modified algorithm for dfj style parallelism

diff --git a/Robust/src/Benchmarks/oooJava/DelaunayRefinement/DirectedEdgeGraph.java b/Robust/src/Benchmarks/oooJava/DelaunayRefinement/DirectedEdgeGraph.java
index 9bc02ff05e06d935e986ffd504431feb714df2aa..05c8057f696e11a334a8185d3a22d0eceae695d7 100644 (file)
--- a/Robust/src/Benchmarks/oooJava/DelaunayRefinement/DirectedEdgeGraph.java
+++ b/Robust/src/Benchmarks/oooJava/DelaunayRefinement/DirectedEdgeGraph.java
@@ -1,8 +1,8 @@
 public class DirectedEdgeGraph implements EdgeGraph {
 public class DirectedEdgeGraph implements EdgeGraph {

-  HashSet nodes;
+

   public DirectedEdgeGraph() {
     // nodes = Collections.synchronizedSet(new HashSet());
   public DirectedEdgeGraph() {
     // nodes = Collections.synchronizedSet(new HashSet());

-    nodes = new HashSet();
+    // nodes = new HashSet();

   }
 
   public boolean addEdge(Edge_d e) {
   }
 
   public boolean addEdge(Edge_d e) {


@@ -90,16 +90,18 @@ public class DirectedEdgeGraph implements EdgeGraph {
     return retval;
   }
 
     return retval;
   }
 

-  public Iterator iterator() {
-    return nodes.iterator();
-  }
+  //public Iterator iterator() {
+  //  return nodes.iterator();
+  //}

 
   public boolean addNode(Node n) {
 
   public boolean addNode(Node n) {

-    return nodes.add((EdgeGraphNode) n);
+    boolean notInAlready = !n.inGraph;
+    n.inGraph = true;
+    return notInAlready;

   }
 
   public boolean containsNode(Node n) {
   }
 
   public boolean containsNode(Node n) {

-    return nodes.contains(n);
+    return n.inGraph;

   }
 
   public Object getNodeData(Node n) {
   }
 
   public Object getNodeData(Node n) {


@@ -107,14 +109,14 @@ public class DirectedEdgeGraph implements EdgeGraph {
     return egn.data;
   }
 
     return egn.data;
   }
 

-  public int getNumNodes() {
-    return nodes.size();
-  }
+  //public int getNumNodes() {
+  //  return nodes.size();
+  //}

 
 

-  public Node getRandom() {
-    // return (Node)Sets.getAny(nodes);
-    return (Node) nodes.iterator().next();
-  }
+  //public Node getRandom() {
+  //  // return (Node)Sets.getAny(nodes);
+  //  return (Node) nodes.iterator().next();
+  //}

 
   public boolean hasNeighbor(Node src, Node dest) {
     EdgeGraphNode esrc = (EdgeGraphNode) src;
 
   public boolean hasNeighbor(Node src, Node dest) {
     EdgeGraphNode esrc = (EdgeGraphNode) src;


@@ -123,8 +125,9 @@ public class DirectedEdgeGraph implements EdgeGraph {
   }
 
   public boolean removeNode(Node n) {
   }
 
   public boolean removeNode(Node n) {

+    boolean wasIn = n.inGraph;

     removeConnectingEdges((EdgeGraphNode) n);
     removeConnectingEdges((EdgeGraphNode) n);

-    return nodes.remove(n);
+    return wasIn;

   }
 
   protected void removeConnectingEdges(EdgeGraphNode n) {
   }
 
   protected void removeConnectingEdges(EdgeGraphNode n) {

diff --git a/Robust/src/Benchmarks/oooJava/DelaunayRefinement/Node.java b/Robust/src/Benchmarks/oooJava/DelaunayRefinement/Node.java
index 5f71f4f86aa7bad3112f8729ecb360ea4b390b1c..68ac2f06fed860f267912479fa1d3199f5da3a52 100644 (file)
--- a/Robust/src/Benchmarks/oooJava/DelaunayRefinement/Node.java
+++ b/Robust/src/Benchmarks/oooJava/DelaunayRefinement/Node.java
@@ -1,5 +1,10 @@
 public class Node {
 public class Node {

+  public boolean inGraph;

   
   

+  public Node() {
+    inGraph = false;
+  }
+

   //None of the program actually uses getData/setData so I use leave Node as a 
   //wrapper interface.
 //  public abstract Object getData();
   //None of the program actually uses getData/setData so I use leave Node as a 
   //wrapper interface.
 //  public abstract Object getData();

diff --git a/Robust/src/Benchmarks/oooJava/DelaunayRefinement/SerialDelaunayRefinement.java b/Robust/src/Benchmarks/oooJava/DelaunayRefinement/SerialDelaunayRefinement.java
index 97be45cc1cc390d1f96c2159281cae401f56ea51..67d2eee4d191b06ca8fb854fc324a739c9f554e1 100644 (file)
--- a/Robust/src/Benchmarks/oooJava/DelaunayRefinement/SerialDelaunayRefinement.java
+++ b/Robust/src/Benchmarks/oooJava/DelaunayRefinement/SerialDelaunayRefinement.java
@@ -44,7 +44,9 @@ public class SerialDelaunayRefinement {
       if (runtime < mintime) {
         mintime = runtime;
       }
       if (runtime < mintime) {
         mintime = runtime;
       }

+      System.out.println( "Post-run garbage collection started..." );

       System.gc();
       System.gc();

+      System.out.println( "done gc" );

     }
 
     System.out.println("minimum runtime: " + mintime + " ms");
     }
 
     System.out.println("minimum runtime: " + mintime + " ms");


@@ -65,8 +67,8 @@ public class SerialDelaunayRefinement {
       System.out.println("http://iss.ices.utexas.edu/lonestar/delaunayrefinement.html");
       System.out.println();
     }
       System.out.println("http://iss.ices.utexas.edu/lonestar/delaunayrefinement.html");
       System.out.println();
     }

-    if (args.length < 1) {
-      System.out.println("Arguments: <input file> [verify]");
+    if (args.length < 2) {
+      System.out.println("Arguments: <input file> <num workers> [verify]");

       System.exit(-1);
     }
 
       System.exit(-1);
     }
 


@@ -75,115 +77,158 @@ public class SerialDelaunayRefinement {
     Mesh m = new Mesh();
     m.read(mesh, args[0]);
 
     Mesh m = new Mesh();
     m.read(mesh, args[0]);
 

-    //treat LinkedList as a stack
+    int numWorkers = Integer.parseInt( args[1] );
+

     Stack worklist = new Stack();
     Stack worklist = new Stack();

-    //    LinkedList worklist = new LinkedList();

 
 

-    // worklist.addAll(Mesh.getBad(mesh));
+    // REPLACE worklist.addAll(Mesh.getBad(mesh)); WITH...

     HashMapIterator it = m.getBad(mesh).iterator();
     while (it.hasNext()) {
       worklist.push(it.next());
     }
     
     if (isFirstRun) {
     HashMapIterator it = m.getBad(mesh).iterator();
     while (it.hasNext()) {
       worklist.push(it.next());
     }
     
     if (isFirstRun) {

-      System.out.println("configuration: " + mesh.getNumNodes() + " total triangles, " + worklist.size() + " bad triangles");
+      System.out.println("configuration: " + 
+                         mesh.getNumNodes() + " total triangles, " +
+                         worklist.size() + " bad triangles");

       System.out.println();
     }
 
       System.out.println();
     }
 

+    System.out.println( "Post-config garbage collection started..." );

     System.gc();
     System.gc();

+    System.out.println( "done gc" );
+

 
 

-//    long id = Time.getNewTimeId();
+    // long id = Time.getNewTimeId();

     long startTime = System.currentTimeMillis();
     while (!worklist.isEmpty()) {
     long startTime = System.currentTimeMillis();
     while (!worklist.isEmpty()) {

-      
-      Node[] bad_elements = new Node[23];
-      for(int i=0;i<23;i++) {
+
+      // Phase 1, grab enough work from list for
+      // each worker in the parent
+      Node[] nodesForBadTris = new Node[numWorkers];
+      for(int i=0;i<numWorkers;i++) {

         if(worklist.isEmpty()) {
         if(worklist.isEmpty()) {

-          bad_elements[i] = null; 
+          nodesForBadTris[i] = null; 

         } else {
         } else {

-          bad_elements[i] = (Node) worklist.pop();
+          nodesForBadTris[i] = (Node) worklist.pop();

         }
       }
       
         }
       }
       

-  //      Node bad_element = (Node) worklist.pop();
-      for(int i=0;i<23;i++) {
-        Node bad_element = bad_elements[i];
-        if (bad_element != null && mesh.containsNode(bad_element)) {
+      // Phase 2, read mesh and compute cavities in parallel
+      Cavity[] cavities = new Cavity[numWorkers];
+      for(int i=0;i<numWorkers;i++) {
+        
+        Node nodeForBadTri = nodesForBadTris[i];
+        if (nodeForBadTri != null 
+            //&& mesh.containsNode(nodeForBadTri)
+            && nodeForBadTri.inGraph
+            ) {

           
           

-          sese P {
-          //takes < 1 sec 
-          Cavity cavity = new Cavity(mesh);
+          sese computeCavity {
+            //takes < 1 sec 
+            Cavity cavity = new Cavity(mesh);

           
           

-          //Appears to only call getters (only possible conflict is inherent in Hashmap)
-          cavity.initialize(bad_element);
+            //Appears to only call getters (only possible conflict is inherent in Hashmap)
+            cavity.initialize(nodeForBadTri);

           
           

-          //Takes up 15% of computation
-          //Problem:: Build is recursive upon building neighbor upon neighbor upon neighbor
-          //This is could be a problem....
-          //TODO check dimensions problem
-          cavity.build();
+            //Takes up 15% of computation
+            //Problem:: Build is recursive upon building neighbor upon neighbor upon neighbor
+            //This is could be a problem....
+            //TODO check dimensions problem
+            cavity.build();

           
           

-          //Takes up a whooping 50% of computation time and changes NOTHING but cavity :D
-          cavity.update();                    
+            //Takes up a whooping 50% of computation time and changes NOTHING but cavity :D
+            cavity.update();                    

           }
   
           }
   

-          sese S {
-            //28% of runtime #Removes stuff out of our mesh
-            middle(mesh, cavity);  
-            
-            //1.5% of runtime # adds stuff back to the work queue. 
-            end(mesh, worklist, bad_element, cavity); 
+          sese storeCavity {
+            cavities[i] = cavity;

           }
         }
           }
         }

-      

       }
       }

-    }
+      
+      // Phase 3, apply cavities to mesh, if still applicable
+      // this phase can proceed in parallel when a cavity's
+      // start nodes are still present
+      for(int i=0;i<numWorkers;i++) {
+
+        Cavity cavity = cavities[i];
+
+        Node nodeForBadTri = null;
+        
+        sese applyCavity {
+
+          // go ahead with applying cavity when all of its
+          // pre-nodes are still in
+          if( cavity.getPre().allNodesStillInCompleteGraph() ) {
+
+            //remove old data
+            Node node;
+    
+            //Takes up 8.9% of runtime
+            for (Iterator iterator = cavity.getPre().getNodes().iterator(); iterator.hasNext();) {
+              node = (Node) iterator.next();
+              mesh.removeNode(node);
+            }
+ 
+            //add new data
+            //Takes up 1.7% of runtime
+            for (Iterator iterator1 = cavity.getPost().getNodes().iterator(); iterator1.hasNext();) {
+              node = (Node) iterator1.next();
+              mesh.addNode(node);
+            }
+ 
+            //Takes up 7.8% of runtime
+            Edge_d edge;
+            for (Iterator iterator2 = cavity.getPost().getEdges().iterator(); iterator2.hasNext();) {
+              edge = (Edge_d) iterator2.next();
+              mesh.addEdge(edge);
+            }
+
+          } else {
+            // otherwise forget the cavity and reschedule the bad triangle
+            nodeForBadTri = nodesForBadTris[i];
+          }
+        }
+         
+
+        sese scheduleMoreBad {
+          
+          // if we couldn't even apply this cavity, just
+          // throw it back on the worklist
+          if( nodeForBadTri != null ) {
+ 
+            if( nodeForBadTri.inGraph ) {
+              worklist.push( nodeForBadTri );
+            }
+
+          } else {
+            // otherwise we did apply the cavity, but we
+            // may have introduced new bad triangles
+            HashMapIterator it2 = cavity.getPost().newBad(mesh).iterator();
+            while (it2.hasNext()) {
+              worklist.push((Node)it2.next());
+            }
+          }
+        } // end scheduleMoreBad
+      } // end phase 3
+
+    } // end while( !worklist.isEmpty() )
+

     long time = System.currentTimeMillis() - startTime;
     System.out.println("runtime: " + time + " ms");
     //TODO note how we only verify on first run...
     long time = System.currentTimeMillis() - startTime;
     System.out.println("runtime: " + time + " ms");
     //TODO note how we only verify on first run...

-    if (isFirstRun && args.length > 1) {
+    //TODO verify is outside timing, do it each time
+    // since we MIGHT compute something different when
+    // we have a bug
+    if (//isFirstRun && 
+        args.length > 2) {

       verify(mesh);
     }
     isFirstRun = false;
     return time;
   }
 
       verify(mesh);
     }
     isFirstRun = false;
     return time;
   }
 

-  private void end(EdgeGraph mesh, Stack worklist, Node bad_element, Cavity cavity) {
-    HashMapIterator it2 = cavity.getPost().newBad(mesh).iterator();
-    while (it2.hasNext()) {
-      worklist.push((Node)it2.next());
-    }
- 
-    if (mesh.containsNode(bad_element)) {
-      worklist.push((Node) bad_element);
-    }
-  }
-
-  private void middle(EdgeGraph mesh, Cavity cavity) {
-    //remove old data
-    Node node;
-    
-    //Takes up 8.9% of runtime
-    for (Iterator iterator = cavity.getPre().getNodes().iterator(); iterator.hasNext();) {
-      node = (Node) iterator.next();
-      mesh.removeNode(node);
-    }
- 
-    //add new data
-    //Takes up 1.7% of runtime
-    for (Iterator iterator1 = cavity.getPost().getNodes().iterator(); iterator1.hasNext();) {
-      node = (Node) iterator1.next();
-      mesh.addNode(node);
-    }
- 
-    
-    //Takes up 7.8% of runtime
-    Edge_d edge;
-    for (Iterator iterator2 = cavity.getPost().getEdges().iterator(); iterator2.hasNext();) {
-      edge = (Edge_d) iterator2.next();
-      mesh.addEdge(edge);
-    }
-  }

 
   public void verify(EdgeGraph result) {
     //Put in cuz of static issues.
 
   public void verify(EdgeGraph result) {
     //Put in cuz of static issues.

diff --git a/Robust/src/Benchmarks/oooJava/DelaunayRefinement/Subgraph.java b/Robust/src/Benchmarks/oooJava/DelaunayRefinement/Subgraph.java
index 01e90903d7e27a4561775ccba4399017a5b27cae..4c55e61e221c707b68f2605573e8fd442f941e7b 100644 (file)
--- a/Robust/src/Benchmarks/oooJava/DelaunayRefinement/Subgraph.java
+++ b/Robust/src/Benchmarks/oooJava/DelaunayRefinement/Subgraph.java
@@ -49,6 +49,17 @@ public class Subgraph {
     edges.clear();
   }
 
     edges.clear();
   }
 

+
+  public boolean allNodesStillInCompleteGraph() {
+    for( Iterator i = nodes.iterator(); i.hasNext(); ) {
+      Node node = (Node) i.next();
+      if( !node.inGraph ) {
+        return false;
+      }
+    }
+    return true;
+  }
+

   public HashSet newBad(EdgeGraph mesh) {
     HashSet ret = new HashSet();
     for (Iterator iter = nodes.iterator(); iter.hasNext();) {
   public HashSet newBad(EdgeGraph mesh) {
     HashSet ret = new HashSet();
     for (Iterator iter = nodes.iterator(); iter.hasNext();) {