Intel(R) - Computational and Systems Biology at MIT

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6 Intel® Math Kernel Library User’s GuideHere are several cases with recommendations depending on the threading model youemploy:Table 6-1How to avoid conflicts in the execution environment for your threadingmodelThreading modelYou thread the program using OS threads(pthreads on the Linux* OS).You thread the program using OpenMP directivesand/or pragmas and compile the program using acompiler other than a compiler from Intel.There are multiple programs running on amultiple-cpu system, as in the case of a parallelizedprogram running using MPI for communication inwhich each processor is treated as a node.DiscussionIf more than one thread calls the library, and thefunction being called is threaded, it may beimportant that you turn off Intel MKL threading. Setthe number of threads to one by any of the availablemeans (see Techniques to Set the Number ofThreads).This is more problematic in that setting ofOMP_NUM_THREADS in the environment affects boththe compiler's threading library and libguide(libiomp). In this case, you should try to choosethe Threading layer library that matches the layeredIntel MKL with the OpenMP compiler you employ (seeLinking Examples on how to do this). If this isimpossible, the sequential version of Intel MKL canbe used as the Threading layer. To do this, youshould link with the appropriate Threading layerlibrary: libmkl_sequential.a orlibmkl_sequential.so (see the High-levelDirectory Structure section in chapter 3).The threading software will see multiple processorson the system even though each processor has aseparate MPI process running on it. In this case, setthe number of threads to one by any of the availablemeans (see Techniques to Set the Number ofThreads).To avoid correctness and performance problems, you are also strongly encouraged todynamically link with the Intel® Legacy OpenMP run-time library libguide and Intel®Compatibility OpenMP run-time library libiomp.Setting the Number of Threads Using OpenMP* EnvironmentVariableYou can set the number of threads using the environment variable OMP_NUM_THREADS. Tochange the number of threads, in the command shell in which the program is going to run,enter:6-4
Managing Performance and Memory 6export OMP_NUM_THREADS= for certain shells, such asbash.orset OMP_NUM_THREADS= for other shells, such as csh ortcsh.See Using Additional Threading Control on how to set the number of threads using IntelMKL environment variables, for example, MKL_NUM_THREADS.Changing the Number of Threads at Run TimeIt is not possible to change the number of processors during run time using theenvironment variables. However, you can call OpenMP API functions from your program tochange the number of threads during run time. The following sample code demonstrateschanging the number of threads during run time using the omp_set_num_threads()routine. See also Techniques to Set the Number of Threads.To run this example, use the omp.h header file from the Intel® Compiler package. If youdo not have the Intel Compiler but wish to explore the functionality in the example, useFortran API for omp_set_num_threads() rather than the C version.Example 6-1 Changing the number of processors for threading#include "omp.h"#include "mkl.h"#include #define SIZE 1000void main(int args, char *argv[]){double *a, *b, *c;a = new double [SIZE*SIZE];b = new double [SIZE*SIZE];c = new double [SIZE*SIZE];6-5
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IndexAAbsoft compiler, linking with
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Intel(R) - Computational and Systems Biology at MIT

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