Intel(R) - Computational and Systems Biology at MIT

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7 Intel® Math Kernel Library User’s GuideThe wrapper for FFT is more complicated because of supporting the lifecycle for FFTdescriptor objects. To compute a single Fourier transform, an application needs to call theFFT software several times with the same copy of native FFT descriptor. The wrapperprovides the handler class to hold the native descriptor while virtual machine runs Javabytecode.The wrapper for VSL RNG is similar to the one for FFT. The wrapper provides the handlerclass to hold the native descriptor of the stream state.The wrapper for the convolution and correlation functions mitigates the same difficulty ofthe VSL interface, which assumes similar lifecycle for "task descriptors". The wrapperutilizes the ESSL-like interface for those functions, which is simpler for the case of1-dimensional data. The JNI stub additionally enwraps the MKL functions into the ESSL-likewrappers written in C and so "packs" the lifecycle of a task descriptor into a single call tothe native method.The wrappers meet the JNI Specification versions 1.1 and 5.0 and so must work withvirtually every modern implementation of Java.The examples and the Java part of the wrappers are written for the Java languagedescribed in “The Java Language Specification (First Edition)” and extended with thefeature of "inner classes" (this refers to late 1990s). This level of language version issupported by all versions of Sun's Java Software Development Kit (SDK) and compatibleimplementations starting from the version 1.1.5, that is, by all modern versions of Java.The level of C language is "Standard C" (that is, C89) with additional assumptions aboutinteger and floating-point data types required by the Intel MKL interfaces and the JNIheader files. That is, the native float and double data types are required to be the sameas JNI jfloat and jdouble data types, respectively, and the native int is required to be4-byte long.Running the examplesThe Java examples support all the C and C++ compilers that the Intel MKL does. Themakefile intended to run the examples also needs the make utility, which is typicallyprovided with the Linux* OS.To run Java examples, Java SDK is required for compiling and running Java code. A Javaimplementation must be installed on the computer or available via the network. You maydownload the SDK from the vendor website.The examples must work for all versions of Java 2 SE SDK. However, they were tested onlywith the following Java implementations:• from the Sun Microsystems Corporation (http://sun.com)• from the BEA (http://bea.com)See the Intel MKL Release Notes about the supported versions of these Java SDKs.7-12
Language-specific Usage Options 7NOTE. The implementation from the Sun Microsystems Corporationsupports only processors using IA-32 and Intel® 64 architectures. Theimplementation from BEA supports Intel® Itanium® 2 processors aswell.Also note that the Java runtime environment* (JRE*) system, which may be pre-installedon your computer, is not enough. You need the JDK* developer toolkit that supports thefollowing set of tools:• java• javac• javah• javadocTo make these tools available for the examples makefile, you have to setup the JAVA_HOMEenvironment variable and to add JDK binaries directory to the system PATH, for example:export JAVA_HOME=/home//jdk1.5.0_09export PATH=${JAVA_HOME}/bin:${PATH}You may also need to clear the JDK_HOME environment variable, if it is assigned a value:unset JDK_HOMETo start the examples, use the makefile found in the Intel MKL Java examples directory:make {so32|soem64t|so64} [function=…] [compiler=…]If started without specifying a target (any of the choices, like so32), the makefile prints thehelp info, which explains the targets as well as the function and compiler parameters.For the examples list, see the examples.lst file in the same directory.Known limitationsThere are three kinds of limitations:• functionality• performance• known bugs.Functionality. It is possible that some MKL functions will not work fine if called from Javaenvironment via a wrapper, like those provided with the Intel MKL Java examples. Onlythose specific CBLAS, FFT, VML, VSL RNG, and the convolution/correlation functions listed7-13
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Overview 1Intel® Math Kernel Libra
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