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

Example 66 with MatrixCharacteristics

use of org.apache.sysml.runtime.matrix.MatrixCharacteristics 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 67 with MatrixCharacteristics

use of org.apache.sysml.runtime.matrix.MatrixCharacteristics 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 68 with MatrixCharacteristics

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

the class ResultMergeRemoteSpark method executeParallelMerge.

@Override
public MatrixObject executeParallelMerge(int par) {
    // always create new matrix object (required for nested parallelism)
    MatrixObject moNew = null;
    if (LOG.isTraceEnabled())
        LOG.trace("ResultMerge (remote, spark): Execute serial merge for output " + _output.hashCode() + " (fname=" + _output.getFileName() + ")");
    try {
        if (_inputs != null && _inputs.length > 0) {
            // prepare compare
            MetaDataFormat metadata = (MetaDataFormat) _output.getMetaData();
            MatrixCharacteristics mcOld = metadata.getMatrixCharacteristics();
            MatrixObject compare = (mcOld.getNonZeros() == 0) ? null : _output;
            // actual merge
            RDDObject ro = executeMerge(compare, _inputs, mcOld.getRows(), mcOld.getCols(), mcOld.getRowsPerBlock(), mcOld.getColsPerBlock());
            // create new output matrix (e.g., to prevent potential export<->read file access conflict
            moNew = new MatrixObject(_output.getValueType(), _outputFName);
            OutputInfo oiOld = metadata.getOutputInfo();
            InputInfo iiOld = metadata.getInputInfo();
            MatrixCharacteristics mc = new MatrixCharacteristics(mcOld);
            mc.setNonZeros(_isAccum ? -1 : computeNonZeros(_output, Arrays.asList(_inputs)));
            MetaDataFormat meta = new MetaDataFormat(mc, oiOld, iiOld);
            moNew.setMetaData(meta);
            moNew.setRDDHandle(ro);
        } else {
            // return old matrix, to prevent copy
            moNew = _output;
        }
    } catch (Exception ex) {
        throw new DMLRuntimeException(ex);
    }
    return moNew;
}

Example 69 with MatrixCharacteristics

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

the class VariableCPInstruction method writeCSVFile.

/**
 * Helper function to write CSV files to HDFS.
 *
 * @param ec execution context
 * @param fname file name
 */
private void writeCSVFile(ExecutionContext ec, String fname) {
    MatrixObject mo = ec.getMatrixObject(getInput1().getName());
    String outFmt = "csv";
    if (mo.isDirty()) {
        // there exist data computed in CP that is not backed up on HDFS
        // i.e., it is either in-memory or in evicted space
        mo.exportData(fname, outFmt, _formatProperties);
    } else {
        try {
            OutputInfo oi = ((MetaDataFormat) mo.getMetaData()).getOutputInfo();
            MatrixCharacteristics mc = ((MetaDataFormat) mo.getMetaData()).getMatrixCharacteristics();
            if (oi == OutputInfo.CSVOutputInfo) {
                WriterTextCSV writer = new WriterTextCSV((CSVFileFormatProperties) _formatProperties);
                writer.addHeaderToCSV(mo.getFileName(), fname, mc.getRows(), mc.getCols());
            } else if (oi == OutputInfo.BinaryBlockOutputInfo || oi == OutputInfo.TextCellOutputInfo) {
                mo.exportData(fname, outFmt, _formatProperties);
            } else {
                throw new DMLRuntimeException("Unexpected data format (" + OutputInfo.outputInfoToString(oi) + "): can not export into CSV format.");
            }
            // Write Metadata file
            MapReduceTool.writeMetaDataFile(fname + ".mtd", mo.getValueType(), mc, OutputInfo.CSVOutputInfo, _formatProperties);
        } catch (IOException e) {
            throw new DMLRuntimeException(e);
        }
    }
}

Example 70 with MatrixCharacteristics

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

the class VariableCPInstruction method writeMMFile.

/**
 * Helper function to write MM files to HDFS.
 *
 * @param ec execution context
 * @param fname file name
 */
private void writeMMFile(ExecutionContext ec, String fname) {
    MatrixObject mo = ec.getMatrixObject(getInput1().getName());
    String outFmt = "matrixmarket";
    if (mo.isDirty()) {
        // there exist data computed in CP that is not backed up on HDFS
        // i.e., it is either in-memory or in evicted space
        mo.exportData(fname, outFmt);
    } else {
        OutputInfo oi = ((MetaDataFormat) mo.getMetaData()).getOutputInfo();
        MatrixCharacteristics mc = mo.getMatrixCharacteristics();
        if (oi == OutputInfo.TextCellOutputInfo) {
            try {
                WriterMatrixMarket.mergeTextcellToMatrixMarket(mo.getFileName(), fname, mc.getRows(), mc.getCols(), mc.getNonZeros());
            } catch (IOException e) {
                throw new DMLRuntimeException(e);
            }
        } else if (oi == OutputInfo.BinaryBlockOutputInfo) {
            mo.exportData(fname, outFmt);
        } else {
            throw new DMLRuntimeException("Unexpected data format (" + OutputInfo.outputInfoToString(oi) + "): can not export into MatrixMarket format.");
        }
    }
}