Examples with DimensionMismatchException org.apache.commons.math3.exception.DimensionMismatchException used on opensource projects

Example 1 with DimensionMismatchException

use of org.apache.commons.math3.exception.DimensionMismatchException in project gatk by broadinstitute.

the class CoverageModelWPreconditionerSpark method operate.

@Override
public INDArray operate(@Nonnull final INDArray W_tl) throws DimensionMismatchException {
    if (W_tl.rank() != 2 || W_tl.shape()[0] != numTargets || W_tl.shape()[1] != numLatents) {
        throw new DimensionMismatchException(W_tl.length(), numTargets * numLatents);
    }
    long startTimeRFFT = System.nanoTime();
    /* forward rfft */
    final INDArray W_kl = Nd4j.create(fftSize, numLatents);
    IntStream.range(0, numLatents).parallel().forEach(li -> W_kl.get(NDArrayIndex.all(), NDArrayIndex.point(li)).assign(Nd4j.create(F_tt.getForwardFFT(W_tl.get(NDArrayIndex.all(), NDArrayIndex.point(li))), new int[] { fftSize, 1 })));
    long endTimeRFFT = System.nanoTime();
    /* apply the preconditioner in the Fourier space */
    long startTimePrecond = System.nanoTime();
    final Map<LinearlySpacedIndexBlock, INDArray> W_kl_map = CoverageModelSparkUtils.partitionINDArrayToMap(fourierSpaceBlocks, W_kl);
    final Broadcast<Map<LinearlySpacedIndexBlock, INDArray>> W_kl_bc = ctx.broadcast(W_kl_map);
    final JavaPairRDD<LinearlySpacedIndexBlock, INDArray> preconditionedWRDD = linOpPairRDD.mapToPair(p -> {
        final INDArray W_kl_chuck = W_kl_bc.value().get(p._1);
        final INDArray linOp_chunk = p._2;
        final int blockSize = linOp_chunk.shape()[0];
        final List<INDArray> linOpWList = IntStream.range(0, blockSize).parallel().mapToObj(k -> CoverageModelEMWorkspaceMathUtils.linsolve(linOp_chunk.get(NDArrayIndex.point(k)), W_kl_chuck.get(NDArrayIndex.point(k)))).collect(Collectors.toList());
        return new Tuple2<>(p._1, Nd4j.vstack(linOpWList));
    });
    W_kl.assign(CoverageModelSparkUtils.assembleINDArrayBlocksFromRDD(preconditionedWRDD, 0));
    W_kl_bc.destroy();
    //        final JavaPairRDD<LinearlySpacedIndexBlock, INDArray> W_kl_RDD = CoverageModelSparkUtils.rddFromINDArray(W_kl,
    //                fourierSpaceBlocks, ctx, true);
    //        W_kl.assign(CoverageModelSparkUtils.assembleINDArrayBlocks(linOpPairRDD.join((W_kl_RDD))
    //                .mapValues(p -> {
    //                    final INDArray linOp = p._1;
    //                    final INDArray W = p._2;
    //                    final int blockSize = linOp.shape()[0];
    //                    final List<INDArray> linOpWList = IntStream.range(0, blockSize).parallel().mapToObj(k ->
    //                            CoverageModelEMWorkspaceMathUtils.linsolve(linOp.get(NDArrayIndex.point(k)),
    //                                    W.get(NDArrayIndex.point(k))))
    //                            .collect(Collectors.toList());
    //                    return Nd4j.vstack(linOpWList);
    //                }), false));
    //        W_kl_RDD.unpersist();
    long endTimePrecond = System.nanoTime();
    /* irfft */
    long startTimeIRFFT = System.nanoTime();
    final INDArray res = Nd4j.create(numTargets, numLatents);
    IntStream.range(0, numLatents).parallel().forEach(li -> res.get(NDArrayIndex.all(), NDArrayIndex.point(li)).assign(F_tt.getInverseFFT(W_kl.get(NDArrayIndex.all(), NDArrayIndex.point(li)))));
    long endTimeIRFFT = System.nanoTime();
    logger.debug("Local FFT timing: " + (endTimeRFFT - startTimeRFFT + endTimeIRFFT - startTimeIRFFT) / 1000000 + " ms");
    logger.debug("Spark preconditioner application timing: " + (endTimePrecond - startTimePrecond) / 1000000 + " ms");
    return res;
}

Example 2 with DimensionMismatchException

use of org.apache.commons.math3.exception.DimensionMismatchException in project gatk by broadinstitute.

the class CoverageModelWLinearOperatorSpark method operate.

@Override
public INDArray operate(@Nonnull final INDArray W_tl) throws DimensionMismatchException {
    if (W_tl.rank() != 2 || W_tl.shape()[0] != numTargets || W_tl.shape()[1] != numLatents)
        throw new DimensionMismatchException(W_tl.length(), numTargets * numLatents);
    /* Z F W */
    final long startTimeZFW = System.nanoTime();
    final INDArray Z_F_W_tl = Nd4j.create(numTargets, numLatents);
    IntStream.range(0, numLatents).parallel().forEach(li -> Z_F_W_tl.get(NDArrayIndex.all(), NDArrayIndex.point(li)).assign(F_tt.operate(W_tl.get(NDArrayIndex.all(), NDArrayIndex.point(li)))));
    Z_F_W_tl.assign(Nd4j.gemm(Z_F_W_tl, Z_ll, false, false));
    final long endTimeZFW = System.nanoTime();
    /* perform a broadcast hash join */
    final long startTimeQW = System.nanoTime();
    final Map<LinearlySpacedIndexBlock, INDArray> W_tl_map = CoverageModelSparkUtils.partitionINDArrayToMap(targetSpaceBlocks, W_tl);
    final Broadcast<Map<LinearlySpacedIndexBlock, INDArray>> W_tl_bc = ctx.broadcast(W_tl_map);
    final INDArray Q_W_tl = CoverageModelSparkUtils.assembleINDArrayBlocksFromRDD(computeRDD.mapValues(cb -> {
        final INDArray W_tl_chunk = W_tl_bc.value().get(cb.getTargetSpaceBlock());
        final INDArray Q_tll_chunk = cb.getINDArrayFromCache(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.Q_tll);
        final Collection<INDArray> W_Q_chunk = IntStream.range(0, cb.getTargetSpaceBlock().getNumElements()).parallel().mapToObj(ti -> Q_tll_chunk.get(NDArrayIndex.point(ti)).mmul(W_tl_chunk.get(NDArrayIndex.point(ti)).transpose())).collect(Collectors.toList());
        return Nd4j.vstack(W_Q_chunk);
    }), 0);
    W_tl_bc.destroy();
    //        final JavaPairRDD<LinearlySpacedIndexBlock, INDArray> W_tl_RDD = CoverageModelSparkUtils.rddFromINDArray(W_tl,
    //                targetSpaceBlocks, ctx, true);
    //        final INDArray Q_W_tl = CoverageModelSparkUtils.assembleINDArrayBlocks(
    //                computeRDD.join(W_tl_RDD).mapValues(p -> {
    //                    final CoverageModelEMComputeBlock cb = p._1;
    //                    final INDArray W_tl_chunk = p._2;
    //                    final INDArray Q_tll_chunk = cb.getINDArrayFromCache("Q_tll");
    //                    return Nd4j.vstack(IntStream.range(0, cb.getTargetSpaceBlock().getNumElements()).parallel()
    //                            .mapToObj(ti -> Q_tll_chunk.get(NDArrayIndex.point(ti)).mmul(W_tl_chunk.get(NDArrayIndex.point(ti)).transpose()))
    //                            .collect(Collectors.toList()));
    //                }), false);
    //        W_tl_RDD.unpersist();
    final long endTimeQW = System.nanoTime();
    logger.debug("Local [Z] [F] [W] timing: " + (endTimeZFW - startTimeZFW) / 1000000 + " ms");
    logger.debug("Spark [Q] [W] timing: " + (endTimeQW - startTimeQW) / 1000000 + " ms");
    return Q_W_tl.addi(Z_F_W_tl);
}

Example 3 with DimensionMismatchException

use of org.apache.commons.math3.exception.DimensionMismatchException in project gatk-protected by broadinstitute.

the class CoverageModelWLinearOperatorLocal method operate.

@Override
public INDArray operate(@Nonnull final INDArray W_tl) throws DimensionMismatchException {
    if (W_tl.rank() != 2 || W_tl.shape()[0] != numTargets || W_tl.shape()[1] != numLatents)
        throw new DimensionMismatchException(W_tl.length(), numTargets * numLatents);
    final INDArray fx = Nd4j.create(numTargets, numLatents);
    final INDArray res = Nd4j.create(numTargets, numLatents);
    /* F W */
    final long startTimeFW = System.nanoTime();
    IntStream.range(0, numLatents).parallel().forEach(li -> fx.get(NDArrayIndex.all(), NDArrayIndex.point(li)).assign(F_tt.operate(W_tl.get(NDArrayIndex.all(), NDArrayIndex.point(li)))));
    final long endTimeFW = System.nanoTime();
    /* Q W + Z F W */
    final long startTimeCalc = System.nanoTime();
    IntStream.range(0, numTargets).parallel().forEach(ti -> res.get(NDArrayIndex.point(ti)).assign(Q_tll.get(NDArrayIndex.point(ti)).mmul(W_tl.get(NDArrayIndex.point(ti)).transpose()).addi(Z_ll.mmul(fx.get(NDArrayIndex.point(ti)).transpose())).transpose()));
    final long endTimeCalc = System.nanoTime();
    logger.debug("Local [F] [W] timing: " + (endTimeFW - startTimeFW) / 1000000 + " ms");
    logger.debug("Local [Q] [W] + [Z] [F] [W] timing: " + (endTimeCalc - startTimeCalc) / 1000000 + " ms");
    return res;
}

Example 4 with DimensionMismatchException

use of org.apache.commons.math3.exception.DimensionMismatchException in project gatk by broadinstitute.

the class CoverageModelWLinearOperatorLocal method operate.

@Override
public INDArray operate(@Nonnull final INDArray W_tl) throws DimensionMismatchException {
    if (W_tl.rank() != 2 || W_tl.shape()[0] != numTargets || W_tl.shape()[1] != numLatents)
        throw new DimensionMismatchException(W_tl.length(), numTargets * numLatents);
    final INDArray fx = Nd4j.create(numTargets, numLatents);
    final INDArray res = Nd4j.create(numTargets, numLatents);
    /* F W */
    final long startTimeFW = System.nanoTime();
    IntStream.range(0, numLatents).parallel().forEach(li -> fx.get(NDArrayIndex.all(), NDArrayIndex.point(li)).assign(F_tt.operate(W_tl.get(NDArrayIndex.all(), NDArrayIndex.point(li)))));
    final long endTimeFW = System.nanoTime();
    /* Q W + Z F W */
    final long startTimeCalc = System.nanoTime();
    IntStream.range(0, numTargets).parallel().forEach(ti -> res.get(NDArrayIndex.point(ti)).assign(Q_tll.get(NDArrayIndex.point(ti)).mmul(W_tl.get(NDArrayIndex.point(ti)).transpose()).addi(Z_ll.mmul(fx.get(NDArrayIndex.point(ti)).transpose())).transpose()));
    final long endTimeCalc = System.nanoTime();
    logger.debug("Local [F] [W] timing: " + (endTimeFW - startTimeFW) / 1000000 + " ms");
    logger.debug("Local [Q] [W] + [Z] [F] [W] timing: " + (endTimeCalc - startTimeCalc) / 1000000 + " ms");
    return res;
}

Example 5 with DimensionMismatchException

use of org.apache.commons.math3.exception.DimensionMismatchException in project gatk by broadinstitute.

the class CoverageModelWPreconditionerLocal method operate.

@Override
public INDArray operate(@Nonnull final INDArray W_tl) throws DimensionMismatchException {
    if (W_tl.rank() != 2 || W_tl.shape()[0] != numTargets || W_tl.shape()[1] != numLatents) {
        throw new DimensionMismatchException(W_tl.length(), numTargets * numLatents);
    }
    /* take a Fourier transform in target space */
    long startTimeRFFT = System.nanoTime();
    final INDArray W_kl = Nd4j.create(fftSize, numLatents);
    IntStream.range(0, numLatents).parallel().forEach(li -> W_kl.get(NDArrayIndex.all(), NDArrayIndex.point(li)).assign(Nd4j.create(F_tt.getForwardFFT(W_tl.get(NDArrayIndex.all(), NDArrayIndex.point(li))), new int[] { fftSize, 1 })));
    long endTimeRFFT = System.nanoTime();
    /* apply the preconditioner in the Fourier space */
    long startTimePrecond = System.nanoTime();
    IntStream.range(0, fftSize).parallel().forEach(k -> {
        final INDArray res = CoverageModelEMWorkspaceMathUtils.linsolve(Z_ll.mul(orderedFourierFactors[k]).addi(Q_ll), W_kl.get(NDArrayIndex.point(k)));
        W_kl.get(NDArrayIndex.point(k)).assign(res);
    });
    long endTimePrecond = System.nanoTime();
    /* irfft */
    long startTimeIRFFT = System.nanoTime();
    final INDArray res = Nd4j.create(numTargets, numLatents);
    IntStream.range(0, numLatents).parallel().forEach(li -> res.get(NDArrayIndex.all(), NDArrayIndex.point(li)).assign(F_tt.getInverseFFT(W_kl.get(NDArrayIndex.all(), NDArrayIndex.point(li)))));
    long endTimeIRFFT = System.nanoTime();
    logger.debug("Local FFT timing: " + (endTimeRFFT - startTimeRFFT + endTimeIRFFT - startTimeIRFFT) / 1000000 + " ms");
    logger.debug("Local preconditioner application timing: " + (endTimePrecond - startTimePrecond) / 1000000 + " ms");
    return res;
}