Intel(R) - Computational and Systems Biology at MIT

6 Intel® Math Kernel Library User’s GuideApplications based on IA-32 or Intel® 64 architecture. The addresses of the first elements ofarrays and the leading dimension values, in bytes (n*element_size), of two-dimensionalarrays should be divisible by cache line size, which equals• 32 bytes for Pentium® III processor• 64 bytes for Pentium® 4 processor• 128 bytes for processor using Intel® 64 architecture.Applications based on IA-64 architecture. The sufficient conditions are as follows:• For the C-style FFT, the distance L between arrays that represent real and imaginaryparts is not divisible by 64. The best case is when L=k*64 + 16• Leading dimension values, in bytes (n*element_size), of two-dimensional arrays arenot power of two.Hardware Configuration TipsDual-Core Intel® Xeon® processor 5100 series systems. To get the best Intel MKLperformance on Dual-Core Intel® Xeon® processor 5100 series systems, you are advisedto enable the Hardware DPL (streaming data) Prefetcher functionality of this processor.Configuration of this functionality is accomplished through appropriate BIOS settings wheresupported. Check your BIOS documentation for details.The use of Hyper-Threading Technology. Hyper-Threading Technology (HT Technology) isespecially effective when each thread is performing different types of operations and whenthere are under-utilized resources on the processor. Intel MKL fits neither of these criteriaas the threaded portions of the library execute at high efficiencies using most of theavailable resources and perform identical operations on each thread. You may obtainhigher performance when using Intel MKL without HT Technology enabled. See UsingIntel® MKL Parallelism for information on the default number of threads, changing thisnumber, and other relevant details.If you run with HT enabled, performance may be especially impacted if you run on fewerthreads than physical cores. For example, as there are two threads to every physical core,the thread scheduler may assign two threads to some cores and ignore others altogether. Ifyou are using the OpenMP* library of the Intel Compiler, read the respective User Guide onhow to best set the affinity to avoid this situation. For Intel MKL, you are recommended toset KMP_AFFINITY=granularity=fine,compact,1,0.6-14