Uploaded image for project: 'Spark'
  1. Spark
  2. SPARK-20859

SQL Loader does not recognize multidimensional columns in postgresql (like integer[]][])

    XMLWordPrintableJSON

Details

    • Bug
    • Status: Resolved
    • Major
    • Resolution: Incomplete
    • 2.1.1
    • None
    • SQL

    Description

      The fix in SPARK-14536 is not accepting columns like integer[][] (multidimensional arrays)

      To reproduce this error:

      1) Create a SQL table in postgresql

      CREATE TABLE arrays_test
(
  eid integer NOT NULL,
  simple integer[],
  multi integer[][]
);

      2) Insert a row like this one:

      insert into arrays_test (eid, simple, multi)
values
(1, '{1, 1}', NULL);

      3) Execute a SPQL query like this one and observe how it works:

      from pyspark import SparkConf
from pyspark import SparkContext
from pyspark.sql import SQLContext

master = "spark://spark211:7077"  # local is OK too
conf = (
    SparkConf()
        .setMaster(master)
        .setAppName("Connection Test 5")
        .set("spark.jars.packages", "org.postgresql:postgresql:9.4.1212")   ## This one works ok
        .set("spark.driver.memory", "2G")
        .set("spark.executor.memory", "2G")
        .set("spark.driver.cores", "10")
)

sc = SparkContext(conf=conf)
# sc.setLogLevel("ALL")

print "====>", 1
print(sc)

sqlContext = SQLContext(sc)

print "====>", 2
print sqlContext

url = "postgresql://localhost:5432/test"   # change properly
url = 'jdbc:'+url
properties = {'user': 'user', 'password': 'password'}   # change user and password if needed

df = sqlContext.read.format("jdbc"). \
    option("url", url). \
    option("driver", "org.postgresql.Driver"). \
    option("useUnicode", "true"). \
    option("continueBatchOnError","true"). \
    option("useSSL", "false"). \
    option("user", "user"). \
    option("password", "password"). \
    option("dbtable", "arrays_test"). \
    option("partitionColumn", "eid"). \
    option("lowerBound", "1000015"). \
    option("upperBound", "6026289"). \
    option("numPartitions", "100"). \
    load()

print "====>", 3

df.registerTempTable("arrays_test")
df = sqlContext.sql("SELECT * FROM arrays_test limit 5")


print "====>", 4
print df.collect()

      4) Observe how it works.

      5) Now, to reproduce the error, insert a multi dimensional array into the SQL table:

      insert into arrays_test (eid, simple, multi)
values
(2, '{1, 1}', '{{1, 1},{2, 2}}');

      6) Execute step 3) again.

      7) Observe the exception

      17/05/23 15:23:38 ERROR TaskSetManager: Task 0 in stage 0.0 failed 4 times; aborting job
Traceback (most recent call last):
  File "/home/pablo/develop/physiosigns/livebetter/modelling2/modelling2/scripts/runSparkTest2.py", line 65, in <module>
    print df.collect()
  File "/home/pablo/myProgs/virt-pablo/local/lib/python2.7/site-packages/pyspark/sql/dataframe.py", line 391, in collect
    port = self._jdf.collectToPython()
  File "/home/pablo/myProgs/virt-pablo/local/lib/python2.7/site-packages/py4j/java_gateway.py", line 1133, in __call__
    answer, self.gateway_client, self.target_id, self.name)
  File "/home/pablo/myProgs/virt-pablo/local/lib/python2.7/site-packages/pyspark/sql/utils.py", line 63, in deco
    return f(*a, **kw)
  File "/home/pablo/myProgs/virt-pablo/local/lib/python2.7/site-packages/py4j/protocol.py", line 319, in get_return_value
    format(target_id, ".", name), value)
py4j.protocol.Py4JJavaError: An error occurred while calling o49.collectToPython.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 4 times, most recent failure: Lost task 0.3 in stage 0.0 (TID 3, 172.17.0.58, executor 0): java.lang.ClassCastException: [Ljava.lang.Integer; cannot be cast to java.lang.Integer
	at scala.runtime.BoxesRunTime.unboxToInt(BoxesRunTime.java:101)
	at org.apache.spark.sql.catalyst.util.GenericArrayData.getInt(GenericArrayData.scala:62)
	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.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
	at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:99)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
	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:748)

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:1925)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:1938)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:1951)
	at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:333)
	at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
	at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply$mcI$sp(Dataset.scala:2768)
	at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply(Dataset.scala:2765)
	at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply(Dataset.scala:2765)
	at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
	at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2788)
	at org.apache.spark.sql.Dataset.collectToPython(Dataset.scala:2765)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:280)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:214)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassCastException: [Ljava.lang.Integer; cannot be cast to java.lang.Integer
	at scala.runtime.BoxesRunTime.unboxToInt(BoxesRunTime.java:101)
	at org.apache.spark.sql.catalyst.util.GenericArrayData.getInt(GenericArrayData.scala:62)
	at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
	at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
	at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
	at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
	at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:99)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	... 1 more

      Attachments

        Issue Links

          incorporates

          Bug - A problem which impairs or prevents the functions of the product. SPARK-14536 NPE in JDBCRDD when array column contains nulls (postgresql)

          • Major - Major loss of function.
          • Resolved

          Bug - A problem which impairs or prevents the functions of the product. SPARK-20846 Incorrect posgres sql array column schema inferred from table.

          • Major - Major loss of function.
          • Resolved

          Activity

            People

              Unassigned Unassigned
              pabloa Pablo Alcaraz
              Votes:
              1 Vote for this issue
              Watchers:
              4 Start watching this issue

              Dates

                Created:
                Updated:
                Resolved: