Repository: systemml Updated Branches: refs/heads/master 0505fd38c -> d9c09e771
[SYSTEMML-1947] Performance cp read sparse binary matrices (seq, par) A previous performance improvement for reading ultra-sparse binary block matrices (SYSTEMML-1838) changed the block format of temporary reuse blocks from MCSR to CSR. For specific scenarios of sparse matrices with a number of columns lower or equal the blocksize, this caused a fallback from efficient row copies to the default path of value appends. This was problematic because it leads to repeated reallocations in the presence of skew that are unnecessary for matrices with a single column block. This patch improves this codepath for all sparse block formats, including the currently used CSR blocks. By leveraging efficient row copies without redundant deep copy or reallocations, this modification significantly reduces GC overhead. On a scenario of reading the Mnist8m dataset (19GB, sp=0.25) from HDFS, this patch improved performance from 30.1s (19s GC) to 20.3s (11s GC). Project: http://git-wip-us.apache.org/repos/asf/systemml/repo Commit: http://git-wip-us.apache.org/repos/asf/systemml/commit/d9c09e77 Tree: http://git-wip-us.apache.org/repos/asf/systemml/tree/d9c09e77 Diff: http://git-wip-us.apache.org/repos/asf/systemml/diff/d9c09e77 Branch: refs/heads/master Commit: d9c09e77196516c17c80813c7ed60378a1515f51 Parents: 0505fd3 Author: Matthias Boehm <mboe...@gmail.com> Authored: Sun Oct 8 20:16:55 2017 -0700 Committer: Matthias Boehm <mboe...@gmail.com> Committed: Sun Oct 8 20:17:10 2017 -0700 ---------------------------------------------------------------------- .../sysml/runtime/io/ReaderBinaryBlock.java | 2 +- .../runtime/io/ReaderBinaryBlockParallel.java | 20 ++++++++++---------- .../sysml/runtime/matrix/data/MatrixBlock.java | 11 +++++++---- 3 files changed, 18 insertions(+), 15 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/systemml/blob/d9c09e77/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlock.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlock.java b/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlock.java index e0c217a..5b5b8ca 100644 --- a/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlock.java +++ b/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlock.java @@ -110,7 +110,7 @@ public class ReaderBinaryBlock extends MatrixReader MatrixBlock value = new MatrixBlock(brlen, bclen, sparse); if( sparse ) { value.allocateAndResetSparseRowsBlock(true, SparseBlock.Type.CSR); - value.getSparseBlock().allocate(0, 1024); + value.getSparseBlock().allocate(0, brlen*bclen); } return value; } http://git-wip-us.apache.org/repos/asf/systemml/blob/d9c09e77/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlockParallel.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlockParallel.java b/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlockParallel.java index 16260a8..374e795 100644 --- a/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlockParallel.java +++ b/src/main/java/org/apache/sysml/runtime/io/ReaderBinaryBlockParallel.java @@ -62,10 +62,10 @@ public class ReaderBinaryBlockParallel extends ReaderBinaryBlock JobConf job = new JobConf(ConfigurationManager.getCachedJobConf()); Path path = new Path( (_localFS ? "file:///" : "") + fname); FileSystem fs = IOUtilFunctions.getFileSystem(path, job); - + //check existence and non-empty file checkValidInputFile(fs, path); - + //core read readBinaryBlockMatrixFromHDFS(path, job, fs, ret, rlen, clen, brlen, bclen); @@ -79,7 +79,7 @@ public class ReaderBinaryBlockParallel extends ReaderBinaryBlock private static void readBinaryBlockMatrixFromHDFS( Path path, JobConf job, FileSystem fs, MatrixBlock dest, long rlen, long clen, int brlen, int bclen ) throws IOException, DMLRuntimeException - { + { //set up preferred custom serialization framework for binary block format if( MRJobConfiguration.USE_BINARYBLOCK_SERIALIZATION ) MRJobConfiguration.addBinaryBlockSerializationFramework( job ); @@ -95,7 +95,7 @@ public class ReaderBinaryBlockParallel extends ReaderBinaryBlock } //wait until all tasks have been executed - List<Future<Object>> rt = pool.invokeAll(tasks); + List<Future<Object>> rt = pool.invokeAll(tasks); //check for exceptions and aggregate nnz long lnnz = 0; @@ -158,15 +158,15 @@ public class ReaderBinaryBlockParallel extends ReaderBinaryBlock int row_offset = (int)(key.getRowIndex()-1)*_brlen; int col_offset = (int)(key.getColumnIndex()-1)*_bclen; - int rows = value.getNumRows(); int cols = value.getNumColumns(); //bound check per block - if( row_offset + rows < 0 || row_offset + rows > _rlen || col_offset + cols<0 || col_offset + cols > _clen ) - { - throw new IOException("Matrix block ["+(row_offset+1)+":"+(row_offset+rows)+","+(col_offset+1)+":"+(col_offset+cols)+"] " + - "out of overall matrix range [1:"+_rlen+",1:"+_clen+"]."); + if( row_offset + rows < 0 || row_offset + rows > _rlen + || col_offset + cols<0 || col_offset + cols > _clen ) { + throw new IOException("Matrix block ["+(row_offset+1)+":" + +(row_offset+rows)+","+(col_offset+1)+":"+(col_offset+cols)+"] " + + "out of overall matrix range [1:"+_rlen+",1:"+_clen+"]."); } //copy block to result @@ -196,7 +196,7 @@ public class ReaderBinaryBlockParallel extends ReaderBinaryBlock else { _dest.copy( row_offset, row_offset+rows-1, - col_offset, col_offset+cols-1, value, false ); + col_offset, col_offset+cols-1, value, false ); } //aggregate nnz http://git-wip-us.apache.org/repos/asf/systemml/blob/d9c09e77/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 5b1e663..aee9956 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 @@ -725,11 +725,14 @@ public class MatrixBlock extends MatrixValue implements CacheBlock, Externalizab { if( b.isEmpty(i) ) continue; int aix = rowoffset+i; - + //single block append (avoid re-allocations) - if( sparseBlock.isEmpty(aix) && coloffset==0 - && b instanceof SparseBlockMCSR ) { - sparseBlock.set(aix, b.get(i), deep); + if( sparseBlock.isEmpty(aix) && coloffset==0 ) { + //note: the deep copy flag is only relevant for MCSR due to + //shallow references of b.get(i); other block formats do not + //require a redundant copy because b.get(i) created a new row. + boolean ldeep = (deep && b instanceof SparseBlockMCSR); + sparseBlock.set(aix, b.get(i), ldeep); } else { //general case int pos = b.pos(i);
