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Commit a68be997 authored by Jeffrey Phillips Freeman's avatar Jeffrey Phillips Freeman 💥
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feat: moved Correlation matrix to root of project.

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CHANGELOG.md
View file @ a68be997
# Aparapi Examples Changelog
## 1.4.1
* Updated parent pon to v6.
......@@ -14,13 +15,13 @@
## 1.3.4
* Updated to aparapi-jni 1.1.2 thus fixing `UnsatisfiedLinkError` which occured only on Windows.
* Synced to Aparapi 1.3.4
* Updated to aparapi-jni 1.1.2 thus fixing `UnsatisfiedLinkError` which occured only on Windows.
## 1.3.3
* Fixed "`CXXABI_1.3.8' not found " error encountered on some older systems.
* Synced to Aparapi 1.3.3
* Fixed "`CXXABI_1.3.8' not found " error encountered on some older systems.
## 1.3.2
......@@ -42,12 +43,15 @@
## 1.1.2
* Synced to Aparapi 1.1.2
* Fixed some bugs causing the OpenCL kernel to be compiled twice.
## 1.1.0
## 1.1.1
* Synced to Aparapi 1.1.1
* Changed package to com.aparapi
## 1.1.0
* Synced to Aparapi 1.1.0
* Changed group id and package to com.aparapi
\ No newline at end of file
examples/correlation-matrix/.project deleted 100644 → 0
View file @ 3652780c
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>correlation-matrix</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
examples/correlation-matrix/CC-4257_FINAL_060612.pdf deleted 100644 → 0
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File suppressed by a .gitattributes entry or the file's encoding is unsupported.
examples/correlation-matrix/build.xml deleted 100644 → 0
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<?xml version="1.0"?>
<project name="correlation-matrix" default="junit" basedir=".">
<!--
USER CONFIGURABLE PROPERTIES
-->
<property name="libs.root" value="${basedir}/.libs" />
<property name="commons.lang.jar" value="commons-lang3-3.1.jar" />
<property name="log4j.jar" value="log4j-1.2.17.jar" />
<property name="lucene.jar" value="lucene-core-3.5.0.jar" />
<property name="junit.jar" value="junit-4.10.jar" />
<property name="commons.lang.url" value="http://repo1.maven.org/maven2/org/apache/commons/commons-lang3/3.1/${commons.lang.jar}" />
<property name="log4j.url" value="http://repo1.maven.org/maven2/log4j/log4j/1.2.17/${log4j.jar}" />
<property name="lucene.url" value="http://repo1.maven.org/maven2/org/apache/lucene/lucene-core/3.5.0/${lucene.jar}" />
<property name="junit.url" value="http://repo1.maven.org/maven2/junit/junit/4.10/${junit.jar}" />
<!--
SYSTEM PROPERTIES
-->
<echo>OS Name: ${os.name}</echo>
<echo>OS Version: ${os.version}</echo>
<echo>OS Arch: ${os.arch}</echo>
<echo>Java Version: ${java.version}</echo>
<!-- Ideally this would be the latest version of Java but not everyone is going to have it installed -->
<!-- Additionally we want to avoid "Class not found: javac1.8" errors from old Ant versions (i.e. Eclipse) -->
<property name="build.compiler" value="javac1.7" />
<property name="ant.build.javac.source" value="1.7" />
<property name="ant.build.javac.target" value="1.7" />
<path id="classpath">
<pathelement path="${basedir}/../../com.aparapi/dist/aparapi.jar" />
<pathelement path="${libs.root}/${commons.lang.jar}" />
<pathelement path="${libs.root}/${log4j.jar}" />
<pathelement path="${libs.root}/${lucene.jar}" />
<pathelement path="${libs.root}/${junit.jar}" />
<pathelement path="classes" />
</path>
<target name="install.deps">
<mkdir dir="${libs.root}" />
<!-- Cleanup all existing deps -->
<delete failonerror="false" includeEmptyDirs="true">
<fileset dir="${libs.root}" includes="*/" />
</delete>
<!-- Download and unzip requested deps -->
<get src="${commons.lang.url}" dest="${libs.root}/${commons.lang.jar}" />
<get src="${log4j.url}" dest="${libs.root}/${log4j.jar}" />
<get src="${lucene.url}" dest="${libs.root}/${lucene.jar}" />
<get src="${junit.url}" dest="${libs.root}/${junit.jar}" />
</target>
<target name="clean">
<delete dir="classes" />
<delete dir="junit" />
<delete file="correlation-matrix.jar" />
</target>
<target name="junit" depends="clean">
<mkdir dir="classes" />
<mkdir dir="junit/data" />
<!-- Runtime Code -->
<javac debug="true" debuglevel="lines,vars,source" srcdir="src/java" destdir="classes" includeAntRuntime="false" classpathref="classpath">
<compilerarg value="-Xlint" />
<compilerarg value="-Xlint:-path" />
</javac>
<!-- JUnit Tests -->
<javac debug="true" debuglevel="lines,vars,source" srcdir="src/test" destdir="classes" includeAntRuntime="false" classpathref="classpath">
<compilerarg value="-Xlint" />
<compilerarg value="-Xlint:-path" />
</javac>
<copy todir="classes" file="src/java/log4j.xml" />
<!-- Even though fork is slower we need to set the library path and this requires fork -->
<junit printsummary="false" fork="true" haltonfailure="false" failureproperty="tests.failed" showoutput="true">
<sysproperty key="java.library.path" value="${basedir}/../../com.aparapi.jni/dist" />
<!-- USER DEFINED PROPERTIES -->
<sysproperty key="numRows" value="1024" />
<sysproperty key="numColumns" value="16384" />
<sysproperty key="useGPU" value="true" />
<formatter type="xml" />
<classpath refid="classpath" />
<batchtest todir="junit/data">
<fileset dir="src/test" />
</batchtest>
</junit>
<junitreport todir="junit/data">
<fileset dir="junit/data" />
</junitreport>
</target>
</project>
\ No newline at end of file
examples/correlation-matrix/src/java/log4j.xml deleted 100644 → 0
View file @ 3652780c
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
<!--
| For more configuration information and examples see the Jakarta Log4j
| website: http://jakarta.apache.org/log4j
-->
<log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/" debug="false">
<!-- ============================== -->
<!-- Append messages to the console -->
<!-- ============================== -->
<appender name="CONSOLE" class="org.apache.log4j.ConsoleAppender">
<param name="Threshold" value="DEBUG"/>
<param name="Target" value="System.out"/>
<param name="Encoding" value="UTF-8"/>
<layout class="org.apache.log4j.PatternLayout">
<!-- The default pattern: Date Priority [Category] (Thread) Message\n -->
<param name="ConversionPattern" value="%d %-5p [%c{1}] %m%n"/>
<!-- The full pattern: Date MS Priority [Category] (Thread:NDC) Message\n
<param name="ConversionPattern" value="%d %-5r %-5p [%c] (%t:%x) %m%n"/>
-->
</layout>
</appender>
<appender name="FILE" class="org.apache.log4j.FileAppender">
<param name="File" value="log/corrmatrix.log"/>
<param name="Append" value="true"/>
<param name="Encoding" value="UTF-8"/>
<layout class="org.apache.log4j.PatternLayout">
<!-- The default pattern: Date Priority [Category] (Thread) Message\n -->
<param name="ConversionPattern" value="%d %-5p [%c] %m%n"/>
<!-- The full pattern: Date MS Priority [Category] (Thread:NDC) Message\n
<param name="ConversionPattern" value="%d %-5r %-5p [%c] (%t:%x) %m%n"/>
-->
</layout>
</appender>
<!-- Limit categories -->
<logger name="gov.pnnl">
<level value="DEBUG"/>
</logger>
<!-- ======================= -->
<!-- Setup the Root category -->
<!-- ======================= -->
<root>
<appender-ref ref="CONSOLE"/>
<!-- <appender-ref ref="FILE"/> -->
</root>
</log4j:configuration>
\ No newline at end of file
pom.xml
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......@@ -81,7 +81,7 @@
<dependency>
<groupId>com.aparapi</groupId>
<artifactId>aparapi</artifactId>
<version>1.4.2-SNAPSHOT</version>
<version>1.4.1</version>
</dependency>
<dependency>
<groupId>org.jogamp.gluegen</groupId>
......@@ -98,6 +98,25 @@
<artifactId>gluegen</artifactId>
<version>2.3.2</version>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-core</artifactId>
<version>3.6.2</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.6</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
</dependencies>
<build>
......
src/main/java/com/aparapi/examples/All.java
View file @ a68be997
......@@ -82,6 +82,7 @@ public class All {
System.out.println(" 33) NBody - Sequential");
System.out.println(" 34) OOPN Body");
System.out.println(" 35) Map-reduce");
System.out.println(" 36) Correlation Matrix");
System.out.println();
Scanner in = new Scanner(System.in);
......@@ -217,6 +218,9 @@ public class All {
case "35":
com.aparapi.examples.mapreduce.Main.main(args);
break;
case "36":
com.aparapi.examples.matrix.Main.main(args);
break;
default:
System.out.println("Invalid selection.");
}
......
examples/correlation-matrix/src/java/gov/pnnl/aparapi/matrix/CorrMatrixHost.java → src/main/java/com/aparapi/examples/matrix/CorrMatrixHost.java
View file @ a68be997
/**
* Copyright (c) 2016 - 2017 Syncleus, Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* This material was prepared as an account of work sponsored by an agency of the United States Government.
* Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of
......@@ -6,7 +21,7 @@
* completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents
* that its use would not infringe privately owned rights.
*/
package gov.pnnl.aparapi.matrix;
package com.aparapi.examples.matrix;
import org.apache.log4j.Logger;
......@@ -40,7 +55,7 @@ public class CorrMatrixHost {
* @return result Matrix
* @throws Exception
*/
public static int[][] intersectionMatrix(final long[][] matrixA, final long[][] matrixB, final EXECUTION_MODE executionMode) throws Exception {
public static int[][] intersectionMatrix(final long[][] matrixA, final long[][] matrixB, final EXECUTION_MODE executionMode) {
// Basic validation
if (matrixA == null) {
......@@ -225,7 +240,7 @@ public class CorrMatrixHost {
for (int i = aSubRowStart; i < aSubRowEnd; i++) {
if (matrixA_numLongs != matrixA[i].length) {
throw new Exception("All rows in the matrix need be the same length");
throw new IllegalStateException("All rows in the matrix need be the same length");
}
System.arraycopy(matrixA[i], 0, subMatrixA, (i - aSubRowStart) * matrixA_numLongs, matrixA_numLongs);
......@@ -236,7 +251,7 @@ public class CorrMatrixHost {
for (int i = bSubRowStart; i < bSubRowEnd; i++) {
if (matrixA_numLongs != matrixB[i].length) {
throw new Exception("All rows in the matrix need be the same length");
throw new IllegalStateException("All rows in the matrix need be the same length");
}
System.arraycopy(matrixB[i], 0, subMatrixB, (i - bSubRowStart) * matrixB_numLongs, matrixB_numLongs);
......
examples/correlation-matrix/src/java/gov/pnnl/aparapi/matrix/CorrMatrixKernel.java → src/main/java/com/aparapi/examples/matrix/CorrMatrixKernel.java
View file @ a68be997
/**
* Copyright (c) 2016 - 2017 Syncleus, Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* This material was prepared as an account of work sponsored by an agency of the United States Government.
* Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of
......@@ -6,7 +21,7 @@
* completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents
* that its use would not infringe privately owned rights.
*/
package gov.pnnl.aparapi.matrix;
package com.aparapi.examples.matrix;
import com.aparapi.Kernel;
......
src/main/java/com/aparapi/examples/matrix/Main.java 0 → 100644
View file @ a68be997
/**
* Copyright (c) 2016 - 2017 Syncleus, Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* This material was prepared as an account of work sponsored by an agency of the United States Government.
* Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of
* their employees, nor any jurisdiction or organization that has cooperated in the development of these materials,
* makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy,
* completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents
* that its use would not infringe privately owned rights.
*/
package com.aparapi.examples.matrix;
import com.aparapi.Kernel.EXECUTION_MODE;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.lucene.util.OpenBitSet;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Random;
/**
* This test class performs the following functions:
*
* 1) Create a randomly populated set of matrices for correlation/co-occurrence computation
* 2) Execute the CPU-based computation using Lucene OpenBitSets
* 3) Execute the GPU-based computation using Aparapi CorrMatrix host and kernel
* 4) Verify the results of OpenBitSet and CorrMatrix by comparing matrices to each other
*
* @author ryan.lamothe at gmail.com
*
*/
public class Main {
/**
* NumTerms and NumLongs (documents) need to be adjusted manually right now to force 'striping' to occur (see Host code for details)
*/
public static void main(String[] _args) {
final List<Pair<OpenBitSet, OpenBitSet>> obsPairs = new ArrayList<Pair<OpenBitSet, OpenBitSet>>();
;
final Random rand = new Random();
int[][] obsResultMatrix;
/*
* Populate test data
*/
System.out.println("----------");
System.out.println("Populating test matrix data using settings from build.xml...");
System.out.println("----------");
final int numTerms = Integer.getInteger("numRows", 300); // # Rows
// numLongs*64 for number of actual documents since these are 'packed' longs
final int numLongs = Integer.getInteger("numColumns", 10000); // # Columns
for (int i = 0; i < numTerms; ++i) {
final long[] bits = new long[numLongs];
for (int j = 0; j < numLongs; ++j) {
bits[j] = rand.nextLong();
}
obsPairs.add(i, new ImmutablePair<OpenBitSet, OpenBitSet>(new OpenBitSet(bits, numLongs), new OpenBitSet(bits, numLongs)));
}
/*
* OpenBitSet calculations
*/
System.out.println("Executing OpenBitSet intersectionCount");
final long startTime = System.currentTimeMillis();
obsResultMatrix = new int[obsPairs.size()][obsPairs.size()];
// This is an N^2 comparison loop
// FIXME This entire loop needs to be parallelized to show an apples-to-apples comparison to Aparapi
for (int i = 0; i < obsPairs.size(); i++) {
final Pair<OpenBitSet, OpenBitSet> docFreqVector1 = obsPairs.get(i);
for (int j = 0; j < obsPairs.size(); j++) {
final Pair<OpenBitSet, OpenBitSet> docFreqVector2 = obsPairs.get(j);
// # of matches in both sets of documents
final int result = (int) OpenBitSet.intersectionCount(docFreqVector1.getLeft(), docFreqVector2.getRight());
obsResultMatrix[i][j] = result;
}
}
final long endTime = System.currentTimeMillis() - startTime;
System.out.println("OpenBitSet Gross Execution Time: " + endTime + " ms <------OpenBitSet");
System.out.println("----------");
/*
* GPU calculations
*/
System.out.println("Executing Aparapi intersectionCount");
final long[][] matrixA = new long[obsPairs.size()][];
final long[][] matrixB = new long[obsPairs.size()][];
// Convert OpenBitSet pairs to long primitive arrays for use with Aparapi
// TODO It would be nice if we could find a way to put the obsPairs onto the GPU directly :)
for (int i = 0; i < obsPairs.size(); i++) {
final OpenBitSet obsA = obsPairs.get(i).getLeft();
final OpenBitSet obsB = obsPairs.get(i).getRight();
matrixA[i] = obsA.getBits();
matrixB[i] = obsB.getBits();
}
// The reason for setting this property is because the CorrMatrix host/kernel code
// came from a GUI where a user could select "Use Hardware Acceleration" instead
// of the application forcing the setting globally on the command-line
final int[][] gpuResultMatrix;
gpuResultMatrix = CorrMatrixHost.intersectionMatrix(matrixA, matrixB, EXECUTION_MODE.GPU);
// Compare the two result arrays to make sure we are generating the same output
System.out.println("[i][j] -> OpenBitSet Result : GPU Result Array");
for (int i = 0; i < obsResultMatrix.length; i++) {
for (int j = 0; j < obsResultMatrix[i].length; j++)
if (obsResultMatrix[i][j] != gpuResultMatrix[i][j]) {
System.out.println("[" + i + "][" + j + "] -> " + obsResultMatrix[i][j] + " : " + gpuResultMatrix[i][j]);
}
}
System.out.println("Any elements not listed matched!");
}
}
src/main/resources/log4j.properties 0 → 100644
View file @ a68be997
# Root logger option
log4j.rootLogger=DEBUG, stdout
# Direct log messages to stdout
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
log4j.appender.stdout.Target=System.out
log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
\ No newline at end of file
examples/correlation-matrix/src/test/gov/pnnl/aparapi/test/CorrMatrixTest.java → src/test/java/com/aparapi/examples/matrix/CorrMatrixTest.java
View file @ a68be997
/**
* Copyright (c) 2016 - 2017 Syncleus, Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/**
* This material was prepared as an account of work sponsored by an agency of the United States Government.
* Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of
......@@ -6,9 +21,7 @@
* completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents
* that its use would not infringe privately owned rights.
*/
package gov.pnnl.aparapi.test;
import gov.pnnl.aparapi.matrix.CorrMatrixHost;
package com.aparapi.examples.matrix;
import java.io.File;
import java.io.PrintWriter;
......@@ -29,12 +42,12 @@ import com.aparapi.Kernel.EXECUTION_MODE;
/**
* This test class performs the following functions:
*
*
* 1) Create a randomly populated set of matrices for correlation/co-occurrence computation
* 2) Execute the CPU-based computation using Lucene OpenBitSets
* 3) Execute the GPU-based computation using Aparapi CorrMatrix host and kernel
* 4) Verify the results of OpenBitSet and CorrMatrix by comparing matrices to each other
*
*
* @author ryan.lamothe at gmail.com
*
*/
......@@ -126,11 +139,7 @@ public class CorrMatrixTest {
// came from a GUI where a user could select "Use Hardware Acceleration" instead
// of the application forcing the setting globally on the command-line
final int[][] gpuResultMatrix;
if (Boolean.getBoolean("useGPU")) {
gpuResultMatrix = CorrMatrixHost.intersectionMatrix(matrixA, matrixB, EXECUTION_MODE.GPU);
} else {
gpuResultMatrix = CorrMatrixHost.intersectionMatrix(matrixA, matrixB, EXECUTION_MODE.CPU);
}
gpuResultMatrix = CorrMatrixHost.intersectionMatrix(matrixA, matrixB, EXECUTION_MODE.GPU);
// Compare the two result arrays to make sure we are generating the same output
for (int i = 0; i < obsResultMatrix.length; i++) {
......
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