[SPARK-32802][SQL] Avoid using SpecificInternalRow in RunLengthEncoding#Encoder #29654

sunchao · 2020-09-05T23:54:05Z

What changes were proposed in this pull request?

Currently RunLengthEncoding#Encoder uses SpecificInternalRow as a holder for the current value when calculating compression stats and doing the actual compression. It calls ColumnType.copyField and ColumnType.getField on the internal row which incurs extra cost comparing to directly operating on the internal type. This proposes to replace the SpecificInternalRow with T#InternalType to avoid the extra cost.

Why are the changes needed?

Operating on SpecificInternalRow carries certain cost and negatively impact performance when using RunLengthEncoding for compression.

With the change I see some improvements through CompressionSchemeBenchmark:

 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
 BOOLEAN Encode:                           Best Time(ms)   Avg Time(ms)   Stdev(ms)    Rate(M/s)   Per Row(ns)   Relative
 ------------------------------------------------------------------------------------------------------------------------
-PassThrough(1.000)                                    1              1           0      51957.0           0.0       1.0X
-RunLengthEncoding(2.502)                            549            555           9        122.2           8.2       0.0X
-BooleanBitSet(0.125)                                296            301           3        226.6           4.4       0.0X
+PassThrough(1.000)                                    2              2           0      42985.4           0.0       1.0X
+RunLengthEncoding(2.517)                            487            500          10        137.7           7.3       0.0X
+BooleanBitSet(0.125)                                348            353           4        192.8           5.2       0.0X

 OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5
 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
 SHORT Encode (Lower Skew):                Best Time(ms)   Avg Time(ms)   Stdev(ms)    Rate(M/s)   Per Row(ns)   Relative
 ------------------------------------------------------------------------------------------------------------------------
-PassThrough(1.000)                                    3              3           0      22779.9           0.0       1.0X
-RunLengthEncoding(1.520)                           1186           1192           9         56.6          17.7       0.0X
+PassThrough(1.000)                                    3              4           0      21216.6           0.0       1.0X
+RunLengthEncoding(1.493)                            882            931          50         76.1          13.1       0.0X

 OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5
 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
 SHORT Encode (Higher Skew):               Best Time(ms)   Avg Time(ms)   Stdev(ms)    Rate(M/s)   Per Row(ns)   Relative
 ------------------------------------------------------------------------------------------------------------------------
-PassThrough(1.000)                                    3              4           0      21352.2           0.0       1.0X
-RunLengthEncoding(2.009)                           1173           1175           3         57.2          17.5       0.0X
+PassThrough(1.000)                                    3              3           0      22388.6           0.0       1.0X
+RunLengthEncoding(2.015)                            924            941          23         72.6          13.8       0.0X

 OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5
 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
 INT Encode (Lower Skew):                  Best Time(ms)   Avg Time(ms)   Stdev(ms)    Rate(M/s)   Per Row(ns)   Relative
 ------------------------------------------------------------------------------------------------------------------------
-PassThrough(1.000)                                    9             10           1       7410.1           0.1       1.0X
-RunLengthEncoding(1.000)                           1499           1502           4         44.8          22.3       0.0X
-DictionaryEncoding(0.500)                           621            630          11        108.0           9.3       0.0X
-IntDelta(0.250)                                     134            149          10        502.0           2.0       0.1X
+PassThrough(1.000)                                    9             10           1       7575.9           0.1       1.0X
+RunLengthEncoding(1.002)                            952            966          12         70.5          14.2       0.0X
+DictionaryEncoding(0.500)                           561            567           6        119.7           8.4       0.0X
+IntDelta(0.250)                                     129            134           3        521.9           1.9       0.1X

 OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5
 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
 INT Encode (Higher Skew):                 Best Time(ms)   Avg Time(ms)   Stdev(ms)    Rate(M/s)   Per Row(ns)   Relative
 ------------------------------------------------------------------------------------------------------------------------
-PassThrough(1.000)                                    9             10           1       7668.3           0.1       1.0X
-RunLengthEncoding(1.332)                           1561           1685         175         43.0          23.3       0.0X
-DictionaryEncoding(0.501)                           616            642          21        108.9           9.2       0.0X
-IntDelta(0.250)                                     126            131           2        533.4           1.9       0.1X
+PassThrough(1.000)                                    9             10           1       7494.1           0.1       1.0X
+RunLengthEncoding(1.336)                            974            987          13         68.9          14.5       0.0X
+DictionaryEncoding(0.501)                           709            719          10         94.6          10.6       0.0X
+IntDelta(0.250)                                     127            132           4        528.4           1.9       0.1X

 OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5
 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
 LONG Encode (Lower Skew):                 Best Time(ms)   Avg Time(ms)   Stdev(ms)    Rate(M/s)   Per Row(ns)   Relative
 ------------------------------------------------------------------------------------------------------------------------
-PassThrough(1.000)                                   18             19           1       3803.0           0.3       1.0X
-RunLengthEncoding(0.754)                           1526           1540          20         44.0          22.7       0.0X
-DictionaryEncoding(0.250)                           735            759          33         91.3          11.0       0.0X
-LongDelta(0.125)                                    126            129           2        530.8           1.9       0.1X
+PassThrough(1.000)                                   19             21           1       3543.5           0.3       1.0X
+RunLengthEncoding(0.747)                           1049           1058          12         63.9          15.6       0.0X
+DictionaryEncoding(0.250)                           620            634          17        108.2           9.2       0.0X
+LongDelta(0.125)                                    129            132           2        520.1           1.9       0.1X

 OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5
 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
 LONG Encode (Higher Skew):                Best Time(ms)   Avg Time(ms)   Stdev(ms)    Rate(M/s)   Per Row(ns)   Relative
 ------------------------------------------------------------------------------------------------------------------------
-PassThrough(1.000)                                   18             20           1       3705.4           0.3       1.0X
-RunLengthEncoding(1.002)                           1665           1669           6         40.3          24.8       0.0X
-DictionaryEncoding(0.251)                           890            901          11         75.4          13.3       0.0X
-LongDelta(0.125)                                    125            130           3        537.2           1.9       0.1X
+PassThrough(1.000)                                   18             20           2       3726.8           0.3       1.0X
+RunLengthEncoding(0.999)                           1076           1077           2         62.4          16.0       0.0X
+DictionaryEncoding(0.251)                           904            919          19         74.3          13.5       0.0X
+LongDelta(0.125)                                    125            131           4        536.5           1.9       0.1X

 OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5
 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
 STRING Encode:                            Best Time(ms)   Avg Time(ms)   Stdev(ms)    Rate(M/s)   Per Row(ns)   Relative
 ------------------------------------------------------------------------------------------------------------------------
-PassThrough(1.000)                                   27             30           2       2497.1           0.4       1.0X
-RunLengthEncoding(0.892)                           3443           3587         204         19.5          51.3       0.0X
-DictionaryEncoding(0.167)                          2286           2290           6         29.4          34.1       0.0X
+PassThrough(1.000)                                   28             31           2       2430.2           0.4       1.0X
+RunLengthEncoding(0.889)                           1798           1800           3         37.3          26.8       0.0X
+DictionaryEncoding(0.167)                          1956           1959           4         34.3          29.1       0.0X

In the above diff, new results are with changes in this PR. It can be seen that encoding performance has improved quite a lot especially for string type.

Does this PR introduce any user-facing change?

No.

How was this patch tested?

Relies on existing unit tests.

…ncoding#Encoder

SparkQA · 2020-09-06T01:16:40Z

Test build #128322 has finished for PR 29654 at commit f3f6fc5.

This patch fails Spark unit tests.
This patch merges cleanly.
This patch adds no public classes.

SparkQA · 2020-09-08T23:37:55Z

Test build #128422 has finished for PR 29654 at commit 903992b.

This patch passes all tests.
This patch merges cleanly.
This patch adds no public classes.

.../src/main/scala/org/apache/spark/sql/execution/columnar/compression/compressionSchemes.scala

SparkQA · 2020-09-09T07:05:02Z

Test build #128432 has finished for PR 29654 at commit 2e18856.

This patch fails due to an unknown error code, -9.
This patch merges cleanly.
This patch adds no public classes.

sunchao · 2020-09-10T16:58:04Z

@maropu could you review this PR? thanks!

maropu · 2020-09-10T23:57:49Z

The performance gain and the code changes look good to me. It would be nice to have more reviews. cc: @rednaxelafx @kiszk @srowen

maropu · 2020-09-11T00:04:19Z

Have you checked the performance on jdk8, too? Could you update the golden files?

benchmarks/CompressionSchemeBenchmark-results.txt
benchmarks/CompressionSchemeBenchmark-jdk11-results.txt

srowen · 2020-09-11T00:17:34Z

I don't know enough to review the logic but it looks plausible.

kiszk · 2020-09-11T11:03:44Z

.../src/main/scala/org/apache/spark/sql/execution/columnar/compression/compressionSchemes.scala

-      if (lastValue.isNullAt(0)) {
-        columnType.copyField(row, ordinal, lastValue, 0)
+      if (lastValue == null) {
+        lastValue = columnType.clone(columnType.getField(row, ordinal))


Do we need clone() here? While I guess that this is for UTF8String, lastValue is used only for keeping a value. Thus, it is ok with just keeping the reference for UTF8String.

@kiszk Yes it is because UTF8String. We reuse InternalRow during each iteration and since UTF8String is backed by the same memory region in the InternalRow, it will be updated each time as we load a new row, which is not correct.

got it, thank you for your clarification.

kiszk · 2020-09-11T11:07:47Z

Looks good. I have one question.

sunchao · 2020-09-11T20:02:52Z

Have you checked the performance on jdk8, too? Could you update the golden files?

benchmarks/CompressionSchemeBenchmark-results.txt

benchmarks/CompressionSchemeBenchmark-jdk11-results.txt

Haven't checked jdk8. Let me do that and update the golden files.

maropu

cc: @dongjoon-hyun

viirya · 2020-09-11T23:55:21Z

cc @cloud-fan

sunchao · 2020-09-11T23:59:38Z

Thanks. I think the CI failure is not related. Probably it is caused by #29640

srowen · 2020-09-12T00:22:03Z

Wait, where do you see the CI failure?

sunchao · 2020-09-12T00:27:54Z

@srowen I see this in the "Python lint" section, and this happened to two of my PRs which do not touch Python at all.

I think it is just a simple fix. Let me come up with a PR quickly.

srowen · 2020-09-12T00:30:15Z

OK right I see it locally anyway. I can submit a fix, I have the PR now.

sunchao · 2020-09-12T00:31:21Z

OK right I see it locally anyway. I can submit a fix, I have the PR now.

Oops. I just filed #29733

SparkQA · 2020-09-12T02:18:09Z

Test build #128582 has finished for PR 29654 at commit bcda6c2.

This patch passes all tests.
This patch merges cleanly.
This patch adds no public classes.

dongjoon-hyun

+1, LGTM. Thank you, @sunchao and all.
Merged to master for Apache Spark 3.1.0 on December 2020.

cc @cloud-fan and @gatorsmile

cloud-fan · 2020-09-14T04:30:53Z

.../src/main/scala/org/apache/spark/sql/execution/columnar/compression/compressionSchemes.scala

@@ -182,8 +181,7 @@ private[columnar] case object RunLengthEncoding extends CompressionScheme {
    private var _uncompressedSize = 0
    private var _compressedSize = 0

-    // Using `MutableRow` to store the last value to avoid boxing/unboxing cost.


do you mean the overhead of boxing is smaller than the overhead of indirections introduced by SpecificInternalRow?

The benchmark result does. Please let us know if we need other validation, @cloud-fan .

I'm fine with it, but it's better to spell out this key finding in the PR description, so that people don't need to infer it from the benchmark results by themselves.

Yea, I also think this finding looks interesting. I'm not sure that this rule (the overhead of boxing is smaller than the overhead of indirections) always hold on any JVM implementations, but I think its importatnt to notice this performance property for future developement.

Thanks for the comments @cloud-fan @dongjoon-hyun and @maropu , and yes my bad for not putting enough info in the PR description. The comment is pretty old and I'm not sure what has changed over the years. By examine flamegraph from a test run I observed boxing both before and after the change:

Before:

After:

Even though the time spent on the boxing part is noticeably less after the change (it could have sth to do with my sample size though).

Perhaps we can open a JIRA to investigate this further? we could have more room for improvement if we can completely eliminate the boxing/unboxing.

@sunchao It is hard to guess the difference of boxing between two flamegraphs, can you show the percentage of boxing in each flamegraph?

@viirya Sure. Here's complete graphs

Before:

After:

Ah sorry @viirya just noticed you were asking for percentage. I calculated. Before the change it was 2.76% and after it is 1.31%.

This is nice :-)

…ng#Encoder ### What changes were proposed in this pull request? Currently `RunLengthEncoding#Encoder` uses `SpecificInternalRow` as a holder for the current value when calculating compression stats and doing the actual compression. It calls `ColumnType.copyField` and `ColumnType.getField` on the internal row which incurs extra cost comparing to directly operating on the internal type. This proposes to replace the `SpecificInternalRow` with `T#InternalType` to avoid the extra cost. ### Why are the changes needed? Operating on `SpecificInternalRow` carries certain cost and negatively impact performance when using `RunLengthEncoding` for compression. With the change I see some improvements through `CompressionSchemeBenchmark`: ```diff Intel(R) Core(TM) i9-9880H CPU 2.30GHz BOOLEAN Encode: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------------------------------ -PassThrough(1.000) 1 1 0 51957.0 0.0 1.0X -RunLengthEncoding(2.502) 549 555 9 122.2 8.2 0.0X -BooleanBitSet(0.125) 296 301 3 226.6 4.4 0.0X +PassThrough(1.000) 2 2 0 42985.4 0.0 1.0X +RunLengthEncoding(2.517) 487 500 10 137.7 7.3 0.0X +BooleanBitSet(0.125) 348 353 4 192.8 5.2 0.0X OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5 Intel(R) Core(TM) i9-9880H CPU 2.30GHz SHORT Encode (Lower Skew): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------------------------------ -PassThrough(1.000) 3 3 0 22779.9 0.0 1.0X -RunLengthEncoding(1.520) 1186 1192 9 56.6 17.7 0.0X +PassThrough(1.000) 3 4 0 21216.6 0.0 1.0X +RunLengthEncoding(1.493) 882 931 50 76.1 13.1 0.0X OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5 Intel(R) Core(TM) i9-9880H CPU 2.30GHz SHORT Encode (Higher Skew): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------------------------------ -PassThrough(1.000) 3 4 0 21352.2 0.0 1.0X -RunLengthEncoding(2.009) 1173 1175 3 57.2 17.5 0.0X +PassThrough(1.000) 3 3 0 22388.6 0.0 1.0X +RunLengthEncoding(2.015) 924 941 23 72.6 13.8 0.0X OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5 Intel(R) Core(TM) i9-9880H CPU 2.30GHz INT Encode (Lower Skew): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------------------------------ -PassThrough(1.000) 9 10 1 7410.1 0.1 1.0X -RunLengthEncoding(1.000) 1499 1502 4 44.8 22.3 0.0X -DictionaryEncoding(0.500) 621 630 11 108.0 9.3 0.0X -IntDelta(0.250) 134 149 10 502.0 2.0 0.1X +PassThrough(1.000) 9 10 1 7575.9 0.1 1.0X +RunLengthEncoding(1.002) 952 966 12 70.5 14.2 0.0X +DictionaryEncoding(0.500) 561 567 6 119.7 8.4 0.0X +IntDelta(0.250) 129 134 3 521.9 1.9 0.1X OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5 Intel(R) Core(TM) i9-9880H CPU 2.30GHz INT Encode (Higher Skew): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------------------------------ -PassThrough(1.000) 9 10 1 7668.3 0.1 1.0X -RunLengthEncoding(1.332) 1561 1685 175 43.0 23.3 0.0X -DictionaryEncoding(0.501) 616 642 21 108.9 9.2 0.0X -IntDelta(0.250) 126 131 2 533.4 1.9 0.1X +PassThrough(1.000) 9 10 1 7494.1 0.1 1.0X +RunLengthEncoding(1.336) 974 987 13 68.9 14.5 0.0X +DictionaryEncoding(0.501) 709 719 10 94.6 10.6 0.0X +IntDelta(0.250) 127 132 4 528.4 1.9 0.1X OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5 Intel(R) Core(TM) i9-9880H CPU 2.30GHz LONG Encode (Lower Skew): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------------------------------ -PassThrough(1.000) 18 19 1 3803.0 0.3 1.0X -RunLengthEncoding(0.754) 1526 1540 20 44.0 22.7 0.0X -DictionaryEncoding(0.250) 735 759 33 91.3 11.0 0.0X -LongDelta(0.125) 126 129 2 530.8 1.9 0.1X +PassThrough(1.000) 19 21 1 3543.5 0.3 1.0X +RunLengthEncoding(0.747) 1049 1058 12 63.9 15.6 0.0X +DictionaryEncoding(0.250) 620 634 17 108.2 9.2 0.0X +LongDelta(0.125) 129 132 2 520.1 1.9 0.1X OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5 Intel(R) Core(TM) i9-9880H CPU 2.30GHz LONG Encode (Higher Skew): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------------------------------ -PassThrough(1.000) 18 20 1 3705.4 0.3 1.0X -RunLengthEncoding(1.002) 1665 1669 6 40.3 24.8 0.0X -DictionaryEncoding(0.251) 890 901 11 75.4 13.3 0.0X -LongDelta(0.125) 125 130 3 537.2 1.9 0.1X +PassThrough(1.000) 18 20 2 3726.8 0.3 1.0X +RunLengthEncoding(0.999) 1076 1077 2 62.4 16.0 0.0X +DictionaryEncoding(0.251) 904 919 19 74.3 13.5 0.0X +LongDelta(0.125) 125 131 4 536.5 1.9 0.1X OpenJDK 64-Bit Server VM 11.0.8+10-LTS on Mac OS X 10.15.5 Intel(R) Core(TM) i9-9880H CPU 2.30GHz STRING Encode: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative ------------------------------------------------------------------------------------------------------------------------ -PassThrough(1.000) 27 30 2 2497.1 0.4 1.0X -RunLengthEncoding(0.892) 3443 3587 204 19.5 51.3 0.0X -DictionaryEncoding(0.167) 2286 2290 6 29.4 34.1 0.0X +PassThrough(1.000) 28 31 2 2430.2 0.4 1.0X +RunLengthEncoding(0.889) 1798 1800 3 37.3 26.8 0.0X +DictionaryEncoding(0.167) 1956 1959 4 34.3 29.1 0.0X ``` In the above diff, new results are with changes in this PR. It can be seen that encoding performance has improved quite a lot especially for string type. ### Does this PR introduce _any_ user-facing change? No. ### How was this patch tested? Relies on existing unit tests. Closes apache#29654 from sunchao/SPARK-32802. Authored-by: Chao Sun <sunchao@apache.org> Signed-off-by: Dongjoon Hyun <dongjoon@apache.org>

[WIP][SPARK-32802][SQL] Avoid using SpecificInternalRow in RunLengthE…

f3f6fc5

…ncoding#Encoder

probot-autolabeler bot added the SQL label Sep 5, 2020

Clone value for String type

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maropu reviewed Sep 9, 2020

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sunchao changed the title ~~[WIP][SPARK-32802][SQL] Avoid using SpecificInternalRow in RunLengthEncoding#Encoder~~ [SPARK-32802][SQL] Avoid using SpecificInternalRow in RunLengthEncoding#Encoder Sep 9, 2020

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sunchao added 2 commits September 11, 2020 13:03

cleanup

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Update benchmark golden file for JDK-11 and JDK-8

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[SPARK-32802][SQL] Avoid using SpecificInternalRow in RunLengthEncoding#Encoder #29654

[SPARK-32802][SQL] Avoid using SpecificInternalRow in RunLengthEncoding#Encoder #29654

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[SPARK-32802][SQL] Avoid using SpecificInternalRow in RunLengthEncoding#Encoder #29654

[SPARK-32802][SQL] Avoid using SpecificInternalRow in RunLengthEncoding#Encoder #29654

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sunchao commented Sep 5, 2020 • edited Loading

What changes were proposed in this pull request?

Why are the changes needed?

Does this PR introduce any user-facing change?

How was this patch tested?

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