Examples with MatrixIndexes org.apache.sysml.runtime.matrix.data.MatrixIndexes used on opensource projects

Example 36 with MatrixIndexes

use of org.apache.sysml.runtime.matrix.data.MatrixIndexes in project incubator-systemml by apache.

the class ResultMergeLocalFile method createBinaryCellStagingFile.

@SuppressWarnings("deprecation")
private static void createBinaryCellStagingFile(String fnameStaging, MatrixObject mo, long ID) throws IOException, DMLRuntimeException {
    JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
    Path path = new Path(mo.getFileName());
    FileSystem fs = IOUtilFunctions.getFileSystem(path, job);
    LinkedList<Cell> buffer = new LinkedList<>();
    MatrixIndexes key = new MatrixIndexes();
    MatrixCell value = new MatrixCell();
    MatrixCharacteristics mc = mo.getMatrixCharacteristics();
    int brlen = mc.getRowsPerBlock();
    int bclen = mc.getColsPerBlock();
    for (Path lpath : IOUtilFunctions.getSequenceFilePaths(fs, path)) {
        SequenceFile.Reader reader = new SequenceFile.Reader(fs, lpath, job);
        try {
            while (reader.next(key, value)) {
                Cell tmp = new Cell(key.getRowIndex(), key.getColumnIndex(), value.getValue());
                buffer.addLast(tmp);
                if (// periodic flush
                buffer.size() > StagingFileUtils.CELL_BUFFER_SIZE) {
                    appendCellBufferToStagingArea(fnameStaging, ID, buffer, brlen, bclen);
                    buffer.clear();
                }
            }
            // final flush
            if (!buffer.isEmpty()) {
                appendCellBufferToStagingArea(fnameStaging, ID, buffer, brlen, bclen);
                buffer.clear();
            }
        } finally {
            IOUtilFunctions.closeSilently(reader);
        }
    }
}

Example 37 with MatrixIndexes

use of org.apache.sysml.runtime.matrix.data.MatrixIndexes in project incubator-systemml by apache.

the class ResultMergeLocalFile method createBinaryBlockResultFile.

@SuppressWarnings("deprecation")
private void createBinaryBlockResultFile(String fnameStaging, String fnameStagingCompare, String fnameNew, MetaDataFormat metadata, boolean withCompare) throws IOException, DMLRuntimeException {
    JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
    Path path = new Path(fnameNew);
    FileSystem fs = IOUtilFunctions.getFileSystem(path, job);
    MatrixCharacteristics mc = metadata.getMatrixCharacteristics();
    long rlen = mc.getRows();
    long clen = mc.getCols();
    int brlen = mc.getRowsPerBlock();
    int bclen = mc.getColsPerBlock();
    // beware ca 50ms
    SequenceFile.Writer writer = new SequenceFile.Writer(fs, job, path, MatrixIndexes.class, MatrixBlock.class);
    try {
        MatrixIndexes indexes = new MatrixIndexes();
        for (long brow = 1; brow <= (long) Math.ceil(rlen / (double) brlen); brow++) for (long bcol = 1; bcol <= (long) Math.ceil(clen / (double) bclen); bcol++) {
            File dir = new File(fnameStaging + "/" + brow + "_" + bcol);
            File dir2 = new File(fnameStagingCompare + "/" + brow + "_" + bcol);
            MatrixBlock mb = null;
            if (dir.exists()) {
                if (// WITH COMPARE BLOCK
                withCompare && dir2.exists()) {
                    // copy only values that are different from the original
                    String[] lnames2 = dir2.list();
                    if (// there should be exactly 1 compare block
                    lnames2.length != 1)
                        throw new DMLRuntimeException("Unable to merge results because multiple compare blocks found.");
                    mb = LocalFileUtils.readMatrixBlockFromLocal(dir2 + "/" + lnames2[0]);
                    boolean appendOnly = mb.isInSparseFormat();
                    DenseBlock compare = DataConverter.convertToDenseBlock(mb, false);
                    for (String lname : dir.list()) {
                        MatrixBlock tmp = LocalFileUtils.readMatrixBlockFromLocal(dir + "/" + lname);
                        mergeWithComp(mb, tmp, compare);
                    }
                    // sort sparse due to append-only
                    if (appendOnly && !_isAccum)
                        mb.sortSparseRows();
                    // change sparsity if required after
                    mb.examSparsity();
                } else // WITHOUT COMPARE BLOCK
                {
                    // copy all non-zeros from all workers
                    boolean appendOnly = false;
                    for (String lname : dir.list()) {
                        if (mb == null) {
                            mb = LocalFileUtils.readMatrixBlockFromLocal(dir + "/" + lname);
                            appendOnly = mb.isInSparseFormat();
                        } else {
                            MatrixBlock tmp = LocalFileUtils.readMatrixBlockFromLocal(dir + "/" + lname);
                            mergeWithoutComp(mb, tmp, appendOnly);
                        }
                    }
                    // sort sparse due to append-only
                    if (appendOnly && !_isAccum)
                        mb.sortSparseRows();
                    // change sparsity if required after
                    mb.examSparsity();
                }
            } else {
                // NOTE: whenever runtime does not need all blocks anymore, this can be removed
                int maxRow = (int) (((brow - 1) * brlen + brlen < rlen) ? brlen : rlen - (brow - 1) * brlen);
                int maxCol = (int) (((bcol - 1) * bclen + bclen < clen) ? bclen : clen - (bcol - 1) * bclen);
                mb = new MatrixBlock(maxRow, maxCol, true);
            }
            // mb.examSparsity(); //done on write anyway and mb not reused
            indexes.setIndexes(brow, bcol);
            writer.append(indexes, mb);
        }
    } finally {
        IOUtilFunctions.closeSilently(writer);
    }
}

Example 38 with MatrixIndexes

use of org.apache.sysml.runtime.matrix.data.MatrixIndexes in project incubator-systemml by apache.

the class ResultMergeLocalFile method createBinaryCellResultFile.

@SuppressWarnings("deprecation")
private void createBinaryCellResultFile(String fnameStaging, String fnameStagingCompare, String fnameNew, MetaDataFormat metadata, boolean withCompare) throws IOException, DMLRuntimeException {
    JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
    Path path = new Path(fnameNew);
    FileSystem fs = IOUtilFunctions.getFileSystem(path, job);
    MatrixCharacteristics mc = metadata.getMatrixCharacteristics();
    long rlen = mc.getRows();
    long clen = mc.getCols();
    int brlen = mc.getRowsPerBlock();
    int bclen = mc.getColsPerBlock();
    MatrixIndexes indexes = new MatrixIndexes(1, 1);
    MatrixCell cell = new MatrixCell(0);
    // beware ca 50ms
    SequenceFile.Writer out = new SequenceFile.Writer(fs, job, path, MatrixIndexes.class, MatrixCell.class);
    try {
        boolean written = false;
        for (long brow = 1; brow <= (long) Math.ceil(rlen / (double) brlen); brow++) for (long bcol = 1; bcol <= (long) Math.ceil(clen / (double) bclen); bcol++) {
            File dir = new File(fnameStaging + "/" + brow + "_" + bcol);
            File dir2 = new File(fnameStagingCompare + "/" + brow + "_" + bcol);
            MatrixBlock mb = null;
            long row_offset = (brow - 1) * brlen + 1;
            long col_offset = (bcol - 1) * bclen + 1;
            if (dir.exists()) {
                if (// WITH COMPARE BLOCK
                withCompare && dir2.exists()) {
                    // copy only values that are different from the original
                    String[] lnames2 = dir2.list();
                    if (// there should be exactly 1 compare block
                    lnames2.length != 1)
                        throw new DMLRuntimeException("Unable to merge results because multiple compare blocks found.");
                    mb = StagingFileUtils.readCellList2BlockFromLocal(dir2 + "/" + lnames2[0], brlen, bclen);
                    boolean appendOnly = mb.isInSparseFormat();
                    DenseBlock compare = DataConverter.convertToDenseBlock(mb, false);
                    for (String lname : dir.list()) {
                        MatrixBlock tmp = StagingFileUtils.readCellList2BlockFromLocal(dir + "/" + lname, brlen, bclen);
                        mergeWithComp(mb, tmp, compare);
                    }
                    // sort sparse due to append-only
                    if (appendOnly && !_isAccum)
                        mb.sortSparseRows();
                    // change sparsity if required after
                    mb.examSparsity();
                } else // WITHOUT COMPARE BLOCK
                {
                    // copy all non-zeros from all workers
                    boolean appendOnly = false;
                    for (String lname : dir.list()) {
                        if (mb == null) {
                            mb = StagingFileUtils.readCellList2BlockFromLocal(dir + "/" + lname, brlen, bclen);
                            appendOnly = mb.isInSparseFormat();
                        } else {
                            MatrixBlock tmp = StagingFileUtils.readCellList2BlockFromLocal(dir + "/" + lname, brlen, bclen);
                            mergeWithoutComp(mb, tmp, appendOnly);
                        }
                    }
                    // sort sparse due to append-only
                    if (appendOnly && !_isAccum)
                        mb.sortSparseRows();
                    // change sparsity if required after
                    mb.examSparsity();
                }
            }
            // write the block to binary cell
            if (mb != null) {
                if (mb.isInSparseFormat()) {
                    Iterator<IJV> iter = mb.getSparseBlockIterator();
                    while (iter.hasNext()) {
                        IJV lcell = iter.next();
                        indexes.setIndexes(row_offset + lcell.getI(), col_offset + lcell.getJ());
                        cell.setValue(lcell.getV());
                        out.append(indexes, cell);
                        written = true;
                    }
                } else {
                    for (int i = 0; i < brlen; i++) for (int j = 0; j < bclen; j++) {
                        double lvalue = mb.getValueDenseUnsafe(i, j);
                        if (// for nnz
                        lvalue != 0) {
                            indexes.setIndexes(row_offset + i, col_offset + j);
                            cell.setValue(lvalue);
                            out.append(indexes, cell);
                            written = true;
                        }
                    }
                }
            }
        }
        if (!written)
            out.append(indexes, cell);
    } finally {
        IOUtilFunctions.closeSilently(out);
    }
}

Example 39 with MatrixIndexes

use of org.apache.sysml.runtime.matrix.data.MatrixIndexes in project incubator-systemml by apache.

the class ResultMergeRemoteSpark method setRDDHandleForMerge.

@SuppressWarnings("unchecked")
private static void setRDDHandleForMerge(MatrixObject mo, SparkExecutionContext sec) {
    InputInfo iinfo = InputInfo.BinaryBlockInputInfo;
    JavaSparkContext sc = sec.getSparkContext();
    JavaPairRDD<MatrixIndexes, MatrixBlock> rdd = (JavaPairRDD<MatrixIndexes, MatrixBlock>) sc.hadoopFile(mo.getFileName(), iinfo.inputFormatClass, iinfo.inputKeyClass, iinfo.inputValueClass);
    RDDObject rddhandle = new RDDObject(rdd);
    rddhandle.setHDFSFile(true);
    mo.setRDDHandle(rddhandle);
}

Example 40 with MatrixIndexes

use of org.apache.sysml.runtime.matrix.data.MatrixIndexes in project incubator-systemml by apache.

the class PairWritableBlock method readFields.

@Override
public void readFields(DataInput in) throws IOException {
    indexes = new MatrixIndexes();
    indexes.readFields(in);
    block = new MatrixBlock();
    block.readFields(in);
}