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

Example 16 with MatrixCharacteristics

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

the class RandSPInstruction method generateSample.

/**
	 * Helper function to construct a sample.
	 * 
	 * @param sec spark execution context
	 * @throws DMLRuntimeException if DMLRuntimeException occurs
	 */
private void generateSample(SparkExecutionContext sec) throws DMLRuntimeException {
    if (maxValue < rows && !replace)
        throw new DMLRuntimeException("Sample (size=" + rows + ") larger than population (size=" + maxValue + ") can only be generated with replacement.");
    if (LOG.isTraceEnabled())
        LOG.trace("Process RandSPInstruction sample with range=" + maxValue + ", size=" + rows + ", replace=" + replace + ", seed=" + seed);
    // sampling rate that guarantees a sample of size >= sampleSizeLowerBound 99.99% of the time.
    double fraction = SamplingUtils.computeFractionForSampleSize((int) rows, UtilFunctions.toLong(maxValue), replace);
    Well1024a bigrand = LibMatrixDatagen.setupSeedsForRand(seed);
    // divide the population range across numPartitions by creating SampleTasks
    double hdfsBlockSize = InfrastructureAnalyzer.getHDFSBlockSize();
    long outputSize = MatrixBlock.estimateSizeDenseInMemory(rows, 1);
    int numPartitions = (int) Math.ceil((double) outputSize / hdfsBlockSize);
    long partitionSize = (long) Math.ceil(maxValue / numPartitions);
    ArrayList<SampleTask> offsets = new ArrayList<SampleTask>();
    long st = 1;
    while (st <= maxValue) {
        SampleTask s = new SampleTask();
        s.range_start = st;
        s.seed = bigrand.nextLong();
        offsets.add(s);
        st = st + partitionSize;
    }
    JavaRDD<SampleTask> offsetRDD = sec.getSparkContext().parallelize(offsets, numPartitions);
    // Construct the sample in a distributed manner
    JavaRDD<Double> rdd = offsetRDD.flatMap((new GenerateSampleBlock(replace, fraction, (long) maxValue, partitionSize)));
    // Randomize the sampled elements
    JavaRDD<Double> randomizedRDD = rdd.mapToPair(new AttachRandom()).sortByKey().values();
    // Trim the sampled list to required size & attach matrix indexes to randomized elements
    JavaPairRDD<MatrixIndexes, MatrixCell> miRDD = randomizedRDD.zipWithIndex().filter(new TrimSample(rows)).mapToPair(new Double2MatrixCell());
    MatrixCharacteristics mcOut = new MatrixCharacteristics(rows, 1, rowsInBlock, colsInBlock, rows);
    // Construct BinaryBlock representation
    JavaPairRDD<MatrixIndexes, MatrixBlock> mbRDD = RDDConverterUtils.binaryCellToBinaryBlock(sec.getSparkContext(), miRDD, mcOut, true);
    MatrixCharacteristics retDims = sec.getMatrixCharacteristics(output.getName());
    retDims.setNonZeros(rows);
    sec.setRDDHandleForVariable(output.getName(), mbRDD);
}

Example 17 with MatrixCharacteristics

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

the class TernarySPInstruction method processInstruction.

@Override
public void processInstruction(ExecutionContext ec) throws DMLRuntimeException {
    SparkExecutionContext sec = (SparkExecutionContext) ec;
    //get input rdd handle
    JavaPairRDD<MatrixIndexes, MatrixBlock> in1 = sec.getBinaryBlockRDDHandleForVariable(input1.getName());
    JavaPairRDD<MatrixIndexes, MatrixBlock> in2 = null;
    JavaPairRDD<MatrixIndexes, MatrixBlock> in3 = null;
    double scalar_input2 = -1, scalar_input3 = -1;
    Ternary.OperationTypes ctableOp = Ternary.findCtableOperationByInputDataTypes(input1.getDataType(), input2.getDataType(), input3.getDataType());
    ctableOp = _isExpand ? Ternary.OperationTypes.CTABLE_EXPAND_SCALAR_WEIGHT : ctableOp;
    MatrixCharacteristics mc1 = sec.getMatrixCharacteristics(input1.getName());
    MatrixCharacteristics mcOut = sec.getMatrixCharacteristics(output.getName());
    // First get the block sizes and then set them as -1 to allow for binary cell reblock
    int brlen = mc1.getRowsPerBlock();
    int bclen = mc1.getColsPerBlock();
    JavaPairRDD<MatrixIndexes, ArrayList<MatrixBlock>> inputMBs = null;
    JavaPairRDD<MatrixIndexes, CTableMap> ctables = null;
    JavaPairRDD<MatrixIndexes, Double> bincellsNoFilter = null;
    boolean setLineage2 = false;
    boolean setLineage3 = false;
    switch(ctableOp) {
        case //(VECTOR)
        CTABLE_TRANSFORM:
            // F=ctable(A,B,W) 
            in2 = sec.getBinaryBlockRDDHandleForVariable(input2.getName());
            in3 = sec.getBinaryBlockRDDHandleForVariable(input3.getName());
            setLineage2 = true;
            setLineage3 = true;
            inputMBs = in1.cogroup(in2).cogroup(in3).mapToPair(new MapThreeMBIterableIntoAL());
            ctables = inputMBs.mapToPair(new PerformCTableMapSideOperation(ctableOp, scalar_input2, scalar_input3, this.instString, (SimpleOperator) _optr, _ignoreZeros));
            break;
        case //(VECTOR)
        CTABLE_EXPAND_SCALAR_WEIGHT:
            // F = ctable(seq,A) or F = ctable(seq,B,1)
            scalar_input3 = sec.getScalarInput(input3.getName(), input3.getValueType(), input3.isLiteral()).getDoubleValue();
            if (scalar_input3 == 1) {
                in2 = sec.getBinaryBlockRDDHandleForVariable(input2.getName());
                setLineage2 = true;
                bincellsNoFilter = in2.flatMapToPair(new ExpandScalarCtableOperation(brlen));
                break;
            }
        case //(VECTOR/MATRIX)
        CTABLE_TRANSFORM_SCALAR_WEIGHT:
            // F = ctable(A,B) or F = ctable(A,B,1)
            in2 = sec.getBinaryBlockRDDHandleForVariable(input2.getName());
            setLineage2 = true;
            scalar_input3 = sec.getScalarInput(input3.getName(), input3.getValueType(), input3.isLiteral()).getDoubleValue();
            inputMBs = in1.cogroup(in2).mapToPair(new MapTwoMBIterableIntoAL());
            ctables = inputMBs.mapToPair(new PerformCTableMapSideOperation(ctableOp, scalar_input2, scalar_input3, this.instString, (SimpleOperator) _optr, _ignoreZeros));
            break;
        case //(VECTOR)
        CTABLE_TRANSFORM_HISTOGRAM:
            // F=ctable(A,1) or F = ctable(A,1,1)
            scalar_input2 = sec.getScalarInput(input2.getName(), input2.getValueType(), input2.isLiteral()).getDoubleValue();
            scalar_input3 = sec.getScalarInput(input3.getName(), input3.getValueType(), input3.isLiteral()).getDoubleValue();
            inputMBs = in1.mapToPair(new MapMBIntoAL());
            ctables = inputMBs.mapToPair(new PerformCTableMapSideOperation(ctableOp, scalar_input2, scalar_input3, this.instString, (SimpleOperator) _optr, _ignoreZeros));
            break;
        case //(VECTOR)
        CTABLE_TRANSFORM_WEIGHTED_HISTOGRAM:
            // F=ctable(A,1,W)
            in3 = sec.getBinaryBlockRDDHandleForVariable(input3.getName());
            setLineage3 = true;
            scalar_input2 = sec.getScalarInput(input2.getName(), input2.getValueType(), input2.isLiteral()).getDoubleValue();
            inputMBs = in1.cogroup(in3).mapToPair(new MapTwoMBIterableIntoAL());
            ctables = inputMBs.mapToPair(new PerformCTableMapSideOperation(ctableOp, scalar_input2, scalar_input3, this.instString, (SimpleOperator) _optr, _ignoreZeros));
            break;
        default:
            throw new DMLRuntimeException("Encountered an invalid ctable operation (" + ctableOp + ") while executing instruction: " + this.toString());
    }
    // Now perform aggregation on ctables to get binaryCells 
    if (bincellsNoFilter == null && ctables != null) {
        bincellsNoFilter = ctables.values().flatMapToPair(new ExtractBinaryCellsFromCTable());
        bincellsNoFilter = RDDAggregateUtils.sumCellsByKeyStable(bincellsNoFilter);
    } else if (!(bincellsNoFilter != null && ctables == null)) {
        throw new DMLRuntimeException("Incorrect ctable operation");
    }
    // handle known/unknown dimensions
    long outputDim1 = (_dim1Literal ? (long) Double.parseDouble(_outDim1) : (sec.getScalarInput(_outDim1, ValueType.DOUBLE, false)).getLongValue());
    long outputDim2 = (_dim2Literal ? (long) Double.parseDouble(_outDim2) : (sec.getScalarInput(_outDim2, ValueType.DOUBLE, false)).getLongValue());
    MatrixCharacteristics mcBinaryCells = null;
    boolean findDimensions = (outputDim1 == -1 && outputDim2 == -1);
    if (!findDimensions) {
        if ((outputDim1 == -1 && outputDim2 != -1) || (outputDim1 != -1 && outputDim2 == -1))
            throw new DMLRuntimeException("Incorrect output dimensions passed to TernarySPInstruction:" + outputDim1 + " " + outputDim2);
        else
            mcBinaryCells = new MatrixCharacteristics(outputDim1, outputDim2, brlen, bclen);
        // filtering according to given dimensions
        bincellsNoFilter = bincellsNoFilter.filter(new FilterCells(mcBinaryCells.getRows(), mcBinaryCells.getCols()));
    }
    // convert double values to matrix cell
    JavaPairRDD<MatrixIndexes, MatrixCell> binaryCells = bincellsNoFilter.mapToPair(new ConvertToBinaryCell());
    // find dimensions if necessary (w/ cache for reblock)
    if (findDimensions) {
        binaryCells = SparkUtils.cacheBinaryCellRDD(binaryCells);
        mcBinaryCells = SparkUtils.computeMatrixCharacteristics(binaryCells);
    }
    //store output rdd handle
    sec.setRDDHandleForVariable(output.getName(), binaryCells);
    mcOut.set(mcBinaryCells);
    // Since we are outputing binary cells, we set block sizes = -1
    mcOut.setRowsPerBlock(-1);
    mcOut.setColsPerBlock(-1);
    sec.addLineageRDD(output.getName(), input1.getName());
    if (setLineage2)
        sec.addLineageRDD(output.getName(), input2.getName());
    if (setLineage3)
        sec.addLineageRDD(output.getName(), input3.getName());
}

Example 18 with MatrixCharacteristics

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

the class Tsmm2SPInstruction method processInstruction.

@Override
public void processInstruction(ExecutionContext ec) throws DMLRuntimeException {
    SparkExecutionContext sec = (SparkExecutionContext) ec;
    //get input
    JavaPairRDD<MatrixIndexes, MatrixBlock> in = sec.getBinaryBlockRDDHandleForVariable(input1.getName());
    MatrixCharacteristics mc = sec.getMatrixCharacteristics(input1.getName());
    //execute tsmm2 instruction 
    //step 1: first pass of X, filter-collect-broadcast excess blocks 
    JavaPairRDD<MatrixIndexes, MatrixBlock> tmp1 = in.filter(new IsBlockInRange(_type.isLeft() ? 1 : mc.getRowsPerBlock() + 1, mc.getRows(), _type.isLeft() ? mc.getColsPerBlock() + 1 : 1, mc.getCols(), mc)).mapToPair(new ShiftTSMMIndexesFunction(_type));
    PartitionedBlock<MatrixBlock> pmb = SparkExecutionContext.toPartitionedMatrixBlock(tmp1, (int) (_type.isLeft() ? mc.getRows() : mc.getRows() - mc.getRowsPerBlock()), (int) (_type.isLeft() ? mc.getCols() - mc.getColsPerBlock() : mc.getCols()), mc.getRowsPerBlock(), mc.getColsPerBlock(), -1L);
    Broadcast<PartitionedBlock<MatrixBlock>> bpmb = sec.getSparkContext().broadcast(pmb);
    //step 2: second pass of X, compute tsmm/mapmm and aggregate result blocks
    int outputDim = (int) (_type.isLeft() ? mc.getCols() : mc.getRows());
    if (OptimizerUtils.estimateSize(outputDim, outputDim) <= 32 * 1024 * 1024) {
        //default: <=32MB
        //output large blocks and reduceAll to avoid skew on combineByKey
        JavaRDD<MatrixBlock> tmp2 = in.map(new RDDTSMM2ExtFunction(bpmb, _type, outputDim, (int) mc.getRowsPerBlock()));
        MatrixBlock out = RDDAggregateUtils.sumStable(tmp2);
        //put output block into symbol table (no lineage because single block)
        //this also includes implicit maintenance of matrix characteristics
        sec.setMatrixOutput(output.getName(), out);
    } else {
        //output individual output blocks and aggregate by key (no action)
        JavaPairRDD<MatrixIndexes, MatrixBlock> tmp2 = in.flatMapToPair(new RDDTSMM2Function(bpmb, _type));
        JavaPairRDD<MatrixIndexes, MatrixBlock> out = RDDAggregateUtils.sumByKeyStable(tmp2, false);
        //put output RDD handle into symbol table
        sec.getMatrixCharacteristics(output.getName()).set(outputDim, outputDim, mc.getRowsPerBlock(), mc.getColsPerBlock());
        sec.setRDDHandleForVariable(output.getName(), out);
        sec.addLineageRDD(output.getName(), input1.getName());
    }
}

Example 19 with MatrixCharacteristics

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

the class ReorgSPInstruction method updateReorgMatrixCharacteristics.

private void updateReorgMatrixCharacteristics(SparkExecutionContext sec) throws DMLRuntimeException {
    MatrixCharacteristics mc1 = sec.getMatrixCharacteristics(input1.getName());
    MatrixCharacteristics mcOut = sec.getMatrixCharacteristics(output.getName());
    //infer initially unknown dimensions from inputs
    if (!mcOut.dimsKnown()) {
        if (!mc1.dimsKnown())
            throw new DMLRuntimeException("Unable to compute output matrix characteristics from input.");
        if (getOpcode().equalsIgnoreCase("r'"))
            mcOut.set(mc1.getCols(), mc1.getRows(), mc1.getColsPerBlock(), mc1.getRowsPerBlock());
        else if (getOpcode().equalsIgnoreCase("rdiag"))
            mcOut.set(mc1.getRows(), (mc1.getCols() > 1) ? 1 : mc1.getRows(), mc1.getRowsPerBlock(), mc1.getColsPerBlock());
        else if (getOpcode().equalsIgnoreCase("rsort")) {
            boolean ixret = sec.getScalarInput(_ixret.getName(), _ixret.getValueType(), _ixret.isLiteral()).getBooleanValue();
            mcOut.set(mc1.getRows(), ixret ? 1 : mc1.getCols(), mc1.getRowsPerBlock(), mc1.getColsPerBlock());
        }
    }
    //infer initially unknown nnz from input
    if (!mcOut.nnzKnown() && mc1.nnzKnown()) {
        boolean sortIx = getOpcode().equalsIgnoreCase("rsort") && sec.getScalarInput(_ixret.getName(), _ixret.getValueType(), _ixret.isLiteral()).getBooleanValue();
        if (sortIx)
            mcOut.setNonZeros(mc1.getRows());
        else
            //default (r', rdiag, rsort data)
            mcOut.setNonZeros(mc1.getNonZeros());
    }
}

Example 20 with MatrixCharacteristics

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

the class RmmSPInstruction method processInstruction.

@Override
public void processInstruction(ExecutionContext ec) throws DMLRuntimeException {
    SparkExecutionContext sec = (SparkExecutionContext) ec;
    //get input rdds
    MatrixCharacteristics mc1 = sec.getMatrixCharacteristics(input1.getName());
    MatrixCharacteristics mc2 = sec.getMatrixCharacteristics(input2.getName());
    JavaPairRDD<MatrixIndexes, MatrixBlock> in1 = sec.getBinaryBlockRDDHandleForVariable(input1.getName());
    JavaPairRDD<MatrixIndexes, MatrixBlock> in2 = sec.getBinaryBlockRDDHandleForVariable(input2.getName());
    //execute Spark RMM instruction
    //step 1: prepare join keys (w/ replication), i/j/k 
    JavaPairRDD<TripleIndexes, MatrixBlock> tmp1 = in1.flatMapToPair(new RmmReplicateFunction(mc2.getCols(), mc2.getColsPerBlock(), true));
    JavaPairRDD<TripleIndexes, MatrixBlock> tmp2 = in2.flatMapToPair(new RmmReplicateFunction(mc1.getRows(), mc1.getRowsPerBlock(), false));
    //step 2: join prepared datasets, multiply, and aggregate
    JavaPairRDD<MatrixIndexes, MatrixBlock> out = //join by result block 
    tmp1.join(tmp2).mapToPair(//do matrix multiplication
    new RmmMultiplyFunction());
    //aggregation per result block
    out = RDDAggregateUtils.sumByKeyStable(out, false);
    //put output block into symbol table (no lineage because single block)
    updateBinaryMMOutputMatrixCharacteristics(sec, true);
    sec.setRDDHandleForVariable(output.getName(), out);
    sec.addLineageRDD(output.getName(), input1.getName());
    sec.addLineageRDD(output.getName(), input2.getName());
}