http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/runtime/matrix/data/MatrixBlock.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/matrix/data/MatrixBlock.java b/src/main/java/org/apache/sysml/runtime/matrix/data/MatrixBlock.java index 4e82891..f307d78 100644 --- a/src/main/java/org/apache/sysml/runtime/matrix/data/MatrixBlock.java +++ b/src/main/java/org/apache/sysml/runtime/matrix/data/MatrixBlock.java @@ -125,9 +125,9 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab protected long nonZeros = 0; //matrix data (sparse or dense) - protected double[] denseBlock = null; + protected DenseBlock denseBlock = null; protected SparseBlock sparseBlock = null; - + //sparse-block-specific attributes (allocation only) protected int estimatedNNzsPerRow = -1; @@ -236,7 +236,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab rlen = rl; clen = cl; sparse = (val == 0) ? sp : false; - nonZeros = (val == 0) ? 0 : rl*cl; + nonZeros = (val == 0) ? 0 : rl*cl; estimatedNNzsPerRow = (estnnz < 0 || !sparse) ? -1 : (int)Math.ceil((double)estnnz/(double)rlen); @@ -260,15 +260,14 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } private void resetDense(double val) { - //handle to dense block allocation - if( denseBlock != null && denseBlock.length<rlen*clen && val==0) - denseBlock = null; - else if( val != 0 ) - allocateDenseBlock(false); - - //reset dense block to given value + //handle to dense block allocation and + //reset dense block to given value if( denseBlock != null ) - Arrays.fill(denseBlock, 0, rlen*clen, val); + denseBlock.reset(rlen, clen, val); + else if( val != 0 ) { + allocateDenseBlock(false); + denseBlock.set(val); + } } /** @@ -292,8 +291,9 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab allocateDenseBlock(); //copy and compute nnz + double[] data = getDenseBlockValues(); for(int i=0, ix=0; i < r; i++, ix+=clen) - System.arraycopy(arr[i], 0, denseBlock, ix, arr[i].length); + System.arraycopy(arr[i], 0, data, ix, arr[i].length); recomputeNonZeros(); } @@ -318,7 +318,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab allocateDenseBlock(); //copy and compute nnz - System.arraycopy(arr, 0, denseBlock, 0, arr.length); + System.arraycopy(arr, 0, getDenseBlockValues(), 0, arr.length); recomputeNonZeros(); } @@ -340,7 +340,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab return this; } - public void allocateDenseBlock(boolean clearNNZ) + public boolean allocateDenseBlock(boolean clearNNZ) { long limit = (long)rlen * clen; @@ -354,16 +354,18 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } //allocate block if non-existing or too small (guaranteed to be 0-initialized), - if(denseBlock == null || denseBlock.length < limit) { - denseBlock = new double[(int)limit]; - } + boolean reset = (denseBlock == null || denseBlock.capacity() < limit); + if( denseBlock == null ) + denseBlock = DenseBlockFactory.createDenseBlock(rlen, clen); + else if( denseBlock.capacity() < limit ) + denseBlock.reset(rlen, clen); //clear nnz if necessary - if( clearNNZ ) { + if( clearNNZ ) nonZeros = 0; - } - sparse = false; + + return reset; } public void allocateSparseRowsBlock() { @@ -519,15 +521,16 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab //////// // Data handling - public double[] getDenseBlock() { - if( sparse ) - return null; + public DenseBlock getDenseBlock() { return denseBlock; } + public double[] getDenseBlockValues() { + return (denseBlock != null) ? + denseBlock.values(0) : null; + } + public SparseBlock getSparseBlock() { - if( !sparse ) - return null; return sparseBlock; } @@ -580,26 +583,17 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab quickSetValue(r, c, v); } - public double quickGetValue(int r, int c) - { - if(sparse) - { - if( sparseBlock==null ) - return 0; + public double quickGetValue(int r, int c) { + if( sparse && sparseBlock!=null ) return sparseBlock.get(r, c); - } - else - { - if( denseBlock==null ) - return 0; - return denseBlock[r*clen+c]; - } + else if( !sparse && denseBlock!=null ) + return denseBlock.get(r, c); + return 0; } public void quickSetValue(int r, int c, double v) { - if(sparse) - { + if(sparse) { //early abort if( (sparseBlock==null || sparseBlock.isEmpty(r)) && v==0 ) return; @@ -612,32 +606,28 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab if( sparseBlock.set(r, c, v) ) nonZeros += (v!=0) ? 1 : -1; } - else - { + else { //early abort if( denseBlock==null && v==0 ) - return; + return; //allocate and init dense block (w/o overwriting nnz) allocateDenseBlock(false); //set value and maintain nnz - int index=r*clen+c; - if( denseBlock[index]==0 ) + if( denseBlock.get(r, c)==0 ) nonZeros++; - denseBlock[index] = v; + denseBlock.set(r, c, v); if( v==0 ) nonZeros--; } } - public double getValueDenseUnsafe(int r, int c) - { + public double getValueDenseUnsafe(int r, int c) { if(denseBlock==null) return 0; - return denseBlock[r*clen+c]; + return denseBlock.get(r, c); } - /** * This can be only called when you know you have properly allocated spaces for a dense representation @@ -648,16 +638,14 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab * @param c column * @param v value */ - public void setValueDenseUnsafe(int r, int c, double v) - { - denseBlock[r*clen+c]=v; + public void setValueDenseUnsafe(int r, int c, double v) { + denseBlock.set(r, c, v); } - public double getValueSparseUnsafe(int r, int c) - { + public double getValueSparseUnsafe(int r, int c) { if(sparseBlock==null || sparseBlock.isEmpty(r)) return 0; - return sparseBlock.get(r, c); + return sparseBlock.get(r, c); } /** @@ -680,7 +668,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab allocateDenseBlock(false); //set value and maintain nnz - denseBlock[r*clen+c] = v; + denseBlock.set(r, c, v); nonZeros++; } else //SPARSE @@ -756,13 +744,13 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab else sparseBlock.allocate(aix, sparseBlock.size(aix)+len); for( int j=pos; j<pos+len; j++ ) - sparseBlock.append(aix, coloffset+ix[j], val[j]); + sparseBlock.append(aix, coloffset+ix[j], val[j]); } } } else //SPARSE <- DENSE { - double[] b = that.denseBlock; + double[] b = that.getDenseBlockValues(); final int bm = that.rlen; final int bn = that.clen; for( int i=0, aix=rowoffset, bix=0; i<bm; i++, aix++, bix+=bn ) @@ -1015,10 +1003,6 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab return evalSparseFormatOnDisk(lrlen, lclen, nonZeros); } - public void examSparsity() throws DMLRuntimeException { - examSparsity(null); - } - /** * Evaluates if this matrix block should be in sparse format in * memory. Depending on the current representation, the state of the @@ -1026,10 +1010,9 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab * Note that this consumes for the time of execution memory for both * representations. * - * @param opcode extended opcode * @throws DMLRuntimeException if DMLRuntimeException occurs */ - public void examSparsity(String opcode) + public void examSparsity() throws DMLRuntimeException { //determine target representation @@ -1100,12 +1083,13 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab private void denseToSparse() { + double[] a = getDenseBlockValues(); + //set target representation, early abort on empty blocks sparse = true; - if( denseBlock==null ) + if( a == null ) return; - double[] a = denseBlock; final int m = rlen; final int n = clen; @@ -1147,12 +1131,12 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } //allocate dense target block, but keep nnz (no need to maintain) - allocateDenseBlock(false); - Arrays.fill(denseBlock, 0, limit, 0); + if( !allocateDenseBlock(false) ) + denseBlock.reset(); //copy sparse to dense SparseBlock a = sparseBlock; - double[] c = denseBlock; + double[] c = getDenseBlockValues(); for( int i=0, cix=0; i<rlen; i++, cix+=clen) if( !a.isEmpty(i) ) { @@ -1176,26 +1160,12 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab * @return number of non-zeros */ public long recomputeNonZeros() { - return recomputeNonZeros(null); - } - - public long recomputeNonZeros(String opcode) { - long t1 = opcode != null && DMLScript.STATISTICS && DMLScript.FINEGRAINED_STATISTICS ? System.nanoTime() : 0; - if( sparse && sparseBlock!=null ) { //SPARSE (max long) + if( sparse && sparseBlock!=null ) { //SPARSE //note: rlen might be <= sparseBlock.numRows() nonZeros = sparseBlock.size(0, sparseBlock.numRows()); } - else if( !sparse && denseBlock!=null ) { //DENSE (max int) - double[] a = denseBlock; - final int limit=rlen*clen; - int nnz = 0; - for(int i=0; i<limit; i++) - nnz += (a[i]!=0) ? 1 : 0; - nonZeros = nnz; - } - if(opcode != null && DMLScript.STATISTICS && DMLScript.FINEGRAINED_STATISTICS) { - long t2 = System.nanoTime(); - GPUStatistics.maintainCPMiscTimes(opcode, CPInstruction.MISC_TIMER_RECOMPUTE_NNZ, t2-t1); + else if( !sparse && denseBlock!=null ) { //DENSE + nonZeros = denseBlock.countNonZeros(); } return nonZeros; } @@ -1217,7 +1187,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab */ public long recomputeNonZeros(int rl, int ru, int cl, int cu) { - if( sparse && sparseBlock!=null ) //SPARSE (max long) + if( sparse && sparseBlock!=null ) //SPARSE { long nnz = 0; if( cl==0 && cu==clen-1 ) { //specific case: all cols @@ -1234,21 +1204,8 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } return nnz; } - else if( !sparse && denseBlock!=null ) //DENSE (max int) - { - double[] a = denseBlock; - final int n = clen; - int nnz = 0; - if( cl==0 && cu==n-1 ) { //specific case: all cols - for( int i=rl*n; i<(ru+1)*n; i++ ) - nnz += (a[i]!=0) ? 1 : 0; - } - else { - for( int i=rl, ix=rl*n; i<=ru; i++, ix+=n ) - for( int j=cl; j<=cu; j++ ) - nnz += (a[ix+j]!=0) ? 1 : 0; - } - return nnz; + else if( !sparse && denseBlock!=null ) { //DENSE + return denseBlock.countNonZeros(rl, ru+1, cl, cu+1); } return 0; //empty block @@ -1359,13 +1316,11 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab private void copyDenseToDense(MatrixBlock that) { nonZeros = that.nonZeros; - int limit = rlen*clen; //plain reset to 0 for empty input - if( that.isEmptyBlock(false) ) - { + if( that.isEmptyBlock(false) ) { if(denseBlock!=null) - Arrays.fill(denseBlock, 0, limit, 0); + denseBlock.reset(rlen, clen); return; } @@ -1373,16 +1328,15 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab allocateDenseBlock(false); //actual copy - System.arraycopy(that.denseBlock, 0, denseBlock, 0, limit); + System.arraycopy(that.getDenseBlockValues(), 0, getDenseBlockValues(), 0, rlen*clen); } private void copySparseToDense(MatrixBlock that) { this.nonZeros=that.nonZeros; - if( that.isEmptyBlock(false) ) - { + if( that.isEmptyBlock(false) ) { if(denseBlock!=null) - Arrays.fill(denseBlock, 0); + denseBlock.reset(rlen, clen); return; } @@ -1390,39 +1344,34 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab allocateDenseBlock(false); int start=0; - for(int r=0; r<Math.min(that.sparseBlock.numRows(), rlen); r++, start+=clen) - { + double[] c = getDenseBlockValues(); + for(int r=0; r<Math.min(that.sparseBlock.numRows(), rlen); r++, start+=clen) { if(that.sparseBlock.isEmpty(r)) continue; int pos = that.sparseBlock.pos(r); int len = that.sparseBlock.size(r); int[] aix = that.sparseBlock.indexes(r); double[] avals = that.sparseBlock.values(r); - - for(int i=pos; i<pos+len; i++) { - denseBlock[start+aix[i]]=avals[i]; - } + for(int i=pos; i<pos+len; i++) + c[start+aix[i]]=avals[i]; } } private void copyDenseToSparse(MatrixBlock that) { nonZeros = that.nonZeros; - if( that.isEmptyBlock(false) ) - { + if( that.isEmptyBlock(false) ) { resetSparse(); return; } allocateSparseRowsBlock(false); - for(int i=0, ix=0; i<rlen; i++) - { + double[] b = that.getDenseBlockValues(); + for(int i=0, ix=0; i<rlen; i++) { sparseBlock.reset(i, estimatedNNzsPerRow, clen); - - for(int j=0; j<clen; j++) - { - double val = that.denseBlock[ix++]; + for(int j=0; j<clen; j++) { + double val = b[ix++]; if( val != 0 ) { //create sparse row only if required sparseBlock.allocate(i, estimatedNNzsPerRow, clen); @@ -1547,21 +1496,17 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab //copy values SparseBlock a = src.sparseBlock; - for( int i=0, ix=rl*clen; i<src.rlen; i++, ix+=clen ) - { - if( !a.isEmpty(i) ) - { - int apos = a.pos(i); - int alen = a.size(i); - int[] aix = a.indexes(i); - double[] avals = a.values(i); - - for( int j=apos; j<apos+alen; j++ ) - denseBlock[ix+cl+aix[j]] = avals[j]; - - if(awareDestNZ) - nonZeros += alen; - } + double[] c = getDenseBlockValues(); + for( int i=0, ix=rl*clen; i<src.rlen; i++, ix+=clen ) { + if( a.isEmpty(i) ) continue; + int apos = a.pos(i); + int alen = a.size(i); + int[] aix = a.indexes(i); + double[] avals = a.values(i); + for( int j=apos; j<apos+alen; j++ ) + c[ix+cl+aix[j]] = avals[j]; + if(awareDestNZ) + nonZeros += alen; } } @@ -1571,33 +1516,34 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab if( src.isEmptyBlock(false) ) { if( awareDestNZ && sparseBlock != null ) copyEmptyToSparse(rl, ru, cl, cu, true); - return; + return; } //allocate output block - //no need to clear for awareDestNZ since overwritten + //no need to clear for awareDestNZ since overwritten allocateSparseRowsBlock(false); //copy values - SparseBlock a = sparseBlock; + SparseBlock c = sparseBlock; + double[] a = src.getDenseBlockValues(); for( int i=0, ix=0; i<src.rlen; i++, ix+=src.clen ) { int rix = rl + i; - if( a instanceof SparseBlockMCSR - && a.isEmpty(rix) ) //special case MCSR append + if( c instanceof SparseBlockMCSR + && c.isEmpty(rix) ) //special case MCSR append { //count nnz per row (fits likely in L1 cache) int lnnz = 0; for( int j=0; j<src.clen; j++ ) - lnnz += (src.denseBlock[ix+j]!=0) ? 1 : 0; + lnnz += (a[ix+j]!=0) ? 1 : 0; //allocate row once and copy values if( lnnz > 0 ) { - a.allocate(rix, lnnz); + c.allocate(rix, lnnz); for( int j=0; j<src.clen; j++ ) { - double val = src.denseBlock[ix+j]; + double val = a[ix+j]; if( val != 0 ) - a.append(rix, cl+j, val); + c.append(rix, cl+j, val); } if( awareDestNZ ) nonZeros += lnnz; @@ -1605,22 +1551,22 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } else if( awareDestNZ ) //general case (w/ awareness NNZ) { - int lnnz = a.size(rix); + int lnnz = c.size(rix); if( cl==cu ) { - double val = src.denseBlock[ix]; - a.set(rix, cl, val); + double val = a[ix]; + c.set(rix, cl, val); } else { - a.setIndexRange(rix, cl, cu+1, src.denseBlock, ix, src.clen); + c.setIndexRange(rix, cl, cu+1, a, ix, src.clen); } - nonZeros += (a.size(rix) - lnnz); + nonZeros += (c.size(rix) - lnnz); } else //general case (w/o awareness NNZ) { for( int j=0; j<src.clen; j++ ) { - double val = src.denseBlock[ix+j]; + double val = a[ix+j]; if( val != 0 ) - a.set(rix, cl+j, val); + c.set(rix, cl+j, val); } } } @@ -1646,12 +1592,14 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab nonZeros = nonZeros - recomputeNonZeros(rl, ru, cl, cu) + src.nonZeros; //copy values + double[] a = src.getDenseBlockValues(); + double[] c = getDenseBlockValues(); int rowLen = cu-cl+1; if(clen == src.clen) //optimization for equal width - System.arraycopy(src.denseBlock, 0, denseBlock, rl*clen+cl, src.rlen*src.clen); + System.arraycopy(a, 0, c, rl*clen+cl, src.rlen*src.clen); else for( int i=0, ix1=0, ix2=rl*clen+cl; i<src.rlen; i++, ix1+=src.clen, ix2+=clen ) { - System.arraycopy(src.denseBlock, ix1, denseBlock, ix2, rowLen); + System.arraycopy(a, ix1, c, ix2, rowLen); } } @@ -1680,14 +1628,14 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } } - private void copyEmptyToDense(int rl, int ru, int cl, int cu) - { + private void copyEmptyToDense(int rl, int ru, int cl, int cu) { int rowLen = cu-cl+1; + double[] a = getDenseBlockValues(); if(clen == rowLen) //optimization for equal width - Arrays.fill(denseBlock, rl*clen+cl, ru*clen+cu+1, 0); + Arrays.fill(a, rl*clen+cl, ru*clen+cu+1, 0); else for( int i=rl, ix2=rl*clen+cl; i<=ru; i++, ix2+=clen ) - Arrays.fill(denseBlock, ix2, ix2+rowLen, 0); + Arrays.fill(a, ix2, ix2+rowLen, 0); } public void merge(CacheBlock that, boolean appendOnly) @@ -1745,7 +1693,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { if( that.sparse ) //DENSE <- SPARSE { - double[] a = denseBlock; + double[] a = getDenseBlockValues(); SparseBlock b = that.sparseBlock; int m = rlen; int n = clen; @@ -1764,8 +1712,8 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } else //DENSE <- DENSE { - double[] a = denseBlock; - double[] b = that.denseBlock; + double[] a = getDenseBlockValues(); + double[] b = that.getDenseBlockValues(); int len = rlen * clen; for( int i=0; i<len; i++ ) @@ -1812,7 +1760,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab else //SPARSE <- DENSE { SparseBlock a = sparseBlock; - double[] b = that.denseBlock; + double[] b = that.getDenseBlockValues(); int m = rlen; int n = clen; @@ -1894,14 +1842,15 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab private void readDenseBlock(DataInput in) throws IOException, DMLRuntimeException { - allocateDenseBlock(true); //allocate block, clear nnz + if( !allocateDenseBlock(false) ) //allocate block + denseBlock.reset(rlen, clen); int limit = rlen*clen; - + double[] a = getDenseBlockValues(); if( in instanceof MatrixBlockDataInput ) //fast deserialize { MatrixBlockDataInput mbin = (MatrixBlockDataInput)in; - nonZeros = mbin.readDoubleArray(limit, denseBlock); + nonZeros = mbin.readDoubleArray(limit, a); } else if( in instanceof DataInputBuffer && MRJobConfiguration.USE_BINARYBLOCK_SERIALIZATION ) { @@ -1910,20 +1859,17 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab FastBufferedDataInputStream mbin = null; try { mbin = new FastBufferedDataInputStream(din); - nonZeros = mbin.readDoubleArray(limit, denseBlock); + nonZeros = mbin.readDoubleArray(limit, a); } finally { IOUtilFunctions.closeSilently(mbin); } } - else //default deserialize - { + else { //default deserialize + long nnz = 0; for( int i=0; i<limit; i++ ) - { - denseBlock[i]=in.readDouble(); - if(denseBlock[i]!=0) - nonZeros++; - } + nnz += ((a[i] = in.readDouble()) != 0) ? 1 : 0; + nonZeros = nnz; } } @@ -1964,22 +1910,21 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab private void readSparseToDense(DataInput in) throws IOException, DMLRuntimeException { - allocateDenseBlock(false); //allocate block - Arrays.fill(denseBlock, 0); + if( !allocateDenseBlock(false) ) //allocate block + denseBlock.reset(rlen, clen); - for(int r=0; r<rlen; r++) - { + double[] a = getDenseBlockValues(); + for(int r=0; r<rlen; r++) { int nr = in.readInt(); - for( int j=0; j<nr; j++ ) - { + for( int j=0; j<nr; j++ ) { int c = in.readInt(); - double val = in.readDouble(); - denseBlock[r*clen+c] = val; + double val = in.readDouble(); + a[r*clen+c] = val; } } } - private void readUltraSparseBlock(DataInput in) + private void readUltraSparseBlock(DataInput in) throws IOException { //allocate ultra-sparse block in CSR to avoid unnecessary size overhead @@ -2010,26 +1955,25 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab private void readUltraSparseToDense(DataInput in) throws IOException, DMLRuntimeException { - allocateDenseBlock(false); //allocate block - Arrays.fill(denseBlock, 0); + if( !allocateDenseBlock(false) ) //allocate block + denseBlock.reset(rlen, clen); - if( clen > 1 ) //ULTRA-SPARSE BLOCK - { + double[] a = getDenseBlockValues(); + if( clen > 1 ) { //ULTRA-SPARSE BLOCK //block: read ijv-triples for(long i=0; i<nonZeros; i++) { int r = in.readInt(); int c = in.readInt(); double val = in.readDouble(); - denseBlock[r*clen+c] = val; + a[r*clen+c] = val; } } - else //ULTRA-SPARSE COL - { + else { //ULTRA-SPARSE COL //col: read iv-pairs for(long i=0; i<nonZeros; i++) { int r = in.readInt(); double val = in.readDouble(); - denseBlock[r] = val; + a[r] = val; } } } @@ -2085,11 +2029,12 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab out.writeByte( BlockType.DENSE_BLOCK.ordinal() ); int limit=rlen*clen; + double[] a = getDenseBlockValues(); if( out instanceof MatrixBlockDataOutput ) //fast serialize - ((MatrixBlockDataOutput)out).writeDoubleArray(limit, denseBlock); + ((MatrixBlockDataOutput)out).writeDoubleArray(limit, a); else //general case (if fast serialize not supported) for(int i=0; i<limit; i++) - out.writeDouble(denseBlock[i]); + out.writeDouble(a[i]); } private void writeSparseBlock(DataOutput out) @@ -2215,28 +2160,32 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab writeNnzInfo( out, true ); long wnnz = 0; - + double[] a = getDenseBlockValues(); if( clen > 1 ) //ULTRA-SPARSE BLOCK { //block: write ijv-triples for(int r=0, ix=0; r<rlen; r++) - for(int c=0; c<clen; c++, ix++) - if( denseBlock[ix]!=0 ) { + for(int c=0; c<clen; c++, ix++) { + double aval = a[ix]; + if( aval != 0 ) { out.writeInt(r); out.writeInt(c); - out.writeDouble(denseBlock[ix]); + out.writeDouble(aval); wnnz++; } + } } else //ULTRA-SPARSE COL { //col: write iv-pairs - for(int r=0; r<rlen; r++) - if( denseBlock[r]!=0 ) { + for(int r=0; r<rlen; r++) { + double aval = a[r]; + if( aval != 0 ) { out.writeInt(r); - out.writeDouble(denseBlock[r]); + out.writeDouble(aval); wnnz++; } + } } //validity check (nnz must exactly match written nnz) @@ -2251,23 +2200,16 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab out.writeByte( BlockType.SPARSE_BLOCK.ordinal() ); //block type writeNnzInfo( out, false ); - int start=0; - for(int r=0; r<rlen; r++) - { - //count nonzeros - int nr=0; - for(int i=start; i<start+clen; i++) - if(denseBlock[i]!=0.0) - nr++; + double[] a = getDenseBlockValues(); + for(int r=0, ix=0; r<rlen; r++, ix+=clen) { + int nr = (int)denseBlock.countNonZeros(r, r+1, 0, clen); out.writeInt(nr); - for(int c=0; c<clen; c++) - { - if(denseBlock[start]!=0.0) - { + for(int c=0; c<clen; c++) { + double aval = a[ix+c]; + if( aval != 0 ) { out.writeInt(c); - out.writeDouble(denseBlock[start]); + out.writeDouble(aval); } - start++; } } } @@ -2769,9 +2711,9 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab else //DENSE <- DENSE { //allocate dense output block - ret.allocateDenseBlock(); - double[] a = denseBlock; - double[] c = ret.denseBlock; + ret.allocateDenseBlock(); + double[] a = getDenseBlockValues(); + double[] c = ret.getDenseBlockValues(); int len = m * n; //unary op, incl nnz maintenance @@ -2861,14 +2803,15 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } else { - int limit=rlen*clen; - nonZeros=0; - for(int i=0; i<limit; i++) - { - denseBlock[i]=op.fn.execute(denseBlock[i]); - if(denseBlock[i]!=0) - nonZeros++; + double[] a = getDenseBlockValues(); + int limit = rlen*clen; + long nnz = 0; + for(int i=0; i<limit; i++) { + a[i] = op.fn.execute(a[i]); + if(a[i] != 0) + nnz++; } + nonZeros = nnz; } } @@ -2892,11 +2835,12 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab allocateDenseBlock(); //compute values in-place and update nnz + double[] a = getDenseBlockValues(); final int limit = rlen*clen; int lnnz = 0; for( int i=0; i<limit; i++ ) { - denseBlock[i] = op.fn.execute(denseBlock[i]); - if( denseBlock[i]!=0 ) + a[i] = op.fn.execute(a[i]); + if( a[i]!=0 ) lnnz++; } nonZeros = lnnz; @@ -2989,9 +2933,8 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab }else if(aggOp.correctionLocation==CorrectionLocationType.LASTCOLUMN) { if(aggOp.increOp.fn instanceof Builtin - && ( ((Builtin)(aggOp.increOp.fn)).bFunc == Builtin.BuiltinCode.MAXINDEX - || ((Builtin)(aggOp.increOp.fn)).bFunc == Builtin.BuiltinCode.MININDEX ) - ){ + && ( ((Builtin)(aggOp.increOp.fn)).bFunc == Builtin.BuiltinCode.MAXINDEX + || ((Builtin)(aggOp.increOp.fn)).bFunc == Builtin.BuiltinCode.MININDEX ) ) { // *** HACK ALERT *** HACK ALERT *** HACK ALERT *** // rowIndexMax() and its siblings don't fit very well into the standard // aggregate framework. We (ab)use the "correction factor" argument to @@ -3038,10 +2981,8 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } else if(aggOp.correctionLocation==CorrectionLocationType.NONE) { - //e.g., ak+ kahan plus as used in sum, mapmult, mmcj and tsmm - if(aggOp.increOp.fn instanceof KahanPlus) - { + if(aggOp.increOp.fn instanceof KahanPlus) { LibMatrixAgg.aggregateBinaryMatrix(newWithCor, this, cor); } else @@ -3066,7 +3007,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab buffer._correction = cor.quickGetValue(r, c); buffer = (KahanObject) aggOp.increOp.fn.execute(buffer, bvals[j]); quickSetValue(r, c, buffer._sum); - cor.quickSetValue(r, c, buffer._correction); + cor.quickSetValue(r, c, buffer._correction); } } } @@ -3075,8 +3016,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab else //DENSE or SPARSE (!sparsesafe) { for(int r=0; r<rlen; r++) - for(int c=0; c<clen; c++) - { + for(int c=0; c<clen; c++) { buffer._sum=this.quickGetValue(r, c); buffer._correction=cor.quickGetValue(r, c); buffer=(KahanObject) aggOp.increOp.fn.execute(buffer, newWithCor.quickGetValue(r, c)); @@ -3217,7 +3157,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab KahanObject buffer=new KahanObject(0, 0); if(aggOp.correctionLocation==CorrectionLocationType.LASTROW) - { + { if( aggOp.increOp.fn instanceof KahanPlus ) { LibMatrixAgg.aggregateBinaryMatrix(newWithCor, this, aggOp); @@ -3445,60 +3385,44 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { //GENERIC case (any reorg operator) CellIndex temp = new CellIndex(0, 0); - if(sparse) - { - if(sparseBlock != null) - { - for(int r=0; r<Math.min(rlen, sparseBlock.numRows()); r++) - { - if(sparseBlock.isEmpty(r)) - continue; - - int apos = sparseBlock.pos(r); - int alen = sparseBlock.size(r); - int[] aix = sparseBlock.indexes(r); - double[] avals = sparseBlock.values(r); - - for(int i=apos; i<apos+alen; i++) { - tempCellIndex.set(r, aix[i]); - op.fn.execute(tempCellIndex, temp); - result.appendValue(temp.row, temp.column, avals[i]); - } + if(sparse && sparseBlock != null) { + for(int r=0; r<Math.min(rlen, sparseBlock.numRows()); r++) { + if(sparseBlock.isEmpty(r)) continue; + int apos = sparseBlock.pos(r); + int alen = sparseBlock.size(r); + int[] aix = sparseBlock.indexes(r); + double[] avals = sparseBlock.values(r); + for(int i=apos; i<apos+alen; i++) { + tempCellIndex.set(r, aix[i]); + op.fn.execute(tempCellIndex, temp); + result.appendValue(temp.row, temp.column, avals[i]); } } } - else - { - if( denseBlock != null ) + else if( !sparse && denseBlock != null ) { + if( result.isInSparseFormat() ) //SPARSE<-DENSE { - if( result.isInSparseFormat() ) //SPARSE<-DENSE - { - double[] a = denseBlock; - for( int i=0, aix=0; i<rlen; i++ ) - for( int j=0; j<clen; j++, aix++ ) - { - temp.set(i, j); - op.fn.execute(temp, temp); - result.appendValue(temp.row, temp.column, a[aix]); - } - } - else //DENSE<-DENSE - { - result.allocateDenseBlock(); - Arrays.fill(result.denseBlock, 0); - double[] a = denseBlock; - double[] c = result.denseBlock; - int n = result.clen; - - for( int i=0, aix=0; i<rlen; i++ ) - for( int j=0; j<clen; j++, aix++ ) - { - temp.set(i, j); - op.fn.execute(temp, temp); - c[temp.row*n+temp.column] = a[aix]; - } - result.nonZeros = nonZeros; - } + double[] a = getDenseBlockValues(); + for( int i=0, aix=0; i<rlen; i++ ) + for( int j=0; j<clen; j++, aix++ ) { + temp.set(i, j); + op.fn.execute(temp, temp); + result.appendValue(temp.row, temp.column, a[aix]); + } + } + else //DENSE<-DENSE + { + result.allocateDenseBlock(); + double[] a = getDenseBlockValues(); + double[] c = result.getDenseBlockValues(); + int n = result.clen; + for( int i=0, aix=0; i<rlen; i++ ) + for( int j=0; j<clen; j++, aix++ ) { + temp.set(i, j); + op.fn.execute(temp, temp); + c[temp.row*n+temp.column] = a[aix]; + } + result.nonZeros = nonZeros; } } } @@ -3686,8 +3610,8 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab throws DMLRuntimeException { return leftIndexingOperations( - rhsMatrix, (int)ixrange.rowStart, (int)ixrange.rowEnd, - (int)ixrange.colStart, (int)ixrange.colEnd, ret, update, opcode); + rhsMatrix, (int)ixrange.rowStart, (int)ixrange.rowEnd, + (int)ixrange.colStart, (int)ixrange.colEnd, ret, update, opcode); } public MatrixBlock leftIndexingOperations(MatrixBlock rhsMatrix, int rl, int ru, @@ -3713,9 +3637,9 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab (rl+1) +":" + (ru+1) + ", " + (cl+1) + ":" + (cu+1) + "]."); } - MatrixBlock result = ret; + MatrixBlock result = ret; boolean sp = estimateSparsityOnLeftIndexing(rlen, clen, nonZeros, - rhsMatrix.getNumRows(), rhsMatrix.getNumColumns(), rhsMatrix.getNonZeros()); + rhsMatrix.getNumRows(), rhsMatrix.getNumColumns(), rhsMatrix.getNonZeros()); if( !update.isInPlace() ) //general case { @@ -3748,14 +3672,13 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab // since this was factors slower, we still use a full copy and subsequently // copy(..., true) - however, this can be changed in the future once we // improved the performance of zeroout. - //result = (MatrixBlockDSM) zeroOutOperations(result, new IndexRange(rowLower,rowUpper, colLower, colUpper ), false); MatrixBlock src = (MatrixBlock)rhsMatrix; - if(rl==ru && cl==cu) { //specific case: cell update + if(rl==ru && cl==cu) { //specific case: cell update //copy single value and update nnz result.quickSetValue(rl, cl, src.quickGetValue(0, 0)); - } + } else { //general case long t1 = opcode != null && DMLScript.STATISTICS && DMLScript.FINEGRAINED_STATISTICS ? System.nanoTime() : 0; boolean isCSRCopy = false; @@ -3764,8 +3687,12 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab SparseBlockCSR sblock = (SparseBlockCSR) result.sparseBlock; if( src.sparse ) sblock.setIndexRange(rl, ru+1, cl, cu+1, src.getSparseBlock()); - else //dense - sblock.setIndexRange(rl, ru+1, cl, cu+1, src.getDenseBlock(), 0, src.getNumRows()*src.getNumColumns()); + else { //dense + double[] data = (src.getDenseBlock()!=null) ? + src.getDenseBlockValues() : null; + sblock.setIndexRange(rl, ru+1, cl, cu+1, data, + 0, src.getNumRows()*src.getNumColumns()); + } result.nonZeros = sblock.size(); isCSRCopy = true; } @@ -3903,11 +3830,12 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { //note: always dense dest dest.allocateDenseBlock(); + double[] c = dest.getDenseBlockValues(); for( int i=rl; i<=ru; i++ ) { if( !sparseBlock.isEmpty(i) ) { double val = sparseBlock.get(i, cl); if( val != 0 ) { - dest.denseBlock[i-rl] = val; + c[i-rl] = val; dest.nonZeros++; } } @@ -3950,7 +3878,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { if( clen==1 ) //vector -> vector { - System.arraycopy(denseBlock, rl, dest.denseBlock, 0, ru-rl+1); + System.arraycopy(getDenseBlockValues(), rl, dest.getDenseBlockValues(), 0, ru-rl+1); } else //matrix -> vector { @@ -3958,19 +3886,20 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab //for( int i=rl*clen+cl, ix=0; i<=ru*clen+cu; i+=clen, ix++ ) // dest.denseBlock[ix] = denseBlock[i]; int len = clen; + double[] a = getDenseBlockValues(); + double[] c = dest.getDenseBlockValues(); for( int i=rl*len+cl, ix=0; i<=ru*len+cu; i+=len, ix++ ) - dest.denseBlock[ix] = denseBlock[i]; + c[ix] = a[i]; } } else // GENERAL RANGE INDEXING { - //IBM JVM bug (JDK7) causes crash for certain cl/cu values (e.g., divide by zero for 4) - //for(int i = rl, ix1 = rl*clen+cl, ix2=0; i <= ru; i++, ix1+=clen, ix2+=dest.clen) - // System.arraycopy(denseBlock, ix1, dest.denseBlock, ix2, dest.clen); int len1 = clen; int len2 = dest.clen; + double[] a = getDenseBlockValues(); + double[] c = dest.getDenseBlockValues(); for(int i = rl, ix1 = rl*len1+cl, ix2=0; i <= ru; i++, ix1+=len1, ix2+=len2) - System.arraycopy(denseBlock, ix1, dest.denseBlock, ix2, len2); + System.arraycopy(a, ix1, c, ix2, len2); } //compute nnz of output (not maintained due to native calls) @@ -4039,15 +3968,16 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { if(denseBlock!=null) { + double[] a = getDenseBlockValues(); int i=((int)range.rowStart)*clen; int r=(int) range.rowStart; for(; r<Math.min(rowCut, range.rowEnd+1); r++) { int c=(int) range.colStart; for(; c<Math.min(colCut, range.colEnd+1); c++) - topleft.appendValue(r+normalBlockRowFactor-rowCut, c+normalBlockColFactor-colCut, denseBlock[i+c]); + topleft.appendValue(r+normalBlockRowFactor-rowCut, c+normalBlockColFactor-colCut, a[i+c]); for(; c<=range.colEnd; c++) - topright.appendValue(r+normalBlockRowFactor-rowCut, c-colCut, denseBlock[i+c]); + topright.appendValue(r+normalBlockRowFactor-rowCut, c-colCut, a[i+c]); i+=clen; } @@ -4055,9 +3985,9 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { int c=(int) range.colStart; for(; c<Math.min(colCut, range.colEnd+1); c++) - bottomleft.appendValue(r-rowCut, c+normalBlockColFactor-colCut, denseBlock[i+c]); + bottomleft.appendValue(r-rowCut, c+normalBlockColFactor-colCut, a[i+c]); for(; c<=range.colEnd; c++) - bottomright.appendValue(r-rowCut, c-colCut, denseBlock[i+c]); + bottomright.appendValue(r-rowCut, c-colCut, a[i+c]); i+=clen; } } @@ -4207,13 +4137,14 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { if(denseBlock!=null) { + double[] a = getDenseBlockValues(); if(complementary)//if selection { int offset=((int)range.rowStart)*clen; for(int r=(int) range.rowStart; r<=range.rowEnd; r++) { for(int c=(int) range.colStart; c<=range.colEnd; c++) - ((MatrixBlock) result).appendValue(r, c, denseBlock[offset+c]); + ((MatrixBlock) result).appendValue(r, c, a[offset+c]); offset+=clen; } }else @@ -4222,20 +4153,20 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab int r=0; for(; r<(int)range.rowStart; r++) for(int c=0; c<clen; c++, offset++) - ((MatrixBlock) result).appendValue(r, c, denseBlock[offset]); + ((MatrixBlock) result).appendValue(r, c, a[offset]); for(; r<=(int)range.rowEnd; r++) { for(int c=0; c<(int)range.colStart; c++) - ((MatrixBlock) result).appendValue(r, c, denseBlock[offset+c]); + ((MatrixBlock) result).appendValue(r, c, a[offset+c]); for(int c=(int)range.colEnd+1; c<clen; c++) - ((MatrixBlock) result).appendValue(r, c, denseBlock[offset+c]); + ((MatrixBlock) result).appendValue(r, c, a[offset+c]); offset+=clen; } for(; r<rlen; r++) for(int c=0; c<clen; c++, offset++) - ((MatrixBlock) result).appendValue(r, c, denseBlock[offset]); + ((MatrixBlock) result).appendValue(r, c, a[offset]); } } @@ -4348,6 +4279,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { if(denseBlock!=null) { + double[] a = getDenseBlockValues(); int limit=rlen*clen; for(int i=0; i<limit; i++) { @@ -4355,7 +4287,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab c=i%clen; tempCellIndex.set(r, c); op.indexFn.execute(tempCellIndex, tempCellIndex); - incrementalAggregateUnaryHelp(op.aggOp, result, tempCellIndex.row, tempCellIndex.column, denseBlock[i], buffer); + incrementalAggregateUnaryHelp(op.aggOp, result, tempCellIndex.row, tempCellIndex.column, a[i], buffer); } } } @@ -4473,7 +4405,9 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab } else if( !sparse && denseBlock!=null ) { //DENSE nonZeros -= recomputeNonZeros(1, rlen-1, 0, clen-1); - denseBlock = Arrays.copyOfRange(denseBlock, 0, clen); + DenseBlock tmp = DenseBlockFactory.createDenseBlock(1, clen); + tmp.set(0, getDenseBlockValues()); + denseBlock = tmp; } rlen -= step; } @@ -4492,15 +4426,16 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab lnnz += ((tmp[i] = sparseBlock.get(i, 0))!=0)? 1 : 0; cleanupBlock(true, true); sparse = false; - denseBlock = tmp; + denseBlock = DenseBlockFactory.createDenseBlock(tmp, rlen, 1); nonZeros = lnnz; } else if( !sparse && denseBlock!=null ) { //DENSE double[] tmp = new double[rlen]; + double[] a = getDenseBlockValues(); int lnnz = 0; for( int i=0, aix=0; i<rlen; i++, aix+=clen ) - lnnz += ((tmp[i] = denseBlock[aix])!=0)? 1 : 0; - denseBlock = tmp; + lnnz += ((tmp[i] = a[aix])!=0)? 1 : 0; + denseBlock = DenseBlockFactory.createDenseBlock(tmp, rlen, 1); nonZeros = lnnz; } clen -= step; @@ -4546,8 +4481,9 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab else if(denseBlock!=null) //DENSE { //always vector (see check above) + double[] a = getDenseBlockValues(); for(int i=0; i<rlen; i++) - op.fn.execute(cmobj, denseBlock[i]); + op.fn.execute(cmobj, a[i]); } return cmobj; @@ -4575,17 +4511,18 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab else if(denseBlock!=null) //DENSE { //always vectors (see check above) + double[] a = getDenseBlockValues(); if( !weights.sparse ) { - //both dense vectors (default case) + double[] w = weights.getDenseBlockValues(); if(weights.denseBlock!=null) for( int i=0; i<rlen; i++ ) - op.fn.execute(cmobj, denseBlock[i], weights.denseBlock[i]); + op.fn.execute(cmobj, a[i], w[i]); } else { for(int i=0; i<rlen; i++) - op.fn.execute(cmobj, denseBlock[i], weights.quickGetValue(i,0) ); + op.fn.execute(cmobj, a[i], weights.quickGetValue(i,0) ); } } @@ -4614,17 +4551,17 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab else if(denseBlock!=null) //DENSE { //always vectors (see check above) - if( !that.sparse ) - { - //both dense vectors (default case) - if(that.denseBlock!=null) + double[] a = getDenseBlockValues(); + if( !that.sparse ) { + if(that.denseBlock!=null) { + double[] b = that.getDenseBlockValues(); for( int i=0; i<rlen; i++ ) - op.fn.execute(covobj, denseBlock[i], that.denseBlock[i]); + op.fn.execute(covobj, a[i], b[i]); + } } - else - { + else { for(int i=0; i<rlen; i++) - op.fn.execute(covobj, denseBlock[i], that.quickGetValue(i,0)); + op.fn.execute(covobj, a[i], that.quickGetValue(i,0)); } } @@ -4658,17 +4595,21 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab else if(denseBlock!=null) //DENSE { //always vectors (see check above) + double[] a = getDenseBlockValues(); + if( !that.sparse && !weights.sparse ) { - //all dense vectors (default case) - if(that.denseBlock!=null) + double[] w = weights.getDenseBlockValues(); + if(that.denseBlock!=null) { + double[] b = that.getDenseBlockValues(); for( int i=0; i<rlen; i++ ) - op.fn.execute(covobj, denseBlock[i], that.denseBlock[i], weights.denseBlock[i]); + op.fn.execute(covobj, a[i], b[i], w[i]); + } } else { for(int i=0; i<rlen; i++) - op.fn.execute(covobj, denseBlock[i], that.quickGetValue(i,0), weights.quickGetValue(i,0)); + op.fn.execute(covobj, a[i], that.quickGetValue(i,0), weights.quickGetValue(i,0)); } } @@ -5122,7 +5063,7 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab ret.sparse = false; ret.allocateDenseBlock(); SparseBlock a = sparseBlock; - double[] c = ret.denseBlock; + double[] c = ret.getDenseBlockValues(); //initialize with replacement (since all 0 values, see SPARSITY_TURN_POINT) Arrays.fill(c, replacement); @@ -5148,8 +5089,8 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { int mn = ret.rlen * ret.clen; ret.allocateDenseBlock(); - double[] a = denseBlock; - double[] c = ret.denseBlock; + double[] a = getDenseBlockValues(); + double[] c = ret.getDenseBlockValues(); for( int i=0; i<mn; i++ ) { @@ -5769,24 +5710,13 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab sb.append(clen); sb.append("\n"); - if(sparse) - { - if( sparseBlock != null ) { - //overloaded implementation in sparse blocks - sb.append(sparseBlock.toString()); - } + if( sparse && sparseBlock != null ) { + //overloaded implementation in sparse blocks + sb.append(sparseBlock.toString()); } - else - { - if(denseBlock!=null) { - for(int i=0, ix=0; i<rlen; i++, ix+=clen) { - for(int j=0; j<clen; j++) { - sb.append(this.denseBlock[ix+j]); - sb.append("\t"); - } - sb.append("\n"); - } - } + else if( !sparse && denseBlock!=null ) { + //overloaded implementation in dense blocks + sb.append(denseBlock.toString()); } return sb.toString();
http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/runtime/util/ConvolutionUtils.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/util/ConvolutionUtils.java b/src/main/java/org/apache/sysml/runtime/util/ConvolutionUtils.java index 046dbac..87f1240 100644 --- a/src/main/java/org/apache/sysml/runtime/util/ConvolutionUtils.java +++ b/src/main/java/org/apache/sysml/runtime/util/ConvolutionUtils.java @@ -127,7 +127,7 @@ public class ConvolutionUtils { } } else { - double [] inputArr = src.getDenseBlock(); + double [] inputArr = src.getDenseBlockValues(); if(op.fn == Plus.getPlusFnObject()) { for(int i = destPos; i < src_ru*destNumCols; i++) { dest[i] += inputArr[i]; @@ -163,7 +163,7 @@ public class ConvolutionUtils { } } else { - double [] inputArr = src.getDenseBlock(); + double [] inputArr = src.getDenseBlockValues(); for(int i = destPos; i < src_ru*destNumCols; i++) { dest[i] = scalarOp.executeScalar(inputArr[i]); } @@ -186,7 +186,7 @@ public class ConvolutionUtils { } } else { - double [] biasArr = bias.getDenseBlock(); + double [] biasArr = bias.getDenseBlockValues(); for(int n = src_rl; n < src_ru; n++) { for(int k = 0; k < K; k++) { int fromIndex = n*K*PQ + k*PQ; http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/runtime/util/DataConverter.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/util/DataConverter.java b/src/main/java/org/apache/sysml/runtime/util/DataConverter.java index c558ebd..fdc7af0 100644 --- a/src/main/java/org/apache/sysml/runtime/util/DataConverter.java +++ b/src/main/java/org/apache/sysml/runtime/util/DataConverter.java @@ -233,19 +233,18 @@ public class DataConverter if( mb.getNonZeros() > 0 ) { - if( mb.isInSparseFormat() ) - { + if( mb.isInSparseFormat() ) { Iterator<IJV> iter = mb.getSparseBlockIterator(); while( iter.hasNext() ) { IJV cell = iter.next(); ret[cell.getI()][cell.getJ()] = cell.getV(); } } - else - { - for( int i=0; i<rows; i++ ) - for( int j=0; j<cols; j++ ) - ret[i][j] = mb.getValueDenseUnsafe(i, j); + else { + double[] a = mb.getDenseBlockValues(); + for( int i=0, ix=0; i<rows; i++ ) + for( int j=0; j<cols; j++, ix++ ) + ret[i][j] = a[ix]; } } @@ -332,7 +331,7 @@ public class DataConverter int rows = mb.getNumRows(); int cols = mb.getNumColumns(); double[] ret = (!mb.isInSparseFormat() && mb.isAllocated() && !deep) ? - mb.getDenseBlock() : new double[rows*cols]; //0-initialized + mb.getDenseBlockValues() : new double[rows*cols]; //0-initialized if( !mb.isEmptyBlock(false) ) { @@ -345,7 +344,7 @@ public class DataConverter } else if( deep ) { //memcopy row major representation if at least 1 non-zero - System.arraycopy(mb.getDenseBlock(), 0, ret, 0, rows*cols); + System.arraycopy(mb.getDenseBlockValues(), 0, ret, 0, rows*cols); } } @@ -542,7 +541,7 @@ public class DataConverter // special case double schema (without cell-object creation, // cache-friendly row-column copy) double[][] a = new double[n][]; - double[] c = mb.getDenseBlock(); + double[] c = mb.getDenseBlockValues(); for( int j=0; j<n; j++ ) a[j] = (double[])frame.getColumnData(j); int blocksizeIJ = 16; //blocks of a+overhead/c in L1 cache @@ -680,14 +679,14 @@ public class DataConverter // allows for a shallow copy since the physical representation // of row-major matrix and column-major frame match exactly frame.reset(); - frame.appendColumns(new double[][]{mb.getDenseBlock()}); + frame.appendColumns(new double[][]{mb.getDenseBlockValues()}); } else if( dFreq == schema.length ) { // special case double schema (without cell-object creation, // col pre-allocation, and cache-friendly row-column copy) int m = mb.getNumRows(); int n = mb.getNumColumns(); - double[] a = mb.getDenseBlock(); + double[] a = mb.getDenseBlockValues(); double[][] c = new double[n][m]; int blocksizeIJ = 16; //blocks of a/c+overhead in L1 cache if( !mb.isEmptyBlock(false) ) @@ -780,7 +779,7 @@ public class DataConverter { MatrixBlock mb = mo.acquireRead(); double[][] data = DataConverter.convertToDoubleMatrix(mb); - mo.release(); + mo.release(); return new Array2DRowRealMatrix(data, false); } @@ -801,7 +800,7 @@ public class DataConverter } else { //memcopy row major representation if at least 1 non-zero - System.arraycopy(mb.getDenseBlock(), 0, dest, destPos, rows*cols); + System.arraycopy(mb.getDenseBlockValues(), 0, dest, destPos, rows*cols); } } http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/runtime/util/FastBufferedDataOutputStream.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/util/FastBufferedDataOutputStream.java b/src/main/java/org/apache/sysml/runtime/util/FastBufferedDataOutputStream.java index 9130e15..6173587 100644 --- a/src/main/java/org/apache/sysml/runtime/util/FastBufferedDataOutputStream.java +++ b/src/main/java/org/apache/sysml/runtime/util/FastBufferedDataOutputStream.java @@ -74,22 +74,22 @@ public class FastBufferedDataOutputStream extends FilterOutputStream implements _buff[_count++] = (byte)b; } - @Override - public void write(byte[] b, int off, int len) - throws IOException - { + @Override + public void write(byte[] b, int off, int len) + throws IOException + { if (len >= _bufflen) { - flushBuffer(); - out.write(b, off, len); - return; + flushBuffer(); + out.write(b, off, len); + return; } if (len > _bufflen - _count) { - flushBuffer(); + flushBuffer(); } System.arraycopy(b, off, _buff, _count, len); _count += len; - } - + } + @Override public void flush() throws IOException http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/runtime/util/SortUtils.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/util/SortUtils.java b/src/main/java/org/apache/sysml/runtime/util/SortUtils.java index ff90784..28db1cd 100644 --- a/src/main/java/org/apache/sysml/runtime/util/SortUtils.java +++ b/src/main/java/org/apache/sysml/runtime/util/SortUtils.java @@ -48,7 +48,7 @@ public class SortUtils public static boolean isSorted(MatrixBlock in) { return in.isInSparseFormat() ? false : !in.isAllocated() ? true : - isSorted(0, in.getNumRows()*in.getNumColumns(), in.getDenseBlock()); + isSorted(0, in.getNumRows()*in.getNumColumns(), in.getDenseBlockValues()); } public static int compare(double[] d1, double[] d2) { http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/udf/lib/CumSumProd.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/udf/lib/CumSumProd.java b/src/main/java/org/apache/sysml/udf/lib/CumSumProd.java index e6a0aaa..e9edb0a 100644 --- a/src/main/java/org/apache/sysml/udf/lib/CumSumProd.java +++ b/src/main/java/org/apache/sysml/udf/lib/CumSumProd.java @@ -114,7 +114,7 @@ public class CumSumProd extends PackageFunction { allocateOutput(); // Copy X to Y - denseBlock = retMB.getDenseBlock(); + denseBlock = retMB.getDenseBlockValues(); if(X.isInSparseFormat()) { Iterator<IJV> iter = X.getSparseBlockIterator(); while(iter.hasNext()) { @@ -124,7 +124,7 @@ public class CumSumProd extends PackageFunction { } else { if(X.getDenseBlock() != null) - System.arraycopy(X.getDenseBlock(), 0, denseBlock, 0, denseBlock.length); + System.arraycopy(X.getDenseBlockValues(), 0, denseBlock, 0, denseBlock.length); } if(!isReverse) { @@ -181,7 +181,7 @@ public class CumSumProd extends PackageFunction { } } else { - double [] CBlk = C.getDenseBlock(); + double [] CBlk = C.getDenseBlockValues(); if(CBlk != null) { if(!isCVector) { for(int j = i*numRetCols; j < (i+1)*numRetCols; j++) { @@ -219,7 +219,7 @@ public class CumSumProd extends PackageFunction { } } else { - double [] CBlk = C.getDenseBlock(); + double [] CBlk = C.getDenseBlockValues(); if(CBlk != null) { if(!isCVector) { for(int j = i*numRetCols; j < (i+1)*numRetCols; j++) { http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/udf/lib/MultiInputCbind.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/udf/lib/MultiInputCbind.java b/src/main/java/org/apache/sysml/udf/lib/MultiInputCbind.java index 30d3571..e56523c 100644 --- a/src/main/java/org/apache/sysml/udf/lib/MultiInputCbind.java +++ b/src/main/java/org/apache/sysml/udf/lib/MultiInputCbind.java @@ -96,7 +96,7 @@ public class MultiInputCbind extends PackageFunction { allocateOutput(); // Performs cbind (cbind (cbind ( X1, X2 ), X3 ), X4) - double [] retData = retMB.getDenseBlock(); + double [] retData = retMB.getDenseBlockValues(); try { int startColumn = 0; for(int inputID = 2; inputID < numInputs + 2; inputID++) { @@ -126,7 +126,7 @@ public class MultiInputCbind extends PackageFunction { } } else { - double [] denseBlock = in.getDenseBlock(); + double [] denseBlock = in.getDenseBlockValues(); if(denseBlock != null) { if(spagetize) { // Perform matrix(X1, rows=length(X1), cols=1) operation before cbind http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/udf/lib/RowClassMeet.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/udf/lib/RowClassMeet.java b/src/main/java/org/apache/sysml/udf/lib/RowClassMeet.java index 273c7d8..671752f 100644 --- a/src/main/java/org/apache/sysml/udf/lib/RowClassMeet.java +++ b/src/main/java/org/apache/sysml/udf/lib/RowClassMeet.java @@ -98,8 +98,8 @@ public class RowClassMeet extends PackageFunction { int nc = Math.max(A.getNumColumns(), B.getNumColumns()); MatrixBlock C = new MatrixBlock(nr, nc, false).allocateBlock(); MatrixBlock N = new MatrixBlock(nr, nc, false).allocateBlock(); - double[] dC = C.getDenseBlock(); - double[] dN = N.getDenseBlock(); + double[] dC = C.getDenseBlockValues(); + double[] dN = N.getDenseBlockValues(); //wrap both A and B into side inputs for efficient sparse access SideInput sB = CodegenUtils.createSideInput(B); boolean mv = (B.getNumRows() == 1); @@ -128,7 +128,7 @@ public class RowClassMeet extends PackageFunction { } } else { - double [] denseBlk = A.getDenseBlock(); + double [] denseBlk = A.getDenseBlockValues(); if(denseBlk == null) break; for(int j = 0; j < numCols; j++) { int aVal = (int) denseBlk[ai+j]; http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/java/org/apache/sysml/udf/lib/SGDNesterovUpdate.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/udf/lib/SGDNesterovUpdate.java b/src/main/java/org/apache/sysml/udf/lib/SGDNesterovUpdate.java index 1a16b57..a644969 100644 --- a/src/main/java/org/apache/sysml/udf/lib/SGDNesterovUpdate.java +++ b/src/main/java/org/apache/sysml/udf/lib/SGDNesterovUpdate.java @@ -86,11 +86,11 @@ public class SGDNesterovUpdate extends PackageFunction { // v = mu * v - lr * dX - lr*lambda*X updatedV = new Matrix( "tmp_" + rand.nextLong(), v.getNumRows(), v.getNumColumns(), ValueType.Double ); MatrixBlock updatedVMB = allocateDenseMatrixBlock(updatedV); - double [] updatedVData = updatedVMB.getDenseBlock(); + double [] updatedVData = updatedVMB.getDenseBlockValues(); if(isDense(v) && isDense(dX) && isDense(X)) { - double [] vArr = v.getDenseBlock(); - double [] dXArr = dX.getDenseBlock(); - double [] XArr = X.getDenseBlock(); + double [] vArr = v.getDenseBlockValues(); + double [] dXArr = dX.getDenseBlockValues(); + double [] XArr = X.getDenseBlockValues(); int nnz = 0; for(int i = 0; i < updatedVData.length; i++) { updatedVData[i] = mu*vArr[i] - lr*dXArr[i] - lr*lambda*XArr[i]; @@ -110,10 +110,10 @@ public class SGDNesterovUpdate extends PackageFunction { // X = X - mu * v_prev + (1 + mu) * v updatedX = new Matrix( "tmp_" + rand.nextLong(), X.getNumRows(), X.getNumColumns(), ValueType.Double ); MatrixBlock updatedXMB = allocateDenseMatrixBlock(updatedX); - double [] updatedXData = updatedXMB.getDenseBlock(); + double [] updatedXData = updatedXMB.getDenseBlockValues(); if(isDense(X) && isDense(v)) { - double [] XArr = X.getDenseBlock(); - double [] vPrevArr = v.getDenseBlock(); + double [] XArr = X.getDenseBlockValues(); + double [] vPrevArr = v.getDenseBlockValues(); int nnz = 0; double muPlus1 = mu+1; for(int i = 0; i < updatedXData.length; i++) { updatedXData[i] = XArr[i] - mu*vPrevArr[i] + muPlus1*updatedVData[i]; @@ -123,7 +123,7 @@ public class SGDNesterovUpdate extends PackageFunction { } else if(isDense(v)) { copy(X, updatedXData); - double [] vPrevArr = v.getDenseBlock(); + double [] vPrevArr = v.getDenseBlockValues(); int nnz = 0; double muPlus1 = mu+1; for(int i = 0; i < updatedXData.length; i++) { updatedXData[i] += - mu*vPrevArr[i] + muPlus1*updatedVData[i]; @@ -172,7 +172,7 @@ public class SGDNesterovUpdate extends PackageFunction { } } else { - double [] denseBlock = in.getDenseBlock(); + double [] denseBlock = in.getDenseBlockValues(); if(denseBlock != null) { // If not empty block for(int i = 0; i < out.length; i++) { @@ -192,7 +192,7 @@ public class SGDNesterovUpdate extends PackageFunction { } } else { - double [] denseBlock = src.getDenseBlock(); + double [] denseBlock = src.getDenseBlockValues(); if(denseBlock != null) { // If not empty block System.arraycopy(denseBlock, 0, dest, 0, dest.length); http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/main/scala/org/apache/sysml/api/dl/Utils.scala ---------------------------------------------------------------------- diff --git a/src/main/scala/org/apache/sysml/api/dl/Utils.scala b/src/main/scala/org/apache/sysml/api/dl/Utils.scala index 5d43730..19596c3 100644 --- a/src/main/scala/org/apache/sysml/api/dl/Utils.scala +++ b/src/main/scala/org/apache/sysml/api/dl/Utils.scala @@ -126,7 +126,7 @@ object Utils { def allocateDeconvolutionWeight(data: java.util.List[java.lang.Float], F: Int, C: Int, H: Int, W: Int): (MatrixBlock, CopyFloatToDoubleArray) = { val mb = new MatrixBlock(C, F * H * W, false) mb.allocateDenseBlock() - val arr = mb.getDenseBlock + val arr = mb.getDenseBlockValues val thread = new CopyCaffeDeconvFloatToSystemMLDeconvDoubleArray(data, F, C, H, W, arr) thread.start return (mb, thread) @@ -135,7 +135,7 @@ object Utils { def allocateMatrixBlock(data: java.util.List[java.lang.Float], rows: Int, cols: Int, transpose: Boolean): (MatrixBlock, CopyFloatToDoubleArray) = { val mb = new MatrixBlock(rows, cols, false) mb.allocateDenseBlock() - val arr = mb.getDenseBlock + val arr = mb.getDenseBlockValues val thread = new CopyFloatToDoubleArray(data, rows, cols, transpose, arr) thread.start return (mb, thread) http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/test/java/org/apache/sysml/test/integration/functions/codegen/CPlanVectorPrimitivesTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/sysml/test/integration/functions/codegen/CPlanVectorPrimitivesTest.java b/src/test/java/org/apache/sysml/test/integration/functions/codegen/CPlanVectorPrimitivesTest.java index 36f9f58..c2c4704 100644 --- a/src/test/java/org/apache/sysml/test/integration/functions/codegen/CPlanVectorPrimitivesTest.java +++ b/src/test/java/org/apache/sysml/test/integration/functions/codegen/CPlanVectorPrimitivesTest.java @@ -662,7 +662,7 @@ public class CPlanVectorPrimitivesTest extends AutomatedTestBase for( int i=0; i<m; i++ ) { //execute vector primitive via reflection Double ret1 = (Double) ((type1 == InputType.VECTOR_DENSE) ? - me.invoke(null, in.getDenseBlock(), i*n, n) : + me.invoke(null, in.getDenseBlockValues(), i*n, n) : me.invoke(null, in.getSparseBlock().values(i), in.getSparseBlock().indexes(i), in.getSparseBlock().pos(i), in.getSparseBlock().size(i), n)); @@ -700,7 +700,7 @@ public class CPlanVectorPrimitivesTest extends AutomatedTestBase for( int i=0; i<m; i++ ) { //execute vector primitive via reflection double[] ret1 = (double[]) ((type1 == InputType.VECTOR_DENSE) ? - me.invoke(null, in.getDenseBlock(), i*n, n) : + me.invoke(null, in.getDenseBlockValues(), i*n, n) : me.invoke(null, in.getSparseBlock().values(i), in.getSparseBlock().indexes(i), in.getSparseBlock().pos(i), in.getSparseBlock().size(i), n)); @@ -749,11 +749,11 @@ public class CPlanVectorPrimitivesTest extends AutomatedTestBase //execute vector primitive via reflection double[] ret1 = null; if( type1==InputType.SCALAR && type2==InputType.VECTOR_DENSE ) - ret1 = (double[]) me.invoke(null, inA.max(), inB.getDenseBlock(), i*n, n); + ret1 = (double[]) me.invoke(null, inA.max(), inB.getDenseBlockValues(), i*n, n); else if( type1==InputType.VECTOR_DENSE && type2==InputType.SCALAR ) - ret1 = (double[]) me.invoke(null, inA.getDenseBlock(), inB.max(), i*n, n); + ret1 = (double[]) me.invoke(null, inA.getDenseBlockValues(), inB.max(), i*n, n); else if( type1==InputType.VECTOR_DENSE && type2==InputType.VECTOR_DENSE ) - ret1 = (double[]) me.invoke(null, inA.getDenseBlock(), inB.getDenseBlock(), i*n, i*n, n); + ret1 = (double[]) me.invoke(null, inA.getDenseBlockValues(), inB.getDenseBlockValues(), i*n, i*n, n); else if( type1==InputType.VECTOR_SPARSE && type2==InputType.SCALAR ) ret1 = (double[]) me.invoke(null, inA.getSparseBlock().values(i), inB.max(), inA.getSparseBlock().indexes(i), inA.getSparseBlock().pos(i), inA.getSparseBlock().size(i), n); @@ -761,7 +761,7 @@ public class CPlanVectorPrimitivesTest extends AutomatedTestBase ret1 = (double[]) me.invoke(null, inA.max(), inB.getSparseBlock().values(i), inB.getSparseBlock().indexes(i), inB.getSparseBlock().pos(i), inB.getSparseBlock().size(i), n); else if( type1==InputType.VECTOR_SPARSE && type2==InputType.VECTOR_DENSE ) - ret1 = (double[]) me.invoke(null, inA.getSparseBlock().values(i), inB.getDenseBlock(), + ret1 = (double[]) me.invoke(null, inA.getSparseBlock().values(i), inB.getDenseBlockValues(), inA.getSparseBlock().indexes(i), inA.getSparseBlock().pos(i), i*n, inA.getSparseBlock().size(i), n); //execute comparison operation http://git-wip-us.apache.org/repos/asf/systemml/blob/e6424695/src/test/java/org/apache/sysml/test/integration/functions/unary/matrix/SVDFactorizeTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/sysml/test/integration/functions/unary/matrix/SVDFactorizeTest.java b/src/test/java/org/apache/sysml/test/integration/functions/unary/matrix/SVDFactorizeTest.java index 8623d32..12bd853 100644 --- a/src/test/java/org/apache/sysml/test/integration/functions/unary/matrix/SVDFactorizeTest.java +++ b/src/test/java/org/apache/sysml/test/integration/functions/unary/matrix/SVDFactorizeTest.java @@ -34,15 +34,15 @@ public class SVDFactorizeTest extends AutomatedTestBase private static final String TEST_CLASS_DIR = TEST_DIR + SVDFactorizeTest.class.getSimpleName() + "/"; private final static int rows1 = 500; - private final static int rows2 = 2500; + private final static int rows2 = 1500; private final static int cols1 = 400; - private final static int cols2 = 2200; + private final static int cols2 = 1200; private final static double sparsity = 0.9; @Override public void setUp() { addTestConfiguration(TEST_NAME1, - new TestConfiguration(TEST_CLASS_DIR, TEST_NAME1, new String[] { "D" }) ); + new TestConfiguration(TEST_CLASS_DIR, TEST_NAME1, new String[] { "D" })); } @Test @@ -86,7 +86,7 @@ public class SVDFactorizeTest extends AutomatedTestBase } private void runTestSVDFactorize( int rows, int cols, RUNTIME_PLATFORM rt) - { + { RUNTIME_PLATFORM rtold = rtplatform; rtplatform = rt; @@ -109,10 +109,9 @@ public class SVDFactorizeTest extends AutomatedTestBase // Expected matrix = 1x1 zero matrix double[][] D = new double[1][1]; D[0][0] = 0.0; - writeExpectedMatrix("D", D); + writeExpectedMatrix("D", D); - boolean exceptionExpected = false; - runTest(true, exceptionExpected, null, -1); + runTest(true, false, null, -1); compareResults(1e-8); } finally { @@ -121,5 +120,4 @@ public class SVDFactorizeTest extends AutomatedTestBase } } - }
