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From "Sean Owen (JIRA)" <j...@apache.org>
Subject [jira] [Resolved] (SPARK-18263) Configuring spark.kryo.registrator programmatically doesn't take effect
Date Tue, 08 Nov 2016 08:37:58 GMT

     [ https://issues.apache.org/jira/browse/SPARK-18263?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]

Sean Owen resolved SPARK-18263.
-------------------------------
    Resolution: Not A Problem

> Configuring spark.kryo.registrator programmatically doesn't take effect
> -----------------------------------------------------------------------
>
>                 Key: SPARK-18263
>                 URL: https://issues.apache.org/jira/browse/SPARK-18263
>             Project: Spark
>          Issue Type: Bug
>          Components: Spark Core
>    Affects Versions: 2.0.1
>         Environment: spark-2.0.1-bin-hadoop2.6
> scala-2.11.8
>            Reporter: inred
>
> it run ok with spark-shell --conf spark.serializer=org.apache.spark.serializer.KryoSerializer
\
>     --conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator
\
> but in IDE
>  val spark = SparkSession.builder.master("local[*]").appName("Anno BDG").getOrCreate()
> spark.conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
> spark.conf.set("spark.kryo.registrator", "org.bdgenomics.adam.serialization.ADAMKryoRegistrator")
> it reports the following error:
> java.io.NotSerializableException: org.bdgenomics.formats.avro.AlignmentRecord
> Serialization stack:
> object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord, value: {"readInFragment":
0, "contigName": "chr10", "start": 61758687, "oldPosition": null, "end": 61758727, "mapq":
25, "readName": "NB501244AR:119:HJY3WBGXY:2:11112:6137:19359", "sequence": "AAAATACTGAGACTTATCAGAATTTCAGGCTAAAGCAACC",
"qual": "AAAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEE", "cigar": "40M", "oldCigar": null, "basesTrimmedFromStart":
0, "basesTrimmedFromEnd": 0, "readPaired": false, "properPair": false, "readMapped": true,
"mateMapped": false, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand":
false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false,
"supplementaryAlignment": false, "mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:U\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX1:i:0\tX0:i:1", "recordGroupName": null, "recordGroupSample":
null, "mateAlignmentStart": null, "mateAlignmentEnd": null, "mateContigName": null, "inferredInsertSize":
null})
> at org.apache.spark.serializer.SerializationDebugger$.improveException(SerializationDebugger.scala:40)
> at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:46)
> at org.apache.spark.serializer.SerializationStream.writeValue(Serializer.scala:135)
> at org.apache.spark.storage.DiskBlockObjectWriter.write(DiskBlockObjectWriter.scala:185)
> at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:150)
> at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
> at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
> at org.apache.spark.scheduler.Task.run(Task.scala:86)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> 2016-11-04 10:30:56 ERROR TaskSetManager:70 - Task 0.0 in stage 2.0 (TID 9) had a not
serializable result: org.bdgenomics.formats.avro.AlignmentRecord
> Serialization stack:
> object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord, value: {"readInFragment":
0, "contigName": "chr1", "start": 10001, "oldPosition": null, "end": 10041, "mapq": 0, "readName":
"NB501244AR:119:HJY3WBGXY:3:11508:7857:8792", "sequence": "AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC",
"qual": "///E////6E////EEAEEE/EEEEEEEEEEEEAEAAA/A", "cigar": "40M", "oldCigar": null, "basesTrimmedFromStart":
0, "basesTrimmedFromEnd": 0, "readPaired": false, "properPair": false, "readMapped": true,
"mateMapped": false, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand":
true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false,
"supplementaryAlignment": false, "mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:R\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX0:i:594", "recordGroupName": null, "recordGroupSample":
null, "mateAlignmentStart": null, "mateAlignmentEnd": null, "mateContigName": null, "inferredInsertSize":
null}); not retrying
> 2016-11-04 10:30:56 ERROR TaskSetManager:70 - Task 4.0 in stage 2.0 (TID 13) had a not
serializable result: org.bdgenomics.formats.avro.AlignmentRecord
> Serialization stack:
> object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord, value: {"readInFragment":
0, "contigName": "chr10", "start": 61758687, "oldPosition": null, "end": 61758727, "mapq":
25, "readName": "NB501244AR:119:HJY3WBGXY:2:11112:6137:19359", "sequence": "AAAATACTGAGACTTATCAGAATTTCAGGCTAAAGCAACC",
"qual": "AAAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEE", "cigar": "40M", "oldCigar": null, "basesTrimmedFromStart":
0, "basesTrimmedFromEnd": 0, "readPaired": false, "properPair": false, "readMapped": true,
"mateMapped": false, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand":
false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false,
"supplementaryAlignment": false, "mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:U\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX1:i:0\tX0:i:1", "recordGroupName": null, "recordGroupSample":
null, "mateAlignmentStart": null, "mateAlignmentEnd": null, "mateContigName": null, "inferredInsertSize":
null}); not retrying
> 2016-11-04 10:30:56 ERROR TaskSetManager:70 - Task 3.0 in stage 2.0 (TID 12) had a not
serializable result: org.bdgenomics.formats.avro.AlignmentRecord
> Serialization stack:
> object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord, value: {"readInFragment":
0, "contigName": "chr7", "start": 68163823, "oldPosition": null, "end": 68163863, "mapq":
0, "readName": "NB501244AR:119:HJY3WBGXY:4:21602:16293:18064", "sequence": "TGTGAGGGTGTTGCCCAAAAGAGATTAACATTTGAGTCAG",
"qual": "AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE", "cigar": "40M", "oldCigar": null, "basesTrimmedFromStart":
0, "basesTrimmedFromEnd": 0, "readPaired": false, "properPair": false, "readMapped": true,
"mateMapped": false, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand":
false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false,
"supplementaryAlignment": false, "mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:R\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tXA:Z:chr3,-84617448,40M,0;\tX1:i:0\tX0:i:2", "recordGroupName":
null, "recordGroupSample": null, "mateAlignmentStart": null, "mateAlignmentEnd": null, "mateContigName":
null, "inferredInsertSize": null}); not retrying
> 2016-11-04 10:30:56 ERROR TaskSetManager:70 - Task 2.0 in stage 2.0 (TID 11) had a not
serializable result: org.bdgenomics.formats.avro.AlignmentRecord
> Serialization stack:
> object not serializable (class: org.bdgenomics.formats.avro.AlignmentRecord, value: {"readInFragment":
0, "contigName": "chr4", "start": 181076278, "oldPosition": null, "end": 181076318, "mapq":
25, "readName": "NB501244AR:119:HJY3WBGXY:2:23302:26459:8305", "sequence": "CACTGTGTTTTACTTCTATTTTAAAAAACCTGAAGGCTAT",
"qual": "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA", "cigar": "40M", "oldCigar": null, "basesTrimmedFromStart":
0, "basesTrimmedFromEnd": 0, "readPaired": false, "properPair": false, "readMapped": true,
"mateMapped": false, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand":
true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false,
"supplementaryAlignment": false, "mismatchingPositions": "40", "origQual": null, "attributes":
"XT:A:U\tXO:i:0\tXM:i:0\tNM:i:0\tXG:i:0\tX1:i:0\tX0:i:1", "recordGroupName": null, "recordGroupSample":
null, "mateAlignmentStart": null, "mateAlignmentEnd": null, "mateContigName": null, "inferredInsertSize":
null}); not retrying
> Process finished with exit code 1



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