[Pyxida-cvs-commits] Pyxida/src/edu/harvard/syrah/pyxida/knn Zone.java, 1.3, 1.4 KnnSim.java, 1.5, 1.6 HyperCubeZoneManager.java, 1.4, 1.5

[Jonathan L. <le...@us...>]

Update of /cvsroot/pyxida/Pyxida/src/edu/harvard/syrah/pyxida/knn
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26088/src/edu/harvard/syrah/pyxida/knn

Modified Files:
	Zone.java KnnSim.java HyperCubeZoneManager.java 
Log Message:
Trimmed memory use with KNN

Index: Zone.java
===================================================================
RCS file: /cvsroot/pyxida/Pyxida/src/edu/harvard/syrah/pyxida/knn/Zone.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Zone.java	14 Mar 2007 18:12:26 -0000	1.3
--- Zone.java	20 Mar 2007 13:17:26 -0000	1.4
***************
*** 34,40 ****
    
    // max guys per interval
!   public static final int maxNodesPerInterval = 10;
    
    // remember this many slots of nodes
    public static final int intervalCount = 10;
    
--- 34,43 ----
    
    // max guys per interval
!   // TODO Set to 10
!   public static final int maxNodesPerInterval = 1000;
    
    // remember this many slots of nodes
+   // Note: if you make this large, you may want to change the memory allocation
+   // below so to be a little more judicious
    public static final int intervalCount = 10;
    
***************
*** 42,46 ****
    // maxNodesPerInterval x intervalCount pointers to NodeDescs
    
!   final Vector<List<NodeDesc>> intervalSet; 
    
    int currentInterval = 0;
--- 45,50 ----
    // maxNodesPerInterval x intervalCount pointers to NodeDescs
    
!   final Vector<List<NodeDesc>> intervalSet;
!   //final NodeDesc[][] intervalSet;
    
    int currentInterval = 0;
***************
*** 51,57 ****
    public Zone (long _id) {
      id = _id;
!     intervalSet = new Vector<List<NodeDesc>> ();
      for (int i = 0; i < intervalCount; i++) {
!       intervalSet.add(new ArrayList<NodeDesc>());
      }
    }
--- 55,62 ----
    public Zone (long _id) {
      id = _id;
! 
!     intervalSet = new Vector<List<NodeDesc>> (intervalCount);
      for (int i = 0; i < intervalCount; i++) {
!       intervalSet.add(new ArrayList<NodeDesc>(0));
      }
    }
***************
*** 60,64 ****
      if (node == null) return;
      long intervalFloor = stamp / rotateSetInterval;
!     
      if (intervalFloor > currentIntervalFloor ||
        intervalSet.get(currentInterval).size() >= maxNodesPerInterval) {
--- 65,69 ----
      if (node == null) return;
      long intervalFloor = stamp / rotateSetInterval;
! 
      if (intervalFloor > currentIntervalFloor ||
        intervalSet.get(currentInterval).size() >= maxNodesPerInterval) {
***************
*** 66,75 ****
        currentInterval++;
        if (currentInterval == intervalCount) currentInterval = 0;
!       nodeCount -= intervalSet.get(currentInterval).size();
!       intervalSet.get(currentInterval).clear();
        currentIntervalFloor = intervalFloor;
      }
      
      intervalSet.get(currentInterval).add(node);
      nodeCount++;
    }
--- 71,84 ----
        currentInterval++;
        if (currentInterval == intervalCount) currentInterval = 0;
!       
!       ArrayList<NodeDesc> current = (ArrayList)intervalSet.get(currentInterval);
!       nodeCount -= current.size();
!       current.clear();
!       current.trimToSize();
        currentIntervalFloor = intervalFloor;
      }
      
      intervalSet.get(currentInterval).add(node);
+     
      nodeCount++;
    }
***************
*** 80,84 ****
      int intervalsPassed = 0;
      
!     while (distance2nearbyNodes.size() < maxNearbyNodes && intervalsPassed < intervalCount) {
        for (NodeDesc nearbyNode : intervalSet.get(interval)) {
          if (!probeSrc.equals(nearbyNode) && probeSrc.coord != null && nearbyNode.coord != null) {
--- 89,93 ----
      int intervalsPassed = 0;
      
!     while ( (maxNearbyNodes==0 || distance2nearbyNodes.size() < maxNearbyNodes) && intervalsPassed < intervalCount) {
        for (NodeDesc nearbyNode : intervalSet.get(interval)) {
          if (!probeSrc.equals(nearbyNode) && probeSrc.coord != null && nearbyNode.coord != null) {

Index: HyperCubeZoneManager.java
===================================================================
RCS file: /cvsroot/pyxida/Pyxida/src/edu/harvard/syrah/pyxida/knn/HyperCubeZoneManager.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** HyperCubeZoneManager.java	14 Mar 2007 18:12:26 -0000	1.4
--- HyperCubeZoneManager.java	20 Mar 2007 13:17:26 -0000	1.5
***************
*** 30,39 ****
    final Map<Long,List<Long>> zone2adjacentZones;
    
!   public HyperCubeZoneManager (int _dimensions, double _dimensionSideLength, int _zonesPerDimension, boolean _useAdjacentZones) {
      dimensions = _dimensions;
  		dimensionSideLength = _dimensionSideLength;
      halfDimensionSideLength = dimensionSideLength / 2.;
! 		zonesPerDimension = _zonesPerDimension;
!     zoneEdgeLength = _dimensionSideLength / _zonesPerDimension;
      useAdjacentZones = _useAdjacentZones;
      zoneMap = new HashMap<Long,Zone> ();
--- 30,40 ----
    final Map<Long,List<Long>> zone2adjacentZones;
    
!   public HyperCubeZoneManager (int _dimensions, double _dimensionSideLength, double _zoneEdgeLength, boolean _useAdjacentZones) {
      dimensions = _dimensions;
  		dimensionSideLength = _dimensionSideLength;
      halfDimensionSideLength = dimensionSideLength / 2.;
!     zoneEdgeLength = _zoneEdgeLength;
! 		zonesPerDimension = (int)Math.floor(_dimensionSideLength / _zoneEdgeLength);
!     
      useAdjacentZones = _useAdjacentZones;
      zoneMap = new HashMap<Long,Zone> ();
***************
*** 78,82 ****
      //slog.info ("added "+distance2nearbyNodes.size()+" from our zone "+zoneId);
      
!     if (useAdjacentZones && distance2nearbyNodes.size() < maxReturnSize) {
        List<Long> adjacentZones = zone2adjacentZones.get(zoneId);
        // compute our adjacent zones in case ours is empty
--- 79,83 ----
      //slog.info ("added "+distance2nearbyNodes.size()+" from our zone "+zoneId);
      
!     if (useAdjacentZones && (maxReturnSize == 0 || distance2nearbyNodes.size() < maxReturnSize)) {
        List<Long> adjacentZones = zone2adjacentZones.get(zoneId);
        // compute our adjacent zones in case ours is empty
***************
*** 92,96 ****
          //slog.info ("total "+distance2nearbyNodes.size()+" from zone "+adjacentZoneId);
          
!         if (distance2nearbyNodes.size() >= maxReturnSize) {
            return;
          }
--- 93,97 ----
          //slog.info ("total "+distance2nearbyNodes.size()+" from zone "+adjacentZoneId);
          
!         if (maxReturnSize == 0 || distance2nearbyNodes.size() >= maxReturnSize) {
            return;
          }

Index: KnnSim.java
===================================================================
RCS file: /cvsroot/pyxida/Pyxida/src/edu/harvard/syrah/pyxida/knn/KnnSim.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** KnnSim.java	20 Mar 2007 12:27:53 -0000	1.5
--- KnnSim.java	20 Mar 2007 13:17:26 -0000	1.6
***************
*** 35,43 ****
  	// Number of guys we would be returning to client.
  	// We will see how many of the true NN of the same size we find.
! 	int returnSetSize = 50;
    String coordFilename = null;
!   boolean useAdjacentZones = true;
    double dimensionSideLength = 10000;
!   int zonesPerDimension = 2;
    
    final static protected int NFDigits = 3;
--- 35,44 ----
  	// Number of guys we would be returning to client.
  	// We will see how many of the true NN of the same size we find.
! 	int returnSetSize = 0;
    String coordFilename = null;
!   boolean useAdjacentZones = false;
    double dimensionSideLength = 10000;
!   double zoneEdgeLength = 25.;
!   double zoneTargetRTT = 100.;
    
    final static protected int NFDigits = 3;
***************
*** 65,68 ****
--- 66,71 ----
            " -h toggle height use ("+NCClient.USE_HEIGHT+")\n"+
            " -s dimension side length ("+dimensionSideLength+")\n"+
+           " -e zone edge length ("+zoneEdgeLength+")\n"+
+           " -t zone target RTT ("+zoneTargetRTT+")\n"+
            " -a toggle adjacent zone use ("+useAdjacentZones+")\n"+
            " -r return set size ("+returnSetSize+")\n"+
***************
*** 73,77 ****
    public KnnSim (String[] args) {
      int c;    
!     Getopt g = new Getopt ("KnnSim", args, "d:hz:s:ar:c:");
      
      while ((c = g.getopt()) != -1) {
--- 76,80 ----
    public KnnSim (String[] args) {
      int c;    
!     Getopt g = new Getopt ("KnnSim", args, "d:he:s:ar:c:");
      
      while ((c = g.getopt()) != -1) {
***************
*** 83,88 ****
          NCClient.USE_HEIGHT = !NCClient.USE_HEIGHT;
          break;
!       case 'z':
!         zonesPerDimension = Integer.parseInt(g.getOptarg());
          break;
        case 's':
--- 86,91 ----
          NCClient.USE_HEIGHT = !NCClient.USE_HEIGHT;
          break;
!       case 'e':
!         zoneEdgeLength = Double.parseDouble(g.getOptarg());
          break;
        case 's':
***************
*** 102,121 ****
        }
      }
      
      if (coordFilename == null) printUsage ("coordinate file required");
      if (dimensions <= 0) printUsage ("invalid number of dimensions");
      if (zonesPerDimension <= 1) printUsage ("zones per dimension invalid");
      if (dimensionSideLength < 1.) printUsage ("dimension side length invalid");
!     if (returnSetSize < 1) printUsage ("return set size invalid");
      
      dimsPlusHeight = NCClient.USE_HEIGHT?(dimensions+1):dimensions;
      
!     slog.info("PARAMS dims="+dimensions+
        " height="+NCClient.USE_HEIGHT+
        " dimensionSideLength="+dimensionSideLength+
        " zonesPerDimension="+zonesPerDimension+
        " useAdjacentZones="+useAdjacentZones+
        " returnSetSize="+returnSetSize+
!       " coordFile="+coordFilename);
      
      slog.info ("reading coordinate file "+coordFilename);
--- 105,131 ----
        }
      }
+ 
+     if (dimensionSideLength % zoneEdgeLength != 0.) 
+       printUsage ("zone edge length must divide dimension side length evenly.");
      
+     int zonesPerDimension = (int)(Math.floor(dimensionSideLength / zoneEdgeLength)); 
+         
      if (coordFilename == null) printUsage ("coordinate file required");
      if (dimensions <= 0) printUsage ("invalid number of dimensions");
      if (zonesPerDimension <= 1) printUsage ("zones per dimension invalid");
      if (dimensionSideLength < 1.) printUsage ("dimension side length invalid");
!     if (returnSetSize < 0) printUsage ("return set size invalid");
      
      dimsPlusHeight = NCClient.USE_HEIGHT?(dimensions+1):dimensions;
      
!     String params = "PARAMS dims="+dimensions+
        " height="+NCClient.USE_HEIGHT+
        " dimensionSideLength="+dimensionSideLength+
        " zonesPerDimension="+zonesPerDimension+
+       " zoneEdgeLength="+zoneEdgeLength+
        " useAdjacentZones="+useAdjacentZones+
        " returnSetSize="+returnSetSize+
!       " coordFile="+coordFilename;
!     System.out.println ("# "+params);
      
      slog.info ("reading coordinate file "+coordFilename);
***************
*** 125,129 ****
      
  
!     zm = new HyperCubeZoneManager (dimensions, dimensionSideLength, zonesPerDimension, useAdjacentZones);
      
      slog.info ("adding nodes to zones");
--- 135,139 ----
      
  
!     zm = new HyperCubeZoneManager (dimensions, dimensionSideLength, zoneEdgeLength, useAdjacentZones);
      
      slog.info ("adding nodes to zones");
***************
*** 137,146 ****
      for (NodeDesc me : nodes) {
        SortedMap<Double,NodeDesc> distance2node = new TreeMap<Double,NodeDesc>();
        for (NodeDesc node : nodes) {
          if (me != node) {
            double distance = me.coord.distanceTo(node.coord);
!           distance2node.put(distance, node);
          }
        }
        node2distance2node.put(me, distance2node);
      }
--- 147,173 ----
      for (NodeDesc me : nodes) {
        SortedMap<Double,NodeDesc> distance2node = new TreeMap<Double,NodeDesc>();
+       double nearestDistance = Double.MAX_VALUE;
+       NodeDesc nearestNode = null;
        for (NodeDesc node : nodes) {
          if (me != node) {
            double distance = me.coord.distanceTo(node.coord);
!           if (distance < nearestDistance) {
!             nearestDistance = distance;
!             nearestNode = node;
!           }
          }
        }
+ 
+       distance2node.put(nearestDistance, nearestNode);
+       
+       /*
+       SortedMap<Double,NodeDesc> distance2node = new TreeMap<Double,NodeDesc>();
+       int count = 0;
+       final int MAX_NEARBY_TNN = 1;
+       for (Map.Entry<Double,NodeDesc> entry : allDistance2node.entrySet()) {
+         distance2node.put(entry.getKey(), entry.getValue());
+         if (count > MAX_NEARBY_TNN) break;
+       }
+       */
        node2distance2node.put(me, distance2node);
      }
***************
*** 153,157 ****
        zm.add (stamp, node);
      }
!     //slog.info (zm.toString());    
    }
    
--- 180,185 ----
        zm.add (stamp, node);
      }
!     //slog.info (zm.toString());
!     //System.out.println (zm.toString());
    }
    
***************
*** 162,173 ****
        SortedMap<Double,NodeDesc> distance2nearbyNodes = new TreeMap<Double,NodeDesc>();
  			
!       zm.query(node,distance2nearbyNodes,returnSetSize);
  
  			// foundSet is who we would be returning to the client
  			//Set<NodeDesc> foundSet = getSetHead (distance2node, returnSetSize);
! 			Set<NodeDesc> tnnSet = getSetHead (node2distance2node.get(node), returnSetSize);
! 
! 			int unionSize = 0;
! 
        /*
        slog.info (node.id+" true nearest neighbors:");
--- 190,204 ----
        SortedMap<Double,NodeDesc> distance2nearbyNodes = new TreeMap<Double,NodeDesc>();
  			
!       zm.query(node,distance2nearbyNodes,0);
  
  			// foundSet is who we would be returning to the client
  			//Set<NodeDesc> foundSet = getSetHead (distance2node, returnSetSize);
! 			SortedMap<Double,NodeDesc> trueDistance2node = node2distance2node.get(node);
! 			double trueNearestDistance = trueDistance2node.firstKey();
!       
! 			double rttSum = 0.;
!       int countLtTargetRtt = 0;
!       int countGtTargetRtt = 0;
!       
        /*
        slog.info (node.id+" true nearest neighbors:");
***************
*** 177,193 ****
        */
        
!       for (NodeDesc foundNode : distance2nearbyNodes.values()) {
          //slog.info (node.id+" union "+foundNode.id);
!         if (tnnSet.contains(foundNode)) {
!           unionSize++;
          }
        }
  
!       double pctOverlap = (double)unionSize / tnnSet.size();
        
        //slog.info (node.id+" unionSize "+unionSize + " pct="+nf.format(pctOverlap));
!       slog.info (node.id+" pct="+nf.format(pctOverlap));
  
! 			// TODO Could also eval mapping with abs(rank difference)
  			// exponentially weighted by tnn rank
  
--- 208,236 ----
        */
        
!       for (Map.Entry<Double, NodeDesc> entry : distance2nearbyNodes.entrySet()) {
          //slog.info (node.id+" union "+foundNode.id);
!         double rtt = entry.getKey();
!         rttSum += rtt;
!         if (rtt < zoneTargetRTT) {
!           countLtTargetRtt++;
!         } else {
!           countGtTargetRtt++;
          }
        }
  
!       double avgRtt = (distance2nearbyNodes.size() > 0) ?
!         rttSum / (double)distance2nearbyNodes.size() : 0.;
        
        //slog.info (node.id+" unionSize "+unionSize + " pct="+nf.format(pctOverlap));
!       String res = node.id+" avgRtt= "+nf.format(avgRtt)+
!         " lt= "+countLtTargetRtt+ " gt= "+countGtTargetRtt+
!         " pctLt= "+ nf.format
!         ((distance2nearbyNodes.size() > 0) ? (double)countLtTargetRtt/(double)distance2nearbyNodes.size() : 0.)+
!         " tN= "+nf.format(trueNearestDistance)+
!         " c= "+node.coord;
!         
!       System.out.println (res);
  
! 			// Could also eval mapping with abs(rank difference)
  			// exponentially weighted by tnn rank