From issues-return-217259-archive-asf-public=cust-asf.ponee.io@spark.apache.org Fri Mar 1 08:25:06 2019 Return-Path: X-Original-To: archive-asf-public@cust-asf.ponee.io Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by mx-eu-01.ponee.io (Postfix) with SMTP id 4BD17180676 for ; Fri, 1 Mar 2019 09:25:05 +0100 (CET) Received: (qmail 13835 invoked by uid 500); 1 Mar 2019 08:25:04 -0000 Mailing-List: contact issues-help@spark.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Delivered-To: mailing list issues@spark.apache.org Received: (qmail 13826 invoked by uid 99); 1 Mar 2019 08:25:04 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd1-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 01 Mar 2019 08:25:03 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd1-us-west.apache.org (ASF Mail Server at spamd1-us-west.apache.org) with ESMTP id 94DB1C0D0F for ; Fri, 1 Mar 2019 08:25:03 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd1-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: -110.301 X-Spam-Level: X-Spam-Status: No, score=-110.301 tagged_above=-999 required=6.31 tests=[ENV_AND_HDR_SPF_MATCH=-0.5, RCVD_IN_DNSWL_MED=-2.3, SPF_PASS=-0.001, USER_IN_DEF_SPF_WL=-7.5, USER_IN_WHITELIST=-100] autolearn=disabled Received: from mx1-lw-eu.apache.org ([10.40.0.8]) by localhost (spamd1-us-west.apache.org [10.40.0.7]) (amavisd-new, port 10024) with ESMTP id dw_mETk9Rs15 for ; Fri, 1 Mar 2019 08:25:02 +0000 (UTC) Received: from mailrelay1-us-west.apache.org (mailrelay1-us-west.apache.org [209.188.14.139]) by mx1-lw-eu.apache.org (ASF Mail Server at mx1-lw-eu.apache.org) with ESMTP id 475885F4D5 for ; Fri, 1 Mar 2019 08:25:01 +0000 (UTC) Received: from jira-lw-us.apache.org (unknown [207.244.88.139]) by mailrelay1-us-west.apache.org (ASF Mail Server at mailrelay1-us-west.apache.org) with ESMTP id 24DCFE01AC for ; Fri, 1 Mar 2019 08:25:00 +0000 (UTC) Received: from jira-lw-us.apache.org (localhost [127.0.0.1]) by jira-lw-us.apache.org (ASF Mail Server at jira-lw-us.apache.org) with ESMTP id 1736F256EE for ; Fri, 1 Mar 2019 08:25:00 +0000 (UTC) Date: Fri, 1 Mar 2019 08:25:00 +0000 (UTC) From: =?utf-8?Q?Piotr_Ko=C5=82aczkowski_=28JIRA=29?= To: issues@spark.apache.org Message-ID: In-Reply-To: References: Subject: [jira] [Created] (SPARK-27018) Checkpointed RDD deleted prematurely when using GBTClassifier MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-JIRA-FingerPrint: 30527f35849b9dde25b450d4833f0394 Piotr Ko=C5=82aczkowski created SPARK-27018: ------------------------------------------ Summary: Checkpointed RDD deleted prematurely when using GBTCl= assifier Key: SPARK-27018 URL: https://issues.apache.org/jira/browse/SPARK-27018 Project: Spark Issue Type: Bug Components: ML Affects Versions: 2.4.0, 2.2.2 Environment: OS: Ubuntu Linux 18.10 Java:=C2=A0java version "1.8.0_201" Java(TM) SE Runtime Environment (build 1.8.0_201-b09) Java HotSpot(TM) 64-Bit Server VM (build 25.201-b09, mixed mode) Reproducible with a single-node Spark in standalone mode. Reproducible with Zepellin or Spark shell. =C2=A0 Reporter: Piotr Ko=C5=82aczkowski Steps to reproduce: {noformat} import org.apache.spark.ml.linalg.Vectors import org.apache.spark.ml.classification.GBTClassifier case class Row(features: org.apache.spark.ml.linalg.Vector, label: Int) sc.setCheckpointDir("/checkpoints") val trainingData =3D sc.parallelize(1 to 2426874, 256).map(x =3D> Row(Vecto= rs.dense(x, x + 1, x * 2 % 10), if (x % 5 =3D=3D 0) 1 else 0)).toDF val classifier =3D new GBTClassifier() .setLabelCol("label") .setFeaturesCol("features") .setProbabilityCol("probability") .setMaxIter(100) .setMaxDepth(10) .setCheckpointInterval(2) classifier.fit(trainingData){noformat} =C2=A0 The last line fails with: {noformat} org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 i= n stage 56.0 failed 10 times, most recent failure: Lost task 0.9 in stage 5= 6.0 (TID 12058, 127.0.0.1, executor 0): java.io.FileNotFoundException: /che= ckpoints/191c9209-0955-440f-8c11-f042bdf7f804/rdd-51 at com.datastax.bdp.fs.hadoop.DseFileSystem$$anonfun$1.applyOrElse(DseFileS= ystem.scala:63) at com.datastax.bdp.fs.hadoop.DseFileSystem$$anonfun$1.applyOrElse(DseFileS= ystem.scala:61) at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scal= a:36) at com.datastax.bdp.fs.hadoop.DseFileSystem.com$datastax$bdp$fs$hadoop$DseF= ileSystem$$translateToHadoopExceptions(DseFileSystem.scala:70) at com.datastax.bdp.fs.hadoop.DseFileSystem$$anonfun$6.apply(DseFileSystem.= scala:264) at com.datastax.bdp.fs.hadoop.DseFileSystem$$anonfun$6.apply(DseFileSystem.= scala:264) at com.datastax.bdp.fs.hadoop.DseFsInputStream.input(DseFsInputStream.scala= :31) at com.datastax.bdp.fs.hadoop.DseFsInputStream.openUnderlyingDataSource(Dse= FsInputStream.scala:39) at com.datastax.bdp.fs.hadoop.DseFileSystem.open(DseFileSystem.scala:269) at org.apache.spark.rdd.ReliableCheckpointRDD$.readCheckpointFile(ReliableC= heckpointRDD.scala:292) at org.apache.spark.rdd.ReliableCheckpointRDD.compute(ReliableCheckpointRDD= .scala:100) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD.iterator(RDD.scala:288) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:322) at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:337) at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:335) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(Blo= ckManager.scala:1165) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(Blo= ckManager.scala:1156) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1= 156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala= :882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.sc= ala:89) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD.iterator(RDD.scala:288) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:337) at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:335) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(Blo= ckManager.scala:1165) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(Blo= ckManager.scala:1156) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1= 156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala= :882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.sc= ala:89) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD.iterator(RDD.scala:288) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:337) at org.apache.spark.rdd.RDD$$anonfun$7.apply(RDD.scala:335) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(Blo= ckManager.scala:1165) at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(Blo= ckManager.scala:1156) at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091) at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1= 156) at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala= :882) at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335) at org.apache.spark.rdd.RDD.iterator(RDD.scala:286) at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.sc= ala:89) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD.iterator(RDD.scala:288) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD.iterator(RDD.scala:288) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD.iterator(RDD.scala:288) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324) at org.apache.spark.rdd.RDD.iterator(RDD.scala:288) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:121) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor= .scala:402) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.jav= a:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.ja= va:624) at java.lang.Thread.run(Thread.java:748){noformat} The problem happens as well when checkpointing directory is placed on the l= ocal file system, on a single-node setup.=C2=A0 Debugging at the FS level showed that the driver requests to recursively de= lete the checkpointed rdd-51 soon before the exception gets thrown by the t= ask. =C2=A0 =C2=A0 -- This message was sent by Atlassian JIRA (v7.6.3#76005) --------------------------------------------------------------------- To unsubscribe, e-mail: issues-unsubscribe@spark.apache.org For 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