Storm [ERROR] Async loop died - python-2.7

I am using storm 0.9.3.
I am running a topology in python, in which spouts read a URL off the Kafka queue and then pass it to a next bolt which fetches that page using python requests module.
Here is my topology definition in java.
public static void main(String[] args) throws Exception {
TopologyBuilder builder = new TopologyBuilder();
builder.setSpout("URLSpout", new URLSpout(), 1);
builder.setBolt("ScrapeBolt", new ScrapeBolt(), 30).shuffleGrouping("URLSpout");
Config conf = new Config();
//conf.setDebug(true);
conf.setMessageTimeoutSecs(50);
conf.setNumWorkers(3);
conf.setMaxSpoutPending(50);
conf.put(Config.TOPOLOGY_RECEIVER_BUFFER_SIZE, 8);
conf.put(Config.TOPOLOGY_TRANSFER_BUFFER_SIZE, 32);
conf.put(Config.TOPOLOGY_EXECUTOR_RECEIVE_BUFFER_SIZE, 16384);
conf.put(Config.TOPOLOGY_EXECUTOR_SEND_BUFFER_SIZE, 16384);
StormSubmitter.submitTopologyWithProgressBar(args[0], conf, builder.createTopology());
}
After the topology is submitted, it runs fine, but after some time the topology halts. When checked the logs, I found these errors.
2015-06-09T17:34:49.733+0530 b.s.util [ERROR] Async loop died!
java.lang.RuntimeException: pid:5736, name:URLSpout exitCode:-1, errorString:
at backtype.storm.spout.ShellSpout.querySubprocess(ShellSpout.java:178) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.spout.ShellSpout.nextTuple(ShellSpout.java:91) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.daemon.executor$fn__3373$fn__3388$fn__3417.invoke(executor.clj:565) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.util$async_loop$fn__464.invoke(util.clj:463) ~[storm-core-0.9.3.jar:0.9.3]
at clojure.lang.AFn.run(AFn.java:24) [clojure-1.5.1.jar:na]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_45-internal]
Caused by: java.lang.RuntimeException: Unknown command received: error
at backtype.storm.spout.ShellSpout.querySubprocess(ShellSpout.java:173) ~[storm-core-0.9.3.jar:0.9.3]
... 5 common frames omitted
2015-06-09T17:34:49.734+0530 b.s.d.executor [ERROR]
java.lang.RuntimeException: pid:5736, name:URLSpout exitCode:-1, errorString:
at backtype.storm.spout.ShellSpout.querySubprocess(ShellSpout.java:178) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.spout.ShellSpout.nextTuple(ShellSpout.java:91) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.daemon.executor$fn__3373$fn__3388$fn__3417.invoke(executor.clj:565) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.util$async_loop$fn__464.invoke(util.clj:463) ~[storm-core-0.9.3.jar:0.9.3]
at clojure.lang.AFn.run(AFn.java:24) [clojure-1.5.1.jar:na]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_45-internal]
Caused by: java.lang.RuntimeException: Unknown command received: error
at backtype.storm.spout.ShellSpout.querySubprocess(ShellSpout.java:173) ~[storm-core-0.9.3.jar:0.9.3]
... 5 common frames omitted
2015-06-09T17:34:49.745+0530 b.s.util [ERROR] Halting process: ("Worker died")
java.lang.RuntimeException: ("Worker died")
at backtype.storm.util$exit_process_BANG_.doInvoke(util.clj:325) [storm-core-0.9.3.jar:0.9.3]
at clojure.lang.RestFn.invoke(RestFn.java:423) [clojure-1.5.1.jar:na]
at backtype.storm.daemon.worker$fn__3812$fn__3813.invoke(worker.clj:456) [storm-core-0.9.3.jar:0.9.3]
at backtype.storm.daemon.executor$mk_executor_data$fn__3274$fn__3275.invoke(executor.clj:240) [storm-core-0.9.3.jar:0.9.3]
at backtype.storm.util$async_loop$fn__464.invoke(util.clj:473) [storm-core-0.9.3.jar:0.9.3]
at clojure.lang.AFn.run(AFn.java:24) [clojure-1.5.1.jar:na]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_45-internal]
And
java.lang.RuntimeException: backtype.storm.multilang.NoOutputException: Pipe to subprocess seems to be broken! No output read.
Serializer Exception:
(Unable to capture error stream)
at backtype.storm.utils.ShellProcess.readShellMsg(ShellProcess.java:101) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.task.ShellBolt$BoltReaderRunnable.run(ShellBolt.java:318) ~[storm-core-0.9.3.jar:0.9.3]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_45-internal]
2015-06-09T17:34:49.779+0530 o.a.s.z.s.NIOServerCnxnFactory [ERROR] Thread Thread[Thread-37,5,main] died
java.lang.RuntimeException: java.lang.InterruptedException
at backtype.storm.util$wrap_in_runtime.invoke(util.clj:44) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.zookeeper$exists_node_QMARK_$fn__1668.invoke(zookeeper.clj:102) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.zookeeper$exists_node_QMARK_.invoke(zookeeper.clj:98) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.zookeeper$mkdirs.invoke(zookeeper.clj:114) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.cluster$mk_distributed_cluster_state$reify__1915.mkdirs(cluster.clj:119) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.cluster$mk_storm_cluster_state$reify__2372.report_error(cluster.clj:397) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.daemon.executor$throttled_report_error_fn$fn__3221.invoke(executor.clj:180) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.daemon.executor$fn__3441$fn$reify__3486.reportError(executor.clj:738) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.task.OutputCollector.reportError(OutputCollector.java:223) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.task.ShellBolt.die(ShellBolt.java:283) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.task.ShellBolt.access$400(ShellBolt.java:69) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.task.ShellBolt$BoltReaderRunnable.run(ShellBolt.java:341) ~[storm-core-0.9.3.jar:0.9.3]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_45-internal]
Caused by: java.lang.InterruptedException: null
at java.lang.Object.wait(Native Method) ~[na:1.8.0_45-internal]
at java.lang.Object.wait(Object.java:502) ~[na:1.8.0_45-internal]
at org.apache.storm.zookeeper.ClientCnxn.submitRequest(ClientCnxn.java:1342) ~[storm-core-0.9.3.jar:0.9.3]
at org.apache.storm.zookeeper.ZooKeeper.exists(ZooKeeper.java:1040) ~[storm-core-0.9.3.jar:0.9.3]
at org.apache.storm.curator.framework.imps.ExistsBuilderImpl$2.call(ExistsBuilderImpl.java:172) ~[storm-core-0.9.3.jar:0.9.3]
at org.apache.storm.curator.framework.imps.ExistsBuilderImpl$2.call(ExistsBuilderImpl.java:161) ~[storm-core-0.9.3.jar:0.9.3]
at org.apache.storm.curator.RetryLoop.callWithRetry(RetryLoop.java:107) ~[storm-core-0.9.3.jar:0.9.3]
at org.apache.storm.curator.framework.imps.ExistsBuilderImpl.pathInForeground(ExistsBuilderImpl.java:157) ~[storm-core-0.9.3.jar:0.9.3]
at org.apache.storm.curator.framework.imps.ExistsBuilderImpl.forPath(ExistsBuilderImpl.java:148) ~[storm-core-0.9.3.jar:0.9.3]
at org.apache.storm.curator.framework.imps.ExistsBuilderImpl.forPath(ExistsBuilderImpl.java:36) ~[storm-core-0.9.3.jar:0.9.3]
at backtype.storm.zookeeper$exists_node_QMARK_$fn__1668.invoke(zookeeper.clj:101) ~[storm-core-0.9.3.jar:0.9.3]
... 11 common frames omitted
2015-06-09T17:34:49.780+0530 b.s.t.ShellBolt [ERROR] Halting process: ShellBolt died.
And
2015-06-09T18:13:15.392+0530 b.s.s.ShellSpout [ERROR] Halting process: ShellSpout died.
java.lang.RuntimeException: subprocess heartbeat timeout
at backtype.storm.spout.ShellSpout$SpoutHeartbeatTimerTask.run(ShellSpout.java:255) [storm-core-0.9.3.jar:0.9.3]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_45-internal]
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308) [na:1.8.0_45-internal]
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180) [na:1.8.0_45-internal]
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294) [na:1.8.0_45-internal]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_45-internal]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_45-internal]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_45-internal]
Can someone,Please help me resolving this?

You're hitting https://issues.apache.org/jira/browse/STORM-796 which is fixed via Storm 0.9.5.
Since Storm 0.9.4 and 0.9.5 contains only bugfixes, so you can upgrade your Storm version from 0.9.3 to 0.9.5 safely.

Related

AWS EMR Hive fails due to serde2/serde

I am running EMR hive query on S3 and it fails saying "Map operator initialization failed"
I tried to set HADOOP_CLASSPATH as below, still no luck.
set HADOOP_CLASSPATH=/usr/lib/hive/lib/*;
Also, adding below jar,
add jar /usr/hive/json-serde-1.3.7-jar-with-dependencies.jar . This jar file is present at the given path.
I am not sure why it is complaining as below:
Caused by: java.lang.NoClassDefFoundError: org/apache/hadoop/hive/serde2/SerDe
The log is as below:
Status: Failed
Vertex failed, vertexName=Map 10, vertexId=vertex_1515176779844_0076_2_02, diagnostics=[Task failed,
taskId=task_1515176779844_0076_2_02_000031, diagnostics=[TaskAttempt 0
failed, info=[Error: Error while running task ( failure ) :
attempt_1515176779844_0076_2_02_000031_0:java.lang.RuntimeException:
java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:211)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.run(TezProcessor.java:168)
at org.apache.tez.runtime.LogicalIOProcessorRuntimeTask.run(LogicalIOProcessorRuntimeTask.java:370)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:73)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:61)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1698)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:61)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:37)
at org.apache.tez.common.CallableWithNdc.call(CallableWithNdc.java:36)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:354)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:184)
... 14 more
Caused by: java.lang.NoClassDefFoundError: org/apache/hadoop/hive/serde2/SerDe
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.hadoop.conf.Configuration.getClassByNameOrNull(Configuration.java:2134)
at org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:2099)
at org.apache.hadoop.hive.ql.plan.PartitionDesc.getDeserializer(PartitionDesc.java:177)
at org.apache.hadoop.hive.ql.exec.MapOperator.getConvertedOI(MapOperator.java:295)
at org.apache.hadoop.hive.ql.exec.MapOperator.setChildren(MapOperator.java:420)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:286)
... 15 more
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hive.serde2.SerDe
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 35 more
], TaskAttempt 1 failed, info=[Error: Error while running task ( failure ) :
attempt_1515176779844_0076_2_02_000031_1:java.lang.RuntimeException:
java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:211)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.run(TezProcessor.java:168)
at org.apache.tez.runtime.LogicalIOProcessorRuntimeTask.run(LogicalIOProcessorRuntimeTask.java:370)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:73)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:61)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1698)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:61)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:37)
at org.apache.tez.common.CallableWithNdc.call(CallableWithNdc.java:36)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:354)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:184)
... 14 more
Caused by: java.lang.NoClassDefFoundError: org/apache/hadoop/hive/serde2/SerDe
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.hadoop.conf.Configuration.getClassByNameOrNull(Configuration.java:2134)
at org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:2099)
at org.apache.hadoop.hive.ql.plan.PartitionDesc.getDeserializer(PartitionDesc.java:177)
at org.apache.hadoop.hive.ql.exec.MapOperator.getConvertedOI(MapOperator.java:295)
at org.apache.hadoop.hive.ql.exec.MapOperator.setChildren(MapOperator.java:420)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:286)
... 15 more
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hive.serde2.SerDe
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 35 more
], TaskAttempt 2 failed, info=[Error: Error while running task ( failure ) :
attempt_1515176779844_0076_2_02_000031_2:java.lang.RuntimeException:
java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:211)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.run(TezProcessor.java:168)
at org.apache.tez.runtime.LogicalIOProcessorRuntimeTask.run(LogicalIOProcessorRuntimeTask.java:370)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:73)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:61)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1698)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:61)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:37)
at org.apache.tez.common.CallableWithNdc.call(CallableWithNdc.java:36)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:354)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:184)
... 14 more
Caused by: java.lang.NoClassDefFoundError: org/apache/hadoop/hive/serde2/SerDe
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.hadoop.conf.Configuration.getClassByNameOrNull(Configuration.java:2134)
at org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:2099)
at org.apache.hadoop.hive.ql.plan.PartitionDesc.getDeserializer(PartitionDesc.java:177)
at org.apache.hadoop.hive.ql.exec.MapOperator.getConvertedOI(MapOperator.java:295)
at org.apache.hadoop.hive.ql.exec.MapOperator.setChildren(MapOperator.java:420)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:286)
... 15 more
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hive.serde2.SerDe
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 35 more
], TaskAttempt 3 failed, info=[Error: Error while running task ( failure ) :
attempt_1515176779844_0076_2_02_000031_3:java.lang.RuntimeException:
java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:211)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.run(TezProcessor.java:168)
at org.apache.tez.runtime.LogicalIOProcessorRuntimeTask.run(LogicalIOProcessorRuntimeTask.java:370)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:73)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:61)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1698)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:61)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:37)
at org.apache.tez.common.CallableWithNdc.call(CallableWithNdc.java:36)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:354)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:184)
... 14 more
Caused by: java.lang.NoClassDefFoundError: org/apache/hadoop/hive/serde2/SerDe
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.hadoop.conf.Configuration.getClassByNameOrNull(Configuration.java:2134)
at org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:2099)
at org.apache.hadoop.hive.ql.plan.PartitionDesc.getDeserializer(PartitionDesc.java:177)
at org.apache.hadoop.hive.ql.exec.MapOperator.getConvertedOI(MapOperator.java:295)
at org.apache.hadoop.hive.ql.exec.MapOperator.setChildren(MapOperator.java:420)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:286)
... 15 more
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hive.serde2.SerDe
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 35 more
]], Vertex did not succeed due to OWN_TASK_FAILURE, failedTasks:1 killedTasks:159, Vertex vertex_1515176779844_0076_2_02 [Map 10]
killed/failed due to:OWN_TASK_FAILURE]
Vertex killed, vertexName=Reducer 7, vertexId=vertex_1515176779844_0076_2_04, diagnostics=[Vertex received
Kill while in RUNNING state., Vertex did not succeed due to
OTHER_VERTEX_FAILURE, failedTasks:0 killedTasks:12, Vertex
vertex_1515176779844_0076_2_04 [Reducer 7] killed/failed due
to:OTHER_VERTEX_FAILURE]
Vertex killed, vertexName=Reducer 2, vertexId=vertex_1515176779844_0076_2_06, diagnostics=[Vertex received
Kill while in RUNNING state., Vertex did not succeed due to
OTHER_VERTEX_FAILURE, failedTasks:0 killedTasks:1, Vertex
vertex_1515176779844_0076_2_06 [Reducer 2] killed/failed due
to:OTHER_VERTEX_FAILURE]
Vertex killed, vertexName=Reducer 4, vertexId=vertex_1515176779844_0076_2_08, diagnostics=[Vertex received
Kill while in RUNNING state., Vertex did not succeed due to
OTHER_VERTEX_FAILURE, failedTasks:0 killedTasks:7, Vertex
vertex_1515176779844_0076_2_08 [Reducer 4] killed/failed due
to:OTHER_VERTEX_FAILURE]
Vertex killed, vertexName=Reducer 3, vertexId=vertex_1515176779844_0076_2_07, diagnostics=[Vertex received
Kill while in RUNNING state., Vertex did not succeed due to
OTHER_VERTEX_FAILURE, failedTasks:0 killedTasks:7, Vertex
vertex_1515176779844_0076_2_07 [Reducer 3] killed/failed due
to:OTHER_VERTEX_FAILURE]
Vertex killed, vertexName=Reducer 5, vertexId=vertex_1515176779844_0076_2_10, diagnostics=[Vertex received
Kill while in RUNNING state., Vertex did not succeed due to
OTHER_VERTEX_FAILURE, failedTasks:0 killedTasks:14, Vertex
vertex_1515176779844_0076_2_10 [Reducer 5] killed/failed due
to:OTHER_VERTEX_FAILURE]
Vertex killed, vertexName=Reducer 11, vertexId=vertex_1515176779844_0076_2_09, diagnostics=[Vertex received
Kill while in RUNNING state., Vertex did not succeed due to
OTHER_VERTEX_FAILURE, failedTasks:0 killedTasks:12, Vertex
vertex_1515176779844_0076_2_09 [Reducer 11] killed/failed due
to:OTHER_VERTEX_FAILURE]
Vertex killed, vertexName=Map 6, vertexId=vertex_1515176779844_0076_2_03, diagnostics=[Vertex received
Kill while in RUNNING state., Vertex did not succeed due to
OTHER_VERTEX_FAILURE, failedTasks:0 killedTasks:165, Vertex
vertex_1515176779844_0076_2_03 [Map 6] killed/failed due
to:OTHER_VERTEX_FAILURE]
Vertex killed, vertexName=Map 1, vertexId=vertex_1515176779844_0076_2_05, diagnostics=[Vertex received
Kill while in RUNNING state., Vertex did not succeed due to
OTHER_VERTEX_FAILURE, failedTasks:0 killedTasks:139, Vertex
vertex_1515176779844_0076_2_05 [Map 1] killed/failed due
to:OTHER_VERTEX_FAILURE]
DAG did not succeed due to VERTEX_FAILURE. failedVertices:1 killedVertices:8
FAILED: Execution Error, return code 2 from org.apache.hadoop.hive.ql.exec.tez.TezTask. Vertex failed,
vertexName=Map 10, vertexId=vertex_1515176779844_0076_2_02,
diagnostics=[Task failed, taskId=task_1515176779844_0076_2_02_000031,
diagnostics=[TaskAttempt 0 failed, info=[Error: Error while running
task ( failure ) :
attempt_1515176779844_0076_2_02_000031_0:java.lang.RuntimeException:
java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:211)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.run(TezProcessor.java:168)
at org.apache.tez.runtime.LogicalIOProcessorRuntimeTask.run(LogicalIOProcessorRuntimeTask.java:370)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:73)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:61)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1698)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:61)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:37)
at org.apache.tez.common.CallableWithNdc.call(CallableWithNdc.java:36)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:354)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:184)
... 14 more
Caused by: java.lang.NoClassDefFoundError: org/apache/hadoop/hive/serde2/SerDe
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.hadoop.conf.Configuration.getClassByNameOrNull(Configuration.java:2134)
at org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:2099)
at org.apache.hadoop.hive.ql.plan.PartitionDesc.getDeserializer(PartitionDesc.java:177)
at org.apache.hadoop.hive.ql.exec.MapOperator.getConvertedOI(MapOperator.java:295)
at org.apache.hadoop.hive.ql.exec.MapOperator.setChildren(MapOperator.java:420)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:286)
... 15 more
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.hive.serde2.SerDe
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 35 more
], TaskAttempt 1 failed, info=[Error: Error while running task ( failure ) :
attempt_1515176779844_0076_2_02_000031_1:java.lang.RuntimeException:
java.lang.RuntimeException: Map operator initialization failed

Failed to register classes with Kryo

I am creating a spark context by using-
(ns something
(:require [flambo.conf : conf]
[flambo.api :as f]))
(def c (-> (conf/spark-conf)
(conf/master "spark://formcept008.lan:7077")
(conf/app-name "clustering"))) ;; app-name
(def sc (f/spark-context c))
Then I am creating an RDD-
(f/parallelize sc DATA)
Now when I am performing some action on this data, like (f/take rdd 3) etc, I am getting an error-
17/11/28 14:35:00 ERROR Utils: Exception encountered
org.apache.spark.SparkException: Failed to register classes with Kryo
at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:129)
at org.apache.spark.serializer.KryoSerializerInstance.borrowKryo(KryoSerializer.scala:274)
at org.apache.spark.serializer.KryoSerializerInstance.(KryoSerializer.scala:259)
at org.apache.spark.serializer.KryoSerializer.newInstance(KryoSerializer.scala:175)
at org.apache.spark.rdd.ParallelCollectionPartition$$anonfun$readObject$1.apply$mcV$sp(ParallelCollectionRDD.scala:79)
at org.apache.spark.rdd.ParallelCollectionPartition$$anonfun$readObject$1.apply(ParallelCollectionRDD.scala:70)
at org.apache.spark.rdd.ParallelCollectionPartition$$anonfun$readObject$1.apply(ParallelCollectionRDD.scala:70)
at org.apache.spark.util.Utils$.tryOrIOException(Utils.scala:1273)
at org.apache.spark.rdd.ParallelCollectionPartition.readObject(ParallelCollectionRDD.scala:70)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1909)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1808)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2018)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1942)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1808)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:75)
at org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:114)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:253)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: flambo.kryo.BaseFlamboRegistrator
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$5.apply(KryoSerializer.scala:124)
at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$5.apply(KryoSerializer.scala:124)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186)
at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:186)
at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:124)
... 27 more
17/11/28 14:35:00 ERROR Executor: Exception in task 0.0 in stage 0.0 (TID 0)
java.lang.IllegalStateException: unread block data
at java.io.ObjectInputStream$BlockDataInputStream.setBlockDataMode(ObjectInputStream.java:2449)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1385)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2018)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1942)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1808)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:75)
at org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:114)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:253)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Any thoughts on that, please.
flambo doesn't seem to be in your classpath somehow which is why you're getting:
java.lang.ClassNotFoundException: flambo.kryo.BaseFlamboRegistrator
Are you running this from the REPL or are you using a lein or boot task?
if you're using leiningen check your classpath (lein classpath) and dependency tree (lein deps :tree)
Also, it never hurts to do a lein clean to make sure your target folder isn't causing issues
Stack trace analysis:
The Failed to register classes with Kryo is caused because flambo.kryo.BaseFlamboRegistrator is missing
Solved.
Add all the jars of your project in spark-configuration by using -
(conf/jars (map #(.getPath % (.getURLs(java.lang.ClassLoader/getSystemClassLoader))))
It will register all the classes.
Since this issue is resolved, so closing it.

Error in migrating OWL data into GRAKN

I am trying to migrate a OWL data into GRAKN using the migration script as described here. I started my GRAKN engine and then executed ./migration.sh owl -i /home/file1.owl -k grakn but I get this error:
Migrating data /home/file1.owl using Grakn Engine localhost:4567 into graph grakn
Exception in thread "main" java.lang.RuntimeException: java.lang.IllegalArgumentException: Graph Factory [ai.grakn.factory.TitanInternalFactory] is not valid
at ai.grakn.factory.FactoryBuilder.newFactory(FactoryBuilder.java:101)
at ai.grakn.factory.FactoryBuilder.getGraknGraphFactory(FactoryBuilder.java:82)
at ai.grakn.factory.FactoryBuilder.getFactory(FactoryBuilder.java:62)
at ai.grakn.factory.GraknSessionImpl.configureGraphFactoryRemote(GraknSessionImpl.java:153)
at ai.grakn.factory.GraknSessionImpl.configureGraphFactory(GraknSessionImpl.java:134)
at ai.grakn.factory.GraknSessionImpl.getConfiguredFactory(GraknSessionImpl.java:90)
at ai.grakn.factory.GraknSessionImpl.open(GraknSessionImpl.java:79)
at ai.grakn.migration.owl.Main.runOwl(Main.java:64)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Collections$2.tryAdvance(Collections.java:4717)
at java.util.Collections$2.forEachRemaining(Collections.java:4725)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at ai.grakn.migration.owl.Main.main(Main.java:52)
Caused by: java.lang.reflect.InvocationTargetException
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 ai.grakn.factory.FactoryBuilder.newFactory(FactoryBuilder.java:99)
... 19 more
Caused by: java.lang.IllegalArgumentException: Could not instantiate implementation: com.thinkaurelius.titan.diskstorage.cassandra.astyanax.AstyanaxStoreManager
at com.thinkaurelius.titan.util.system.ConfigurationUtil.instantiate(ConfigurationUtil.java:55)
at com.thinkaurelius.titan.diskstorage.Backend.getImplementationClass(Backend.java:473)
at com.thinkaurelius.titan.diskstorage.Backend.getStorageManager(Backend.java:407)
at com.thinkaurelius.titan.graphdb.configuration.GraphDatabaseConfiguration.<init>(GraphDatabaseConfiguration.java:1325)
at com.thinkaurelius.titan.core.TitanFactory.open(TitanFactory.java:94)
at com.thinkaurelius.titan.core.TitanFactory.open(TitanFactory.java:84)
at com.thinkaurelius.titan.core.TitanFactory$Builder.open(TitanFactory.java:139)
at ai.grakn.factory.TitanInternalFactory.configureGraph(TitanInternalFactory.java:113)
at ai.grakn.factory.TitanInternalFactory.newTitanGraph(TitanInternalFactory.java:88)
at ai.grakn.factory.TitanInternalFactory.buildTinkerPopGraph(TitanInternalFactory.java:84)
at ai.grakn.factory.TitanInternalFactory.buildTinkerPopGraph(TitanInternalFactory.java:60)
at ai.grakn.factory.AbstractInternalFactory.getTinkerPopGraph(AbstractInternalFactory.java:141)
at ai.grakn.factory.AbstractInternalFactory.getTinkerPopGraph(AbstractInternalFactory.java:135)
at ai.grakn.factory.AbstractInternalFactory.getGraph(AbstractInternalFactory.java:110)
at ai.grakn.factory.AbstractInternalFactory.open(AbstractInternalFactory.java:95)
at ai.grakn.factory.SystemKeyspace.loadSystemOntology(SystemKeyspace.java:114)
at ai.grakn.factory.FactoryBuilder.newFactory(FactoryBuilder.java:107)
at ai.grakn.factory.FactoryBuilder.getGraknGraphFactory(FactoryBuilder.java:82)
at ai.grakn.factory.AbstractInternalFactory.getSystemFactory(AbstractInternalFactory.java:80)
at ai.grakn.factory.AbstractInternalFactory.<init>(AbstractInternalFactory.java:74)
at ai.grakn.factory.TitanInternalFactory.<init>(TitanInternalFactory.java:64)
... 24 more
Caused by: java.lang.reflect.InvocationTargetException
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 com.thinkaurelius.titan.util.system.ConfigurationUtil.instantiate(ConfigurationUtil.java:44)
... 44 more
Caused by: com.thinkaurelius.titan.diskstorage.TemporaryBackendException: Temporary failure in storage backend
at com.thinkaurelius.titan.diskstorage.cassandra.astyanax.AstyanaxStoreManager.ensureKeyspaceExists(AstyanaxStoreManager.java:580)
at com.thinkaurelius.titan.diskstorage.cassandra.astyanax.AstyanaxStoreManager.<init>(AstyanaxStoreManager.java:291)
... 49 more
Is there any mistake in the command I am executing to do the migration? What can I do to resolve this issue?
UPDATE: I was able to resolve the above issue but now I am getting following error in trying to start the graql shell:
Exception in thread "graql-session-0" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextNode(HashMap.java:1437)
at java.util.HashMap$ValueIterator.next(HashMap.java:1466)
at ai.grakn.graph.internal.AbstractGraknGraph.loadOntologyCacheIntoTransactionCache(AbstractGraknGraph.java:337)
at ai.grakn.graph.internal.AbstractGraknGraph.getConceptLog(AbstractGraknGraph.java:307)
at ai.grakn.graph.internal.AbstractGraknGraph.buildType(AbstractGraknGraph.java:450)
at ai.grakn.graph.internal.AbstractGraknGraph.getTypeByLabel(AbstractGraknGraph.java:548)
at ai.grakn.graph.internal.AbstractGraknGraph.getMetaConcept(AbstractGraknGraph.java:608)
at ai.grakn.engine.session.GraqlSession.getTypes(GraqlSession.java:371)
at ai.grakn.engine.session.GraqlSession.sendTypes(GraqlSession.java:348)
at ai.grakn.engine.session.GraqlSession.lambda$new$48(GraqlSession.java:105)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

Trying to write dataframe to file, getting org.apache.spark.SparkException: Task failed while writing rows

I have a org.apache.spark.sql.DataFrame called pres2 (about 1000 lines long, generated on an AWS 3-node EMR cluster (v5.3.1) running Spark 2.1.0) which looks like this:
+-------------------+--------------------+----------+
| CreatedAt| tweet|prediction|
+-------------------+--------------------+----------+
|2015-10-12 20:58:52|This Saturday is ...| 1.0|
|2015-10-13 17:28:45|Sleep with a spoo...| 1.0|
(etc.)
I am trying to write said dataframe to a .csv file and I keep getting errors similar to described (but not resolved) here. I have tried writing this data frame in many different ways and I still get the error shown below. These methods include:
pres2.write.format("com.databricks.spark.csv").save("someFile.csv")
pres2.write.mode("overwrite").format("com.databricks.spark.csv").save("someFile.csv")
pres2.write.mode("append").format("com.databricks.spark.csv").save("someFile.csv")
In addition to trying to save it with that basic method to HDFS, I have also tried hdfs://[hostname]/[path] to no avail, although I can see a file of 0 bytes in HDFS. I also have tried to save to an S3 bucket, which similarly didn't work.
I can only conclude that I just have something screwed up with my cluster, but I have repeated this on other, similar clusters and with the new EMR v5.4.0. Is there anything that I have done obviously wrong based on the errors below (generated for the first write method shown above, but they all look pretty similar)?
17/03/10 16:24:02 WARN TaskSetManager: Lost task 0.0 in stage 23.0 (TID 149, ip-addy .ec2.internal, executor 9): org.apache.spark.SparkException: Task failed while writing rows
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:204)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:129)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:128)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.spark.SparkException: Failed to execute user defined function($anonfun$createTransformFunc$2: (string) => array<string>)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$SingleDirectoryWriteTask.execute(FileFormatWriter.scala:243)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:190)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:188)
at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1341)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:193)
... 8 more
Caused by: java.lang.NullPointerException
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:142)
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:140)
... 16 more
17/03/10 16:24:03 ERROR TaskSetManager: Task 0 in stage 23.0 failed 4 times; aborting job
17/03/10 16:24:03 ERROR FileFormatWriter: Aborting job null.
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 23.0 failed 4 times, most recent failure: Lost task 0.3 in stage 23.0 (TID 152, ip-addy, executor 9): org.apache.spark.SparkException: Task failed while writing rows
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:204)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:129)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:128)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.spark.SparkException: Failed to execute user defined function($anonfun$createTransformFunc$2: (string) => array<string>)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$SingleDirectoryWriteTask.execute(FileFormatWriter.scala:243)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:190)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:188)
at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1341)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:193)
... 8 more
Caused by: java.lang.NullPointerException
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:142)
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:140)
... 16 more
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1951)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:127)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:121)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:121)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:121)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:101)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:114)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:114)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:135)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:132)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:113)
at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:87)
at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:87)
at org.apache.spark.sql.execution.datasources.DataSource.write(DataSource.scala:492)
at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:215)
at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:198)
at $line94.$read$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw.<init>(<console>:80)
at $line94.$read$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw.<init>(<console>:85)
at $line94.$read$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw.<init>(<console>:87)
at $line94.$read$$iw$$iw$$iw$$iw$$iw$$iw$$iw.<init>(<console>:89)
at $line94.$read$$iw$$iw$$iw$$iw$$iw$$iw.<init>(<console>:91)
at $line94.$read$$iw$$iw$$iw$$iw$$iw.<init>(<console>:93)
at $line94.$read$$iw$$iw$$iw$$iw.<init>(<console>:95)
at $line94.$read$$iw$$iw$$iw.<init>(<console>:97)
at $line94.$read$$iw$$iw.<init>(<console>:99)
at $line94.$read$$iw.<init>(<console>:101)
at $line94.$read.<init>(<console>:103)
at $line94.$read$.<init>(<console>:107)
at $line94.$read$.<clinit>(<console>)
at $line94.$eval$.$print$lzycompute(<console>:7)
at $line94.$eval$.$print(<console>:6)
at $line94.$eval.$print(<console>)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at scala.tools.nsc.interpreter.IMain$ReadEvalPrint.call(IMain.scala:786)
at scala.tools.nsc.interpreter.IMain$Request.loadAndRun(IMain.scala:1047)
at scala.tools.nsc.interpreter.IMain$WrappedRequest$$anonfun$loadAndRunReq$1.apply(IMain.scala:638)
at scala.tools.nsc.interpreter.IMain$WrappedRequest$$anonfun$loadAndRunReq$1.apply(IMain.scala:637)
at scala.reflect.internal.util.ScalaClassLoader$class.asContext(ScalaClassLoader.scala:31)
at scala.reflect.internal.util.AbstractFileClassLoader.asContext(AbstractFileClassLoader.scala:19)
at scala.tools.nsc.interpreter.IMain$WrappedRequest.loadAndRunReq(IMain.scala:637)
at scala.tools.nsc.interpreter.IMain.interpret(IMain.scala:569)
at scala.tools.nsc.interpreter.IMain.interpret(IMain.scala:565)
at scala.tools.nsc.interpreter.ILoop.interpretStartingWith(ILoop.scala:807)
at scala.tools.nsc.interpreter.ILoop.command(ILoop.scala:681)
at scala.tools.nsc.interpreter.ILoop.processLine(ILoop.scala:395)
at scala.tools.nsc.interpreter.ILoop.loop(ILoop.scala:415)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply$mcZ$sp(ILoop.scala:923)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:909)
at scala.tools.nsc.interpreter.ILoop$$anonfun$process$1.apply(ILoop.scala:909)
at scala.reflect.internal.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:97)
at scala.tools.nsc.interpreter.ILoop.process(ILoop.scala:909)
at org.apache.spark.repl.Main$.doMain(Main.scala:68)
at org.apache.spark.repl.Main$.main(Main.scala:51)
at org.apache.spark.repl.Main.main(Main.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:738)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:187)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:212)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:126)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: org.apache.spark.SparkException: Task failed while writing rows
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:204)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:129)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:128)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.spark.SparkException: Failed to execute user defined function($anonfun$createTransformFunc$2: (string) => array<string>)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$SingleDirectoryWriteTask.execute(FileFormatWriter.scala:243)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:190)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:188)
at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1341)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:193)
... 8 more
Caused by: java.lang.NullPointerException
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:142)
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:140)
... 16 more
org.apache.spark.SparkException: Job aborted.
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:147)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:121)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:121)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:121)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:101)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:114)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:114)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:135)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:132)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:113)
at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:87)
at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:87)
at org.apache.spark.sql.execution.datasources.DataSource.write(DataSource.scala:492)
at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:215)
at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:198)
... 50 elided
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 23.0 failed 4 times, most recent failure: Lost task 0.3 in stage 23.0 (TID 152, ip-addy, executor 9): org.apache.spark.SparkException: Task failed while writing rows
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:204)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:129)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:128)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.spark.SparkException: Failed to execute user defined function($anonfun$createTransformFunc$2: (string) => array<string>)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$SingleDirectoryWriteTask.execute(FileFormatWriter.scala:243)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:190)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:188)
at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1341)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:193)
... 8 more
Caused by: java.lang.NullPointerException
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:142)
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:140)
... 16 more
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1951)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:127)
... 69 more
Caused by: org.apache.spark.SparkException: Task failed while writing rows
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:204)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:129)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1$$anonfun$3.apply(FileFormatWriter.scala:128)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.spark.SparkException: Failed to execute user defined function($anonfun$createTransformFunc$2: (string) => array<string>)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$SingleDirectoryWriteTask.execute(FileFormatWriter.scala:243)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:190)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:188)
at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1341)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:193)
... 8 more
Caused by: java.lang.NullPointerException
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:142)
at org.apache.spark.ml.feature.RegexTokenizer$$anonfun$createTransformFunc$2.apply(Tokenizer.scala:140)
... 16 more
Incidently, I did try to convert the dataframe to an RDD and save it as a text file, but that generated its own erros (I exceed the 30000 char limit if I post it here).
As you have tried 3 different approaches to save the data, but unfortunately they all are the same, only difference is how to write the file, i.e, create new one, overwrite the existing or to write it in append mode,
I would suggest to perform a short experiment by creating schema file and then by using databrick csv to read the file with schema, then print the data schema using,
df.printSchema()
This will help you understand the datatype of you column, also try to perform it on subset of the original dataset, if that saving, then try to get some analysis on you input data to get more insight what data you are processing.
Adding on top of Uday Shankar Singh, whose comments actually helped me to solve the issue.
Check the dataframe schema with df.printSchema(). In my case, one of the column was not nullable, but I was passing a null value.
Modifying the schema to accept null values, actually resolved this issue. Hope this helps !!
The secret in Java and Scala code is always go to the most nested stack in the stack trace, usually the one where half the stack is missing, and assume that's the cause.
Here the NullPointerException at the bottom is the warning sign. If you have are trying to do some transformation with a regular expression declaring how to spliit up the line, there's probably something wrong there.
I don't think it's the output itself, it's the work generating the output which is failing. Remember: Spark is "lazy", it doesn't do any work until you try to save the RDD.

SolrCloud connection timeout pool

I have solr cloud cluster and it is throwing the following exception, it is happening when solr does something with the replicas
null:org.apache.solr.common.SolrException: org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://10.14.0.72:8080/solr/IE_big_index_shard1_0_replica2
at org.apache.solr.handler.component.SearchHandler.handleRequestBody(SearchHandler.java:407)
at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:155)
at org.apache.solr.core.SolrCore.execute(SolrCore.java:2033)
at org.apache.solr.servlet.HttpSolrCall.execute(HttpSolrCall.java:652)
at org.apache.solr.servlet.HttpSolrCall.call(HttpSolrCall.java:460)
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:229)
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:184)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1668)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:581)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1160)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:511)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1092)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:213)
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:119)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)
at org.eclipse.jetty.server.Server.handle(Server.java:518)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:308)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:244)
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273)
at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:95)
at org.eclipse.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93)
at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.produceAndRun(ExecuteProduceConsume.java:246)
at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:156)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:654)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:572)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://10.14.0.72:8080/solr/IE_big_index_shard1_0_replica2
at org.apache.solr.client.solrj.impl.HttpSolrClient.executeMethod(HttpSolrClient.java:591)
at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:241)
at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:230)
at org.apache.solr.client.solrj.SolrClient.request(SolrClient.java:1219)
at org.apache.solr.handler.component.HttpShardHandler$1.call(HttpShardHandler.java:198)
at org.apache.solr.handler.component.HttpShardHandler$1.call(HttpShardHandler.java:163)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.solr.common.util.ExecutorUtil$MDCAwareThreadPoolExecutor.lambda$execute$0(ExecutorUtil.java:229)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
... 1 more
Caused by: org.apache.http.conn.ConnectionPoolTimeoutException: Timeout waiting for connection from pool
at org.apache.http.impl.conn.PoolingClientConnectionManager.leaseConnection(PoolingClientConnectionManager.java:226)
at org.apache.http.impl.conn.PoolingClientConnectionManager$1.getConnection(PoolingClientConnectionManager.java:195)
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:423)
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:882)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:107)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:55)
at org.apache.solr.client.solrj.impl.HttpSolrClient.executeMethod(HttpSolrClient.java:482)
... 12 more