fix docs

src/main/java/org/apache/sysds/runtime/compress/colgroup/dictionary/IDictionary.java

@@ -291,6 +291,8 @@ public IDictionary binOpRightWithReference(BinaryOperator op, double[] v, IColIn
 
 	/**
 	 * Returns a deep clone of the dictionary.
+	 * 
+	 * @return A deep clone
 	 */
 	public IDictionary clone();
 

src/main/java/org/apache/sysds/runtime/compress/colgroup/scheme/ACLAScheme.java

@@ -44,6 +44,44 @@ public ICLAScheme update(MatrixBlock data) {
 		return update(data, getColIndices());
 	}
 
+
+	@Override
+	public ICLAScheme updateSparse(MatrixBlock data) {
+		// fallback to default
+		return updateSparse(data, getColIndices());
+	}
+
+	@Override
+	public ICLAScheme updateDense(MatrixBlock data) {
+		// fallback to default
+		return updateDense(data, getColIndices());
+	}
+
+	@Override
+	public ICLAScheme updateGeneric(MatrixBlock data) {
+		// fallback to default
+		return updateGeneric(data, getColIndices());
+	}
+
+
+	@Override
+	public ICLAScheme updateSparse(MatrixBlock data, IColIndex columns) {
+		// fallback to default
+		return update(data, columns);
+	}
+
+	@Override
+	public ICLAScheme updateDense(MatrixBlock data, IColIndex columns) {
+		// fallback to default
+		return update(data, columns);
+	}
+
+	@Override
+	public ICLAScheme updateGeneric(MatrixBlock data, IColIndex columns) {
+		// fallback to default
+		return update(data, columns);
+	}
+
 	protected final void validate(MatrixBlock data, IColIndex columns) throws IllegalArgumentException {
 		if(columns.size() != cols.size())
 			throw new IllegalArgumentException(
@@ -54,4 +92,6 @@ protected final void validate(MatrixBlock data, IColIndex columns) throws Illega
 			throw new IllegalArgumentException("Invalid columns to encode with max col:" + nCol+ " list of columns: "+ columns);
 	}
 
+
+
 }

src/main/java/org/apache/sysds/runtime/compress/colgroup/scheme/CompressionScheme.java

@@ -66,7 +66,8 @@ public ICLAScheme get(int i) {
 	 */
 	public CompressedMatrixBlock encode(MatrixBlock mb) {
 		if(mb instanceof CompressedMatrixBlock)
-			throw new NotImplementedException("Not implemented schema encode/apply on an already compressed MatrixBlock");
+			throw new NotImplementedException(
+				"Not implemented schema encode/apply on an already compressed MatrixBlock");
 
 		List<AColGroup> ret = new ArrayList<>(encodings.length);
 
@@ -116,7 +117,8 @@ public CompressedMatrixBlock encode(MatrixBlock mb, int k) {
 	 */
 	public CompressionScheme update(MatrixBlock mb) {
 		if(mb instanceof CompressedMatrixBlock)
-			throw new NotImplementedException("Not implemented schema encode/apply on an already compressed MatrixBlock");
+			throw new NotImplementedException(
+				"Not implemented schema encode/apply on an already compressed MatrixBlock");
 
 		for(int i = 0; i < encodings.length; i++)
 			encodings[i] = encodings[i].update(mb);
@@ -182,18 +184,22 @@ public static CompressionScheme getScheme(CompressedMatrixBlock cmb) {
 	public CompressedMatrixBlock updateAndEncode(MatrixBlock mb, int k) {
 		if(k == 1)
 			return updateAndEncode(mb);
+
 		final ExecutorService pool = CommonThreadPool.get(k);
 		try {
-
+			final int nCol = mb.getNumColumns();
+			AColGroup[] ret = new AColGroup[encodings.length];
 			List<UpdateAndEncodeTask> tasks = new ArrayList<>();
-			for(int i = 0; i < encodings.length; i++)
-				tasks.add(new UpdateAndEncodeTask(i, encodings[i], mb));
+			// int taskSize = Math.max(1, encodings.length / (4 * k));
+			int taskSize = 1;
+			for(int i = 0; i < encodings.length; i += taskSize)
+				tasks.add(new UpdateAndEncodeTask(i, Math.min(encodings.length, i + taskSize), ret, mb));
 
-			List<AColGroup> ret = new ArrayList<>(encodings.length);
-			for(Future<AColGroup> t : pool.invokeAll(tasks))
-				ret.add(t.get());
+			for(Future<Object> t : pool.invokeAll(tasks))
+				t.get();
 
-			return new CompressedMatrixBlock(mb.getNumRows(), mb.getNumColumns(), mb.getNonZeros(), false, ret);
+			List<AColGroup> retA = new ArrayList<>(Arrays.asList(ret));
+			return new CompressedMatrixBlock(mb.getNumRows(), nCol, mb.getNonZeros(), false, retA);
 
 		}
 		catch(Exception e) {
@@ -206,7 +212,8 @@ public CompressedMatrixBlock updateAndEncode(MatrixBlock mb, int k) {
 
 	public CompressedMatrixBlock updateAndEncode(MatrixBlock mb) {
 		if(mb instanceof CompressedMatrixBlock)
-			throw new NotImplementedException("Not implemented schema encode/apply on an already compressed MatrixBlock");
+			throw new NotImplementedException(
+				"Not implemented schema encode/apply on an already compressed MatrixBlock");
 
 		List<AColGroup> ret = new ArrayList<>(encodings.length);
 
@@ -258,21 +265,31 @@ public ICLAScheme call() throws Exception {
 		}
 	}
 
-	protected class UpdateAndEncodeTask implements Callable<AColGroup> {
+	protected class UpdateAndEncodeTask implements Callable<Object> {
 		final int i;
-		final ICLAScheme enc;
+		final int e;
 		final MatrixBlock mb;
+		final AColGroup[] ret;
 
-		protected UpdateAndEncodeTask(int i, ICLAScheme enc, MatrixBlock mb) {
+		protected UpdateAndEncodeTask(int i, int e, AColGroup[] ret, MatrixBlock mb) {
 			this.i = i;
-			this.enc = enc;
+			this.e = e;
 			this.mb = mb;
+			this.ret = ret;
 		}
 
 		@Override
-		public AColGroup call() throws Exception {
-			encodings[i] = enc.update(mb);
-			return enc.encode(mb);
+		public Object call() throws Exception {
+			final boolean dense = mb.getDenseBlock().isContiguous();
+
+			for(int j = i; j < e; j++) {
+				if(dense)
+					encodings[j] = encodings[j].updateDense(mb);
+				else
+					encodings[j] = encodings[j].update(mb);
+				ret[j] = encodings[j].encode(mb);
+			}
+			return null;
 		}
 	}
 }

src/main/java/org/apache/sysds/runtime/compress/colgroup/scheme/DDCSchemeSC.java

@@ -60,44 +60,51 @@ protected final Object getMap() {
 	@Override
 	public ICLAScheme update(MatrixBlock data, IColIndex columns) {
 		validate(data, columns);
-		final int col = columns.get(0);
 		if(data.isEmpty())
 			map.increment(0.0, data.getNumRows());
 		else if(data.isInSparseFormat())
-			updateSparse(data, col);
+			updateSparse(data, columns);
 		else if(data.getDenseBlock().isContiguous())
-			updateDense(data, col);
+			updateDense(data, columns);
 		else
-			updateGeneric(data, col);
+			updateGeneric(data, columns);
 
 		return this;
 	}
 
-	private void updateSparse(MatrixBlock data, int col) {
+	@Override
+	public ICLAScheme updateSparse(MatrixBlock data, IColIndex columns) {
+		final int col = columns.get(0);
 		final int nRow = data.getNumRows();
 		final SparseBlock sb = data.getSparseBlock();
 		for(int i = 0; i < nRow; i++)
 			map.increment(sb.get(i, col));
+		return this;
 	}
 
-	private void updateDense(MatrixBlock data, int col) {
+	@Override
+	public ICLAScheme updateDense(MatrixBlock data, IColIndex columns) {
+		final int col = columns.get(0);
 		final int nRow = data.getNumRows();
 		final double[] vals = data.getDenseBlockValues();
 		final int nCol = data.getNumColumns();
 		final int max = nRow * nCol; // guaranteed lower than intmax.
 		for(int off = col; off < max; off += nCol)
 			map.increment(vals[off]);
-
+		return this;
 	}
 
-	private void updateGeneric(MatrixBlock data, int col) {
+	@Override
+	public ICLAScheme updateGeneric(MatrixBlock data, IColIndex columns) {
+		final int col = columns.get(0);
 		final int nRow = data.getNumRows();
 		final DenseBlock db = data.getDenseBlock();
 		for(int i = 0; i < nRow; i++) {
 			final double[] c = db.values(i);
 			final int off = db.pos(i) + col;
 			map.increment(c[off]);
 		}
+		return this;
 	}
 
 	@Override

src/main/java/org/apache/sysds/runtime/compress/colgroup/scheme/ICLAScheme.java

@@ -43,10 +43,10 @@ public interface ICLAScheme {
 
 	/**
 	 * Encode the given matrix block into the scheme provided in the instance.
-	 * 	 
 	 * 
-	 * The method is unsafe in the sense that if the encoding scheme does not fit, there is no guarantee that an error is
-	 * thrown. To guarantee the encoding scheme, first use update on the matrix block and used the returned scheme to
+	 * 
+	 * The method is unsafe in the sense that if the encoding scheme does not fit, there is no guarantee that an error
+	 * is thrown. To guarantee the encoding scheme, first use update on the matrix block and used the returned scheme to
 	 * ensure consistency.
 	 * 
 	 * @param data The data to encode
@@ -59,8 +59,8 @@ public interface ICLAScheme {
 	/**
 	 * Encode a given matrix block into the scheme provided in the instance but overwrite what columns to use.
 	 * 
-	 * The method is unsafe in the sense that if the encoding scheme does not fit, there is no guarantee that an error is
-	 * thrown. To guarantee the encoding scheme, first use update on the matrix block and used the returned scheme to
+	 * The method is unsafe in the sense that if the encoding scheme does not fit, there is no guarantee that an error
+	 * is thrown. To guarantee the encoding scheme, first use update on the matrix block and used the returned scheme to
 	 * ensure consistency.
 	 * 
 	 * @param data    The data to encode
@@ -75,7 +75,7 @@ public interface ICLAScheme {
 	 * Update the encoding scheme to enable compression of the given data.
 	 * 
 	 * @param data The data to update into the scheme
-	 * @return A updated scheme 
+	 * @return A updated scheme
 	 */
 	public ICLAScheme update(MatrixBlock data);
 
@@ -84,8 +84,20 @@ public interface ICLAScheme {
 	 * 
 	 * @param data    The data to update into the scheme
 	 * @param columns The columns to extract the data from
-	 * @return A updated scheme 
+	 * @return A updated scheme
 	 */
 	public ICLAScheme update(MatrixBlock data, IColIndex columns);
 
+	public ICLAScheme updateSparse(MatrixBlock sparseBlock);
+
+	public ICLAScheme updateDense(MatrixBlock denseBlock);
+
+	public ICLAScheme updateGeneric(MatrixBlock largeDenseBlock);
+
+	public ICLAScheme updateSparse(MatrixBlock sparseBlock, IColIndex columns);
+
+	public ICLAScheme updateDense(MatrixBlock denseBlock, IColIndex columns);
+
+	public ICLAScheme updateGeneric(MatrixBlock largeDenseBlock, IColIndex columns);
+
 }

src/main/java/org/apache/sysds/runtime/compress/io/WriterCompressed.java

@@ -155,8 +155,9 @@ else if(!(src instanceof CompressedMatrixBlock))
 	private void writeSingleBlock(MatrixBlock b, int k) throws IOException {
 		Writer w = getWriter(fname);
 		MatrixIndexes idx = new MatrixIndexes(1, 1);
-		MatrixBlock mc = CompressedMatrixBlockFactory.compress(b, k).getLeft();
-		w.append(idx, new CompressedWriteBlock(mc));
+		if(!(b instanceof CompressedMatrixBlock))
+			b = CompressedMatrixBlockFactory.compress(b, k).getLeft();
+		w.append(idx, new CompressedWriteBlock(b));
 		IOUtilFunctions.closeSilently(w);
 		cleanup();
 	}

src/main/java/org/apache/sysds/runtime/compress/lib/CLALibSeparator.java

@@ -63,7 +63,7 @@ public static SeparatedGroups split(List<AColGroup> gs) {
 	 * Combine a set of separated groups back together.
 	 * 
 	 * @param s A Separated group of indexStructures
-	 * @return
+	 * @return A combined list of columngroups.
 	 */
 	public static List<AColGroup> combine(SeparatedGroups s) {
 		throw new NotImplementedException();