-
Notifications
You must be signed in to change notification settings - Fork 461
/
CompressedMatrixBlock.java
1393 lines (1204 loc) · 46.9 KB
/
CompressedMatrixBlock.java
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/*
* 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.
*/
package org.apache.sysds.runtime.compress;
import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
import java.io.ObjectInput;
import java.io.ObjectOutput;
import java.lang.ref.SoftReference;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.Future;
import org.apache.commons.lang.NotImplementedException;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.commons.math3.random.Well1024a;
import org.apache.sysds.common.Types.CorrectionLocationType;
import org.apache.sysds.conf.ConfigurationManager;
import org.apache.sysds.conf.DMLConfig;
import org.apache.sysds.lops.MMTSJ.MMTSJType;
import org.apache.sysds.lops.MapMultChain.ChainType;
import org.apache.sysds.runtime.DMLRuntimeException;
import org.apache.sysds.runtime.compress.colgroup.AColGroup;
import org.apache.sysds.runtime.compress.colgroup.AColGroup.CompressionType;
import org.apache.sysds.runtime.compress.colgroup.AColGroupValue;
import org.apache.sysds.runtime.compress.colgroup.ColGroupEmpty;
import org.apache.sysds.runtime.compress.colgroup.ColGroupIO;
import org.apache.sysds.runtime.compress.colgroup.ColGroupUncompressed;
import org.apache.sysds.runtime.compress.lib.CLALibAppend;
import org.apache.sysds.runtime.compress.lib.CLALibBinaryCellOp;
import org.apache.sysds.runtime.compress.lib.CLALibCompAgg;
import org.apache.sysds.runtime.compress.lib.CLALibDecompress;
import org.apache.sysds.runtime.compress.lib.CLALibLeftMultBy;
import org.apache.sysds.runtime.compress.lib.CLALibReExpand;
import org.apache.sysds.runtime.compress.lib.CLALibRightMultBy;
import org.apache.sysds.runtime.compress.lib.CLALibScalar;
import org.apache.sysds.runtime.compress.lib.CLALibSlice;
import org.apache.sysds.runtime.compress.lib.CLALibSquash;
import org.apache.sysds.runtime.compress.lib.CLALibUnary;
import org.apache.sysds.runtime.controlprogram.caching.CacheBlock;
import org.apache.sysds.runtime.controlprogram.caching.MatrixObject.UpdateType;
import org.apache.sysds.runtime.controlprogram.parfor.stat.InfrastructureAnalyzer;
import org.apache.sysds.runtime.controlprogram.parfor.stat.Timing;
import org.apache.sysds.runtime.data.DenseBlock;
import org.apache.sysds.runtime.data.SparseBlock;
import org.apache.sysds.runtime.data.SparseRow;
import org.apache.sysds.runtime.functionobjects.MinusMultiply;
import org.apache.sysds.runtime.functionobjects.Multiply;
import org.apache.sysds.runtime.functionobjects.PlusMultiply;
import org.apache.sysds.runtime.functionobjects.SwapIndex;
import org.apache.sysds.runtime.functionobjects.TernaryValueFunction.ValueFunctionWithConstant;
import org.apache.sysds.runtime.instructions.InstructionUtils;
import org.apache.sysds.runtime.instructions.cp.CM_COV_Object;
import org.apache.sysds.runtime.instructions.cp.ScalarObject;
import org.apache.sysds.runtime.instructions.spark.data.IndexedMatrixValue;
import org.apache.sysds.runtime.matrix.data.CTableMap;
import org.apache.sysds.runtime.matrix.data.IJV;
import org.apache.sysds.runtime.matrix.data.LibMatrixBincell;
import org.apache.sysds.runtime.matrix.data.LibMatrixDatagen;
import org.apache.sysds.runtime.matrix.data.LibMatrixReorg;
import org.apache.sysds.runtime.matrix.data.LibMatrixTercell;
import org.apache.sysds.runtime.matrix.data.MatrixBlock;
import org.apache.sysds.runtime.matrix.data.MatrixIndexes;
import org.apache.sysds.runtime.matrix.data.MatrixValue;
import org.apache.sysds.runtime.matrix.data.RandomMatrixGenerator;
import org.apache.sysds.runtime.matrix.operators.AggregateBinaryOperator;
import org.apache.sysds.runtime.matrix.operators.AggregateOperator;
import org.apache.sysds.runtime.matrix.operators.AggregateTernaryOperator;
import org.apache.sysds.runtime.matrix.operators.AggregateUnaryOperator;
import org.apache.sysds.runtime.matrix.operators.BinaryOperator;
import org.apache.sysds.runtime.matrix.operators.CMOperator;
import org.apache.sysds.runtime.matrix.operators.COVOperator;
import org.apache.sysds.runtime.matrix.operators.Operator;
import org.apache.sysds.runtime.matrix.operators.QuaternaryOperator;
import org.apache.sysds.runtime.matrix.operators.ReorgOperator;
import org.apache.sysds.runtime.matrix.operators.ScalarOperator;
import org.apache.sysds.runtime.matrix.operators.TernaryOperator;
import org.apache.sysds.runtime.matrix.operators.UnaryOperator;
import org.apache.sysds.runtime.util.IndexRange;
import org.apache.sysds.utils.DMLCompressionStatistics;
public class CompressedMatrixBlock extends MatrixBlock {
private static final Log LOG = LogFactory.getLog(CompressedMatrixBlock.class.getName());
private static final long serialVersionUID = 73193720143154058L;
/**
* Column groups
*/
protected transient List<AColGroup> _colGroups;
/**
* Boolean specifying if the colGroups are overlapping each other. This happens after a right matrix multiplication.
*/
protected boolean overlappingColGroups = false;
/**
* Soft reference to a decompressed version of this matrix block.
*/
protected transient SoftReference<MatrixBlock> decompressedVersion;
public CompressedMatrixBlock() {
super(true);
sparse = false;
nonZeros = -1;
}
/**
* Main constructor for building a block from scratch.
*
* Use with caution, since it constructs an empty matrix block with nothing inside.
*
* @param rl number of rows in the block
* @param cl number of columns
*/
public CompressedMatrixBlock(int rl, int cl) {
super(true);
rlen = rl;
clen = cl;
sparse = false;
nonZeros = -1;
}
/**
* Copy constructor taking that CompressedMatrixBlock and populate this new compressedMatrixBlock with pointers to
* the same columnGroups.
*
* @param that CompressedMatrixBlock to copy values from
*/
public CompressedMatrixBlock(CompressedMatrixBlock that) {
super(true);
rlen = that.getNumRows();
clen = that.getNumColumns();
this.copyCompressedMatrix(that);
}
/**
* Copy constructor taking an uncompressedMatrixBlock to copy metadata from also while copying metadata, a soft
* reference is constructed to the uncompressed matrixBlock, to allow quick decompressions if the program is not
* under memory pressure.
*
* This method is used in the CompressionFactory.
*
* @param uncompressedMatrixBlock An uncompressed Matrix to copy metadata from.
*/
protected CompressedMatrixBlock(MatrixBlock uncompressedMatrixBlock) {
super(true);
rlen = uncompressedMatrixBlock.getNumRows();
clen = uncompressedMatrixBlock.getNumColumns();
sparse = false;
nonZeros = uncompressedMatrixBlock.getNonZeros();
decompressedVersion = new SoftReference<>(uncompressedMatrixBlock);
}
@Override
public void reset(int rl, int cl, boolean sp, long estnnz, double val) {
throw new DMLCompressionException("Invalid to reset a Compressed MatrixBlock");
}
/**
* Allocate the given column group and remove all references to old column groups.
*
* This is done by simply allocating a ned _colGroups list and adding the given column group
*
* @param cg The column group to use after.
*/
public void allocateColGroup(AColGroup cg) {
_colGroups = new ArrayList<>(1);
_colGroups.add(cg);
}
/**
* Replace the column groups in this CompressedMatrixBlock with the given column groups
*
* @param colGroups new ColGroups in the MatrixBlock
*/
public void allocateColGroupList(List<AColGroup> colGroups) {
_colGroups = colGroups;
}
/**
* Get the column groups of this CompressedMatrixBlock
*
* @return the column groups
*/
public List<AColGroup> getColGroups() {
return _colGroups;
}
/**
* Decompress block into a MatrixBlock
*
* @return a new uncompressed matrix block containing the contents of this block
*/
public MatrixBlock decompress() {
return decompress(1);
}
/**
* Decompress block into a MatrixBlock
*
* @param k degree of parallelism
* @return a new uncompressed matrix block containing the contents of this block
*/
public MatrixBlock decompress(int k) {
// Early out if empty.
if(isEmpty())
return new MatrixBlock(rlen, clen, true, 0);
// Early out if decompressed version already is cached
MatrixBlock ret = getCachedDecompressed();
if(ret != null)
return ret;
ret = CLALibDecompress.decompress(this, k);
// Set soft reference to the decompressed version
decompressedVersion = new SoftReference<>(ret);
return ret;
}
@Override
public void putInto(MatrixBlock target, int rowOffset, int colOffset, boolean sparseCopyShallow) {
CLALibDecompress.decompressTo(this, target, rowOffset, colOffset, 1);
}
/**
* Get the cached decompressed matrix (if it exists otherwise null).
*
* This in practice means that if some other instruction have materialized the decompressed version it can be
* accessed though this method with a guarantee that it did not go through the entire decompression phase.
*
* @return The cached decompressed matrix, if it does not exist return null
*/
public MatrixBlock getCachedDecompressed() {
if(decompressedVersion != null) {
final MatrixBlock mb = decompressedVersion.get();
if(mb != null) {
DMLCompressionStatistics.addDecompressCacheCount();
LOG.trace("Decompressed block was in soft reference.");
return mb;
}
}
return null;
}
public CompressedMatrixBlock squash(int k) {
return CLALibSquash.squash(this, k);
}
@Override
public long recomputeNonZeros() {
if(isOverlapping())
nonZeros = clen * rlen;
else {
long nnz = 0;
for(AColGroup g : _colGroups)
nnz += g.getNumberNonZeros(rlen);
nonZeros = nnz;
}
if(nonZeros == 0) {
ColGroupEmpty cg = ColGroupEmpty.generate(getNumColumns());
allocateColGroup(cg);
}
return nonZeros;
}
@Override
public long recomputeNonZeros(int rl, int ru) {
throw new NotImplementedException();
}
@Override
public long recomputeNonZeros(int rl, int ru, int cl, int cu) {
throw new NotImplementedException();
}
@Override
public long getInMemorySize() {
return estimateCompressedSizeInMemory();
}
@Override
public long estimateSizeInMemory() {
return estimateCompressedSizeInMemory();
}
/**
* Obtain an upper bound on the memory used to store the compressed block.
*
* @return an upper bound on the memory used to store this compressed block considering class overhead.
*/
public long estimateCompressedSizeInMemory() {
long total = baseSizeInMemory();
for(AColGroup grp : _colGroups)
total += grp.estimateInMemorySize();
return total;
}
public static long baseSizeInMemory() {
long total = 16; // Object header
total += getHeaderSize(); // Matrix Block elements
total += 8; // Col Group Ref
total += 8; // v reference
total += 8; // soft reference to decompressed version
total += 1 + 7; // Booleans plus padding
total += 40; // Col Group Array List
return total;
}
@Override
public double quickGetValue(int r, int c) {
if(isOverlapping()) {
double v = 0.0;
for(AColGroup group : _colGroups)
v += group.get(r, c);
return v;
}
else {
for(AColGroup group : _colGroups) {
final int idx = Arrays.binarySearch(group.getColIndices(), c);
if(idx >= 0)
return group.getIdx(r, idx);
}
return 0;
}
}
@Override
public long getExactSizeOnDisk() {
// header information
long ret = 4 + 4 + 8 + 1;
ret += ColGroupIO.getExactSizeOnDisk(_colGroups);
return ret;
}
@Override
public long estimateSizeOnDisk() {
return getExactSizeOnDisk();
}
@Override
public void readFields(DataInput in) throws IOException {
// deserialize compressed block
rlen = in.readInt();
clen = in.readInt();
nonZeros = in.readLong();
overlappingColGroups = in.readBoolean();
_colGroups = ColGroupIO.readGroups(in, rlen);
}
@Override
public void write(DataOutput out) throws IOException {
if(getExactSizeOnDisk() > MatrixBlock.estimateSizeOnDisk(rlen, clen, nonZeros)) {
// If the size of this matrixBlock is smaller in uncompressed format, then
// decompress and save inside an uncompressed column group.
MatrixBlock uncompressed = getUncompressed("for smaller serialization");
ColGroupUncompressed cg = new ColGroupUncompressed(uncompressed);
allocateColGroup(cg);
nonZeros = cg.getNumberNonZeros(rlen);
// clear the soft reference to the decompressed version, since the one column group is perfectly,
// representing the decompressed version.
clearSoftReferenceToDecompressed();
}
// serialize compressed matrix block
out.writeInt(rlen);
out.writeInt(clen);
out.writeLong(nonZeros);
out.writeBoolean(overlappingColGroups);
ColGroupIO.writeGroups(out, _colGroups);
}
/**
* Redirects the default java serialization via externalizable to our default hadoop writable serialization for
* efficient broadcast/rdd de-serialization.
*
* @param is object input
* @throws IOException if IOException occurs
*/
@Override
public void readExternal(ObjectInput is) throws IOException {
readFields(is);
}
/**
* Redirects the default java serialization via externalizable to our default hadoop writable serialization for
* efficient broadcast/rdd serialization.
*
* @param os object output
* @throws IOException if IOException occurs
*/
@Override
public void writeExternal(ObjectOutput os) throws IOException {
write(os);
}
@Override
public MatrixBlock scalarOperations(ScalarOperator sop, MatrixValue result) {
return CLALibScalar.scalarOperations(sop, this, result);
}
@Override
public MatrixBlock binaryOperations(BinaryOperator op, MatrixValue thatValue, MatrixValue result) {
MatrixBlock that = thatValue == null ? null : (MatrixBlock) thatValue;
MatrixBlock ret = result == null ? null : (MatrixBlock) result;
return CLALibBinaryCellOp.binaryOperationsRight(op, this, that, ret);
}
public MatrixBlock binaryOperationsLeft(BinaryOperator op, MatrixValue thatValue, MatrixValue result) {
MatrixBlock that = thatValue == null ? null : (MatrixBlock) thatValue;
MatrixBlock ret = result == null ? null : (MatrixBlock) result;
return CLALibBinaryCellOp.binaryOperationsLeft(op, this, that, ret);
}
@Override
public MatrixBlock append(MatrixBlock[] that, MatrixBlock ret, boolean cbind) {
if(cbind && that.length == 1)
return CLALibAppend.append(this, that[0], InfrastructureAnalyzer.getLocalParallelism());
else {
MatrixBlock left = getUncompressed("append list or r-bind not supported in compressed");
MatrixBlock[] thatUC = new MatrixBlock[that.length];
for(int i = 0; i < that.length; i++)
thatUC[i] = getUncompressed(that[i]);
return left.append(thatUC, ret, cbind);
}
}
@Override
public void append(MatrixValue v2, ArrayList<IndexedMatrixValue> outlist, int blen, boolean cbind, boolean m2IsLast,
int nextNCol) {
MatrixBlock left = getUncompressed("append ArrayList");
MatrixBlock right = getUncompressed(v2);
left.append(right, outlist, blen, cbind, m2IsLast, nextNCol);
}
@Override
public MatrixBlock chainMatrixMultOperations(MatrixBlock v, MatrixBlock w, MatrixBlock out, ChainType ctype, int k) {
checkMMChain(ctype, v, w);
// multi-threaded MMChain of single uncompressed ColGroup
if(_colGroups != null && _colGroups.size() == 1 &&
_colGroups.get(0).getCompType() == CompressionType.UNCOMPRESSED)
return ((ColGroupUncompressed) _colGroups.get(0)).getData().chainMatrixMultOperations(v, w, out, ctype, k);
// prepare result
if(out != null)
out.reset(clen, 1, false);
else
out = new MatrixBlock(clen, 1, false);
// empty block handling
if(isEmpty())
return out;
BinaryOperator bop = new BinaryOperator(Multiply.getMultiplyFnObject(), k);
boolean allowOverlap = ConfigurationManager.getDMLConfig().getBooleanValue(DMLConfig.COMPRESSED_OVERLAPPING) &&
v.getNumColumns() > 1;
MatrixBlock tmp = CLALibRightMultBy.rightMultByMatrix(this, v, null, k, allowOverlap);
if(ctype == ChainType.XtwXv) {
if(tmp instanceof CompressedMatrixBlock)
tmp = CLALibBinaryCellOp.binaryOperationsRight(bop, (CompressedMatrixBlock) tmp, w, null);
else
LibMatrixBincell.bincellOpInPlace(tmp, w, bop);
}
if(tmp instanceof CompressedMatrixBlock)
CLALibLeftMultBy.leftMultByMatrixTransposed(this, (CompressedMatrixBlock) tmp, out, k);
else
CLALibLeftMultBy.leftMultByMatrixTransposed(this, tmp, out, k);
if(out.getNumColumns() != 1)
out = LibMatrixReorg.transposeInPlace(out, k);
out.recomputeNonZeros();
return out;
}
@Override
public MatrixBlock aggregateBinaryOperations(MatrixBlock m1, MatrixBlock m2, MatrixBlock ret,
AggregateBinaryOperator op) {
// create output matrix block
return aggregateBinaryOperations(m1, m2, ret, op, false, false);
}
public MatrixBlock aggregateBinaryOperations(MatrixBlock m1, MatrixBlock m2, MatrixBlock ret,
AggregateBinaryOperator op, boolean transposeLeft, boolean transposeRight) {
validateMatrixMult(m1, m2);
final int k = op.getNumThreads();
final Timing time = LOG.isTraceEnabled() ? new Timing(true) : null;
if(m1 instanceof CompressedMatrixBlock && m2 instanceof CompressedMatrixBlock) {
return doubleCompressedAggregateBinaryOperations((CompressedMatrixBlock) m1, (CompressedMatrixBlock) m2, ret,
op, transposeLeft, transposeRight);
}
boolean transposeOutput = false;
if(transposeLeft || transposeRight) {
if((m1 instanceof CompressedMatrixBlock && transposeLeft) ||
(m2 instanceof CompressedMatrixBlock && transposeRight)) {
// change operation from m1 %*% m2 -> t( t(m2) %*% t(m1) )
transposeOutput = true;
MatrixBlock tmp = m1;
m1 = m2;
m2 = tmp;
boolean tmpLeft = transposeLeft;
transposeLeft = !transposeRight;
transposeRight = !tmpLeft;
}
if(!(m1 instanceof CompressedMatrixBlock) && transposeLeft) {
m1 = LibMatrixReorg.transpose(m1, k);
transposeLeft = false;
}
else if(!(m2 instanceof CompressedMatrixBlock) && transposeRight) {
m2 = LibMatrixReorg.transpose(m2, k);
transposeRight = false;
}
}
final boolean right = (m1 == this);
final MatrixBlock that = right ? m2 : m1;
// create output matrix block
if(right)
ret = CLALibRightMultBy.rightMultByMatrix(this, that, ret, op.getNumThreads());
else
ret = CLALibLeftMultBy.leftMultByMatrix(this, that, ret, op.getNumThreads());
if(LOG.isTraceEnabled())
LOG.trace("MM: Time block w/ sharedDim: " + m1.getNumColumns() + " rowLeft: " + m1.getNumRows() + " colRight:"
+ m2.getNumColumns() + " in " + time.stop() + "ms.");
if(transposeOutput) {
if(ret instanceof CompressedMatrixBlock) {
LOG.warn("Transposing decompression");
ret = ((CompressedMatrixBlock) ret).decompress(k);
}
ret = LibMatrixReorg.transpose(ret, k);
}
return ret;
}
private void validateMatrixMult(MatrixBlock m1, MatrixBlock m2) {
if(!(m1 == this || m2 == this))
throw new DMLRuntimeException("Invalid aggregateBinaryOperation One of either input should be this");
}
private MatrixBlock doubleCompressedAggregateBinaryOperations(CompressedMatrixBlock m1, CompressedMatrixBlock m2,
MatrixBlock ret, AggregateBinaryOperator op, boolean transposeLeft, boolean transposeRight) {
if(!transposeLeft && !transposeRight) {
// If both are not transposed, decompress the right hand side. to enable
// compressed overlapping output.
LOG.warn("Matrix decompression from multiplying two compressed matrices.");
return aggregateBinaryOperations(m1, getUncompressed(m2), ret, op, transposeLeft, transposeRight);
}
else if(transposeLeft && !transposeRight) {
if(m1.getNumColumns() > m2.getNumColumns()) {
ret = CLALibLeftMultBy.leftMultByMatrixTransposed(m1, m2, ret, op.getNumThreads());
ReorgOperator r_op = new ReorgOperator(SwapIndex.getSwapIndexFnObject(), op.getNumThreads());
return ret.reorgOperations(r_op, new MatrixBlock(), 0, 0, 0);
}
else
return CLALibLeftMultBy.leftMultByMatrixTransposed(m2, m1, ret, op.getNumThreads());
}
else if(!transposeLeft && transposeRight) {
throw new DMLCompressionException("Not Implemented compressed Matrix Mult, to produce larger matrix");
// worst situation since it blows up the result matrix in number of rows in
// either compressed matrix.
}
else {
ret = aggregateBinaryOperations(m2, m1, ret, op);
ReorgOperator r_op = new ReorgOperator(SwapIndex.getSwapIndexFnObject(), op.getNumThreads());
return ret.reorgOperations(r_op, new MatrixBlock(), 0, 0, 0);
}
}
@Override
public MatrixBlock aggregateUnaryOperations(AggregateUnaryOperator op, MatrixValue result, int blen,
MatrixIndexes indexesIn, boolean inCP) {
MatrixBlock ret = (result == null) ? null : (MatrixBlock) result;
return CLALibCompAgg.aggregateUnary(this, ret, op, blen, indexesIn, inCP);
}
@Override
public MatrixBlock transposeSelfMatrixMultOperations(MatrixBlock out, MMTSJType tstype, int k) {
// check for transpose type
if(tstype == MMTSJType.LEFT) {
if(isEmpty())
return new MatrixBlock(clen, clen, true);
// create output matrix block
if(out == null)
out = new MatrixBlock(clen, clen, false);
else
out.reset(clen, clen, false);
out.allocateDenseBlock();
CLALibLeftMultBy.leftMultByTransposeSelf(this, out, k);
return out;
}
else {
throw new DMLRuntimeException("Invalid MMTSJ type '" + tstype.toString() + "'.");
}
}
@Override
public MatrixBlock replaceOperations(MatrixValue result, double pattern, double replacement) {
if(isOverlapping())
return getUncompressed("replaceOperations " + pattern + " -> " + replacement).replaceOperations(result,
pattern, replacement);
else {
CompressedMatrixBlock ret = new CompressedMatrixBlock(getNumRows(), getNumColumns());
final List<AColGroup> prev = getColGroups();
final int colGroupsLength = prev.size();
final List<AColGroup> retList = new ArrayList<>(colGroupsLength);
for(int i = 0; i < colGroupsLength; i++)
retList.add(prev.get(i).replace(pattern, replacement));
ret.allocateColGroupList(retList);
ret.recomputeNonZeros();
return ret;
}
}
@Override
public MatrixBlock reorgOperations(ReorgOperator op, MatrixValue ret, int startRow, int startColumn, int 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
printDecompressWarning(op.getClass().getSimpleName() + " -- " + op.fn.getClass().getSimpleName());
MatrixBlock tmp = decompress(op.getNumThreads());
return tmp.reorgOperations(op, ret, startRow, startColumn, length);
}
public ColGroupUncompressed getUncompressedColGroup() {
for(AColGroup grp : _colGroups)
if(grp instanceof ColGroupUncompressed)
return (ColGroupUncompressed) grp;
return null;
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("CompressedMatrixBlock:");
sb.append("\nCols:" + getNumColumns() + " Rows:" + getNumRows() + " Overlapping: " + isOverlapping() + " nnz: "
+ nonZeros);
if(_colGroups != null)
for(AColGroup cg : _colGroups) {
sb.append("\n" + cg);
}
else
sb.append("\nEmptyColGroups");
return sb.toString();
}
public boolean isOverlapping() {
return _colGroups.size() != 1 && overlappingColGroups;
}
public void setOverlapping(boolean overlapping) {
overlappingColGroups = overlapping;
}
@Override
public MatrixBlock slice(int rl, int ru, int cl, int cu, boolean deep, CacheBlock ret) {
validateSliceArgument(rl, ru, cl, cu);
return CLALibSlice.slice(this, rl, ru, cl, cu, deep);
}
@Override
public void slice(ArrayList<IndexedMatrixValue> outlist, IndexRange range, int rowCut, int colCut, int blen,
int boundaryRlen, int boundaryClen) {
MatrixBlock tmp = getUncompressed(
"slice for distribution to spark. (Could be implemented such that it does not decompress)");
tmp.slice(outlist, range, rowCut, colCut, blen, boundaryRlen, boundaryClen);
}
@Override
public MatrixBlock unaryOperations(UnaryOperator op, MatrixValue result) {
return CLALibUnary.unaryOperations(this, op, result);
}
@Override
public boolean containsValue(double pattern) {
if(isOverlapping())
return getUncompressed("ContainsValue").containsValue(pattern);
else {
for(AColGroup g : _colGroups)
if(g.containsValue(pattern))
return true;
return false;
}
}
@Override
public double max() {
AggregateUnaryOperator op = InstructionUtils.parseBasicAggregateUnaryOperator("uamax", 1);
return aggregateUnaryOperations(op, null, 1000, null).getValue(0, 0);
}
@Override
public double min() {
AggregateUnaryOperator op = InstructionUtils.parseBasicAggregateUnaryOperator("uamin", 1);
return aggregateUnaryOperations(op, null, 1000, null).getValue(0, 0);
}
@Override
public double sum() {
AggregateUnaryOperator op = InstructionUtils.parseBasicAggregateUnaryOperator("uak+", 1);
return aggregateUnaryOperations(op, null, 1000, null).getValue(0, 0);
}
@Override
public MatrixBlock colSum() {
MatrixBlock res = new MatrixBlock(1, getNumColumns(), false);
res.allocateDenseBlock();
double[] resV = res.getDenseBlockValues();
AColGroup.colSum(_colGroups, resV, getNumRows());
res.recomputeNonZeros();
return res;
}
@Override
public double sumSq() {
AggregateUnaryOperator op = InstructionUtils.parseBasicAggregateUnaryOperator("uasqk+", 1);
return aggregateUnaryOperations(op, null, 1000, null).getValue(0, 0);
}
@Override
public double prod() {
AggregateUnaryOperator op = InstructionUtils.parseBasicAggregateUnaryOperator("ua*", 1);
return aggregateUnaryOperations(op, null, 1000, null).getValue(0, 0);
}
@Override
public double mean() {
AggregateUnaryOperator op = InstructionUtils.parseBasicAggregateUnaryOperator("uamean", 1);
return aggregateUnaryOperations(op, null, 1000, null).getValue(0, 0);
}
@Override
public MatrixBlock rexpandOperations(MatrixBlock ret, double max, boolean rows, boolean cast, boolean ignore,
int k) {
if(rows) {
printDecompressWarning("rexpandOperations");
MatrixBlock tmp = getUncompressed();
return tmp.rexpandOperations(ret, max, rows, cast, ignore, k);
}
else
return CLALibReExpand.reExpand(this, ret, max, cast, ignore, k);
}
@Override
public boolean isEmptyBlock(boolean safe) {
final long nonZeros = getNonZeros();
return _colGroups == null || nonZeros == 0 || (nonZeros == -1 && recomputeNonZeros() == 0);
}
@Override
public MatrixBlock binaryOperationsInPlace(BinaryOperator op, MatrixValue thatValue) {
printDecompressWarning("binaryOperationsInPlace", (MatrixBlock) thatValue);
MatrixBlock left = new MatrixBlock();
left.copy(getUncompressed());
MatrixBlock right = getUncompressed(thatValue);
left.binaryOperationsInPlace(op, right);
return left;
}
@Override
public void incrementalAggregate(AggregateOperator aggOp, MatrixValue correction, MatrixValue newWithCorrection,
boolean deep) {
printDecompressWarning("IncrementalAggregate not supported");
MatrixBlock left = getUncompressed();
MatrixBlock correctionMatrixBlock = getUncompressed(correction);
MatrixBlock newWithCorrectionMatrixBlock = getUncompressed(newWithCorrection);
left.incrementalAggregate(aggOp, correctionMatrixBlock, newWithCorrectionMatrixBlock, deep);
}
@Override
public void incrementalAggregate(AggregateOperator aggOp, MatrixValue newWithCorrection) {
printDecompressWarning("IncrementalAggregate not supported");
MatrixBlock left = getUncompressed();
MatrixBlock newWithCorrectionMatrixBlock = getUncompressed(newWithCorrection);
left.incrementalAggregate(aggOp, newWithCorrectionMatrixBlock);
}
@Override
public void permutationMatrixMultOperations(MatrixValue m2Val, MatrixValue out1Val, MatrixValue out2Val, int k) {
printDecompressWarning("permutationMatrixMultOperations", (MatrixBlock) m2Val);
MatrixBlock left = getUncompressed();
MatrixBlock right = getUncompressed(m2Val);
left.permutationMatrixMultOperations(right, out1Val, out2Val, k);
}
@Override
public MatrixBlock leftIndexingOperations(MatrixBlock rhsMatrix, int rl, int ru, int cl, int cu, MatrixBlock ret,
UpdateType update) {
printDecompressWarning("leftIndexingOperations");
MatrixBlock left = getUncompressed();
MatrixBlock right = getUncompressed(rhsMatrix);
return left.leftIndexingOperations(right, rl, ru, cl, cu, ret, update);
}
@Override
public MatrixBlock leftIndexingOperations(ScalarObject scalar, int rl, int cl, MatrixBlock ret, UpdateType update) {
printDecompressWarning("leftIndexingOperations");
MatrixBlock tmp = getUncompressed();
return tmp.leftIndexingOperations(scalar, rl, cl, ret, update);
}
@Override
public MatrixBlock zeroOutOperations(MatrixValue result, IndexRange range, boolean complementary) {
printDecompressWarning("zeroOutOperations");
MatrixBlock tmp = getUncompressed();
return tmp.zeroOutOperations(result, range, complementary);
}
@Override
public CM_COV_Object cmOperations(CMOperator op) {
if(isEmpty())
return super.cmOperations(op);
else if(_colGroups.size() == 1 && _colGroups.get(0) instanceof AColGroupValue) {
AColGroupValue g = (AColGroupValue) _colGroups.get(0);
MatrixBlock vals = g.getValuesAsBlock();
MatrixBlock counts = getCountsAsBlock(g.getCounts());
if(counts.isEmpty())
return vals.cmOperations(op);
return vals.cmOperations(op, counts);
}
else
return getUncompressed("cmOperations").cmOperations(op);
}
private static MatrixBlock getCountsAsBlock(int[] counts) {
if(counts != null) {
MatrixBlock ret = new MatrixBlock(counts.length, 1, false);
for(int i = 0; i < counts.length; i++)
ret.quickSetValue(i, 0, counts[i]);
return ret;
}
else
return new MatrixBlock(1, 1, false);
}
@Override
public CM_COV_Object cmOperations(CMOperator op, MatrixBlock weights) {
printDecompressWarning("cmOperations");
MatrixBlock right = getUncompressed(weights);
if(isEmpty())
return super.cmOperations(op, right);
AColGroup grp = _colGroups.get(0);
if(grp instanceof ColGroupUncompressed)
return ((ColGroupUncompressed) grp).getData().cmOperations(op);
return getUncompressed().cmOperations(op, right);
}
@Override
public CM_COV_Object covOperations(COVOperator op, MatrixBlock that) {
MatrixBlock right = getUncompressed(that);
return getUncompressed("covOperations").covOperations(op, right);
}
@Override
public CM_COV_Object covOperations(COVOperator op, MatrixBlock that, MatrixBlock weights) {
MatrixBlock right1 = getUncompressed(that);
MatrixBlock right2 = getUncompressed(weights);
return getUncompressed("covOperations").covOperations(op, right1, right2);
}
@Override
public MatrixBlock sortOperations(MatrixValue weights, MatrixBlock result) {
MatrixBlock right = getUncompressed(weights);
return getUncompressed("sortOperations").sortOperations(right, result);
}
@Override
public MatrixBlock aggregateTernaryOperations(MatrixBlock m1, MatrixBlock m2, MatrixBlock m3, MatrixBlock ret,
AggregateTernaryOperator op, boolean inCP) {
boolean m1C = m1 instanceof CompressedMatrixBlock;
boolean m2C = m2 instanceof CompressedMatrixBlock;
boolean m3C = m3 instanceof CompressedMatrixBlock;
printDecompressWarning("aggregateTernaryOperations " + op.aggOp.getClass().getSimpleName() + " "
+ op.indexFn.getClass().getSimpleName() + " " + op.aggOp.increOp.fn.getClass().getSimpleName() + " "
+ op.binaryFn.getClass().getSimpleName() + " m1,m2,m3 " + m1C + " " + m2C + " " + m3C);
MatrixBlock left = getUncompressed(m1);
MatrixBlock right1 = getUncompressed(m2);
MatrixBlock right2 = getUncompressed(m3);
ret = left.aggregateTernaryOperations(left, right1, right2, ret, op, inCP);
if(ret.getNumRows() == 0 || ret.getNumColumns() == 0)
throw new DMLCompressionException("Invalid output");
return ret;
}
@Override
public MatrixBlock uaggouterchainOperations(MatrixBlock mbLeft, MatrixBlock mbRight, MatrixBlock mbOut,
BinaryOperator bOp, AggregateUnaryOperator uaggOp) {
printDecompressWarning("uaggouterchainOperations");
MatrixBlock left = getUncompressed();
MatrixBlock right = getUncompressed(mbRight);
return left.uaggouterchainOperations(left, right, mbOut, bOp, uaggOp);
}
@Override
public MatrixBlock groupedAggOperations(MatrixValue tgt, MatrixValue wghts, MatrixValue ret, int ngroups,
Operator op, int k) {
printDecompressWarning("groupedAggOperations");
MatrixBlock left = getUncompressed();
MatrixBlock right = getUncompressed(wghts);
return left.groupedAggOperations(left, right, ret, ngroups, op, k);
}
@Override
public MatrixBlock removeEmptyOperations(MatrixBlock ret, boolean rows, boolean emptyReturn, MatrixBlock select) {
printDecompressWarning("removeEmptyOperations");
MatrixBlock tmp = getUncompressed();
return tmp.removeEmptyOperations(ret, rows, emptyReturn, select);
}
@Override
public void ctableOperations(Operator op, double scalar, MatrixValue that, CTableMap resultMap,
MatrixBlock resultBlock) {
printDecompressWarning("ctableOperations Var 1");
MatrixBlock left = getUncompressed();
MatrixBlock right = getUncompressed(that);
left.ctableOperations(op, scalar, right, resultMap, resultBlock);
}
@Override
public void ctableOperations(Operator op, double scalar, double scalar2, CTableMap resultMap,
MatrixBlock resultBlock) {
printDecompressWarning("ctableOperations Var 2");
MatrixBlock tmp = getUncompressed();
tmp.ctableOperations(op, scalar, scalar2, resultMap, resultBlock);
}
@Override
public void ctableOperations(Operator op, MatrixIndexes ix1, double scalar, boolean left, int brlen,
CTableMap resultMap, MatrixBlock resultBlock) {
printDecompressWarning("ctableOperations Var 3");
MatrixBlock tmp = getUncompressed();
tmp.ctableOperations(op, ix1, scalar, left, brlen, resultMap, resultBlock);
}
@Override
public void ctableOperations(Operator op, MatrixValue that, double scalar, boolean ignoreZeros, CTableMap resultMap,
MatrixBlock resultBlock) {
printDecompressWarning("ctableOperations Var 4");
MatrixBlock left = getUncompressed();
MatrixBlock right = getUncompressed(that);
left.ctableOperations(op, right, scalar, ignoreZeros, resultMap, resultBlock);
}
@Override
public MatrixBlock ctableSeqOperations(MatrixValue thatMatrix, double thatScalar, MatrixBlock resultBlock,
boolean updateClen) {
printDecompressWarning("ctableOperations Var 5");
MatrixBlock left = getUncompressed();
MatrixBlock right = getUncompressed(thatMatrix);
return left.ctableSeqOperations(right, thatScalar, resultBlock, updateClen);
}
@Override
public void ctableOperations(Operator op, MatrixValue that, MatrixValue that2, CTableMap resultMap,
MatrixBlock resultBlock) {
MatrixBlock left = getUncompressed("ctableOperations Var 7");
MatrixBlock right1 = getUncompressed(that);
MatrixBlock right2 = getUncompressed(that2);
left.ctableOperations(op, right1, right2, resultMap, resultBlock);
}
@Override