This is likely a factor of your hadoop config and Spark rather then anything specific with GraphFrames.
You might have better luck getting assistance if you could isolate the code to a simple case that manifests the problem (without GraphFrames), and repost. ________________________________ From: Ankur Srivastava <ankur.srivast...@gmail.com> Sent: Thursday, January 5, 2017 3:45:59 PM To: Felix Cheung; d...@spark.apache.org Cc: user@spark.apache.org Subject: Re: Spark GraphFrame ConnectedComponents Adding DEV mailing list to see if this is a defect with ConnectedComponent or if they can recommend any solution. Thanks Ankur On Thu, Jan 5, 2017 at 1:10 PM, Ankur Srivastava <ankur.srivast...@gmail.com<mailto:ankur.srivast...@gmail.com>> wrote: Yes I did try it out and it choses the local file system as my checkpoint location starts with s3n:// I am not sure how can I make it load the S3FileSystem. On Thu, Jan 5, 2017 at 12:12 PM, Felix Cheung <felixcheun...@hotmail.com<mailto:felixcheun...@hotmail.com>> wrote: Right, I'd agree, it seems to be only with delete. Could you by chance run just the delete to see if it fails FileSystem.get(sc.hadoopConfiguration) .delete(new Path(somepath), true) ________________________________ From: Ankur Srivastava <ankur.srivast...@gmail.com<mailto:ankur.srivast...@gmail.com>> Sent: Thursday, January 5, 2017 10:05:03 AM To: Felix Cheung Cc: user@spark.apache.org<mailto:user@spark.apache.org> Subject: Re: Spark GraphFrame ConnectedComponents Yes it works to read the vertices and edges data from S3 location and is also able to write the checkpoint files to S3. It only fails when deleting the data and that is because it tries to use the default file system. I tried looking up how to update the default file system but could not find anything in that regard. Thanks Ankur On Thu, Jan 5, 2017 at 12:55 AM, Felix Cheung <felixcheun...@hotmail.com<mailto:felixcheun...@hotmail.com>> wrote: >From the stack it looks to be an error from the explicit call to >hadoop.fs.FileSystem. Is the URL scheme for s3n registered? Does it work when you try to read from s3 from Spark? _____________________________ From: Ankur Srivastava <ankur.srivast...@gmail.com<mailto:ankur.srivast...@gmail.com>> Sent: Wednesday, January 4, 2017 9:23 PM Subject: Re: Spark GraphFrame ConnectedComponents To: Felix Cheung <felixcheun...@hotmail.com<mailto:felixcheun...@hotmail.com>> Cc: <user@spark.apache.org<mailto:user@spark.apache.org>> This is the exact trace from the driver logs Exception in thread "main" java.lang.IllegalArgumentException: Wrong FS: s3n://<checkpoint-folder>/8ac233e4-10f9-4eb3-aa53-df6d9d7ea7be/connected-components-c1dbc2b0/3, expected: file:/// at org.apache.hadoop.fs.FileSystem.checkPath(FileSystem.java:645) at org.apache.hadoop.fs.RawLocalFileSystem.pathToFile(RawLocalFileSystem.java:80) at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:529) at org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:747) at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:524) at org.apache.hadoop.fs.ChecksumFileSystem.delete(ChecksumFileSystem.java:534) at org.graphframes.lib.ConnectedComponents$.org$graphframes$lib$ConnectedComponents$$run(ConnectedComponents.scala:340) at org.graphframes.lib.ConnectedComponents.run(ConnectedComponents.scala:139) at GraphTest.main(GraphTest.java:31) ----------- Application Class at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731) at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181) at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) And I am running spark v 1.6.2 and graphframes v 0.3.0-spark1.6-s_2.10 Thanks Ankur On Wed, Jan 4, 2017 at 8:03 PM, Ankur Srivastava <ankur.srivast...@gmail.com<mailto:ankur.srivast...@gmail.com>> wrote: Hi I am rerunning the pipeline to generate the exact trace, I have below part of trace from last run: Exception in thread "main" java.lang.IllegalArgumentException: Wrong FS: s3n://<folder-path>, expected: file:/// at org.apache.hadoop.fs.FileSystem.checkPath(FileSystem.java:642) at org.apache.hadoop.fs.RawLocalFileSystem.pathToFile(RawLocalFileSystem.java:69) at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:516) at org.apache.hadoop.fs.ChecksumFileSystem.delete(ChecksumFileSystem.java:528) Also I think the error is happening in this part of the code "ConnectedComponents.scala:339" I am referring the code @https://github.com/graphframes/graphframes/blob/master/src/main/scala/org/graphframes/lib/ConnectedComponents.scala if (shouldCheckpoint && (iteration % checkpointInterval == 0)) { // TODO: remove this after DataFrame.checkpoint is implemented val out = s"${checkpointDir.get}/$iteration" ee.write.parquet(out) // may hit S3 eventually consistent issue ee = sqlContext.read.parquet(out) // remove previous checkpoint if (iteration > checkpointInterval) { FileSystem.get(sc.hadoopConfiguration) .delete(new Path(s"${checkpointDir.get}/${iteration - checkpointInterval}"), true) } System.gc() // hint Spark to clean shuffle directories } Thanks Ankur On Wed, Jan 4, 2017 at 5:19 PM, Felix Cheung <felixcheun...@hotmail.com<mailto:felixcheun...@hotmail.com>> wrote: Do you have more of the exception stack? ________________________________ From: Ankur Srivastava <ankur.srivast...@gmail.com<mailto:ankur.srivast...@gmail.com>> Sent: Wednesday, January 4, 2017 4:40:02 PM To: user@spark.apache.org<mailto:user@spark.apache.org> Subject: Spark GraphFrame ConnectedComponents Hi, I am trying to use the ConnectedComponent algorithm of GraphFrames but by default it needs a checkpoint directory. As I am running my spark cluster with S3 as the DFS and do not have access to HDFS file system I tried using a s3 directory as checkpoint directory but I run into below exception: Exception in thread "main"java.lang.IllegalArgumentException: Wrong FS: s3n://<folder-path>, expected: file:/// at org.apache.hadoop.fs.FileSystem.checkPath(FileSystem.java:642) at org.apache.hadoop.fs.RawLocalFileSystem.pathToFile(RawLocalFileSystem.java:69) If I set checkpoint interval to -1 to avoid checkpointing the driver just hangs after 3 or 4 iterations. Is there some way I can set the default FileSystem to S3 for Spark or any other option? Thanks Ankur
