It appears a provided scope dependency on spark-sql leaks old parquet versions was causing the runtime error below. After including new parquet-column and parquet-hadoop compile scope dependencies (in addition to parquet-avro, which we already have at compile scope), our build succeeds.
https://github.com/bigdatagenomics/adam/pull/2232 <https://github.com/bigdatagenomics/adam/pull/2232> However, when running via spark-submit I run into a similar runtime error Caused by: java.lang.NoSuchMethodError: org.apache.parquet.schema.Types$PrimitiveBuilder.as(Lorg/apache/parquet/schema/LogicalTypeAnnotation;)Lorg/apache/parquet/schema/Types$Builder; at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:161) at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:226) at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:182) at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:141) at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:244) at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:135) at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:126) at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121) at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388) at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349) at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35) at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350) at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120) at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83) at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:123) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Will bumping our library dependency version to 1.11 require a new version of Spark, built against Parquet 1.11? Please accept my apologies if this is heading out-of-scope for the Parquet mailing list. michael > On Nov 20, 2019, at 10:00 AM, Michael Heuer <[email protected]> wrote: > > I am willing to do some benchmarking on genomic data at scale but am not > quite sure what the Spark target version for 1.11.0 might be. Will Parquet > 1.11.0 be compatible in Spark 2.4.x? > > Updating from 1.10.1 to 1.11.0 breaks at runtime in our build > > … > D 0, localhost, executor driver): java.lang.NoClassDefFoundError: > org/apache/parquet/schema/LogicalTypeAnnotation > at > org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121) > at > org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388) > at > org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349) > at > org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35) > at > org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350) > at > org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120) > at > org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83) > at > org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78) > at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) > at org.apache.spark.scheduler.Task.run(Task.scala:123) > at > org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) > at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) > Caused by: java.lang.ClassNotFoundException: > org.apache.parquet.schema.LogicalTypeAnnotation > at java.net.URLClassLoader.findClass(URLClassLoader.java:382) > at java.lang.ClassLoader.loadClass(ClassLoader.java:424) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) > at java.lang.ClassLoader.loadClass(ClassLoader.java:357) > > michael > > >> On Nov 20, 2019, at 3:29 AM, Gabor Szadovszky <[email protected]> wrote: >> >> Thanks, Fokko. >> >> Ryan, we did not do such measurements yet. I'm afraid, I won't have enough >> time to do that in the next couple of weeks. >> >> Cheers, >> Gabor >> >> On Tue, Nov 19, 2019 at 6:14 PM Driesprong, Fokko <[email protected]> >> wrote: >> >>> Thanks Gabor for the explanation. I'd like to change my vote to +1 >>> (non-binding). >>> >>> Cheers, Fokko >>> >>> Op di 19 nov. 2019 om 18:03 schreef Ryan Blue <[email protected]> >>> >>>> Gabor, what I meant was: have we tried this with real data to see the >>>> effect? I think those results would be helpful. >>>> >>>> On Mon, Nov 18, 2019 at 11:35 PM Gabor Szadovszky <[email protected]> >>>> wrote: >>>> >>>>> Hi Ryan, >>>>> >>>>> It is not easy to calculate. For the column indexes feature we >>> introduced >>>>> two new structures saved before the footer: column indexes and offset >>>>> indexes. If the min/max values are not too long, then the truncation >>>> might >>>>> not decrease the file size because of the offset indexes. Moreover, we >>>> also >>>>> introduced parquet.page.row.count.limit which might increase the number >>>> of >>>>> pages which leads to increasing the file size. >>>>> The footer itself is also changed and we are saving more values in it: >>>> the >>>>> offset values to the column/offset indexes, the new logical type >>>>> structures, the CRC checksums (we might have some others). >>>>> So, the size of the files with small amount of data will be increased >>>>> (because of the larger footer). The size of the files where the values >>>> can >>>>> be encoded very well (RLE) will probably be increased (because we will >>>> have >>>>> more pages). The size of some files where the values are long (>64bytes >>>> by >>>>> default) might be decreased because of truncating the min/max values. >>>>> >>>>> Regards, >>>>> Gabor >>>>> >>>>> On Mon, Nov 18, 2019 at 6:46 PM Ryan Blue <[email protected]> >>>>> wrote: >>>>> >>>>>> Gabor, do we have an idea of the additional overhead for a non-test >>>> data >>>>>> file? It should be easy to validate that this doesn't introduce an >>>>>> unreasonable amount of overhead. In some cases, it should actually be >>>>>> smaller since the column indexes are truncated and page stats are >>> not. >>>>>> >>>>>> On Mon, Nov 18, 2019 at 1:00 AM Gabor Szadovszky >>>>>> <[email protected]> wrote: >>>>>> >>>>>>> Hi Fokko, >>>>>>> >>>>>>> For the first point. The referenced constructor is private and >>>> Iceberg >>>>>> uses >>>>>>> it via reflection. It is not a breaking change. I think, parquet-mr >>>>> shall >>>>>>> not keep private methods only because of clients might use them via >>>>>>> reflection. >>>>>>> >>>>>>> About the checksum. I've agreed on having the CRC checksum write >>>>> enabled >>>>>> by >>>>>>> default because the benchmarks did not show significant performance >>>>>>> penalties. See https://github.com/apache/parquet-mr/pull/647 for >>>>>> details. >>>>>>> >>>>>>> About the file size change. 1.11.0 is introducing column indexes, >>> CRC >>>>>>> checksum, removing the statistics from the page headers and maybe >>>> other >>>>>>> changes that impact file size. If only file size is in question I >>>>> cannot >>>>>>> see a breaking change here. >>>>>>> >>>>>>> Regards, >>>>>>> Gabor >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Sun, Nov 17, 2019 at 9:27 PM Driesprong, Fokko >>>> <[email protected] >>>>>> >>>>>>> wrote: >>>>>>> >>>>>>>> Unfortunately, a -1 from my side (non-binding) >>>>>>>> >>>>>>>> I've updated Iceberg to Parquet 1.11.0, and found three things: >>>>>>>> >>>>>>>> - We've broken backward compatibility of the constructor of >>>>>>>> ColumnChunkPageWriteStore >>>>>>>> < >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://github.com/apache/parquet-mr/commit/e7db9e20f52c925a207ea62d6dda6dc4e870294e#diff-d007a18083a2431c30a5416f248e0a4bR80 >>>>>>>>> . >>>>>>>> This required a change >>>>>>>> < >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://github.com/apache/incubator-iceberg/pull/297/files#diff-b877faa96f292b851c75fe8bcc1912f8R176 >>>>>>>>> >>>>>>>> to the code. This isn't a hard blocker, but if there will be a >>>> new >>>>>> RC, >>>>>>>> I've >>>>>>>> submitted a patch: >>>> https://github.com/apache/parquet-mr/pull/699 >>>>>>>> - Related, that we need to put in the changelog, is that >>>> checksums >>>>>> are >>>>>>>> enabled by default: >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://github.com/apache/parquet-mr/blob/master/parquet-column/src/main/java/org/apache/parquet/column/ParquetProperties.java#L54 >>>>>>>> This >>>>>>>> will impact performance. I would suggest disabling it by >>>> default: >>>>>>>> https://github.com/apache/parquet-mr/pull/700 >>>>>>>> < >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://github.com/apache/parquet-mr/commit/e7db9e20f52c925a207ea62d6dda6dc4e870294e#diff-d007a18083a2431c30a5416f248e0a4bR277 >>>>>>>>> >>>>>>>> - Binary compatibility. While updating Iceberg, I've noticed >>>> that >>>>>> the >>>>>>>> split-test was failing: >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://github.com/apache/incubator-iceberg/pull/297/files#diff-4b64b7014f259be41b26cfb73d3e6e93L199 >>>>>>>> The >>>>>>>> two records are now divided over four Spark partitions. >>>> Something >>>>> in >>>>>>> the >>>>>>>> output has changed since the files are bigger now. Has anyone >>>> any >>>>>> idea >>>>>>>> to >>>>>>>> check what's changed, or a way to check this? The only thing I >>>> can >>>>>>>> think of >>>>>>>> is the checksum mentioned above. >>>>>>>> >>>>>>>> $ ls -lah ~/Desktop/parquet-1-1* >>>>>>>> -rw-r--r-- 1 fokkodriesprong staff 562B 17 nov 21:09 >>>>>>>> /Users/fokkodriesprong/Desktop/parquet-1-10-1.parquet >>>>>>>> -rw-r--r-- 1 fokkodriesprong staff 611B 17 nov 21:05 >>>>>>>> /Users/fokkodriesprong/Desktop/parquet-1-11-0.parquet >>>>>>>> >>>>>>>> $ parquet-tools cat >>>>>> /Users/fokkodriesprong/Desktop/parquet-1-10-1.parquet >>>>>>>> id = 1 >>>>>>>> data = a >>>>>>>> >>>>>>>> $ parquet-tools cat >>>>>> /Users/fokkodriesprong/Desktop/parquet-1-11-0.parquet >>>>>>>> id = 1 >>>>>>>> data = a >>>>>>>> >>>>>>>> A binary diff here: >>>>>>>> https://gist.github.com/Fokko/1c209f158299dc2fb5878c5bae4bf6d8 >>>>>>>> >>>>>>>> Cheers, Fokko >>>>>>>> >>>>>>>> Op za 16 nov. 2019 om 04:18 schreef Junjie Chen < >>>>>>> [email protected] >>>>>>>>> : >>>>>>>> >>>>>>>>> +1 >>>>>>>>> Verified signature, checksum and ran mvn install successfully. >>>>>>>>> >>>>>>>>> Wang, Yuming <[email protected]> 于2019年11月14日周四 >>> 下午2:05写道： >>>>>>>>>> >>>>>>>>>> +1 >>>>>>>>>> Tested Parquet 1.11.0 with Spark SQL module: build/sbt >>>>>>> "sql/test-only" >>>>>>>>> -Phadoop-3.2 >>>>>>>>>> >>>>>>>>>> On 2019/11/13, 21:33, "Gabor Szadovszky" <[email protected]> >>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi everyone, >>>>>>>>>> >>>>>>>>>> I propose the following RC to be released as official >>>> Apache >>>>>>>> Parquet >>>>>>>>> 1.11.0 >>>>>>>>>> release. >>>>>>>>>> >>>>>>>>>> The commit id is 18519eb8e059865652eee3ff0e8593f126701da4 >>>>>>>>>> * This corresponds to the tag: apache-parquet-1.11.0-rc7 >>>>>>>>>> * >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Fparquet-mr%2Ftree%2F18519eb8e059865652eee3ff0e8593f126701da4&data=02%7C01%7Cyumwang%40ebay.com%7C8d588ca5855842a94bed08d7683e1221%7C46326bff992841a0baca17c16c94ea99%7C0%7C0%7C637092488114756267&sdata=ToLFrTB9lU%2FGzH6UpXwy7PAY7kaupbyKAgdghESCfgg%3D&reserved=0 >>>>>>>>>> >>>>>>>>>> The release tarball, signature, and checksums are here: >>>>>>>>>> * >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdist.apache.org%2Frepos%2Fdist%2Fdev%2Fparquet%2Fapache-parquet-1.11.0-rc7&data=02%7C01%7Cyumwang%40ebay.com%7C8d588ca5855842a94bed08d7683e1221%7C46326bff992841a0baca17c16c94ea99%7C0%7C0%7C637092488114756267&sdata=MPaHiYJT7ZcqreAYUkvDvZugthUhRPrySdXpN2ytT5k%3D&reserved=0 >>>>>>>>>> >>>>>>>>>> You can find the KEYS file here: >>>>>>>>>> * >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapache.org%2Fdist%2Fparquet%2FKEYS&data=02%7C01%7Cyumwang%40ebay.com%7C8d588ca5855842a94bed08d7683e1221%7C46326bff992841a0baca17c16c94ea99%7C0%7C0%7C637092488114756267&sdata=IwG4MUGsP2lVzlD4bwZUEPuEAPUg%2FHXRYtxc5CQupBM%3D&reserved=0 >>>>>>>>>> >>>>>>>>>> Binary artifacts are staged in Nexus here: >>>>>>>>>> * >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frepository.apache.org%2Fcontent%2Fgroups%2Fstaging%2Forg%2Fapache%2Fparquet%2F&data=02%7C01%7Cyumwang%40ebay.com%7C8d588ca5855842a94bed08d7683e1221%7C46326bff992841a0baca17c16c94ea99%7C0%7C0%7C637092488114756267&sdata=lHtqLRQqQFwsyoaLSVaJuau5gxPKsCQFFVJaY8H0tZQ%3D&reserved=0 >>>>>>>>>> >>>>>>>>>> This release includes the changes listed at: >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Fparquet-mr%2Fblob%2Fapache-parquet-1.11.0-rc7%2FCHANGES.md&data=02%7C01%7Cyumwang%40ebay.com%7C8d588ca5855842a94bed08d7683e1221%7C46326bff992841a0baca17c16c94ea99%7C0%7C0%7C637092488114756267&sdata=82BplI3bLAL6qArLHvVoYReZOk%2BboSP655rI8VX5Q5I%3D&reserved=0 >>>>>>>>>> >>>>>>>>>> Please download, verify, and test. >>>>>>>>>> >>>>>>>>>> Please vote in the next 72 hours. >>>>>>>>>> >>>>>>>>>> [ ] +1 Release this as Apache Parquet 1.11.0 >>>>>>>>>> [ ] +0 >>>>>>>>>> [ ] -1 Do not release this because... >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Ryan Blue >>>>>> Software Engineer >>>>>> Netflix >>>>>> >>>>> >>>> >>>> >>>> -- >>>> Ryan Blue >>>> Software Engineer >>>> Netflix >>>> >>> >
