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Commit 6fa1b264 authored by Alexander David Hellwig's avatar Alexander David Hellwig
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Merge branch 'ML_clustering' of... 

Merge branch 'ML_clustering' of https://git.rwth-aachen.de/monticore/EmbeddedMontiArc/generators/EMAM2Middleware into ML_clustering
parents aebebd66 7280b84a
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.circleci/config.yml deleted 100644 → 0
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# Java Maven CircleCI 2.0 configuration file
#
# Check https://circleci.com/docs/2.0/language-java/ for more details
#
version: 2
general:
branches:
ignore:
- gh-pages
jobs:
build:
docker:
# specify the version you desire here
- image: circleci/openjdk:8-jdk
cmd: ["/bin/bash"]
# Specify service dependencies here if necessary
# CircleCI maintains a library of pre-built images
# documented at https://circleci.com/docs/2.0/circleci-images/
# - image: circleci/postgres:9.4
working_directory: ~/repo
environment:
# Customize the JVM maximum heap limit
- MAVEN_OPTS: -Xmx3200m
- ES_JAVA_OPTS=-Xms3200m -Xmx3200m
steps:
- checkout
# run tests!
- run: mvn -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=warn -B clean install --settings "settings.xml"
workflows:
version: 2
commit-workflow:
jobs:
- build
scheduled-workflow:
triggers:
- schedule:
cron: "30 1 * * *"
filters:
branches:
only: master
jobs:
- build
.travis.yml deleted 100644 → 0
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script:
- mvn -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=warn -B clean install cobertura:cobertura org.eluder.coveralls:coveralls-maven-plugin:report --settings "settings.xml"
after_success:
- if [ "${TRAVIS_BRANCH}" == "master" ]; then mvn -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=warn -B deploy --debug --settings "./settings.xml"; fi
README.md
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......@@ -5,7 +5,7 @@
This generator takes an EMAM or EMADL model and connects it to a middleware library. If all Ports of two connected Components are marked as middleware Ports, the generator will create 2 executables that can be deployed on different machines.
All communication of these 2 Components will then be tunneled trough the specified middleware:
![MiddlewareAdapter](/uploads/6e9c69e6b56554579551769174df3697/MiddlewareAdapter.png)
It also supports automatic clustering of the subcomponents to deploy on different machines.
## Writing your own Middleware Generator
see [TUTORIAL_ADD_MIDDLEWARE.md](https://git.rwth-aachen.de/monticore/EmbeddedMontiArc/generators/EMAM2Middleware/blob/master/TUTORIAL_ADD_MIDDLEWARE.md)
......@@ -215,21 +215,4 @@ Look at [GenerationTest::testDistributedTargetGenerator](https://git.rwth-aachen
1. If the project was created by a MiddlewareGenerator, run the executable(s) at build/coordinator(/<subcomp.name>)/Coordinator_<(sub)component.name>
2.
## Automatic Clustering
To simplify the creation of distributed systems, the generator can automatically split the model into a given number of clusters.
Supported:
* Spectral Clustering
* ...
Procedure:
* Convert the Symbol Table of a Component into a adjacency matrix
* (Add costs given by type to matrix. E.g. float is cheaper than Matrix of floats)
* Feed into ml library(e.g. [smile ml](https://github.com/haifengl/smile)) with the selected clustering algorithm
* (Compare the result of different algorithms)
* Generate Middleware tags seperating the clusters
* Feed into existing manual clustering architecture
* (generate)
pom.xml
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......@@ -24,6 +24,7 @@
<Embedded-montiarc-math-roscpp-generator.version>0.1.1-SNAPSHOT</Embedded-montiarc-math-roscpp-generator.version>
<EMADL.version>0.2.4</EMADL.version>
<EMADL2CPP.version>0.2.6-SNAPSHOT</EMADL2CPP.version>
<embedded-montiarc-component-clustering.version>0.0.1-SNAPSHOT</embedded-montiarc-component-clustering.version>
<!-- .. Libraries .................................................. -->
<guava.version>18.0</guava.version>
......@@ -64,36 +65,12 @@
<version>${gson.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge</groupId>
<artifactId>javaml</artifactId>
<version>0.1.5</version>
</dependency>
<!--dependency>
<groupId>be.abeel</groupId>
<artifactId>ajt</artifactId>
<version>2.9</version>
</dependency-->
<dependency>
<groupId>com.github.haifengl</groupId>
<artifactId>smile-core</artifactId>
<version>1.5.2</version>
</dependency>
<dependency>
<groupId>com.github.haifengl</groupId>
<artifactId>smile-plot</artifactId>
<version>1.5.2</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
<!--<dependency>
<groupId>com.clust4j</groupId>
<artifactId>clust4j</artifactId>
<version>1.2.4-SNAPSHOT</version>
</dependency>-->
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-core</artifactId>
......@@ -128,13 +105,6 @@
<version>${Embedded-montiarc-math-roscpp-generator.version}</version>
</dependency>
<dependency>
<groupId>org.graphstream</groupId>
<artifactId>gs-core</artifactId>
<version>1.3</version>
<optional>false</optional>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math</artifactId>
......@@ -154,6 +124,12 @@
<version>${EMADL2CPP.version}</version>
</dependency>
<dependency>
<groupId>de.monticore.lang.monticar</groupId>
<artifactId>embedded-montiarc-component-clustering</artifactId>
<version>${embedded-montiarc-component-clustering.version}</version>
</dependency>
<!-- MontiCore Dependencies -->
<dependency>
<groupId>de.se_rwth.commons</groupId>
......@@ -183,16 +159,6 @@
</dependencies>
<repositories>
<repository>
<id>java-ds</id>
<!--
<url>https://raw.githubusercontent.com/alexeygrigorev/maven-repo/master/</url>
-->
<url>https://raw.githubusercontent.com/mgbeyer/maven-repo/master/</url>
</repository>
</repositories>
<!-- == PROJECT BUILD SETTINGS =========================================== -->
<build>
......
src/main/java/com/clust4j/Clust4j.java deleted 100644 → 0
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/*******************************************************************************
* Copyright 2015, 2016 Taylor G Smith
*
* 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.
*******************************************************************************/
package com.clust4j;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
/**
* The absolute super type for all clust4j objects (models and datasets)
* that should be able to commonly serialize their data.
* @author Taylor G Smith
*/
public abstract class Clust4j implements java.io.Serializable {
private static final long serialVersionUID = -4522135376738501625L;
/**
* Load a model from a FileInputStream
* @param fos
* @return
* @throws IOException
* @throws ClassNotFoundException
*/
public static Clust4j loadObject(final FileInputStream fis) throws IOException, ClassNotFoundException {
ObjectInputStream in = null;
Clust4j bm = null;
try {
in = new ObjectInputStream(fis);
bm = (Clust4j) in.readObject();
} finally {
if(null != in)
in.close();
fis.close();
}
return bm;
}
/**
* Save a model to FileOutputStream
* @param fos
* @throws IOException
*/
public void saveObject(final FileOutputStream fos) throws IOException {
ObjectOutputStream out = null;
try {
out = new ObjectOutputStream(fos);
out.writeObject(this);
} finally {
if(null != out)
out.close();
fos.close();
}
}
}
src/main/java/com/clust4j/GlobalState.java deleted 100644 → 0
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/*******************************************************************************
* Copyright 2015, 2016 Taylor G Smith
*
* 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.
*******************************************************************************/
package com.clust4j;
import java.util.Random;
import java.util.concurrent.ForkJoinPool;
import org.apache.commons.math3.util.FastMath;
/**
* A set of global config values used in multiple classes. Some values may
* be set to the user's preference, while others are final.
*
* @author Taylor G Smith
*/
public abstract class GlobalState {
/** The default random state */
public final static Random DEFAULT_RANDOM_STATE = new Random(999);
public final static int MAX_ARRAY_SIZE = 25_000_000;
/**
* Holds static mathematical values
* @author Taylor G Smith
*/
public static abstract class Mathematics {
/** Double.MIN_VALUE is not negative; this is */
public final static double SIGNED_MIN = Double.NEGATIVE_INFINITY;
public final static double MAX = Double.POSITIVE_INFINITY;
public final static double TINY = 2.2250738585072014e-308;
public final static double EPS = 2.2204460492503131e-16;
/*===== Gamma function assistants =====*/
public final static double LOG_PI = FastMath.log(Math.PI);
public final static double LOG_2PI = FastMath.log(2 * Math.PI);
public final static double ROOT_2PI= FastMath.sqrt(2 * Math.PI);
/** Euler's Gamma constant */
public final static double GAMMA = 0.577215664901532860606512090;
public final static double HALF_LOG2_PI = 0.91893853320467274178032973640562;
final static double[] GAMMA_BOUNDS = new double[]{0.001, 12.0};
final static double HIGH_BOUND = 171.624;
/** numerator coefficients for approximation over the interval (1,2) */
private final static double[] p = new double[]{
-1.71618513886549492533811E+0,
2.47656508055759199108314E+1,
-3.79804256470945635097577E+2,
6.29331155312818442661052E+2,
8.66966202790413211295064E+2,
-3.14512729688483675254357E+4,
-3.61444134186911729807069E+4,
6.64561438202405440627855E+4
};
/** denominator coefficients for approximation over the interval (1,2) */
private final static double[] q = new double[]{
-3.08402300119738975254353E+1,
3.15350626979604161529144E+2,
-1.01515636749021914166146E+3,
-3.10777167157231109440444E+3,
2.25381184209801510330112E+4,
4.75584627752788110767815E+3,
-1.34659959864969306392456E+5,
-1.15132259675553483497211E+5
};
/**
* Abramowitz and Stegun 6.1.41
* Asymptotic series should be good to at least 11 or 12 figures
* For error analysis, see Whittiker and Watson
* A Course in Modern Analysis (1927), page 252
*/
private final static double[] c = new double[]{
1.0/12.0,
-1.0/360.0,
1.0/1260.0,
-1.0/1680.0,
1.0/1188.0,
-691.0/360360.0,
1.0/156.0,
-3617.0/122400.0
};
// Any assertion failures will cause exception to be thrown right away
static {
// These should never change
assert GAMMA_BOUNDS.length == 2;
assert p.length == 8;
assert p.length == q.length;
assert c.length == p.length;
}
/**
* Adapted from sklearn_gamma, which was in turn adapted from
* John D. Cook's public domain version of lgamma, from
* http://www.johndcook.com/stand_alone_code.html
* @param x
* @return
*/
public static double gamma(double x) {
if(x <= 0)
throw new IllegalArgumentException("x must exceed 0");
// Check if in first boundary
int boundaryIdx = 0;
if(x < GAMMA_BOUNDS[boundaryIdx++])
return 1.0 / (x * (1.0 + GAMMA * x));
if(x < GAMMA_BOUNDS[boundaryIdx++]) {
double den = 1.0, num = 0.0, res, z, y = x;
int i, n = 0;
boolean lt1 = y < 1.0;
if(lt1)
y += 1.0;
else {
n = ((int)y) - 1;
y -= n;
}
z = y - 1;
for(i = 0; i < p.length; i++) {
num = (num + p[i]) * z;
den = den * z + q[i];
}
res = num/den + 1.0;
// Correction if arg was not initially in (1,2)
if(lt1)
res /= (y - 1.0);
else {
for(i = 0; i < n; i++, y++)
res *= y;
}
return res;
}
if(x > HIGH_BOUND)
return Double.POSITIVE_INFINITY;
return FastMath.exp(lgamma(x));
}
public static double lgamma(double x) {
if(x <= 0)
throw new IllegalArgumentException("x must exceed 0");
double z, sum;
int i;
if(x < GAMMA_BOUNDS[1])
return FastMath.log(FastMath.abs(gamma(x)));
z = 1.0/ (x * x);
sum = c[7];
for(i = 6; i >= 0; i--) {
sum *= z;
sum += c[i];
}
return (x - 0.5) * FastMath.log(x) - x + HALF_LOG2_PI + sum / x;
}
}
/**
* A class to hold configurations for parallelism
* @author Taylor G Smith
*/
public abstract static class ParallelismConf {
/**
* Matrices with number of elements exceeding this number
* will automatically trigger parallel events as supported
* in clustering methods.
*/
public static final int MIN_ELEMENTS = 15000;
/**
* The minimum number of cores to efficiently
* allow parallel operations.
*/
public static final int MIN_PARALLEL_CORES_RECOMMENDED = 8;
/**
* The minimum number of required cores to allow any
* parallelism at all.
*/
public static final int MIN_CORES_REQUIRED = 4;
/**
* The number of available cores on the machine. Used for determining
* whether or not to use parallelism & how large parallel chunks should be. */
public static final int NUM_CORES = Runtime.getRuntime().availableProcessors();
/**
* Whether to allow parallelism at all or quietly force serial jobs where necessary
*/
public static boolean PARALLELISM_ALLOWED = NUM_CORES >= MIN_CORES_REQUIRED;
/**
* Whether parallelization is recommended for this machine.
* Default value is true if availableProcessors is at least 8.
*/
public static final boolean PARALLELISM_RECOMMENDED = NUM_CORES >= MIN_PARALLEL_CORES_RECOMMENDED;
/** If true and the size of the vector exceeds {@value #MAX_SERIAL_VECTOR_LEN},
* auto schedules parallel job for applicable operations. This can slow
* things down on machines with a lower core count, but speed them up
* on machines with a higher core count. More heap space may be required.
* Defaults to {@link #PARALLELISM_RECOMMENDED}
*/
public static boolean ALLOW_AUTO_PARALLELISM = PARALLELISM_RECOMMENDED;
/**
* The global ForkJoin thread pool for parallel recursive tasks. */
final static public ForkJoinPool FJ_THREADPOOL = new ForkJoinPool();
/**
* The max length a vector may be before defaulting to a parallel process, if applicable */
static public int MAX_SERIAL_VECTOR_LEN = 10_000_000;
/**
* The max length a parallel-processed chunk may be */
public static int MAX_PARALLEL_CHUNK_SIZE = MAX_SERIAL_VECTOR_LEN / NUM_CORES; //2_500_000;
}
}
src/main/java/com/clust4j/LICENSE.txt deleted 100644 → 0
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Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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END OF TERMS AND CONDITIONS
src/main/java/com/clust4j/NamedEntity.java deleted 100644 → 0
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/*******************************************************************************
* Copyright 2015, 2016 Taylor G Smith
*
* 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.
*******************************************************************************/
package com.clust4j;
import com.clust4j.log.Loggable;
/**
*
* Models or any {@link Loggable}
* that should be able to "say their name" should
* implement this method.
*
* <p>Other considered names:
* <p><ul><tt>SelfProfessant</tt></ul>
* <p><ul><tt>Parrot</tt></ul>
* <p><ul><tt>EchoChamber</tt></ul>
*
* :-)
*
* <p>
* @author Taylor G Smith
*/
public interface NamedEntity {
public String getName();
}
src/main/java/com/clust4j/algo/AbstractAutonomousClusterer.java deleted 100644 → 0
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/*******************************************************************************
* Copyright 2015, 2016 Taylor G Smith
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.