Merge branch 'master' of github.com:0xdata/h2o

AlicTsai · Dec 5, 2013 · 563389b · 563389b
2 parents f35328e + 6ea8f48
commit 563389b
Showing 1 changed file with 13 additions and 8 deletions.
diff --git a/src/main/java/hex/gram/Gram.java b/src/main/java/hex/gram/Gram.java
@@ -8,6 +8,7 @@
 
 import jsr166y.RecursiveAction;
 import water.*;
+import water.util.Log;
 import water.util.Utils;
 import Jama.CholeskyDecomposition;
 import Jama.Matrix;
@@ -66,7 +67,7 @@ public String toString(){
     } else return Utils.pprint(getXX());
   }
   static public class InPlaceCholesky {
-    final double _xx[][];             // Lower triagle of the symmetric matrix.
+    final double _xx[][];             // Lower triangle of the symmetric matrix.
     private boolean _isSPD;
     private InPlaceCholesky(double xx[][], boolean isspd) { _xx = xx; _isSPD = isspd; }
     static private class BlockTask extends RecursiveAction {
@@ -77,8 +78,6 @@ public BlockTask(double xx[][], int ifr, int ito, int jfr, int jto) {
         _i0 = ifr; _i1 = ito; _j0 = jfr; _j1 = jto;
       }
       @Override public void compute() {
-        //Log.info("TASK THREAD ID -- " + Thread.currentThread().getName());
-        //Log.info("  BLOCK SIZE " + (_i1 - _i0));
         for (int i=_i0; i < _i1; i++) {
           double rowi[] = _xx[i];
           for (int k=_j0; k < _j1; k++) {
@@ -164,7 +163,6 @@ public Cholesky cholesky(Cholesky chol, int parallelize) {
     final Cholesky fchol = chol;
     final int sparseN = _diag.length;
     final int denseN = _fullN - sparseN;
-    boolean spd=true;
     // compute the cholesky of the diagonal and diagonal*dense parts
     if( _diag != null ) for( int i = 0; i < sparseN; ++i ) {
       double d = 1.0 / (chol._diag[i] = Math.sqrt(_diag[i]));
@@ -173,18 +171,25 @@ public Cholesky cholesky(Cholesky chol, int parallelize) {
     }
     Futures fs = new Futures();
     // compute the outer product of diagonal*dense
-    final int chk = Math.max(denseN/10, 1);
     //Log.info("SPARSEN = " + sparseN + "    DENSEN = " + denseN);
 
     for( int i = 0; i < denseN; ++i ) {
       final int fi = i;
       fs.add(new RecursiveAction() {
           @Override protected void compute() {
+            double[] rowi = fchol._xx[fi];
+            int[] nz = new int[sparseN];
+            int   n = 0;
+            for( int k = 0; k < sparseN; ++k )
+              if (rowi[k] != .0) nz[n++] = k;
             for( int j = 0; j <= fi; ++j ) {
+              double[] rowj = fchol._xx[j];
               double s = 0;
-              for( int k = 0; k < sparseN; ++k )
-                s += fchol._xx[fi][k] * fchol._xx[j][k];
-                 fchol._xx[fi][j + sparseN] = _xx[fi][j + sparseN] - s;
+              for ( int z = 0; z < n; z++) {
+                int k = nz[z];
+                s += rowi[k] * rowj[k];
+              }
+              rowi[j + sparseN] = _xx[fi][j + sparseN] - s;
             }
           }
         }.fork());