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Posted to issues@iceberg.apache.org by "aokolnychyi (via GitHub)" <gi...@apache.org> on 2023/05/24 01:05:23 UTC
[GitHub] [iceberg] aokolnychyi opened a new pull request, #7692: Core: Add writer for unordered position deletes
aokolnychyi opened a new pull request, #7692:
URL: https://github.com/apache/iceberg/pull/7692
This PR adds a position delete writer that can handle unordered position deletes. This writer should allow us to avoid a local sort for **_some_** MERGE operations. Specifically, consider MERGE operations where 90% of data are inserts and the table is partitioned but no sort order is defined. Right now, we always request a local sort to order deletes. However, that sort can be useless for inserts if no sort order is defined and fanout writer is enabled. Moreover, ordering inserts may lead to a spill, which is expensive for wide tables and large tasks.
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[GitHub] [iceberg] aokolnychyi commented on a diff in pull request #7692: Core: Add writer for unordered position deletes
Posted by "aokolnychyi (via GitHub)" <gi...@apache.org>.
aokolnychyi commented on code in PR #7692:
URL: https://github.com/apache/iceberg/pull/7692#discussion_r1204815093
##########
core/src/main/java/org/apache/iceberg/deletes/SortingPositionOnlyDeleteWriter.java:
##########
@@ -0,0 +1,111 @@
+/*
+ * 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.iceberg.deletes;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+import org.apache.iceberg.io.DeleteWriteResult;
+import org.apache.iceberg.io.FileWriter;
+import org.apache.iceberg.relocated.com.google.common.collect.Lists;
+import org.apache.iceberg.relocated.com.google.common.collect.Maps;
+import org.apache.iceberg.types.Comparators;
+import org.apache.iceberg.util.CharSequenceWrapper;
+import org.roaringbitmap.longlong.PeekableLongIterator;
+import org.roaringbitmap.longlong.Roaring64Bitmap;
+
+/**
+ * A position delete writer that is capable of handling unordered deletes without rows.
Review Comment:
Will add in this PR.
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[GitHub] [iceberg] aokolnychyi commented on a diff in pull request #7692: Core: Add writer for unordered position deletes
Posted by "aokolnychyi (via GitHub)" <gi...@apache.org>.
aokolnychyi commented on code in PR #7692:
URL: https://github.com/apache/iceberg/pull/7692#discussion_r1204814401
##########
spark/v3.4/spark/src/jmh/java/org/apache/iceberg/spark/source/WritersBenchmark.java:
##########
@@ -363,6 +389,60 @@ public void writeUnpartitionedClusteredPositionDeleteWriter(Blackhole blackhole)
blackhole.consume(writer);
}
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriter(Blackhole blackhole) throws IOException {
+ FileIO io = table().io();
+
+ OutputFileFactory fileFactory = newFileFactory();
+ SparkFileWriterFactory writerFactory =
+ SparkFileWriterFactory.builderFor(table()).dataFileFormat(fileFormat()).build();
+
+ FanoutPositionOnlyDeleteWriter<InternalRow> writer =
+ new FanoutPositionOnlyDeleteWriter<>(
+ writerFactory, fileFactory, io, TARGET_FILE_SIZE_IN_BYTES);
+
+ PositionDelete<InternalRow> positionDelete = PositionDelete.create();
+ try (FanoutPositionOnlyDeleteWriter<InternalRow> closeableWriter = writer) {
+ for (InternalRow row : positionDeleteRows) {
+ String path = row.getString(0);
+ long pos = row.getLong(1);
+ positionDelete.set(path, pos, null);
+ closeableWriter.write(positionDelete, unpartitionedSpec, null);
+ }
+ }
+
+ blackhole.consume(writer);
+ }
+
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriterShuffled(Blackhole blackhole)
Review Comment:
I ran this benchmark (100 data files, 50k deletes each, 5 million deletes total) with a GC profiler and did not see anything bad. Issues will arise when there are lots of unique data files. That's unlikely as we distribute by partition and this writer will still be disabled by default, so users will have to opt in explicitly.
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[GitHub] [iceberg] aokolnychyi commented on a diff in pull request #7692: Core: Add writer for unordered position deletes
Posted by "aokolnychyi (via GitHub)" <gi...@apache.org>.
aokolnychyi commented on code in PR #7692:
URL: https://github.com/apache/iceberg/pull/7692#discussion_r1203260409
##########
spark/v3.4/spark/src/jmh/java/org/apache/iceberg/spark/source/WritersBenchmark.java:
##########
@@ -363,6 +389,60 @@ public void writeUnpartitionedClusteredPositionDeleteWriter(Blackhole blackhole)
blackhole.consume(writer);
}
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriter(Blackhole blackhole) throws IOException {
+ FileIO io = table().io();
+
+ OutputFileFactory fileFactory = newFileFactory();
+ SparkFileWriterFactory writerFactory =
+ SparkFileWriterFactory.builderFor(table()).dataFileFormat(fileFormat()).build();
+
+ FanoutPositionOnlyDeleteWriter<InternalRow> writer =
+ new FanoutPositionOnlyDeleteWriter<>(
+ writerFactory, fileFactory, io, TARGET_FILE_SIZE_IN_BYTES);
+
+ PositionDelete<InternalRow> positionDelete = PositionDelete.create();
+ try (FanoutPositionOnlyDeleteWriter<InternalRow> closeableWriter = writer) {
+ for (InternalRow row : positionDeleteRows) {
+ String path = row.getString(0);
+ long pos = row.getLong(1);
+ positionDelete.set(path, pos, null);
+ closeableWriter.write(positionDelete, unpartitionedSpec, null);
+ }
+ }
+
+ blackhole.consume(writer);
+ }
+
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriterShuffled(Blackhole blackhole)
Review Comment:
We should expect 5-15% overhead for the new buffering writer, which can still be beneficial for the job if we skip local ordering for inserts and potentially avoid spilling. This benchmark also does not take into account the cost to order records, it only tests the write performance. We will use this writer only if fanout is enabled. We should also explore Puffin delete files that would persist bitmaps directly.
```
Benchmark Mode Cnt Score Error Units
ParquetWritersBenchmark.writeUnpartitionedClusteredPositionDeleteWriter ss 5 6.004 ± 0.185 s/op
ParquetWritersBenchmark.writeUnpartitionedFanoutPositionDeleteWriter ss 5 6.503 ± 0.171 s/op
ParquetWritersBenchmark.writeUnpartitionedFanoutPositionDeleteWriterShuffled ss 5 6.616 ± 0.204 s/op
```
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[GitHub] [iceberg] aokolnychyi closed pull request #7692: Core: Add writer for unordered position deletes
Posted by "aokolnychyi (via GitHub)" <gi...@apache.org>.
aokolnychyi closed pull request #7692: Core: Add writer for unordered position deletes
URL: https://github.com/apache/iceberg/pull/7692
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[GitHub] [iceberg] aokolnychyi commented on pull request #7692: Core: Add writer for unordered position deletes
Posted by "aokolnychyi (via GitHub)" <gi...@apache.org>.
aokolnychyi commented on PR #7692:
URL: https://github.com/apache/iceberg/pull/7692#issuecomment-1560321440
cc @singhpk234 @amogh-jahagirdar @RussellSpitzer @szehon-ho @flyrain @rdblue
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[GitHub] [iceberg] aokolnychyi merged pull request #7692: Core: Add writer for unordered position deletes
Posted by "aokolnychyi (via GitHub)" <gi...@apache.org>.
aokolnychyi merged PR #7692:
URL: https://github.com/apache/iceberg/pull/7692
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[GitHub] [iceberg] singhpk234 commented on a diff in pull request #7692: Core: Add writer for unordered position deletes
Posted by "singhpk234 (via GitHub)" <gi...@apache.org>.
singhpk234 commented on code in PR #7692:
URL: https://github.com/apache/iceberg/pull/7692#discussion_r1204772057
##########
spark/v3.4/spark/src/jmh/java/org/apache/iceberg/spark/source/WritersBenchmark.java:
##########
@@ -363,6 +389,60 @@ public void writeUnpartitionedClusteredPositionDeleteWriter(Blackhole blackhole)
blackhole.consume(writer);
}
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriter(Blackhole blackhole) throws IOException {
+ FileIO io = table().io();
+
+ OutputFileFactory fileFactory = newFileFactory();
+ SparkFileWriterFactory writerFactory =
+ SparkFileWriterFactory.builderFor(table()).dataFileFormat(fileFormat()).build();
+
+ FanoutPositionOnlyDeleteWriter<InternalRow> writer =
+ new FanoutPositionOnlyDeleteWriter<>(
+ writerFactory, fileFactory, io, TARGET_FILE_SIZE_IN_BYTES);
+
+ PositionDelete<InternalRow> positionDelete = PositionDelete.create();
+ try (FanoutPositionOnlyDeleteWriter<InternalRow> closeableWriter = writer) {
+ for (InternalRow row : positionDeleteRows) {
+ String path = row.getString(0);
+ long pos = row.getLong(1);
+ positionDelete.set(path, pos, null);
+ closeableWriter.write(positionDelete, unpartitionedSpec, null);
+ }
+ }
+
+ blackhole.consume(writer);
+ }
+
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriterShuffled(Blackhole blackhole)
Review Comment:
> We should also explore Puffin delete files that would persist bitmaps directly
+1
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[GitHub] [iceberg] aokolnychyi commented on a diff in pull request #7692: Core: Add writer for unordered position deletes
Posted by "aokolnychyi (via GitHub)" <gi...@apache.org>.
aokolnychyi commented on code in PR #7692:
URL: https://github.com/apache/iceberg/pull/7692#discussion_r1204814401
##########
spark/v3.4/spark/src/jmh/java/org/apache/iceberg/spark/source/WritersBenchmark.java:
##########
@@ -363,6 +389,60 @@ public void writeUnpartitionedClusteredPositionDeleteWriter(Blackhole blackhole)
blackhole.consume(writer);
}
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriter(Blackhole blackhole) throws IOException {
+ FileIO io = table().io();
+
+ OutputFileFactory fileFactory = newFileFactory();
+ SparkFileWriterFactory writerFactory =
+ SparkFileWriterFactory.builderFor(table()).dataFileFormat(fileFormat()).build();
+
+ FanoutPositionOnlyDeleteWriter<InternalRow> writer =
+ new FanoutPositionOnlyDeleteWriter<>(
+ writerFactory, fileFactory, io, TARGET_FILE_SIZE_IN_BYTES);
+
+ PositionDelete<InternalRow> positionDelete = PositionDelete.create();
+ try (FanoutPositionOnlyDeleteWriter<InternalRow> closeableWriter = writer) {
+ for (InternalRow row : positionDeleteRows) {
+ String path = row.getString(0);
+ long pos = row.getLong(1);
+ positionDelete.set(path, pos, null);
+ closeableWriter.write(positionDelete, unpartitionedSpec, null);
+ }
+ }
+
+ blackhole.consume(writer);
+ }
+
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriterShuffled(Blackhole blackhole)
Review Comment:
I ran this benchmark (100 data files, 50k deletes each, 5 million deletes total) with a GC profiler and did not see anything bad. Issues will arise when there are lots of unique data files. That's unlikely as we distribute by partition and this writer will still be disabled by default, so users will have to opt in explicitly. It ain't perfect for sure but there would be reasonable cases for it.
##########
spark/v3.4/spark/src/jmh/java/org/apache/iceberg/spark/source/WritersBenchmark.java:
##########
@@ -363,6 +389,60 @@ public void writeUnpartitionedClusteredPositionDeleteWriter(Blackhole blackhole)
blackhole.consume(writer);
}
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriter(Blackhole blackhole) throws IOException {
+ FileIO io = table().io();
+
+ OutputFileFactory fileFactory = newFileFactory();
+ SparkFileWriterFactory writerFactory =
+ SparkFileWriterFactory.builderFor(table()).dataFileFormat(fileFormat()).build();
+
+ FanoutPositionOnlyDeleteWriter<InternalRow> writer =
+ new FanoutPositionOnlyDeleteWriter<>(
+ writerFactory, fileFactory, io, TARGET_FILE_SIZE_IN_BYTES);
+
+ PositionDelete<InternalRow> positionDelete = PositionDelete.create();
+ try (FanoutPositionOnlyDeleteWriter<InternalRow> closeableWriter = writer) {
+ for (InternalRow row : positionDeleteRows) {
+ String path = row.getString(0);
+ long pos = row.getLong(1);
+ positionDelete.set(path, pos, null);
+ closeableWriter.write(positionDelete, unpartitionedSpec, null);
+ }
+ }
+
+ blackhole.consume(writer);
+ }
+
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriterShuffled(Blackhole blackhole)
Review Comment:
I ran this benchmark (100 data files, 50k deletes each, 5 million deletes total) with a GC profiler and did not see anything bad. Issues will arise when there are lots of unique data files. That's unlikely as we distribute by partition and this writer will still be disabled by default, so users will have to opt in explicitly. It isn't perfect for sure but there would be reasonable cases for it.
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[GitHub] [iceberg] szehon-ho commented on a diff in pull request #7692: Core: Add writer for unordered position deletes
Posted by "szehon-ho (via GitHub)" <gi...@apache.org>.
szehon-ho commented on code in PR #7692:
URL: https://github.com/apache/iceberg/pull/7692#discussion_r1204801749
##########
core/src/main/java/org/apache/iceberg/deletes/PositionDelete.java:
##########
@@ -38,6 +38,13 @@ public PositionDelete<R> set(CharSequence newPath, long newPos, R newRow) {
return this;
}
+ public PositionDelete<R> set(CharSequence newPath, long newPos) {
+ this.path = newPath;
Review Comment:
Nit question: is it cleaner to have this constructor delegate to the other one?
##########
core/src/main/java/org/apache/iceberg/deletes/SortingPositionOnlyDeleteWriter.java:
##########
@@ -0,0 +1,111 @@
+/*
+ * 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.iceberg.deletes;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+import org.apache.iceberg.io.DeleteWriteResult;
+import org.apache.iceberg.io.FileWriter;
+import org.apache.iceberg.relocated.com.google.common.collect.Lists;
+import org.apache.iceberg.relocated.com.google.common.collect.Maps;
+import org.apache.iceberg.types.Comparators;
+import org.apache.iceberg.util.CharSequenceWrapper;
+import org.roaringbitmap.longlong.PeekableLongIterator;
+import org.roaringbitmap.longlong.Roaring64Bitmap;
+
+/**
+ * A position delete writer that is capable of handling unordered deletes without rows.
Review Comment:
Nit: can we add javadoc to the PositionDeleteWriter, when we get a chance?
##########
spark/v3.4/spark/src/jmh/java/org/apache/iceberg/spark/source/WritersBenchmark.java:
##########
@@ -93,14 +100,33 @@ public void setupBenchmark() {
row -> transform.bind(Types.IntegerType.get()).apply(row.getInt(1))));
this.rows = data;
- this.positionDeleteRows =
- RandomData.generateSpark(DeleteSchemaUtil.pathPosSchema(), NUM_ROWS, 0L);
+ this.positionDeleteRows = generatePositionDeletes(false /* shuffle */);
Review Comment:
Don't shuffle?
##########
spark/v3.4/spark/src/jmh/java/org/apache/iceberg/spark/source/WritersBenchmark.java:
##########
@@ -93,14 +100,33 @@ public void setupBenchmark() {
row -> transform.bind(Types.IntegerType.get()).apply(row.getInt(1))));
this.rows = data;
- this.positionDeleteRows =
- RandomData.generateSpark(DeleteSchemaUtil.pathPosSchema(), NUM_ROWS, 0L);
+ this.positionDeleteRows = generatePositionDeletes(false /* shuffle */);
+ this.shuffledPositionDeleteRows = generatePositionDeletes(true /* shuffle */);
this.unpartitionedSpec = table().specs().get(0);
Preconditions.checkArgument(unpartitionedSpec.isUnpartitioned());
this.partitionedSpec = table().specs().get(1);
}
+ private Iterable<InternalRow> generatePositionDeletes(boolean shuffle) {
+ int numDeletes = NUM_DATA_FILES_PER_POSITION_DELETE_FILE * NUM_DELETED_POSITIONS_PER_DATA_FILE;
+ List<InternalRow> deletes = Lists.newArrayListWithExpectedSize(numDeletes);
+
+ for (int pathIndex = 0; pathIndex < NUM_DATA_FILES_PER_POSITION_DELETE_FILE; pathIndex++) {
+ UTF8String path = UTF8String.fromString("path/to/position/delete/file/" + UUID.randomUUID());
+ int step = 10;
Review Comment:
why not just make this outside?
##########
spark/v3.4/spark/src/jmh/java/org/apache/iceberg/spark/source/WritersBenchmark.java:
##########
@@ -363,6 +389,60 @@ public void writeUnpartitionedClusteredPositionDeleteWriter(Blackhole blackhole)
blackhole.consume(writer);
}
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriter(Blackhole blackhole) throws IOException {
+ FileIO io = table().io();
+
+ OutputFileFactory fileFactory = newFileFactory();
+ SparkFileWriterFactory writerFactory =
+ SparkFileWriterFactory.builderFor(table()).dataFileFormat(fileFormat()).build();
+
+ FanoutPositionOnlyDeleteWriter<InternalRow> writer =
+ new FanoutPositionOnlyDeleteWriter<>(
+ writerFactory, fileFactory, io, TARGET_FILE_SIZE_IN_BYTES);
+
+ PositionDelete<InternalRow> positionDelete = PositionDelete.create();
+ try (FanoutPositionOnlyDeleteWriter<InternalRow> closeableWriter = writer) {
+ for (InternalRow row : positionDeleteRows) {
+ String path = row.getString(0);
+ long pos = row.getLong(1);
+ positionDelete.set(path, pos, null);
+ closeableWriter.write(positionDelete, unpartitionedSpec, null);
+ }
+ }
+
+ blackhole.consume(writer);
+ }
+
+ @Benchmark
+ @Threads(1)
+ public void writeUnpartitionedFanoutPositionDeleteWriterShuffled(Blackhole blackhole)
Review Comment:
About memory overhead (not sure any thing measures it now): Should be just additional space of map (data_file_path => bitmaps)? Will there be cases, esp in fanout, where a writer writes many delete of many data files, that will start to stress it?
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[GitHub] [iceberg] aokolnychyi commented on pull request #7692: Core: Add writer for unordered position deletes
Posted by "aokolnychyi (via GitHub)" <gi...@apache.org>.
aokolnychyi commented on PR #7692:
URL: https://github.com/apache/iceberg/pull/7692#issuecomment-1563072197
Thanks, @singhpk234 @szehon-ho!
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