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[SYSTEMDS-3824] Decompressing Transpose
Sebastian Baunsgaard <[email protected]> introduced a new CLALib for Reorg, specifically Transpose e-strauss <[email protected]> applied minor changes: - a manual rewrite in bultin kmeans script to use argmin (reduced runtime by 18%) - added new decompressing transpose to DenseBlock from SparseBlock for ColGroupDDC - fixed bug in sparsity evaluation in decompressed transposed (switch nrow w/ ncol) - minor bug fix in regarding the cached decompression count
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158 changes: 158 additions & 0 deletions
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src/main/java/org/apache/sysds/runtime/compress/lib/CLALibReorg.java
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| /* | ||
| * Licensed to the Apache Software Foundation (ASF) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The ASF licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, | ||
| * software distributed under the License is distributed on an | ||
| * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY | ||
| * KIND, either express or implied. See the License for the | ||
| * specific language governing permissions and limitations | ||
| * under the License. | ||
| */ | ||
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| package org.apache.sysds.runtime.compress.lib; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.concurrent.ExecutorService; | ||
| import java.util.concurrent.Future; | ||
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| import org.apache.commons.logging.Log; | ||
| import org.apache.commons.logging.LogFactory; | ||
| import org.apache.sysds.runtime.compress.CompressedMatrixBlock; | ||
| import org.apache.sysds.runtime.compress.DMLCompressionException; | ||
| import org.apache.sysds.runtime.compress.colgroup.AColGroup; | ||
| import org.apache.sysds.runtime.data.DenseBlock; | ||
| import org.apache.sysds.runtime.data.SparseBlock; | ||
| import org.apache.sysds.runtime.data.SparseBlockMCSR; | ||
| import org.apache.sysds.runtime.functionobjects.SwapIndex; | ||
| import org.apache.sysds.runtime.matrix.data.LibMatrixReorg; | ||
| import org.apache.sysds.runtime.matrix.data.MatrixBlock; | ||
| import org.apache.sysds.runtime.matrix.operators.ReorgOperator; | ||
| import org.apache.sysds.runtime.util.CommonThreadPool; | ||
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| public class CLALibReorg { | ||
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| protected static final Log LOG = LogFactory.getLog(CLALibReorg.class.getName()); | ||
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| public static boolean warned = false; | ||
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| public static MatrixBlock reorg(CompressedMatrixBlock cmb, ReorgOperator op, MatrixBlock ret, int startRow, | ||
| int startColumn, int length) { | ||
| // SwapIndex is transpose | ||
| if(op.fn instanceof SwapIndex && cmb.getNumColumns() == 1) { | ||
| MatrixBlock tmp = cmb.decompress(op.getNumThreads()); | ||
| long nz = tmp.setNonZeros(tmp.getNonZeros()); | ||
| if(tmp.isInSparseFormat()) | ||
| return LibMatrixReorg.transpose(tmp); // edge case... | ||
| else | ||
| tmp = new MatrixBlock(tmp.getNumColumns(), tmp.getNumRows(), tmp.getDenseBlockValues()); | ||
| tmp.setNonZeros(nz); | ||
| return tmp; | ||
| } | ||
| else if(op.fn instanceof SwapIndex) { | ||
| MatrixBlock tmp = cmb.getCachedDecompressed(); | ||
| if(tmp != null) | ||
| return tmp.reorgOperations(op, ret, startRow, startColumn, length); | ||
| // Allow transpose to be compressed output. In general we need to have a transposed flag on | ||
| // the compressed matrix. https://issues.apache.org/jira/browse/SYSTEMDS-3025 | ||
| return transpose(cmb, ret, op.getNumThreads()); | ||
| } | ||
| else { | ||
| String message = !warned ? op.getClass().getSimpleName() + " -- " + op.fn.getClass().getSimpleName() : null; | ||
| MatrixBlock tmp = cmb.getUncompressed(message, op.getNumThreads()); | ||
| warned = true; | ||
| return tmp.reorgOperations(op, ret, startRow, startColumn, length); | ||
| } | ||
| } | ||
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| private static MatrixBlock transpose(CompressedMatrixBlock cmb, MatrixBlock ret, int k) { | ||
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| final long nnz = cmb.getNonZeros(); | ||
| final int nRow = cmb.getNumRows(); | ||
| final int nCol = cmb.getNumColumns(); | ||
| final boolean sparseOut = MatrixBlock.evalSparseFormatInMemory(nCol,nRow, nnz); | ||
| if(sparseOut) | ||
| return transposeSparse(cmb, ret, k, nRow, nCol, nnz); | ||
| else | ||
| return transposeDense(cmb, ret, k, nRow, nCol, nnz); | ||
| } | ||
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| private static MatrixBlock transposeSparse(CompressedMatrixBlock cmb, MatrixBlock ret, int k, int nRow, int nCol, | ||
| long nnz) { | ||
| if(ret == null) | ||
| ret = new MatrixBlock(nCol, nRow, true, nnz); | ||
| else | ||
| ret.reset(nCol, nRow, true, nnz); | ||
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| ret.allocateAndResetSparseBlock(true, SparseBlock.Type.MCSR); | ||
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| final int nColOut = ret.getNumColumns(); | ||
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| if(k > 1 && cmb.getColGroups().size() > 1) | ||
| decompressToTransposedSparseParallel((SparseBlockMCSR) ret.getSparseBlock(), cmb.getColGroups(), nColOut, k); | ||
| else | ||
| decompressToTransposedSparseSingleThread((SparseBlockMCSR) ret.getSparseBlock(), cmb.getColGroups(), nColOut); | ||
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| return ret; | ||
| } | ||
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| private static MatrixBlock transposeDense(CompressedMatrixBlock cmb, MatrixBlock ret, int k, int nRow, int nCol, | ||
| long nnz) { | ||
| if(ret == null) | ||
| ret = new MatrixBlock(nCol, nRow, false, nnz); | ||
| else | ||
| ret.reset(nCol, nRow, false, nnz); | ||
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| // TODO: parallelize | ||
| ret.allocateDenseBlock(); | ||
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| decompressToTransposedDense(ret.getDenseBlock(), cmb.getColGroups(), nRow, 0, nRow); | ||
| return ret; | ||
| } | ||
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| private static void decompressToTransposedDense(DenseBlock ret, List<AColGroup> groups, int rlen, int rl, int ru) { | ||
| for(int i = 0; i < groups.size(); i++) { | ||
| AColGroup g = groups.get(i); | ||
| g.decompressToDenseBlockTransposed(ret, rl, ru); | ||
| } | ||
| } | ||
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| private static void decompressToTransposedSparseSingleThread(SparseBlockMCSR ret, List<AColGroup> groups, | ||
| int nColOut) { | ||
| for(int i = 0; i < groups.size(); i++) { | ||
| AColGroup g = groups.get(i); | ||
| g.decompressToSparseBlockTransposed(ret, nColOut); | ||
| } | ||
| } | ||
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| private static void decompressToTransposedSparseParallel(SparseBlockMCSR ret, List<AColGroup> groups, int nColOut, | ||
| int k) { | ||
| final ExecutorService pool = CommonThreadPool.get(k); | ||
| try { | ||
| final List<Future<?>> tasks = new ArrayList<>(groups.size()); | ||
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| for(int i = 0; i < groups.size(); i++) { | ||
| final AColGroup g = groups.get(i); | ||
| tasks.add(pool.submit(() -> g.decompressToSparseBlockTransposed(ret, nColOut))); | ||
| } | ||
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| for(Future<?> f : tasks) | ||
| f.get(); | ||
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| } | ||
| catch(Exception e) { | ||
| throw new DMLCompressionException("Failed to parallel decompress transpose sparse", e); | ||
| } | ||
| finally { | ||
| pool.shutdown(); | ||
| } | ||
| } | ||
| } |
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