Intel(R) - Computational and Systems Biology at MIT

More documents

Recommendations

Info

6 Intel® Math Kernel Library User’s GuideOperating on DenormalsIf an Intel MKL function operates on denormals, that is, non-zero numbers that are smallerthan the smallest possible non-zero number supported by a given floating-point format, orproduces denormals during the computation (for instance, if the incoming data is too closeto the underflow threshold), you may experience considerable performance drop. The CPUstate may be set so that floating-point operations on denormals invoke the exceptionhandler that slows down the application.To resolve the issue, before compiling the main program, turn on the -ftz option, if youare using the Intel® compiler or any other compiler that can control this feature. In thiscase, denormals are treated as zeros at processor level and the exception handler is notinvoked. Note, however, that setting this option slightly impacts the accuracy.Another way to bring the performance back to norm is proper scaling of the input data toavoid numbers near the underflow threshold.FFT Optimized RadicesYou can gain performance of Intel MKL FFT if length of the data vector permits factorizationinto powers of optimized radices.In Intel MKL, the list of optimized radices depends upon the architecture:• 2, 3, 4, 5 for IA-32 architecture• 2, 3, 4, 5 for Intel® 64 architecture• 2, 3, 4, 5, 7, 11 for IA-64 architecture.Using Intel® MKL Memory ManagementIntel MKL has the memory management software that controls memory buffers for use bythe library functions. New buffers that the library allocates when certain functions (Level 3BLAS or FFT) are called are not deallocated until the program ends. To get the amount ofmemory allocated by the memory management software, call the MKL_MemStat()function. If at some point your program needs to free memory, it may do so with a call toMKL_FreeBuffers(). If another call is made to a library function that needs a memorybuffer, then the memory manager will again allocate the buffers and they will again remainallocated until either the program ends or the program deallocates the memory.This behavior facilitates better performance. However, some tools may report the behavioras a memory leak. You can release memory in your program through the use of a functionmade available in Intel MKL or you can force memory releasing after each call by setting anenvironment variable.6-16
Managing Performance and Memory 6The memory management software is turned on by default. To disable the software usingthe environment variable, set MKL_DISABLE_FAST_MM to any value, which will causememory to be allocated and freed from call to call. Disabling this feature will negativelyimpact performance of routines such as the level 3 BLAS, especially for small problemsizes.Using one of these methods to release memory will not necessarily stop programs fromreporting memory leaks, and, in fact, may increase the number of such reports in case youmake multiple calls to the library, thereby requiring new allocations with each call. Memorynot released by one of the methods described will be released by the system when theprogram ends.Redefining Memory FunctionsStarting with MKL 9.0, you can replace memory functions that the library uses by defaultwith your own ones. It is possible due to the memory renaming feature.Memory renamingIn general, if users try to employ their own memory management functions instead ofsimilar system functions (malloc, free, calloc, and realloc), actually, the memorygets managed by two independent memory management packages, which may causememory issues. To prevent from such issues, the memory renaming feature wasintroduced in certain Intel® libraries and in particular in Intel MKL. This feature enablesusers to redefine memory management functions.Redefining is possible because Intel MKL actually uses pointers to memory functions(i_malloc, i_free, i_calloc, i_realloc) rather than the functions themselves. Thesepointers initially hold addresses of respective system memory management functions(malloc, free, calloc, realloc) and are visible at the application level. So, the pointervalues can be redefined programmatically.Once a user has redirected these pointers to their own respective memory managementfunctions, the memory will be managed with user-defined functions rather than systemones. As only one (user-defined) memory management package is in operation, the issuesare avoided.Intel MKL memory management by default uses standard C run-time memory functions toallocate or free memory. These functions can be replaced using memory renaming.How to redefine memory functionsTo redefine memory functions, you may use the following procedure:6-17
Page 3 and 4:
INFORMATION IN THIS DOCUMENT IS PRO
Page 7 and 8:
Intel® Math Kernel Library User’
Page 9 and 10:
Overview 1Intel® Math Kernel Libra
Page 11 and 12:
Overview 1Chapter 3Chapter 4Chapter
Page 13 and 14:
Getting Started 2This chapter helps
Page 16 and 17:
2 Intel® Math Kernel Library User
Page 18 and 19:
3 Intel® Math Kernel Library User
Page 20 and 21: 3 Intel® Math Kernel Library User
Page 38 and 39: Configuring YourDevelopment Environ
Page 40 and 41: Configuring Your Development Enviro
Page 42 and 43: Configuring Your Development Enviro
Page 94 and 95: LINPACK and MP LINPACKBenchmarks 10
Page 96 and 97: LINPACK and MP LINPACK Benchmarks 1
Page 106 and 107: A Intel® Math Kernel Library User
Page 108 and 109: IndexAAbsoft compiler, linking with
Page 110: Intel MKL choice, particular cases,
show all

Intel(R) - Computational and Systems Biology at MIT

Create successful ePaper yourself

Delete template?

Save as template?