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Task run failure #50

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maning opened this issue Jun 5, 2018 · 7 comments
Closed

Task run failure #50

maning opened this issue Jun 5, 2018 · 7 comments

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@maning
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maning commented Jun 5, 2018

Running from dev branch and gadle4.7. I get the following:

gradle run

...

> Task :run FAILED

FAILURE: Build failed with an exception.

* Where:
Build file '/Users/maning/projects/git/atlas-checks/build.gradle' line: 314

* What went wrong:
Execution failed for task ':runChecks'.
> Process 'command '/Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/bin/java'' finished with non-zero exit value 52

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

Deprecated Gradle features were used in this build, making it incompatible with Gradle 5.0.
See https://docs.gradle.org/4.7/userguide/command_line_interface.html#sec:command_line_warnings

BUILD FAILED in 11m 55s
7 actionable tasks: 7 executed

@maning
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maning commented Jun 21, 2018

Running on java 1.8.0_172 and gradle 4.8, I did not get the "depracated gradle" message, but a different one. Any hints would be helpful, thanks!
Stack trace below:

maning@hjutoe ~/projects/git/atlas-checks (dev)*$ ./gradlew run -PCheckName=PoolSizeCheck

> Configure project :
Building new check org.openstreetmap.atlas.checks.validation.PoolSizeCheck.java

> Task :run
/Library/Java/JavaVirtualMachines/jdk1.8.0_172.jdk/Contents/Home/bin/java \
-Dfile.encoding=UTF-8 \
-Duser.country=PH \
-Duser.language=en \
-Duser.variant \
-cp \
/Users/maning/projects/git/atlas-checks/build/classes/java/main:/Users/maning/projects/git/atlas-checks/build/resources/main:/Users/maning/.gradle/caches/modules-2/files-2.1/org.openstreetmap.atlas/atlas-generator/4.0.4/7e0b72e0b0c94d65ef8469e150ef1d07273e62be/atlas-generator-4.0.4.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.spark/spark-core_2.10/1.6.0-cdh5.7.0/5be4b4baedf477fdb407f3755a33d19780797bac/spark-core_2.10-1.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.tachyonproject/tachyon-client/0.8.2/a0b0c068488d1a4eae155bd8ce2971cd89212a53/tachyon-client-0.8.2.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-client/2.6.0-cdh5.7.0/a5fea8f1a2f3b60adea961ec048263661e5c8d42/hadoop-client-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-hdfs/2.6.0-cdh5.7.0/5cf1935e1eccefa2be270b500d142d32129cfbb0/hadoop-hdfs-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-mapreduce-client-app/2.6.0-cdh5.7.0/c9ddcb8fe456d35c9ac7db048b2715a50a68c8f7/hadoop-mapreduce-client-app-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-mapreduce-client-jobclient/2.6.0-cdh5.7.0/c8aca96d642b88acc53782e09b2e1f8e7fed9f2a/hadoop-mapreduce-client-jobclient-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-mapreduce-client-shuffle/2.6.0-cdh5.7.0/ae89dc5dd7a698ac792dd9ae3a470bc86efa02be/hadoop-mapreduce-client-shuffle-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-mapreduce-client-common/2.6.0-cdh5.7.0/3a37397b78fc75d37a02bbbcb7c1cf3df5d4d459/hadoop-mapreduce-client-common-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-yarn-client/2.6.0-cdh5.7.0/3c3f5a71090d226b2ef0005c32e60338f933844/hadoop-yarn-client-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-mapreduce-client-core/2.6.0-cdh5.7.0/581ccc38003ddfa4f6d43d1372947429644ca688/hadoop-mapreduce-client-core-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-yarn-server-nodemanager/2.6.0-cdh5.7.0/fad61e38f7399b8a08446fd78497e4b7245b5cc0/hadoop-yarn-server-nodemanager-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-yarn-server-common/2.6.0-cdh5.7.0/a5a2b4e8f12868c65a9ff8b97a6699792e948ed1/hadoop-yarn-server-common-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-yarn-common/2.6.0-cdh5.7.0/6b47c9827c3ce45a6e17751a69c9f9e13663380c/hadoop-yarn-common-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-aws/2.6.0-cdh5.7.0/dae0c7040c010c61c9f68a3e4eb6bb6c0aa3b6f5/hadoop-aws-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-common/2.6.0-cdh5.7.0/eb8cf9b34574fa98571c0c4cbb74d8506d2735db/hadoop-common-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/commons-configuration/commons-configuration/1.6/32cadde23955d7681b0d94a2715846d20b425235/commons-configuration-1.6.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-yarn-api/2.6.0-cdh5.7.0/cb306ef9cda3c5e9647c9d409a70c384fc1d6b96/hadoop-yarn-api-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/commons-lang/commons-lang/2.6/ce1edb914c94ebc388f086c6827e8bdeec71ac2/commons-lang-2.6.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.openstreetmap.atlas/atlas/5.0.15/cce39185e5c4a74c0bc74363298a696e0ec9e48/atlas-5.0.15.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.avro/avro-mapred/1.7.6-cdh5.7.0/4071ad09178fcbf8699a5fed786e42710d9f326a/avro-mapred-1.7.6-cdh5.7.0-hadoop2.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.slf4j/jul-to-slf4j/1.7.5/d2b0f76abde33a62f1dbc19a9da726ffe9a0180e/jul-to-slf4j-1.7.5.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.slf4j/jcl-over-slf4j/1.7.5/cd5970bd13fa85f7bed41ca606d6daf7cbf1365/jcl-over-slf4j-1.7.5.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.curator/curator-recipes/2.7.1/a2c180efc6a38a4f8c9197eb35bb4eb5716cd2fa/curator-recipes-2.7.1.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-auth/2.6.0-cdh5.7.0/682b25d13d8454477d3826633b122af529598ae3/hadoop-auth-2.6.0-cdh5.7.0.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.curator/curator-framework/2.7.1/8c7b1eeb78e43bb91ea737111ba3dec0512be876/curator-framework-2.7.1.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.curator/curator-client/2.7.1/a591dfc085db3e9d4d480381cc7e6ae8a26b34af/curator-client-2.7.1.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.apache.zookeeper/zookeeper/3.4.6/1b2502e29da1ebaade2357cd1de35a855fa3755/zookeeper-3.4.6.jar:/Users/maning/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-log4j1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\
org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob \
-mainClass=org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob \
-master=local \
-configFiles=file:///Users/maning/projects/git/atlas-checks/config/configuration.json \
-outputFormats=flags,geojson,metrics \
-countries=UNK \
-input=file:///Users/maning/projects/git/atlas-checks/data/ \
-sparkOptions=spark.executor.memory->4g,spark.driver.memory->4g,spark.rdd.compress->true \
-output=file:///Users/maning/projects/git/atlas-checks/build/ \
-startedFolder=file:///Users/maning/projects/git/atlas-checks/build/tmp/ \
-compressOutput=false \

> Task :runChecks
2018-06-21 09:44:11 WARN  Command:237 - Unknown switch mainClass -> org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch master -> local
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch configFiles -> file:///Users/maning/projects/git/atlas-checks/config/configuration.json
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch outputFormats -> flags,geojson,metrics
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch countries -> UNK
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch input -> file:///Users/maning/projects/git/atlas-checks/data/
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch sparkOptions -> spark.executor.memory->4g,spark.driver.memory->4g,spark.rdd.compress->true
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch output -> file:///Users/maning/projects/git/atlas-checks/build/
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch startedFolder -> file:///Users/maning/projects/git/atlas-checks/build/tmp/
2018-06-21 09:44:11 INFO  Command:232 - Parsing switch compressOutput -> false
2018-06-21 09:44:11 WARN  Command:261 - Running without switch [Switch: name = additionalSparkOptions, description = Comma separated list of additional Spark options, i.e. key1->value1,key2->value2 Default is: ]
2018-06-21 09:44:11 WARN  Command:261 - Running without switch [Switch: name = sparkContextProvider, description = The class name of the Spark Context Provider Default is: org.openstreetmap.atlas.generator.tools.spark.context.DefaultSparkContextProvider]
2018-06-21 09:44:11 WARN  Command:261 - Running without switch [Switch: name = sensitiveConfiguration, description = Regular expression pattern of spark configuration keys to avoid logging. Default is: .*]
2018-06-21 09:44:11 WARN  Command:261 - Running without switch [Switch: name = inputFolder, description = Path of folder which contains Atlas file(s)]
2018-06-21 09:44:11 WARN  Command:261 - Running without switch [Switch: name = maproulette, description = Map roulette server information, format <Host>:<Port>:<ProjectName>:<ApiKey>, projectName is optional.]
2018-06-21 09:44:11 WARN  Command:261 - Running without switch [Switch: name = configJson, description = Json formatted configuration.]
2018-06-21 09:44:11 WARN  Command:261 - Running without switch [Switch: name = pbfBoundingBox, description = OSM protobuf data will be loaded only in this bounding box]
2018-06-21 09:44:11 WARN  Command:261 - Running without switch [Switch: name = savePbfAtlas, description = Saves intermediate atlas files created when processing OSM protobuf data. Default is: false]
2018-06-21 09:44:12 INFO  SparkJob:154 - Forcing configuration from -sparkOptions: key: "spark.executor.memory", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:154 - Forcing configuration from -sparkOptions: key: "spark.driver.memory", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:154 - Forcing configuration from -sparkOptions: key: "spark.rdd.compress", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:166 - SparkConf ===============================================================
2018-06-21 09:44:12 INFO  SparkJob:175 - SparkConf: key: "spark.master", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:175 - SparkConf: key: "mapreduce.output.fileoutputformat.compress", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:175 - SparkConf: key: "spark.serializer", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:175 - SparkConf: key: "spark.driver.memory", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:175 - SparkConf: key: "spark.executor.memory", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:175 - SparkConf: key: "spark.app.name", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:175 - SparkConf: key: "spark.rdd.compress", value: "**********"
2018-06-21 09:44:12 INFO  SparkJob:178 - SparkConf ===============================================================
2018-06-21 09:44:12 INFO  SparkContext:58 - Running Spark version 1.6.0
2018-06-21 09:44:12 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2018-06-21 09:44:12 INFO  SecurityManager:58 - Changing view acls to: maning
2018-06-21 09:44:12 INFO  SecurityManager:58 - Changing modify acls to: maning
2018-06-21 09:44:12 INFO  SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(maning); users with modify permissions: Set(maning)
2018-06-21 09:44:13 INFO  Utils:58 - Successfully started service 'sparkDriver' on port 49762.
2018-06-21 09:44:13 INFO  Slf4jLogger:80 - Slf4jLogger started
2018-06-21 09:44:13 INFO  Remoting:74 - Starting remoting
2018-06-21 09:44:13 INFO  Remoting:74 - Remoting started; listening on addresses :[akka.tcp://[email protected]:49763]
2018-06-21 09:44:13 INFO  Remoting:74 - Remoting now listens on addresses: [akka.tcp://[email protected]:49763]
2018-06-21 09:44:13 INFO  Utils:58 - Successfully started service 'sparkDriverActorSystem' on port 49763.
2018-06-21 09:44:13 INFO  SparkEnv:58 - Registering MapOutputTracker
2018-06-21 09:44:13 INFO  SparkEnv:58 - Registering BlockManagerMaster
2018-06-21 09:44:13 INFO  DiskBlockManager:58 - Created local directory at /private/var/folders/0q/c_r1c5v53779qm7c293qzl5m0000gn/T/blockmgr-a14fbbbc-23a5-4149-9921-a42303d6cf01
2018-06-21 09:44:13 INFO  MemoryStore:58 - MemoryStore started with capacity 983.1 MB
2018-06-21 09:44:13 INFO  SparkEnv:58 - Registering OutputCommitCoordinator
2018-06-21 09:44:13 INFO  Server:272 - jetty-8.y.z-SNAPSHOT
2018-06-21 09:44:14 INFO  AbstractConnector:338 - Started [email protected]:4040
2018-06-21 09:44:14 INFO  Utils:58 - Successfully started service 'SparkUI' on port 4040.
2018-06-21 09:44:14 INFO  SparkUI:58 - Started SparkUI at http://192.168.1.134:4040
2018-06-21 09:44:14 INFO  Executor:58 - Starting executor ID driver on host localhost
2018-06-21 09:44:14 INFO  Utils:58 - Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 49764.
2018-06-21 09:44:14 INFO  NettyBlockTransferService:58 - Server created on 49764
2018-06-21 09:44:14 INFO  BlockManagerMaster:58 - Trying to register BlockManager
2018-06-21 09:44:14 INFO  BlockManagerMasterEndpoint:58 - Registering block manager localhost:49764 with 983.1 MB RAM, BlockManagerId(driver, localhost, 49764)
2018-06-21 09:44:14 INFO  BlockManagerMaster:58 - Registered BlockManager
2018-06-21 09:44:14 WARN  :389 - Your hostname, hjutoe.local resolves to a loopback/non-reachable address: fe80:0:0:0:206:ba51:34c1:50ab%utun0, but we couldn't find any external IP address!
2018-06-21 09:44:20 WARN  FileSystemPerformanceHelper:51 - Opening rename thread pool!
2018-06-21 09:44:20 INFO  ConfigurationResolver:84 - Loading local configuration file:///Users/maning/projects/git/atlas-checks/config/configuration.json
2018-06-21 09:44:21 INFO  CheckResourceLoader:203 - Loaded 25 BaseCheck in 1.235 seconds
2018-06-21 09:44:21 INFO  CheckResourceLoader:203 - Loaded 25 BaseCheck in 524 milliseconds
2018-06-21 09:44:22 INFO  IntegrityCheckSparkJob:256 - Initialized countries: UNK
2018-06-21 09:44:22 INFO  IntegrityCheckSparkJob:258 - Initialized checks: DuplicateNodeCheck,BuildingRoadIntersectionCheck,PoolSizeCheck,UnusualLayerTagsCheck,IntersectingBuildingsCheck,OneMemberRelationCheck,InvalidTurnRestrictionCheck,DuplicateWaysCheck,SnakeRoadCheck,OrphanNodeCheck,AddressPointMatchCheck,InvalidTurnRestrictionCheck,RoundaboutClosedLoopCheck,WaterbodyAndIslandSizeCheck,SinkIslandCheck,SelfIntersectingPolylineCheck,AreasWithHighwayTagCheck,RoundaboutValenceCheck,DuplicatePointCheck,SinkIslandCheck,EdgeCrossingEdgeCheck,FloatingEdgeCheck,SharpAngleCheck,MalformedRoundaboutCheck,AbbreviatedNameCheck
2018-06-21 09:44:22 INFO  SparkContext:58 - Starting job: foreach at IntegrityCheckSparkJob.java:386
2018-06-21 09:44:22 INFO  DAGScheduler:58 - Got job 0 (foreach at IntegrityCheckSparkJob.java:386) with 1 output partitions
2018-06-21 09:44:22 INFO  DAGScheduler:58 - Final stage: ResultStage 0 (foreach at IntegrityCheckSparkJob.java:386)
2018-06-21 09:44:22 INFO  DAGScheduler:58 - Parents of final stage: List()
2018-06-21 09:44:22 INFO  DAGScheduler:58 - Missing parents: List()
2018-06-21 09:44:22 INFO  DAGScheduler:58 - Submitting ResultStage 0 (MapPartitionsRDD[2] at filter at IntegrityCheckSparkJob.java:383), which has no missing parents
2018-06-21 09:44:22 INFO  MemoryStore:58 - Block broadcast_0 stored as values in memory (estimated size 6.7 KB, free 6.7 KB)
2018-06-21 09:44:22 INFO  MemoryStore:58 - Block broadcast_0_piece0 stored as bytes in memory (estimated size 4.7 KB, free 11.4 KB)
2018-06-21 09:44:22 INFO  BlockManagerInfo:58 - Added broadcast_0_piece0 in memory on localhost:49764 (size: 4.7 KB, free: 983.1 MB)
2018-06-21 09:44:22 INFO  SparkContext:58 - Created broadcast 0 from broadcast at DAGScheduler.scala:1006
2018-06-21 09:44:22 INFO  DAGScheduler:58 - Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at filter at IntegrityCheckSparkJob.java:383)
2018-06-21 09:44:22 INFO  TaskSchedulerImpl:58 - Adding task set 0.0 with 1 tasks
2018-06-21 09:44:22 INFO  TaskSetManager:58 - Starting task 0.0 in stage 0.0 (TID 0, localhost, partition 0,PROCESS_LOCAL, 30379 bytes)
2018-06-21 09:44:22 INFO  Executor:58 - Running task 0.0 in stage 0.0 (TID 0)
2018-06-21 09:44:22 INFO  IntegrityCheckSparkJob:290 - Initialized checks for UNK: SharpAngleCheck,DuplicateWaysCheck,SnakeRoadCheck,DuplicatePointCheck,RoundaboutValenceCheck,MalformedRoundaboutCheck,OrphanNodeCheck,AbbreviatedNameCheck,EdgeCrossingEdgeCheck,AddressPointMatchCheck,AreasWithHighwayTagCheck,UnusualLayerTagsCheck,SelfIntersectingPolylineCheck,FloatingEdgeCheck,IntersectingBuildingsCheck,BuildingRoadIntersectionCheck,PoolSizeCheck,OneMemberRelationCheck,WaterbodyAndIslandSizeCheck,DuplicateNodeCheck,InvalidTurnRestrictionCheck,SinkIslandCheck,InvalidTurnRestrictionCheck,RoundaboutClosedLoopCheck,SinkIslandCheck
2018-06-21 09:44:22 INFO  FileSystemHelper:298 - [F] file:/Users/maning/projects/git/atlas-checks/data/san-francisco_california.osm.pbf
2018-06-21 09:44:22 INFO  FileSystemHelper:298 - [F] file:/Users/maning/projects/git/atlas-checks/data/README.md
2018-06-21 09:44:22 INFO  FileSystemHelper:298 - [F] file:/Users/maning/projects/git/atlas-checks/data/berlin-latest.osm.pbf
2018-06-21 09:44:22 INFO  FileSystemHelper:298 - [F] file:/Users/maning/projects/git/atlas-checks/data/san-francisco_california.osm.pbf
2018-06-21 09:44:22 INFO  FileSystemHelper:298 - [F] file:/Users/maning/projects/git/atlas-checks/data/README.md
2018-06-21 09:44:22 INFO  FileSystemHelper:298 - [F] file:/Users/maning/projects/git/atlas-checks/data/berlin-latest.osm.pbf
2018-06-21 09:44:22 INFO  AtlasDataSource:162 - Loading Atlas from 2 OSM protobuf(s) found in file:///Users/maning/projects/git/atlas-checks/data/
2018-06-21 09:47:56 WARN  NettyRpcEnv:70 - Ignored message: HeartbeatResponse(false)
2018-06-21 09:47:56 WARN  NettyRpcEndpointRef:91 - Error sending message [message = Heartbeat(driver,[Lscala.Tuple2;@65bff167,BlockManagerId(driver, localhost, 49764))] in 1 attempts
org.apache.spark.rpc.RpcTimeoutException: Futures timed out after [10 seconds]. This timeout is controlled by spark.executor.heartbeatInterval
        at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:48)
        at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:63)
        at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
        at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:33)
        at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:76)
        at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:101)
        at org.apache.spark.executor.Executor.org$apache$spark$executor$Executor$$reportHeartBeat(Executor.scala:449)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply$mcV$sp(Executor.scala:470)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply(Executor.scala:470)
        at org.apache.spark.executor.Executor$$anon$1$$anonfun$run$1.apply(Executor.scala:470)
        at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1766)
        at org.apache.spark.executor.Executor$$anon$1.run(Executor.scala:470)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.TimeoutException: Futures timed out after [10 seconds]
        at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:96)
        at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:100)
        at scala.concurrent.Await$$anonfun$result$1.apply(package.scala:107)
        at scala.concurrent.BlockContext$DefaultBlockContext$.blockOn(BlockContext.scala:53)
        at scala.concurrent.Await$.result(package.scala:107)
        at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
        ... 14 more
2018-06-21 09:47:56 WARN  HeartbeatReceiver:70 - Removing executor driver with no recent heartbeats: 145736 ms exceeds timeout 120000 ms
2018-06-21 09:47:56 INFO  OsmPbfProcessor:217 - First pass loading done
2018-06-21 09:47:56 INFO  OsmPbfProcessor:217 - First pass loading done
2018-06-21 09:48:04 ERROR Executor:95 - Exception in task 0.0 in stage 0.0 (TID 0)
java.lang.OutOfMemoryError
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
        at java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:598)
        at java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:677)
        at java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:735)
        at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:714)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
        at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
        at org.openstreetmap.atlas.checks.distributed.AtlasDataSource.load(AtlasDataSource.java:166)
        at org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob.lambda$start$1401df6c$1(IntegrityCheckSparkJob.java:358)
        at org.apache.spark.api.java.JavaPairRDD$$anonfun$pairFunToScalaFun$1.apply(JavaPairRDD.scala:1018)
        at org.apache.spark.api.java.JavaPairRDD$$anonfun$pairFunToScalaFun$1.apply(JavaPairRDD.scala:1018)
        at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        at scala.collection.Iterator$$anon$14.hasNext(Iterator.scala:389)
        at scala.collection.Iterator$class.foreach(Iterator.scala:727)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1$$anonfun$apply$32.apply(RDD.scala:912)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1$$anonfun$apply$32.apply(RDD.scala:912)
        at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1869)
        at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1869)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
        at org.apache.spark.scheduler.Task.run(Task.scala:89)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
        at org.openstreetmap.atlas.geography.atlas.pbf.OsmPbfProcessor.preProcess(OsmPbfProcessor.java:790)
        at org.openstreetmap.atlas.geography.atlas.pbf.OsmPbfProcessor.process(OsmPbfProcessor.java:133)
        at crosby.binary.osmosis.OsmosisBinaryParser.parseDense(OsmosisBinaryParser.java:138)
        at org.openstreetmap.osmosis.osmbinary.BinaryParser.parse(BinaryParser.java:124)
        at org.openstreetmap.osmosis.osmbinary.BinaryParser.handleBlock(BinaryParser.java:68)
        at org.openstreetmap.osmosis.osmbinary.file.FileBlock.process(FileBlock.java:135)
        at org.openstreetmap.osmosis.osmbinary.file.BlockInputStream.process(BlockInputStream.java:34)
        at crosby.binary.osmosis.OsmosisReader.run(OsmosisReader.java:45)
        at org.openstreetmap.atlas.geography.atlas.pbf.OsmPbfLoader.read(OsmPbfLoader.java:70)
        at org.openstreetmap.atlas.checks.distributed.AtlasDataSource.loadPbf(AtlasDataSource.java:180)
        at org.openstreetmap.atlas.checks.distributed.AtlasDataSource.lambda$load$1(AtlasDataSource.java:165)
        at org.openstreetmap.atlas.checks.distributed.AtlasDataSource$$Lambda$134/1829180675.apply(Unknown Source)
        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
        at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:747)
        at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:721)
        at java.util.stream.AbstractTask.compute(AbstractTask.java:316)
        at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
        at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
        at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
        at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
        at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
2018-06-21 09:48:04 ERROR TaskSchedulerImpl:74 - Lost executor driver on localhost: Executor heartbeat timed out after 145736 ms
2018-06-21 09:48:04 WARN  TaskSetManager:70 - Lost task 0.0 in stage 0.0 (TID 0, localhost): ExecutorLostFailure (executor driver exited caused by one of the running tasks) Reason: Executor heartbeat timed out after 145736 ms
2018-06-21 09:48:04 ERROR TaskSetManager:74 - Task 0 in stage 0.0 failed 1 times; aborting job
2018-06-21 09:48:04 INFO  TaskSchedulerImpl:58 - Removed TaskSet 0.0, whose tasks have all completed, from pool 
2018-06-21 09:48:04 WARN  SparkContext:70 - Killing executors is only supported in coarse-grained mode
2018-06-21 09:48:04 INFO  TaskSchedulerImpl:58 - Cancelling stage 0
2018-06-21 09:48:04 INFO  DAGScheduler:58 - ResultStage 0 (foreach at IntegrityCheckSparkJob.java:386) failed in 222.006 s
2018-06-21 09:48:04 INFO  DAGScheduler:58 - Executor lost: driver (epoch 0)
2018-06-21 09:48:04 INFO  BlockManagerMasterEndpoint:58 - Trying to remove executor driver from BlockManagerMaster.
2018-06-21 09:48:04 INFO  BlockManagerMasterEndpoint:58 - Removing block manager BlockManagerId(driver, localhost, 49764)
2018-06-21 09:48:04 INFO  BlockManagerMaster:58 - Removed driver successfully in removeExecutor
2018-06-21 09:48:04 INFO  DAGScheduler:58 - Host added was in lost list earlier: localhost
2018-06-21 09:48:04 INFO  DAGScheduler:58 - Job 0 failed: foreach at IntegrityCheckSparkJob.java:386, took 222.215816 s
2018-06-21 09:48:04 ERROR SparkJob:203 - Unable to prepare output directories.
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost): ExecutorLostFailure (executor driver exited caused by one of the running tasks) Reason: Executor heartbeat timed out after 145736 ms
Driver stacktrace:
        at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1431)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1419)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1418)
        at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
        at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
        at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1418)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:799)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:799)
        at scala.Option.foreach(Option.scala:236)
        at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:799)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1640)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1599)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1588)
        at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
        at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:620)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1843)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1856)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1869)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1940)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1.apply(RDD.scala:912)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1.apply(RDD.scala:910)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)
        at org.apache.spark.rdd.RDD.withScope(RDD.scala:316)
        at org.apache.spark.rdd.RDD.foreach(RDD.scala:910)
        at org.apache.spark.api.java.JavaRDDLike$class.foreach(JavaRDDLike.scala:332)
        at org.apache.spark.api.java.AbstractJavaRDDLike.foreach(JavaRDDLike.scala:46)
        at org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob.start(IntegrityCheckSparkJob.java:386)
        at org.openstreetmap.atlas.generator.tools.spark.SparkJob.onRun(SparkJob.java:196)
        at org.openstreetmap.atlas.utilities.runtime.Command.execute(Command.java:337)
        at org.openstreetmap.atlas.utilities.runtime.Command.run(Command.java:281)
        at org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob.main(IntegrityCheckSparkJob.java:127)
2018-06-21 09:48:04 ERROR SparkUncaughtExceptionHandler:95 - Uncaught exception in thread Thread[Executor task launch worker-0,5,main]
java.lang.OutOfMemoryError
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
        at java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:598)
        at java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:677)
        at java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:735)
        at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:714)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
        at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
        at org.openstreetmap.atlas.checks.distributed.AtlasDataSource.load(AtlasDataSource.java:166)
        at org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob.lambda$start$1401df6c$1(IntegrityCheckSparkJob.java:358)
        at org.apache.spark.api.java.JavaPairRDD$$anonfun$pairFunToScalaFun$1.apply(JavaPairRDD.scala:1018)
        at org.apache.spark.api.java.JavaPairRDD$$anonfun$pairFunToScalaFun$1.apply(JavaPairRDD.scala:1018)
        at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        at scala.collection.Iterator$$anon$14.hasNext(Iterator.scala:389)
        at scala.collection.Iterator$class.foreach(Iterator.scala:727)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1$$anonfun$apply$32.apply(RDD.scala:912)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1$$anonfun$apply$32.apply(RDD.scala:912)
        at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1869)
        at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1869)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
        at org.apache.spark.scheduler.Task.run(Task.scala:89)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
        at org.openstreetmap.atlas.geography.atlas.pbf.OsmPbfProcessor.preProcess(OsmPbfProcessor.java:790)
        at org.openstreetmap.atlas.geography.atlas.pbf.OsmPbfProcessor.process(OsmPbfProcessor.java:133)
        at crosby.binary.osmosis.OsmosisBinaryParser.parseDense(OsmosisBinaryParser.java:138)
        at org.openstreetmap.osmosis.osmbinary.BinaryParser.parse(BinaryParser.java:124)
        at org.openstreetmap.osmosis.osmbinary.BinaryParser.handleBlock(BinaryParser.java:68)
        at org.openstreetmap.osmosis.osmbinary.file.FileBlock.process(FileBlock.java:135)
        at org.openstreetmap.osmosis.osmbinary.file.BlockInputStream.process(BlockInputStream.java:34)
        at crosby.binary.osmosis.OsmosisReader.run(OsmosisReader.java:45)
        at org.openstreetmap.atlas.geography.atlas.pbf.OsmPbfLoader.read(OsmPbfLoader.java:70)
        at org.openstreetmap.atlas.checks.distributed.AtlasDataSource.loadPbf(AtlasDataSource.java:180)
        at org.openstreetmap.atlas.checks.distributed.AtlasDataSource.lambda$load$1(AtlasDataSource.java:165)
        at org.openstreetmap.atlas.checks.distributed.AtlasDataSource$$Lambda$134/1829180675.apply(Unknown Source)
        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
        at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:747)
        at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:721)
        at java.util.stream.AbstractTask.compute(AbstractTask.java:316)
        at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
        at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
        at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
        at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
        at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
2018-06-21 09:48:04 INFO  SparkContext:58 - Invoking stop() from shutdown hook
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/metrics/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/stage/kill,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/api,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/static,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/executors/threadDump/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/executors/threadDump,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/executors/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/executors,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/environment/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/environment,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/storage/rdd/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/storage/rdd,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/storage/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/storage,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/pool/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/pool,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/stage/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/stage,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/jobs/job/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/jobs/job,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/jobs/json,null}
2018-06-21 09:48:04 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/jobs,null}
2018-06-21 09:48:04 INFO  SparkUI:58 - Stopped Spark web UI at http://192.168.1.134:4040
2018-06-21 09:48:04 INFO  MapOutputTrackerMasterEndpoint:58 - MapOutputTrackerMasterEndpoint stopped!
2018-06-21 09:48:04 INFO  SparkContext:58 - SparkContext already stopped.
2018-06-21 09:48:04 INFO  SparkContext:58 - SparkContext already stopped.
2018-06-21 09:48:04 ERROR Command:285 - Command execution failed.
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost): ExecutorLostFailure (executor driver exited caused by one of the running tasks) Reason: Executor heartbeat timed out after 145736 ms
Driver stacktrace:
        at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1431)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1419)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1418)
        at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
        at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
        at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1418)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:799)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:799)
        at scala.Option.foreach(Option.scala:236)
        at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:799)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1640)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1599)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1588)
        at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
        at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:620)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1843)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1856)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1869)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1940)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1.apply(RDD.scala:912)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1.apply(RDD.scala:910)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:111)
        at org.apache.spark.rdd.RDD.withScope(RDD.scala:316)
        at org.apache.spark.rdd.RDD.foreach(RDD.scala:910)
        at org.apache.spark.api.java.JavaRDDLike$class.foreach(JavaRDDLike.scala:332)
        at org.apache.spark.api.java.AbstractJavaRDDLike.foreach(JavaRDDLike.scala:46)
        at org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob.start(IntegrityCheckSparkJob.java:386)
        at org.openstreetmap.atlas.generator.tools.spark.SparkJob.onRun(SparkJob.java:196)
        at org.openstreetmap.atlas.utilities.runtime.Command.execute(Command.java:337)
        at org.openstreetmap.atlas.utilities.runtime.Command.run(Command.java:281)
        at org.openstreetmap.atlas.checks.distributed.IntegrityCheckSparkJob.main(IntegrityCheckSparkJob.java:127)
2018-06-21 09:48:04 INFO  MemoryStore:58 - MemoryStore cleared
2018-06-21 09:48:04 INFO  BlockManager:58 - BlockManager stopped
2018-06-21 09:48:04 INFO  BlockManagerMaster:58 - BlockManagerMaster stopped
2018-06-21 09:48:04 INFO  OutputCommitCoordinator$OutputCommitCoordinatorEndpoint:58 - OutputCommitCoordinator stopped!
2018-06-21 09:48:04 INFO  SparkContext:58 - Successfully stopped SparkContext
2018-06-21 09:48:04 INFO  ShutdownHookManager:58 - Shutdown hook called
2018-06-21 09:48:04 INFO  ShutdownHookManager:58 - Deleting directory /private/var/folders/0q/c_r1c5v53779qm7c293qzl5m0000gn/T/spark-dbe03ce5-065d-4879-99a5-82dccccf725f
<===========--> 90% EXECUTING [3m 55s]
> :run
> :runChecks

FAILURE: Build failed with an exception.

* What went wrong:
Received complete event for an unknown operation (id: 911)

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org
maning@hjutoe ~/projects/git/atlas-checks (dev)*$ 

@MikeGost
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The issue is an OutOfMemory exception when constructing the Atlas file from PBF format. Try one of the following:

  1. The PBF file you're using is too big - the OsmPbfProcessor is not optimized to work on non-sharded PBF files as there are a lot of temporary in-memory objects created when going from PBF to atlas. Try trimming down the the PBF file size (osmosis is a tool that you can do this with) and running the job again.
  2. It's possible you're not allocating enough executor and driver memory for the size of the data. Try setting your spark parameters to something larger and seeing if that resolves the issue. Example:
    spark.executor.memory->12g,spark.driver.memory->12g

@maning
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maning commented Jun 22, 2018

@MikeGost Thanks! Running on the smallest PBF from Geofabrik (Wash DC), I get geojson.

I increased my java resources to use 4 GB, took 10 minutes. Then I get the following errors related to spark. Not sure what I'm doing here. For now all I need is to generate the geojson. Would the succeeding spark errors affect the output?

2018-06-22 09:28:47 INFO  OsmPbfProcessor:217 - Second pass loading done
2018-06-22 09:28:47 INFO  OsmPbfLoader:77 - Finished reading PBF, now retrieve atlas
2018-06-22 09:28:48 INFO  OsmPbfLoader:92 - Finished building atlas 0
2018-06-22 09:29:01 INFO  RunnableCheck:67 - InvalidTurnRestrictionCheck completed in 5.362 seconds.
2018-06-22 09:29:02 INFO  RunnableCheck:67 - OrphanNodeCheck completed in 6.873 seconds.
2018-06-22 09:29:03 INFO  RunnableCheck:67 - OneMemberRelationCheck completed in 6.753 seconds.
2018-06-22 09:29:04 INFO  RunnableCheck:67 - DuplicateNodeCheck completed in 7.951 seconds.
2018-06-22 09:29:04 INFO  RunnableCheck:67 - AddressPointMatchCheck completed in 8.036 seconds.
2018-06-22 09:29:04 INFO  RunnableCheck:67 - RoundaboutValenceCheck completed in 8.235 seconds.
2018-06-22 09:29:05 INFO  RunnableCheck:67 - RoundaboutClosedLoopCheck completed in 9.675 seconds.
2018-06-22 09:29:05 INFO  RunnableCheck:67 - DuplicatePointCheck completed in 9.460 seconds.
2018-06-22 09:29:06 INFO  RunnableCheck:67 - MalformedRoundaboutCheck completed in 9.643 seconds.
2018-06-22 09:29:06 INFO  RunnableCheck:67 - SharpAngleCheck completed in 10.493 seconds.
2018-06-22 09:29:07 INFO  RunnableCheck:67 - FloatingEdgeCheck completed in 11.192 seconds.
2018-06-22 09:29:08 INFO  RunnableCheck:67 - AreasWithHighwayTagCheck completed in 11.935 seconds.
2018-06-22 09:29:08 INFO  RunnableCheck:67 - PoolSizeCheck completed in 12.062 seconds.
2018-06-22 09:29:09 INFO  RunnableCheck:67 - WaterbodyAndIslandSizeCheck completed in 12.908 seconds.
2018-06-22 09:29:09 INFO  RunnableCheck:67 - UnusualLayerTagsCheck completed in 13.115 seconds.
2018-06-22 09:29:09 INFO  RunnableCheck:67 - InvalidTurnRestrictionCheck completed in 13.550 seconds.
2018-06-22 09:29:09 INFO  RunnableCheck:67 - SinkIslandCheck completed in 13.888 seconds.
2018-06-22 09:29:11 INFO  RunnableCheck:67 - SnakeRoadCheck completed in 15.009 seconds.
2018-06-22 09:29:17 INFO  RunnableCheck:67 - AbbreviatedNameCheck completed in 22.042 seconds.
2018-06-22 09:29:22 INFO  RunnableCheck:67 - DuplicateWaysCheck completed in 26.243 seconds.
2018-06-22 09:29:23 INFO  RunnableCheck:67 - EdgeCrossingEdgeCheck completed in 27.154 seconds.
2018-06-22 09:29:23 INFO  RunnableCheck:67 - SinkIslandCheck completed in 27.173 seconds.
2018-06-22 09:29:23 INFO  RunnableCheck:67 - SelfIntersectingPolylineCheck completed in 27.516 seconds.
2018-06-22 09:29:26 INFO  RunnableCheck:67 - BuildingRoadIntersectionCheck completed in 29.827 seconds.
2018-06-22 09:30:03 INFO  RunnableCheck:67 - IntersectingBuildingsCheck completed in 1.125 minutes.
2018-06-22 09:30:04 INFO  IntegrityCheckSparkJob:390 - [UNK] Committing outputs: [{target: file:///Users/maning/projects/git/atlas-checks/build/geojson/UNK, temporary: file:///Users/maning/projects/git/atlas-checks/build/_temp/p0_a0/geojson/UNK}, {target: file:///Users/maning/projects/git/atlas-checks/build/metric/UNK, temporary: file:///Users/maning/projects/git/atlas-checks/build/_temp/p0_a0/metric/UNK}, {target: file:///Users/maning/projects/git/atlas-checks/build/flag/UNK, temporary: file:///Users/maning/projects/git/atlas-checks/build/_temp/p0_a0/flag/UNK}]
2018-06-22 09:30:05 INFO  Executor:58 - Finished task 0.0 in stage 0.0 (TID 0). 915 bytes result sent to driver
2018-06-22 09:30:05 INFO  TaskSetManager:58 - Finished task 0.0 in stage 0.0 (TID 0) in 595127 ms on localhost (1/1)
2018-06-22 09:30:05 INFO  TaskSchedulerImpl:58 - Removed TaskSet 0.0, whose tasks have all completed, from pool 
2018-06-22 09:30:05 INFO  DAGScheduler:58 - ResultStage 0 (foreach at IntegrityCheckSparkJob.java:386) finished in 595.189 s
2018-06-22 09:30:05 INFO  DAGScheduler:58 - Job 0 finished: foreach at IntegrityCheckSparkJob.java:386, took 595.698875 s
2018-06-22 09:30:05 INFO  IntegrityCheckSparkJob:398 - Deleting file:///Users/maning/projects/git/atlas-checks/build/_temp.
2018-06-22 09:30:05 WARN  FileSystemPerformanceHelper:57 - Closing rename thread pool!
2018-06-22 09:30:05 WARN  FileSystemPerformanceHelper:62 - Closed rename thread pool in 0 milliseconds!
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/metrics/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/stage/kill,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/api,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/static,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/executors/threadDump/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/executors/threadDump,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/executors/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/executors,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/environment/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/environment,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/storage/rdd/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/storage/rdd,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/storage/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/storage,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/pool/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/pool,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/stage/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/stage,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/stages,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/jobs/job/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/jobs/job,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/jobs/json,null}
2018-06-22 09:30:05 INFO  ContextHandler:843 - stopped o.s.j.s.ServletContextHandler{/jobs,null}
2018-06-22 09:30:05 INFO  SparkUI:58 - Stopped Spark web UI at http://192.168.1.134:4040
2018-06-22 09:30:05 INFO  MapOutputTrackerMasterEndpoint:58 - MapOutputTrackerMasterEndpoint stopped!
2018-06-22 09:30:05 INFO  MemoryStore:58 - MemoryStore cleared
2018-06-22 09:30:05 INFO  BlockManager:58 - BlockManager stopped
2018-06-22 09:30:05 INFO  BlockManagerMaster:58 - BlockManagerMaster stopped
2018-06-22 09:30:05 INFO  OutputCommitCoordinator$OutputCommitCoordinatorEndpoint:58 - OutputCommitCoordinator stopped!
2018-06-22 09:30:05 INFO  SparkContext:58 - Successfully stopped SparkContext
2018-06-22 09:30:05 INFO  SparkContext:58 - SparkContext already stopped.
2018-06-22 09:30:05 INFO  ShutdownHookManager:58 - Shutdown hook called
2018-06-22 09:30:05 INFO  ShutdownHookManager:58 - Deleting directory /private/var/folders/0q/c_r1c5v53779qm7c293qzl5m0000gn/T/spark-ddd9c2fc-9113-4cb4-a937-c14f5f4bd7c7
<===========--> 90% EXECUTING [10m 26s]
> :run
> :runChecks

FAILURE: Build failed with an exception.

* What went wrong:
Received complete event for an unknown operation (id: 302)

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org
maning@hjutoe ~/projects/git/atlas-checks (dev)*$ 

@MikeGost
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MikeGost commented Jun 22, 2018

@maning - Nice, it looks like the atlas was generated successfully and the checks were run! Were you able to find the geojson output at this location:

/Users/maning/projects/git/atlas-checks/build/geojson/UNK?

I'm not quite sure what went wrong here - don't see the actual issue in the output. It may be worth trying to re-run with the --debug option to get the full stack-trace as the "Try" block suggests from the output you pasted.

I'll follow up tomorrow morning (PST) to create an osmlab-atlas project issue that will help address the original issue you were seeing when passing in non-sharded PBF files.

@maning
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maning commented Jun 22, 2018

Were you able to find the geojson output at this location:
/Users/maning/projects/git/atlas-checks/build/geojson/UNK?

Yes!

It may be worth trying to re-run with the --debug

See this gist (I reached the max limit for comment :))

@MikeGost
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Great - it sounds like you're unblocked for now @maning. I went ahead and created an atlas issue, which should address your scenario: osmlab/atlas#147. Please feel free to update it with context as needed.

I looked through the logs you linked and wasn't able to find the source of the error. It's possible that this is a benign issue or a gradle configuration that can be played with.

I'll leave this issue open for you to comment on and close when you're satisfied with the result.

@maning
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maning commented Jun 27, 2018

Closing as the original problem is resolved.

@maning maning closed this as completed Jun 27, 2018
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