libsmatrix 0.0.1

data/src/Makefile.in

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+# This file is part of the "libsmatrix" project
+#   (c) 2011-2013 Paul Asmuth <paul@paulasmuth.com>
+#
+# Licensed under the MIT License (the "License"); you may not use this
+# file except in compliance with the License. You may obtain a copy of
+# the License at: http://opensource.org/licenses/MIT
+
+UNAME        = $(shell uname)
+SHELL        = /bin/sh
+CC           = clang
+CFLAGS      ?= -Wall -Wextra -O3 -march=native -mtune=native -D NDEBUG -fPIC
+LDFLAGS      = -lpthread -lm
+PREFIX       = $(DESTDIR)/usr/local
+LIBDIR       = $(PREFIX)/lib
+
+LIBFLAGS   = -shared
+LIBEXT     = so
+
+ifeq ($(UNAME), Darwin)
+LIBFLAGS   = -dynamic -bundle
+LIBEXT     = bundle
+endif

data/src/java/Makefile

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+# This file is part of the "libsmatrix" project
+#   (c) 2011-2013 Paul Asmuth <paul@paulasmuth.com>
+#
+# Licensed under the MIT License (the "License"); you may not use this
+# file except in compliance with the License. You may obtain a copy of
+# the License at: http://opensource.org/licenses/MIT
+
+include ../Makefile.in
+
+TARGET     = smatrix_java.$(LIBEXT)
+
+ifeq ($(UNAME), Darwin)
+JNI_FLAGS  = -I /System/Library/Frameworks/JavaVM.framework/Headers -I /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Headers
+endif
+ifeq ($(UNAME), Linux)
+JNI_FLAGS  = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
+endif
+
+all: $(TARGET)
+	mvn package
+
+$(TARGET): ../smatrix.o ../smatrix_jni.c ../smatrix_jni.h
+	$(CC) $(JNI_FLAGS) $(LIBFLAGS) $(LDFLAGS) ../smatrix_jni.c ../smatrix.o -o $(TARGET)
+ifeq ($(UNAME), Darwin)
+	ln -s $(TARGET) smatrix_java.so
+endif
+
+../smatrix.o:
+	cd .. && make
+
+test: $(TARGET)
+	javac -classpath . test/TestSparseMatrix.java
+	java -Djava.library.path=./ -classpath .:./test TestSparseMatrix
+
+.PHONY: test

data/src/java/com/paulasmuth/libsmatrix/SparseMatrix.java

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+/**
+ * This file is part of the "libsmatrix" project
+ *   (c) 2011-2013 Paul Asmuth <paul@paulasmuth.com>
+ *
+ * Licensed under the MIT License (the "License"); you may not use this
+ * file except in compliance with the License. You may obtain a copy of
+ * the License at: http://opensource.org/licenses/MIT
+ */
+package com.paulasmuth.libsmatrix;
+import java.io.File;
+import java.util.SortedMap;
+import java.util.concurrent.ConcurrentSkipListMap;
+
+/**
+ * A libsmatrix sparse matrix
+ */
+public class SparseMatrix {
+  private static String library_path = null;
+  private String filename = null;
+  private long ptr;
+
+  /**
+   * Create a new sparse matrix that will be stored in main memory only.
+   *
+   * @param file_path path to the file or null
+   * @return a new SparseMatrix
+   */
+  public SparseMatrix() {
+    SparseMatrix.loadLibrary();
+    init(null);
+  }
+
+  /**
+   * Create a new sparse matrix that will be persisted to disk. A cache of the
+   * data is still kept in main memory (the cache size can be adjusted by calling
+   * setCacheSize on the instance). 
+   *
+   * If the file pointed to by filename exists it will be opened, otherwise a new
+   * file will be created.
+   *
+   * @param file_path path to the file
+   * @return a new SparseMatrix
+   */
+  public SparseMatrix(String file_path) {
+    SparseMatrix.loadLibrary();
+    filename = file_path;
+    init(file_path);
+  }
+
+  /**
+   * Explcitly set the path to the native shared object (libsmatrix.so).
+   *
+   * @param the path to the native shared object
+   */
+  public static void setLibraryPath(String path) {
+    library_path = path;
+    loadLibrary();
+  }
+
+  /**
+   * HERE BE DRAGONS
+   */
+  public String getFilename() {
+    return filename;
+  }
+
+  /**
+   * HERE BE DRAGONS
+   */
+  public native int get(int x, int y);
+
+  /**
+   * HERE BE DRAGONS
+   */
+  public native void set(int x, int y, int val);
+
+  /**
+   * HERE BE DRAGONS
+   */
+  public native void incr(int x, int y, int val);
+
+  /**
+   * HERE BE DRAGONS
+   */
+  public native void decr(int x, int y, int val);
+
+  /**
+   * HERE BE DRAGONS
+   */
+  public native int getRowLength(int x);
+
+  /**
+   * HERE BE DRAGONS
+   */
+  public SortedMap<Integer,Integer> getRow(int x) {
+    return getRow(x, 0);
+  }
+
+  /**
+   * HERE BE DRAGONS
+   */
+  public SortedMap<Integer,Integer> getRow(int x, int maxlen) {
+    SortedMap<Integer, Integer> map = new ConcurrentSkipListMap<Integer, Integer>() {
+      public void putIntTuple(int k, int v) {
+        this.put(k, v);
+      }
+    };
+
+    getRowNative(x, map, maxlen);
+
+    return map;
+  }
+
+  /**
+   * Close this matrix. Calling any other method on the instance after it was
+   * closed will throw an exception.
+   */
+  public native void close();
+
+  /**
+   * HERE BE DRAGONS
+   */
+  private native void getRowNative(int x, SortedMap<Integer,Integer> map, int maxlen);
+
+  /**
+   * Load the native shared object (libsmatrix.so)
+   */
+  private static void loadLibrary() {
+    if (library_path != null) {
+      File libfile = new File(library_path);
+
+      if (libfile.exists()) {
+        System.load(libfile.getAbsolutePath());
+        return;
+      }
+    }
+
+    System.loadLibrary("smatrix");
+  }
+
+  /**
+   * Initialize a new native matrix
+   */
+  private native void init(String file_path);
+
+}

data/src/java/pom.xml

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+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <name>libsmatrix sparse matrix</name>
+  <url>http://github.com/paulasmuth/libsmatrix</url>
+  <groupId>com.paulasmuth.libsmatrix</groupId>
+  <artifactId>libsmatrix</artifactId>
+  <version>0.3-SNAPSHOT</version>
+  <packaging>jar</packaging>
+
+  <build>
+    <sourceDirectory>src/java</sourceDirectory>
+
+    <plugins>
+      <plugin>
+        <groupId>com.github.github</groupId>
+        <artifactId>site-maven-plugin</artifactId>
+        <version>0.8</version>
+        <!--
+          put this into ~/.m2/settings.xml:
+
+          <settings>
+            <servers>
+              <server>
+                <id>github</id>
+                <username>USERNAME</username>
+                <password>PASSWORD</password>
+              </server>
+            </servers>
+          </settings>
+        -->
+        <configuration>
+            <message>Maven artifacts for ${project.version}</message> 
+            <noJekyll>true</noJekyll>
+            <outputDirectory>${project.build.directory}/mvn-repo</outputDirectory>
+            <branch>refs/heads/mvn-repo</branch>
+            <includes><include>**/*</include></includes>
+            <repositoryName>libsmatrix</repositoryName>
+            <repositoryOwner>paulasmuth</repositoryOwner>
+        </configuration>
+        <executions>
+          <execution>
+            <goals>
+              <goal>site</goal>
+            </goals>
+            <phase>deploy</phase>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+
+  <distributionManagement>
+    <repository>
+      <id>internal.repo</id>
+      <name>Temporary Staging Repository</name>
+      <url>file://${project.build.directory}/mvn-repo</url>
+      <uniqueVersion>false</uniqueVersion>
+    </repository>
+  </distributionManagement>
+
+  <properties>
+    <!-- github server corresponds to entry in ~/.m2/settings.xml -->
+    <github.global.server>github</github.global.server>
+  </properties>
+
+</project>

data/src/java/test/TestSparseMatrix.java

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+/**
+ * This file is part of the "libsmatrix" project
+ *   (c) 2011-2013 Paul Asmuth <paul@paulasmuth.com>
+ *
+ * Licensed under the MIT License (the "License"); you may not use this
+ * file except in compliance with the License. You may obtain a copy of
+ * the License at: http://opensource.org/licenses/MIT
+ */
+import java.util.LinkedList;
+import java.util.Iterator;
+import java.util.SortedMap;
+import com.paulasmuth.libsmatrix.SparseMatrix;
+
+interface TestCase {
+  public String getName();
+  public boolean run(SparseMatrix smx);
+}
+
+class TestSparseMatrix {
+  static LinkedList<TestCase> testCases = new LinkedList<TestCase>();
+
+  static { testCases.add(new TestCase() {
+    public String getName() {
+      return "simple set/get";
+    }
+    public boolean run(SparseMatrix smx) {
+      smx.set(42,23,17);
+      return smx.get(42,23) == 17;
+    }
+  }); }
+
+  static { testCases.add(new TestCase() {
+    public String getName() {
+      return "simple increment 1";
+    }
+    public boolean run(SparseMatrix smx) {
+      smx.set(4231,2634,0);
+      smx.incr(4231,2634,1);
+      return smx.get(4231,2634) == 1;
+    }
+  }); }
+
+  static { testCases.add(new TestCase() {
+    public String getName() {
+      return "simple increment 5";
+    }
+    public boolean run(SparseMatrix smx) {
+      smx.set(1231,2634,0);
+      smx.incr(1231,2634,1);
+      smx.incr(1231,2634,5);
+      return smx.get(1231,2634) == 6;
+    }
+  }); }
+
+  static { testCases.add(new TestCase() {
+    public String getName() {
+      return "1 million increments + 1 million gets";
+    }
+    public boolean run(SparseMatrix smx) {
+      int v = 34;
+      int i;
+      int n;
+
+      for (n = 0; n < 1000; n++) {
+        for (i = 0; i < 1000; i++) {
+          smx.set(i, n, v);
+        }
+      }
+
+      for (n = 0; n < 1000; n++) {
+        for (i = 0; i < 1000; i++) {
+          if ((smx.get(i, n) != v)) {
+            return false;
+          }
+        }
+      }
+
+      return true;
+    }
+  }); }
+
+  static { testCases.add(new TestCase() {
+    public String getName() {
+      return "1000 increments + getRowLength()";
+    }
+    public boolean run(SparseMatrix smx) {
+      int i = 0;
+      int n = 42;
+
+      for (i = 0; i < 1000; i++) {
+        smx.incr(i, n, 1);
+      }
+
+      return smx.getRowLength(n) == 1000;
+    }
+  }); }
+
+  static { testCases.add(new TestCase() {
+    public String getName() {
+      return "1000 increments + getRow()";
+    }
+    public boolean run(SparseMatrix smx) {
+      int i = 0;
+      int n = 85;
+
+      for (i = 0; i < 1000; i++) {
+        smx.incr(i, n, 1);
+      }
+
+      SortedMap<Integer, Integer> row = smx.getRow(n);
+
+      return row.size() == 1000;
+    }
+  }); }
+
+  static { testCases.add(new TestCase() {
+    public String getName() {
+      return "1000 increments + getRow() with maxlen";
+    }
+    public boolean run(SparseMatrix smx) {
+      int i = 0;
+      int n = 83;
+
+      for (i = 0; i < 1000; i++) {
+        smx.incr(i, n, 1);
+      }
+
+      SortedMap<Integer, Integer> row = smx.getRow(n, 230);
+      return row.size() == 230;
+    }
+  }); }
+
+  static { testCases.add(new TestCase() {
+    public String getName() {
+      return "1 million increments; close; 1 million gets";
+    }
+    public boolean run(SparseMatrix smx1) {
+      if (smx1.getFilename() == null) {
+        return true;
+      }
+
+      int v = 123;
+      int i;
+      int n;
+
+      for (n = 0; n < 1000; n++) {
+        for (i = 0; i < 1000; i++) {
+          smx1.set(i, n, v);
+        }
+      }
+
+      SparseMatrix smx2 = new SparseMatrix("/tmp/fnord.smx");
+
+      for (n = 0; n < 1000; n++) {
+        for (i = 0; i < 1000; i++) {
+          if ((smx2.get(i, n) != v)) {
+            smx2.close();
+            return false;
+          }
+        }
+      }
+
+      smx2.close();
+      return true;
+    }
+  }); }
+
+  public static void main(String[] opts) {
+    boolean success = true;
+    SparseMatrix.setLibraryPath("./smatrix_java.so");
+
+    SparseMatrix smx1 = new SparseMatrix();
+    success &= run_tests(smx1);
+    smx1.close();
+
+    SparseMatrix smx2 = new SparseMatrix("/tmp/fnord.smx");
+    success &= run_tests(smx2);
+    smx2.close();
+
+    if (success) {
+      System.out.println("\033[1;32mAll tests finished successfully :)\033[0m");
+      System.exit(0);
+    } else {
+      System.out.println("\033[1;31mTests failed :(\033[0m");
+      System.exit(1);
+    }
+  }
+
+  public static boolean run_tests(SparseMatrix smx) {
+    boolean success = true;
+    Iterator iter = testCases.iterator();
+
+    while (iter.hasNext()) {
+      TestCase testcase = (TestCase) iter.next();
+
+      if (testcase.run(smx)) {
+        System.out.println("\033[1;32m[SUCCESS] " + testcase.getName() + "\033[0m");
+      } else {
+        System.out.println("\033[1;31m[FAILED] "  + testcase.getName() + "\033[0m");
+        success = false;
+      }
+    }
+
+    return success;
+  }
+
+}