[SYSTEMML-2225] Fix reblock ultra-sparse, incl mem efficiency read This patch fixes the robustness of reblocking ultra-sparse matrices by hardening the CSR index lookups, and better handling of empty blocks on reblock. Furthermore, this also includes a fix for avoiding unnecessary csr block creation on initial read for empty blocks.
Project: http://git-wip-us.apache.org/repos/asf/systemml/repo Commit: http://git-wip-us.apache.org/repos/asf/systemml/commit/addd6e12 Tree: http://git-wip-us.apache.org/repos/asf/systemml/tree/addd6e12 Diff: http://git-wip-us.apache.org/repos/asf/systemml/diff/addd6e12 Branch: refs/heads/master Commit: addd6e121ac8d81af0f90859666b9ac1ec1e5009 Parents: c516145 Author: Matthias Boehm <mboe...@gmail.com> Authored: Sat Mar 31 19:06:19 2018 -0700 Committer: Matthias Boehm <mboe...@gmail.com> Committed: Sat Mar 31 21:27:34 2018 -0700 ---------------------------------------------------------------------- .../spark/functions/CopyBlockPairFunction.java | 2 +- .../functions/ExtractBlockForBinaryReblock.java | 31 ++++++++++---------- .../sysml/runtime/matrix/data/MatrixBlock.java | 8 +++-- .../runtime/matrix/data/SparseBlockCSR.java | 7 +++-- 4 files changed, 26 insertions(+), 22 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/systemml/blob/addd6e12/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/CopyBlockPairFunction.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/CopyBlockPairFunction.java b/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/CopyBlockPairFunction.java index 5423a8f..8ff6c2a 100644 --- a/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/CopyBlockPairFunction.java +++ b/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/CopyBlockPairFunction.java @@ -71,7 +71,7 @@ public class CopyBlockPairFunction implements PairFlatMapFunction<Iterator<Tuple MatrixIndexes ix = new MatrixIndexes(arg._1()); MatrixBlock block = null; //always create deep copies in more memory-efficient CSR representation - //if block is already in sparse format + //if block is already in sparse format if( Checkpoint.CHECKPOINT_SPARSE_CSR && arg._2.isInSparseFormat() ) block = new MatrixBlock(arg._2, SparseBlock.Type.CSR, true); else http://git-wip-us.apache.org/repos/asf/systemml/blob/addd6e12/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/ExtractBlockForBinaryReblock.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/ExtractBlockForBinaryReblock.java b/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/ExtractBlockForBinaryReblock.java index a2a1ce0..66a2271 100644 --- a/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/ExtractBlockForBinaryReblock.java +++ b/src/main/java/org/apache/sysml/runtime/instructions/spark/functions/ExtractBlockForBinaryReblock.java @@ -70,37 +70,36 @@ public class ExtractBlockForBinaryReblock implements PairFlatMapFunction<Tuple2< long endRowGlobalCellIndex = getEndGlobalIndex(ixIn.getRowIndex(), true, true); long startColGlobalCellIndex = UtilFunctions.computeCellIndex(ixIn.getColumnIndex(), in_bclen, 0); long endColGlobalCellIndex = getEndGlobalIndex(ixIn.getColumnIndex(), true, false); - assert(startRowGlobalCellIndex <= endRowGlobalCellIndex && startColGlobalCellIndex <= endColGlobalCellIndex); long out_startRowBlockIndex = UtilFunctions.computeBlockIndex(startRowGlobalCellIndex, out_brlen); long out_endRowBlockIndex = UtilFunctions.computeBlockIndex(endRowGlobalCellIndex, out_brlen); long out_startColBlockIndex = UtilFunctions.computeBlockIndex(startColGlobalCellIndex, out_bclen); long out_endColBlockIndex = UtilFunctions.computeBlockIndex(endColGlobalCellIndex, out_bclen); - assert(out_startRowBlockIndex <= out_endRowBlockIndex && out_startColBlockIndex <= out_endColBlockIndex); ArrayList<Tuple2<MatrixIndexes, MatrixBlock>> retVal = new ArrayList<>(); for(long i = out_startRowBlockIndex; i <= out_endRowBlockIndex; i++) { for(long j = out_startColBlockIndex; j <= out_endColBlockIndex; j++) { MatrixIndexes indx = new MatrixIndexes(i, j); - long rowLower = Math.max(UtilFunctions.computeCellIndex(i, out_brlen, 0), startRowGlobalCellIndex); - long rowUpper = Math.min(getEndGlobalIndex(i, false, true), endRowGlobalCellIndex); - long colLower = Math.max(UtilFunctions.computeCellIndex(j, out_bclen, 0), startColGlobalCellIndex); - long colUpper = Math.min(getEndGlobalIndex(j, false, false), endColGlobalCellIndex); - int new_lrlen = UtilFunctions.computeBlockSize(rlen, i, out_brlen); int new_lclen = UtilFunctions.computeBlockSize(clen, j, out_bclen); MatrixBlock blk = new MatrixBlock(new_lrlen, new_lclen, true); - int in_i1 = UtilFunctions.computeCellInBlock(rowLower, in_brlen); - int out_i1 = UtilFunctions.computeCellInBlock(rowLower, out_brlen); - - for(long i1 = rowLower; i1 <= rowUpper; i1++, in_i1++, out_i1++) { - int in_j1 = UtilFunctions.computeCellInBlock(colLower, in_bclen); - int out_j1 = UtilFunctions.computeCellInBlock(colLower, out_bclen); - for(long j1 = colLower; j1 <= colUpper; j1++, in_j1++, out_j1++) { - double val = in.getValue(in_i1, in_j1); - blk.appendValue(out_i1, out_j1, val); + if( !in.isEmptyBlock(false) ) { + long rowLower = Math.max(UtilFunctions.computeCellIndex(i, out_brlen, 0), startRowGlobalCellIndex); + long rowUpper = Math.min(getEndGlobalIndex(i, false, true), endRowGlobalCellIndex); + long colLower = Math.max(UtilFunctions.computeCellIndex(j, out_bclen, 0), startColGlobalCellIndex); + long colUpper = Math.min(getEndGlobalIndex(j, false, false), endColGlobalCellIndex); + int in_i1 = UtilFunctions.computeCellInBlock(rowLower, in_brlen); + int out_i1 = UtilFunctions.computeCellInBlock(rowLower, out_brlen); + + for(long i1 = rowLower; i1 <= rowUpper; i1++, in_i1++, out_i1++) { + int in_j1 = UtilFunctions.computeCellInBlock(colLower, in_bclen); + int out_j1 = UtilFunctions.computeCellInBlock(colLower, out_bclen); + for(long j1 = colLower; j1 <= colUpper; j1++, in_j1++, out_j1++) { + double val = in.quickGetValue(in_i1, in_j1); + blk.appendValue(out_i1, out_j1, val); + } } } retVal.add(new Tuple2<>(indx, blk)); http://git-wip-us.apache.org/repos/asf/systemml/blob/addd6e12/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 f19fbe5..efe2365 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 @@ -184,10 +184,12 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab throw new RuntimeException("Sparse matrix block expected."); //deep copy and change sparse block type - nonZeros = that.nonZeros; - estimatedNNzsPerRow = that.estimatedNNzsPerRow; - sparseBlock = SparseBlockFactory + if( !that.isEmptyBlock(false) ) { + nonZeros = that.nonZeros; + estimatedNNzsPerRow = that.estimatedNNzsPerRow; + sparseBlock = SparseBlockFactory .copySparseBlock(stype, that.sparseBlock, deep); + } } //////// http://git-wip-us.apache.org/repos/asf/systemml/blob/addd6e12/src/main/java/org/apache/sysml/runtime/matrix/data/SparseBlockCSR.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/matrix/data/SparseBlockCSR.java b/src/main/java/org/apache/sysml/runtime/matrix/data/SparseBlockCSR.java index de0c34b..6bbc81d 100644 --- a/src/main/java/org/apache/sysml/runtime/matrix/data/SparseBlockCSR.java +++ b/src/main/java/org/apache/sysml/runtime/matrix/data/SparseBlockCSR.java @@ -734,16 +734,20 @@ public class SparseBlockCSR extends SparseBlock @Override public double get(int r, int c) { + if( isEmpty(r) ) + return 0; int pos = pos(r); int len = size(r); //search for existing col index in [pos,pos+len) - int index = Arrays.binarySearch(_indexes, pos, pos+len, c); + int index = Arrays.binarySearch(_indexes, pos, pos+len, c); return (index >= 0) ? _values[index] : 0; } @Override public SparseRow get(int r) { + if( isEmpty(r) ) + return new SparseRowScalar(); int pos = pos(r); int len = size(r); @@ -751,7 +755,6 @@ public class SparseBlockCSR extends SparseBlock System.arraycopy(_indexes, pos, row.indexes(), 0, len); System.arraycopy(_values, pos, row.values(), 0, len); row.setSize(len); - return row; }
