_rstack_overflow: Not affected + spec_store_bypass: Mitigation of SSB disabled via prctl + spectre_v1: Mitigation of usercopy/swapgs barriers and __user pointer sanitization + spectre_v2: Mitigation of Retpolines; IBPB: conditional; IBRS_FW; STIBP: conditional; RSB filling; PBRSB-eIBRS: Not affected; BHI: Not affected + srbds: Not affected + tsx_async_abort: Not affected

mafft-1.6.2runmafft: Multiple Sequence Alignment - LSU RNADifferenceStandard ErrorStandard DeviationdebugNoGVNO2NoGVNO3OptNoSimplO2OptNoSimplO3OptSimplO2OptSimplO3OptRedO2OptRedO32 x Intel Xeon E5-2620 v2OptPREO2GVNO2NewGVNO2OptPREO3NewGVNO333GVNO3PessimisticO3PessimisticO222.7531.42x0.142.44%38.9331.01x0.392.44%39.2041.00x0.422.16%38.9301.01x0.482.46%39.0931.01x0.412.33%38.9391.01x0.432.48%38.6551.02x0.412.36%38.7941.01x0.372.35%39.1861.00x0.431.89%38.8361.01x0.332.37%39.1241.01x0.462.33%38.7671.01x0.332.39%38.8441.01x0.512.26%38.7761.01x0.482.46%38.4971.02x0.432.21%38.6741.02x0.482.48%39.3451.00x0.492.50%39.2651.00x0.392.42%OpenBenchmarking.org

Timed MAFFT Alignment

Multiple Sequence Alignment - LSU RNA

OpenBenchmarking.orgSeconds, Fewer Is BetterTimed MAFFT Alignment 7.471Multiple Sequence Alignment - LSU RNAOptNoSimplO2OptNoSimplO3OptSimplO2OptSimplO3OptRedO32 x Intel Xeon E5-2620 v2debugNoGVNO2NoGVNO3OptRedO2OptPREO2GVNO2NewGVNO2OptPREO3NewGVNO333GVNO3PessimisticO3PessimisticO2918273645SE +/- 0.39, N = 6SE +/- 0.36, N = 6SE +/- 0.44, N = 4SE +/- 0.36, N = 7SE +/- 0.38, N = 6SE +/- 0.38, N = 6SE +/- 0.14, N = 15SE +/- 0.39, N = 6SE +/- 0.42, N = 4SE +/- 0.37, N = 6SE +/- 0.46, N = 4SE +/- 0.33, N = 8SE +/- 0.51, N = 3SE +/- 0.48, N = 4SE +/- 0.43, N = 4SE +/- 0.48, N = 4SE +/- 0.49, N = 4SE +/- 0.39, N = 638.7238.9239.0338.8838.8938.9122.7538.9339.2038.7939.1238.7738.8438.7838.5038.6739.3539.271. (CC) clang options: -std=c99 -O3 -lm -lpthread

Phoronix Test Suite v10.8.5