Not a problem! Thanks for looking into this. In reading through the source associated with the stacktrace, I also noticed that there's neither user-code, nor beam-to-flink lifecycle code available for initialization. As far as I could tell, it was pure flink down to the coders. Nothing new here, but maybe it bolsters confidence in your diagnosis. I went ahead and logged an issue here: https://issues.apache.org/jira/browse/BEAM-8303.
Let me know what I can do to help - I'm happy to test/verify any fixes you want to try and review any code (bearing in mind I'm a total newb in the beam space). Thanks again, Preston On 9/25/19, 10:34 AM, "Maximilian Michels" <[email protected]> wrote: Hi Preston, Sorry about the name mixup, of course I meant to write Preston not Magnus :) See my reply below. cheers, Max On 25.09.19 08:31, Maximilian Michels wrote: > Hi Magnus, > > Your observation seems to be correct. There is an issue with the file > system registration. > > The two types of errors you are seeing, as well as the successful run, > are just due to the different structure of the generated transforms. The > Flink scheduler will distribute them differently, which results in some > pipelines being placed on task managers which happen to execute the > FileSystems initialization code and others not. > > There is a quick fix to at least initialize the file system in case it > has not been initialized, by adding the loading code here: > https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Fbeam%2Fblob%2F948c6fae909685e09d36b23be643182b34c8df25%2Fsdks%2Fjava%2Fcore%2Fsrc%2Fmain%2Fjava%2Forg%2Fapache%2Fbeam%2Fsdk%2Fio%2FFileSystems.java%23L463&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680782231&sdata=n9zr0jMao6oGcSK0G3QSPcHbcfdZlUAGwKhWCpdKT6Y%3D&reserved=0 > > > However, there we do not have the pipeline options available, which > prevents any configuration. The problem is that the error occurs in the > coder used in a native Flink operation which does not even run user code. > > I believe the only way fix this is to ship the FileSystems > initialization code in CoderTypeSerializer where we are sure to execute > it in time for any coders which depend on it. > > Could you file an issue? I'd be happy to fix this then. > > Thanks, > Max > > On 24.09.19 09:54, Chamikara Jayalath wrote: >> As Magnus mentioned, FileSystems are picked up from the class path and >> registered here. >> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Fbeam%2Fblob%2Fmaster%2Fsdks%2Fjava%2Fcore%2Fsrc%2Fmain%2Fjava%2Forg%2Fapache%2Fbeam%2Fsdk%2Fio%2FFileSystems.java%23L480&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680782231&sdata=RPVRS548zo%2FWdf672K%2FKbqJykjf%2FuWyS84CirzR4b0E%3D&reserved=0 >> >> >> Seems like Flink is invoking this method at following locations. >> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Fbeam%2Fblob%2Fmaster%2Frunners%2Fflink%2Fsrc%2Fmain%2Fjava%2Forg%2Fapache%2Fbeam%2Frunners%2Fflink%2FFlinkPipelineRunner.java%23L142&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680782231&sdata=jiMBDlzvSX2rLY9tZOLtt6QKAmCPTiglWezLKymxJAc%3D&reserved=0 >> >> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Fbeam%2Fblob%2Fmaster%2Frunners%2Fflink%2Fsrc%2Fmain%2Fjava%2Forg%2Fapache%2Fbeam%2Frunners%2Fflink%2FFlinkJobServerDriver.java%23L63&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680782231&sdata=7hBfpu2mrAltIFCiq98hx5kp%2BLN8XYnavbU%2FKzHudnI%3D&reserved=0 >> >> >> I'm not too familiar about Flink sure why S3 is not properly being >> registered when running the Flink job. Ccing some folks who are more >> familiar about Flink. >> >> +Ankur Goenka <mailto:[email protected]> +Maximilian Michels >> <mailto:[email protected]> >> >> Thanks, >> Cham >> >> >> On Sat, Sep 21, 2019 at 9:18 AM Koprivica,Preston Blake >> <[email protected] >> <mailto:[email protected]>> wrote: >> >> Thanks for the reply Magnus. >> >> I'm sorry it wasn't more clear in the original message. I have >> added the aws dependencies and set up the pipeline options with the >> aws options. For the case where I set the write to ignore >> windowing, everything works. But the option is deprecated and the >> comments warn against its usage. >> >> I'm wondering if where no options are set and I see the error that >> that is a case of improperly initialized filesystems in the flink >> runner. Or maybe someone has some different ideas for the culprit. >> >> Get Outlook for Android <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fghei36&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680782231&sdata=AGwyaD%2Bn8MQJlHqYjsefmUDcrgMifcFUVx%2BR%2BOty5Xo%3D&reserved=0> >> >> >> ------------------------------------------------------------------------ >> *From:* Magnus Runesson <[email protected] >> <mailto:[email protected]>> >> *Sent:* Saturday, September 21, 2019 9:06:03 AM >> *To:* [email protected] <mailto:[email protected]> >> <[email protected] <mailto:[email protected]>> >> *Subject:* Re: No filesystem found for scheme s3 using FileIO >> >> Hi! >> >> >> You probably miss the S3 filesystem in your classpath. >> >> If I remember correctly you must include this >> >> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsearch.maven.org%2Fsearch%3Fq%3Da%3Abeam-sdks-java-io-amazon-web-services&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680782231&sdata=K%2FGNviln25aCjv1biaVakcPpvGEgmAzB%2FggezNGiSOo%3D&reserved=0 >> >> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsearch.maven.org%2Fsearch%3Fq%3Da%3Abeam-sdks-java-io-amazon-web-services&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680792233&sdata=ZLJ7QmRWC8XkouQ7r47Ze%2Fy2pxN%2Bcttoi70ilOsJNG0%3D&reserved=0> >> >> package in your classpath/fat-jar. >> >> /Magnus >> >> On 2019-09-19 23:13, Koprivica,Preston Blake wrote: >>> >>> Hello everyone. I’m getting the following error when attempting to >>> use the FileIO apis (beam-2.15.0) and integrating with a 3rd party >>> filesystem, in this case AWS S3:____ >>> >>> __ __ >>> >>> java.lang.IllegalArgumentException: No filesystem found for scheme >>> s3____ >>> >>> at >>> >>> org.apache.beam.sdk.io.FileSystems.getFileSystemInternal(FileSystems.java:456)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.io.FileSystems.matchNewResource(FileSystems.java:526)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.io.FileBasedSink$FileResultCoder.decode(FileBasedSink.java:1149)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.io.FileBasedSink$FileResultCoder.decode(FileBasedSink.java:1105)____ >>> >>> >>> at org.apache.beam.sdk.coders.Coder.decode(Coder.java:159)____ >>> >>> at >>> >>> org.apache.beam.sdk.transforms.join.UnionCoder.decode(UnionCoder.java:83)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.transforms.join.UnionCoder.decode(UnionCoder.java:32)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.decode(WindowedValue.java:543)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.decode(WindowedValue.java:534)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.decode(WindowedValue.java:480)____ >>> >>> >>> at >>> >>> org.apache.beam.runners.flink.translation.types.CoderTypeSerializer.deserialize(CoderTypeSerializer.java:93)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.plugable.NonReusingDeserializationDelegate.read(NonReusingDeserializationDelegate.java:55)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.io.network.api.serialization.SpillingAdaptiveSpanningRecordDeserializer.getNextRecord(SpillingAdaptiveSpanningRecordDeserializer.java:106)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.io.network.api.reader.AbstractRecordReader.getNextRecord(AbstractRecordReader.java:72)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.io.network.api.reader.MutableRecordReader.next(MutableRecordReader.java:47)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.operators.util.ReaderIterator.next(ReaderIterator.java:73)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.operators.FlatMapDriver.run(FlatMapDriver.java:107)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:503)____ >>> >>> at >>> >>> org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:368)____ >>> >>> >>> at >>> org.apache.flink.runtime.taskmanager.Task.run(Task.java:711)____ >>> >>> at java.lang.Thread.run(Thread.java:748)____ >>> >>> __ __ >>> >>> For reference, the write code resembles this:____ >>> >>> __ __ >>> >>> FileIO.Write<?, GenericRecord> write = >>> FileIO.<GenericRecord>write()____ >>> >>> .via(ParquetIO.sink(schema))____ >>> >>> .to(options.getOutputDir()). // will be something >>> like: s3://<bucket>/<path>____ >>> >>> .withSuffix(".parquet");____ >>> >>> __ __ >>> >>> records.apply(String.format("Write(%s)", options.getOutputDir()), >>> write);____ >>> >>> __ __ >>> >>> I have setup the PipelineOptions with all the relevant AWS options >>> and the issue does not appear to be related to ParquetIO.sink() >>> directly. I am able to reliably reproduce the issue using JSON >>> formatted records and TextIO.sink(), as well.____ >>> >>> __ __ >>> >>> Just trying some different knobs, I went ahead and set the >>> following option:____ >>> >>> __ __ >>> >>> write = write.withNoSpilling();____ >>> >>> __ __ >>> >>> This actually seemed to fix the issue, only to have it reemerge as >>> I scaled up the data set size. The stack trace, while very >>> similar, reads:____ >>> >>> __ __ >>> >>> java.lang.IllegalArgumentException: No filesystem found for scheme >>> s3____ >>> >>> at >>> >>> org.apache.beam.sdk.io.FileSystems.getFileSystemInternal(FileSystems.java:456)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.io.FileSystems.matchNewResource(FileSystems.java:526)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.io.FileBasedSink$FileResultCoder.decode(FileBasedSink.java:1149)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.io.FileBasedSink$FileResultCoder.decode(FileBasedSink.java:1105)____ >>> >>> >>> at org.apache.beam.sdk.coders.Coder.decode(Coder.java:159)____ >>> >>> at >>> org.apache.beam.sdk.coders.KvCoder.decode(KvCoder.java:82)____ >>> >>> at >>> org.apache.beam.sdk.coders.KvCoder.decode(KvCoder.java:36)____ >>> >>> at >>> >>> org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.decode(WindowedValue.java:543)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.decode(WindowedValue.java:534)____ >>> >>> >>> at >>> >>> org.apache.beam.sdk.util.WindowedValue$FullWindowedValueCoder.decode(WindowedValue.java:480)____ >>> >>> >>> at >>> >>> org.apache.beam.runners.flink.translation.types.CoderTypeSerializer.deserialize(CoderTypeSerializer.java:93)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.plugable.NonReusingDeserializationDelegate.read(NonReusingDeserializationDelegate.java:55)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.io.network.api.serialization.SpillingAdaptiveSpanningRecordDeserializer.getNextRecord(SpillingAdaptiveSpanningRecordDeserializer.java:106)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.io.network.api.reader.AbstractRecordReader.getNextRecord(AbstractRecordReader.java:72)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.io.network.api.reader.MutableRecordReader.next(MutableRecordReader.java:47)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.operators.util.ReaderIterator.next(ReaderIterator.java:73)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.operators.NoOpDriver.run(NoOpDriver.java:94)____ >>> >>> >>> at >>> >>> org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:503)____ >>> >>> at >>> >>> org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:368)____ >>> >>> >>> at >>> org.apache.flink.runtime.taskmanager.Task.run(Task.java:711)____ >>> >>> at java.lang.Thread.run(Thread.java:748) ____ >>> >>> __ __ >>> >>> I’ll be interested to hear some theories on the >>> differences/similarities in the stacks. And lastly, I tried >>> adding the following deprecated option (with and without the >>> withNoSpilling() option):____ >>> >>> __ __ >>> >>> write = write.withIgnoreWindowing();____ >>> >>> __ __ >>> >>> This seemed to fix the issue altogether but aside from having to >>> rely on a deprecated feature, there is the bigger issue of why?____ >>> >>> __ __ >>> >>> In reading through some of the source, it seems a common pattern >>> to have to manually register the pipeline options to seed the >>> filesystem registry during the setup part of the operator >>> lifecycle, e.g.: >>> >>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Fbeam%2Fblob%2Frelease-2.15.0%2Frunners%2Fflink%2Fsrc%2Fmain%2Fjava%2Forg%2Fapache%2Fbeam%2Frunners%2Fflink%2Ftranslation%2Fwrappers%2Fstreaming%2FDoFnOperator.java%23L304-L313&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680792233&sdata=j1axauYJ3SxfmPrYW1rgwiGxv3mclE75Sf5PpuzpxFc%3D&reserved=0 >>> >>> >>> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fapache%2Fbeam%2Fblob%2Frelease-2.15.0%2Frunners%2Fflink%2Fsrc%2Fmain%2Fjava%2Forg%2Fapache%2Fbeam%2Frunners%2Fflink%2Ftranslation%2Fwrappers%2Fstreaming%2FDoFnOperator.java%23L304-L313&data=02%7C01%7CPreston.B.Koprivica%40cerner.com%7Ccaa86b8ee6f740a8c3cc08d741cdd982%7Cfbc493a80d244454a815f4ca58e8c09d%7C0%7C0%7C637050224680792233&sdata=j1axauYJ3SxfmPrYW1rgwiGxv3mclE75Sf5PpuzpxFc%3D&reserved=0> >>> >>> ____ >>> >>> __ __ >>> >>> Is it possible that I have hit upon a couple scenarios where that >>> has not taken place? Unfortunately, I’m not yet at a position to >>> suggest a fix, but I’m guessing there’s some missing >>> initialization code in one or more of the batch operators. If >>> this is indeed a legitimate issue, I’ll be happy to log an issue, >>> but I’ll hold off until the community gets a chance to look at >>> it.____ >>> >>> __ __ >>> >>> Thanks,____ >>> >>> * Preston ____ >>> >>> CONFIDENTIALITY NOTICE This message and any included attachments >>> are from Cerner Corporation and are intended only for the >>> addressee. The information contained in this message is >>> confidential and may constitute inside or non-public information >>> under international, federal, or state securities laws. >>> Unauthorized forwarding, printing, copying, distribution, or use >>> of such information is strictly prohibited and may be unlawful. If >>> you are not the addressee, please promptly delete this message and >>> notify the sender of the delivery error by e-mail or you may call >>> Cerner's corporate offices in Kansas City, Missouri, U.S.A at (+1) >>> (816)221-1024 <tel:(816)%20221-1024>. >>> CONFIDENTIALITY NOTICE This message and any included attachments are from Cerner Corporation and are intended only for the addressee. The information contained in this message is confidential and may constitute inside or non-public information under international, federal, or state securities laws. Unauthorized forwarding, printing, copying, distribution, or use of such information is strictly prohibited and may be unlawful. If you are not the addressee, please promptly delete this message and notify the sender of the delivery error by e-mail or you may call Cerner's corporate offices in Kansas City, Missouri, U.S.A at (+1) (816)221-1024.
