[WIP] [AMLS] shortest path

scripts/builtin/shortestPath.dml

@@ -0,0 +1,98 @@
+#-------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you 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.
+#
+#-------------------------------------------------------------
+#
+# Computes the minimum distances (shortest-path) between a single 
+# source vertex and every other vertex in the graph.
+# 
+# Grzegorz Malewicz, Matthew H. Austern, Aart J. C. Bilk, 
+# James C. Dehnert, Ikkan Horn, Naty Leiser and Grzegorz Czajkowski:
+# Pregel: A System for Large-Scale Graph Processing
+#
+#------------------------------------------------------------------------------
+#
+#G           Input matrix (double), adjacency matrix of the labeled graph:
+#	     - Such graph can be directed (G is symmetric) or undirected 
+#	     (G is not symmetric).
+#	     - The values of G can be 0/1 (just specifying whether the nodes are
+#	     connected or not) or integer values (representing the weight of the edjes
+#	     or the distances between nodes, 0 if not connected).
+#
+#sourceNode  node index to calculate the shortest paths to all other nodes.
+#
+#maxi        max number of iterations accepted (0 for FALSE, i.e. max number of iterations
+#	     not defined)
+#
+#verbose     flag for verbose debug output 	
+#------------------------------------------------------------------------------
+#
+#C           Output matrix (double) of minimum distances (shortest-path) between vertices:
+#            - The value of the ith row and the jth column of the output matrix is 
+#            the minimum distance shortest-path from vertex i to vertex j.
+#            - When the value of the minimum distance is infinity, the two nodes are not
+#            connected.
+#------------------------------------------------------------------------------
+
+
+m_shortestPath = function(Matrix[Double] G, Integer maxi = 0, Integer sourceNode, Boolean verbose = FALSE) 
+  return (Matrix[Double] C) 
+{	
+  if(verbose) {
+    print("SHORTEST PATH CALCULATION");
+  }
+
+  if(min(G) < 0){
+    stop("All values in G must be positive")
+  }
+
+  if(ncol(G) != nrow(G)){
+    stop("Not correct matrix dimensions")
+  }
+
+  matrixSize = nrow(G)
+
+  G = replace(target=G, pattern=0, replacement=Inf)
+
+  # initialize the matrix of minimum distances with "infinity" values:
+  minDistVector = matrix(Inf,rows=matrixSize,cols=1)
+
+  # update minimum distance from the sourceNode to itself to 0:
+  minDistVector[sourceNode,1] = 0
+
+  iter = 1
+  diff = Inf;
+  while( diff > 0 & (maxi==0 | iter<=maxi) ) {
+    w = t(colMins(G + minDistVector))
+    u = min(w, minDistVector);
+    diff = sum(u != minDistVector)
+    minDistVector = u; # update assignment
+    if( verbose ){
+      print("Shortest Path: iter = "+iter+", #diff = "+diff);
+    }
+    iter = iter + 1;
+  }
+
+  C=minDistVector
+  if(verbose) {
+    print("SHORTEST PATH CALCULATION FINISHED, CHECK OUTPUT MATRIX OF MINIMUM DISTANCES:");
+    print(toString(C))
+  }		
+}
+

src/main/java/org/apache/sysds/common/Builtins.java

@@ -217,6 +217,7 @@ public enum Builtins {
 	SEQ("seq", false),
 	SHERLOCK("sherlock", true),
 	SHERLOCKPREDICT("sherlockPredict", true),
+	SHORTESTPATH("shortestPath", true),
 	SIGMOID("sigmoid", true),   // 1 / (1 + exp(-X))
 	SIGN("sign", false),
 	SIN("sin", false),

src/test/java/org/apache/sysds/test/functions/builtin/BuiltinShortestPathTest.java

@@ -0,0 +1,86 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 org.apache.sysds.test.functions.builtin;
+
+import java.util.HashMap;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import org.apache.sysds.common.Types;
+import org.apache.sysds.lops.LopProperties;
+import org.apache.sysds.runtime.matrix.data.MatrixValue;
+import org.apache.sysds.test.AutomatedTestBase;
+import org.apache.sysds.test.TestConfiguration;
+import org.apache.sysds.test.TestUtils;
+
+public class BuiltinShortestPathTest extends AutomatedTestBase {
+	private final static String TEST_NAME = "shortestPathTest";
+	private final static String TEST_DIR = "functions/builtin/";
+	private static final String TEST_CLASS_DIR = TEST_DIR + BuiltinShortestPathTest.class.getSimpleName() + "/";
+	private final static double eps = 1e-10;
+
+	@Override
+	public void setUp() {
+		TestUtils.clearAssertionInformation();
+		addTestConfiguration(TEST_NAME,new TestConfiguration(TEST_CLASS_DIR, TEST_NAME,new String[]{"r"}));
+	}
+
+	@Test
+	public void testShortestPathNode1CP() {
+		runShortestPathNodeTest(1, new double[][] {{0}, {2}, {5}, {5}});
+	}
+
+	@Test
+	public void testShortestPathNode2CP() {
+		runShortestPathNodeTest(2, new double[][] {{1}, {0}, {4}, {5}});
+	}
+
+	@Test
+	public void testShortestPathNode3CP() {
+		runShortestPathNodeTest(3, new double[][] {{4}, {3}, {0}, {1}});
+	}
+
+
+
+	private void runShortestPathNodeTest(int node, double [][] Res)
+	{
+		loadTestConfiguration(getTestConfiguration(TEST_NAME));
+
+		String HOME = SCRIPT_DIR + TEST_DIR;
+		fullDMLScriptName = HOME + TEST_NAME + ".dml";
+		programArgs = new String[]{ "-args",
+			input("X"), String.valueOf(node), output("R")};
+
+		double[][] X = {{0, 2, 5, 5 }, 
+						{1, 0, 4, 10}, 
+						{0, 3, 0, 1 },
+						{3, 2, 0, 0 }};
+
+		writeInputMatrixWithMTD("X", X, true);
+
+		runTest(true, false, null, -1);
+
+		HashMap<MatrixValue.CellIndex, Double> dmlfile = readDMLMatrixFromOutputDir("R");
+		double[][] Y = TestUtils.convertHashMapToDoubleArray(dmlfile);
+		TestUtils.compareMatrices(Res, Y, eps);
+
+	}
+}

src/test/scripts/functions/builtin/shortestPathTest.dml

@@ -0,0 +1,26 @@
+
+#-------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you 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.
+#
+#-------------------------------------------------------------
+
+X = read($1)
+C = shortestPath(G=X,sourceNode = $2)
+
+write(C, $3)