[SPARK-27733][CORE] Upgrade Avro to version 1.10.1 by iemejia · Pull Request #31232 · apache/spark

iemejia · 2021-01-18T09:40:28Z

What changes were proposed in this pull request?

Update Avro dependency to version 1.10.1

Why are the changes needed?

To catch up multiple improvements of Avro as well as fix security issues on transitive dependencies.

Does this PR introduce any user-facing change?

No

How was this patch tested?

Since there were no API changes required we just run the tests

wangyum · 2021-01-18T09:46:55Z

Why do we need this change?

This is an improvement because Nullable in that class is used to designate class attributes that are nullable (like javax.annotation) and not to refer to nullability of an Avro field.

wangyum · 2021-01-18T10:05:21Z

ok to test.

SparkQA · 2021-01-18T11:45:57Z

Kubernetes integration test starting
URL: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/38778/

SparkQA · 2021-01-18T12:19:45Z

Kubernetes integration test status success
URL: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/38778/

HyukjinKwon · 2021-01-18T12:25:13Z

@iemejia, please fill the PR description.

SparkQA · 2021-01-18T13:47:12Z

Test build #134193 has finished for PR 31232 at commit cb3b0ce.

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

iemejia · 2021-01-18T14:00:01Z

@iemejia, please fill the PR description.

Done thanks for the reminder @HyukjinKwon

iemejia · 2021-01-18T14:00:42Z

All green now PTAL
R: @wangyum @dongjoon-hyun

dongjoon-hyun

Thank you for pinging me, @iemejia .

cc @gengliangwang

gengliangwang · 2021-01-19T05:49:12Z

@iemejia Thanks for the work!
I am +1 with the upgrade. The bug fix from apache/avro#969 is also important.
Please address comments and keep Avro upgrade related changes only in this PR.

SparkQA · 2021-01-19T10:44:56Z

Kubernetes integration test starting
URL: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/38806/

SparkQA · 2021-01-19T11:14:30Z

Kubernetes integration test status success
URL: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/38806/

SparkQA · 2021-01-19T12:44:47Z

Test build #134221 has finished for PR 31232 at commit 6c6b137.

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

iemejia · 2021-01-19T14:43:26Z

Hive error looks like a flake is there a way to re run that CI job/action?

mridulm · 2021-01-19T16:27:14Z

+CC @xkrogen

SparkQA · 2021-01-20T09:49:08Z

Kubernetes integration test starting
URL: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/38846/

SparkQA · 2021-01-20T09:57:56Z

Kubernetes integration test status failure
URL: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder-K8s/38846/

iemejia · 2021-01-20T10:02:28Z

Yay! green again after rebasing. PTAL again

SparkQA · 2021-01-20T11:38:43Z

Test build #134260 has finished for PR 31232 at commit f0ea522.

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

gengliangwang

LGTM. Again, thanks for the work!

gengliangwang · 2021-01-20T11:46:04Z

Also cc @bozhang2820

wangyum · 2021-01-20T15:58:07Z

AvroReadBenchmark result.
Avro 1.8.2:

================================================================================================
SQL Single Numeric Column Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single TINYINT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2478 2526 68 6.3 157.5 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single SMALLINT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2481 2523 59 6.3 157.8 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single INT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2416 2446 42 6.5 153.6 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single BIGINT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2757 2794 53 5.7 175.3 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single FLOAT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2540 2570 41 6.2 161.5 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single DOUBLE Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2570 2583 19 6.1 163.4 1.0X
================================================================================================
Int and String Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Int and String Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of columns 4050 4093 62 2.6 386.2 1.0X
================================================================================================
Partitioned Table Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Partitioned Table: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Data column 2880 2897 24 5.5 183.1 1.0X
Partition column 2522 2532 14 6.2 160.3 1.1X
Both columns 2936 2945 14 5.4 186.6 1.0X
================================================================================================
Repeated String Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Repeated String: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of string length 2923 3065 201 3.6 278.7 1.0X
================================================================================================
String with Nulls Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
String with Nulls Scan (0.0%): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of string length 4868 4944 108 2.2 464.3 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
String with Nulls Scan (50.0%): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of string length 3302 3317 22 3.2 314.9 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
String with Nulls Scan (95.0%): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of string length 2052 2080 39 5.1 195.7 1.0X
================================================================================================
Single Column Scan From Wide Columns
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Single Column Scan from 100 columns: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of single column 3851 3858 10 0.3 3672.5 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Single Column Scan from 200 columns: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of single column 7399 7505 149 0.1 7056.6 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Single Column Scan from 300 columns: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of single column 11134 11168 48 0.1 10618.4 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Filters pushdown: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
w/o filters 8049 8189 145 0.1 8049.3 1.0X
pushdown disabled 7728 7784 57 0.1 7728.5 1.0X
w/ filters 3291 3310 27 0.3 3291.3 2.4X

Avro 1.10.1:

================================================================================================
SQL Single Numeric Column Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single TINYINT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2513 2550 53 6.3 159.8 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single SMALLINT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2451 2505 77 6.4 155.8 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single INT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2474 2476 3 6.4 157.3 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single BIGINT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2845 2860 21 5.5 180.9 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single FLOAT Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2507 2513 8 6.3 159.4 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
SQL Single DOUBLE Column Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum 2527 2531 6 6.2 160.7 1.0X
================================================================================================
Int and String Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Int and String Scan: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of columns 4172 4179 9 2.5 397.9 1.0X
================================================================================================
Partitioned Table Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Partitioned Table: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Data column 2848 2878 43 5.5 181.1 1.0X
Partition column 2526 2557 43 6.2 160.6 1.1X
Both columns 2967 2967 1 5.3 188.6 1.0X
================================================================================================
Repeated String Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Repeated String: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of string length 2788 2868 113 3.8 265.9 1.0X
================================================================================================
String with Nulls Scan
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
String with Nulls Scan (0.0%): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of string length 4594 4667 103 2.3 438.1 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
String with Nulls Scan (50.0%): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of string length 2993 2998 8 3.5 285.4 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
String with Nulls Scan (95.0%): Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of string length 1664 1675 16 6.3 158.7 1.0X
================================================================================================
Single Column Scan From Wide Columns
================================================================================================
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Single Column Scan from 100 columns: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of single column 3845 3860 22 0.3 3666.6 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Single Column Scan from 200 columns: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of single column 7552 7562 15 0.1 7202.0 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Single Column Scan from 300 columns: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
Sum of single column 11295 11337 60 0.1 10771.6 1.0X
Java HotSpot(TM) 64-Bit Server VM 1.8.0_221-b11 on Linux 3.10.0-957.10.1.el7.x86_64
Intel Core Processor (Broadwell, IBRS)
Filters pushdown: Best Time(ms) Avg Time(ms) Stdev(ms) Rate(M/s) Per Row(ns) Relative
------------------------------------------------------------------------------------------------------------------------
w/o filters 8222 8378 171 0.1 8222.4 1.0X
pushdown disabled 8089 8307 293 0.1 8089.4 1.0X
w/ filters 3402 3470 67 0.3 3402.3 2.4X

dongjoon-hyun

+1, LGTM. Thank you, @iemejia and all!
Merged to master for Apache Spark 3.2.0.

dongjoon-hyun · 2021-01-20T23:44:41Z

@iemejia I added you to the Apache Spark contributor group and assigned SPARK-27733 to you. Thanks!

iemejia · 2021-01-21T08:10:49Z

Thanks to you @dongjoon-hyun and @wangyum! This PR seems 'trivial' but when you have lived through the multi project issues/fixes and dependencies you realize this would not have been possible without everybody's work.

iemejia · 2021-01-21T08:34:01Z

@wangyum just for learning's sake what command do you use to calculate the benchmarks?

wangyum · 2021-01-21T08:46:32Z

@iemejia

spark/external/avro/src/test/scala/org/apache/spark/sql/execution/benchmark/AvroReadBenchmark.scala

Lines 29 to 41 in d897825

/**
 * Benchmark to measure Avro read performance.
 * {{{
 * To run this benchmark:
 * 1. without sbt: bin/spark-submit --class <this class>
 * --jars <catalyst test jar>,<core test jar>,<spark-avro jar> <avro test jar>
 * 2. build/sbt "avro/test:runMain <this class>"
 * 3. generate result: SPARK_GENERATE_BENCHMARK_FILES=1 build/sbt "avro/test:runMain <this class>"
 * Results will be written to "benchmarks/AvroReadBenchmark-results.txt".
 * }}}
*/
objectAvroReadBenchmarkextendsSqlBasedBenchmark { 

iemejia · 2021-01-21T21:07:11Z

Thanks for the ref 👍 @wangyum !

### What changes were proposed in this pull request? Update Avro dependency to version 1.10.1 ### Why are the changes needed? To catch up multiple improvements of Avro as well as fix security issues on transitive dependencies. ### Does this PR introduce _any_ user-facing change? No ### How was this patch tested? Since there were no API changes required we just run the tests Closesapache#31232 from iemejia/SPARK-27733-avro-upgrade. Authored-by: Ismaël Mejía <iemejia@gmail.com> Signed-off-by: Dongjoon Hyun <dhyun@apple.com>

Update Avro dependency to version 1.10.1 To catch up multiple improvements of Avro as well as fix security issues on transitive dependencies. No Since there were no API changes required we just run the tests Closesapache#31232 from iemejia/SPARK-27733-avro-upgrade. Authored-by: Ismaël Mejía <iemejia@gmail.com> Signed-off-by: Dongjoon Hyun <dhyun@apple.com>

iemejia mentioned this pull request Jan 18, 2021
[WIP][SPARK-27733][CORE] Upgrade Avro to 1.9.2 #27609
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iemejia force-pushed the SPARK-27733-avro-upgrade branch from cb3b0ce to 6c6b137Compare January 19, 2021 09:47

iemejia mentioned this pull request Jan 19, 2021
Schema registry should not include classes in the org.apache.avro package confluentinc/schema-registry#1432
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[SPARK-27733][CORE] Upgrade Avro to version 1.10.1
f0ea522

iemejia force-pushed the SPARK-27733-avro-upgrade branch from 6c6b137 to f0ea522Compare January 20, 2021 08:31

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[SPARK-26346][BUILD][SQL] Upgrade Parquet to 1.11.1 #26804
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iemejia deleted the SPARK-27733-avro-upgrade branch January 21, 2021 08:04

LorenzoMartini mentioned this pull request Apr 19, 2021
[SPARK-27733][CORE] Upgrade Avro to version 1.10.1 palantir/spark#757
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