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mraad / FileGDB

Read GDB (Esri File GeoDatabase) using Apache Spark
Apache License 2.0
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Parsing GDB files from S3 lake using PySpark and EC2 cluster #1

Open cdibble opened 4 years ago

cdibble commented 4 years ago

Hello-

I am trying to use your package to parse a bunch of .gdb databases that are in S3 (the same AIS ship data as in your example) and write them to a new S3 bucket using parquet so that I can process them later. It works fine with a local PySpark session, but fails when run on the cluster, giving the "Unable to load AWS credentials from any provider in the chain" error. My AWS credentials are available to all of the EC2 instances in the cluster (set as environment variables in bash, then imported to hadoop configuration settings in PySpark via script), though, and I can use the cluster to, say, read a GDB file as a text file.

I launch PySpark with:

pyspark\
      --master spark://10.0.0.7:7077 \
      --jars /usr/local/spark/jars/spark-gdb-0.7.jar,/usr/local/spark/jars/filegdb-0.37.jar,/usr/local/spark/jars/filegdb-0.37-2.11.jar,/usr/local/spark/jars/hadoop-aws-2.7.1.jar,/usr/local/spark/jars/aws-java-sdk-1.7.4.jar\

And then I run the following code successfully:

jvm = spark._jvm # get ref to underlying JVM.
gdb = jvm.com.esri.gdb.FileGDB # get ref to FileGDB Scala object
gdb_path = 'Data/2011/05/Zone14_2011_05.gdb/Zone14_2011_05.gdb' # for testing
gdb_path = "s3a://ais-ship-data-raw/" + gdb_path
ping_table = spark.read \
        .format("com.esri.gdb") \
        .options(path=gdb_path, name="Broadcast") \
        .load()

But it fails when actually executing on the cluster the command:

ping_table.show()

Any ideas on why this is failing? Is support for boto3/s3 access missing? Any pointers would be appreciated. Thanks for the package!

Here's the full stack trace:

>>> ping_table.show()
[Stage 0:>                                                          (0 + 1) / 1]20:03:40 WARN TaskSetManager: Lost task 0.0 in stage 0.0 (TID 0, 10.0.0.7, executor 0): com.amazonaws.AmazonClientException: Unable to load AWS credentials from any provider in the chain
    at com.amazonaws.auth.AWSCredentialsProviderChain.getCredentials(AWSCredentialsProviderChain.java:117)
    at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:3521)
    at com.amazonaws.services.s3.AmazonS3Client.headBucket(AmazonS3Client.java:1031)
    at com.amazonaws.services.s3.AmazonS3Client.doesBucketExist(AmazonS3Client.java:994)
    at org.apache.hadoop.fs.s3a.S3AFileSystem.initialize(S3AFileSystem.java:297)
    at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2669)
    at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:94)
    at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2703)
    at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2685)
    at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:373)
    at org.apache.hadoop.fs.Path.getFileSystem(Path.java:295)
    at com.esri.gdb.GDBIndex$.apply(GDBIndex.scala:130)
    at com.esri.gdb.GDBRDD.compute(GDBRDD.scala:22)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:123)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

20:03:40 ERROR TaskSetManager: Task 0 in stage 0.0 failed 4 times; aborting job
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/spark/python/pyspark/sql/dataframe.py", line 380, in show
    print(self._jdf.showString(n, 20, vertical))
  File "/usr/local/spark/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py", line 1257, in __call__
  File "/usr/local/spark/python/pyspark/sql/utils.py", line 63, in deco
    return f(*a, **kw)
  File "/usr/local/spark/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py", line 328, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling o41.showString.
: 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, 10.0.0.7, executor 0): com.amazonaws.AmazonClientException: Unable to load AWS credentials from any provider in the chain
    at com.amazonaws.auth.AWSCredentialsProviderChain.getCredentials(AWSCredentialsProviderChain.java:117)
    at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:3521)
    at com.amazonaws.services.s3.AmazonS3Client.headBucket(AmazonS3Client.java:1031)
    at com.amazonaws.services.s3.AmazonS3Client.doesBucketExist(AmazonS3Client.java:994)
    at org.apache.hadoop.fs.s3a.S3AFileSystem.initialize(S3AFileSystem.java:297)
    at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2669)
    at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:94)
    at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2703)
    at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2685)
    at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:373)
    at org.apache.hadoop.fs.Path.getFileSystem(Path.java:295)
    at com.esri.gdb.GDBIndex$.apply(GDBIndex.scala:130)
    at com.esri.gdb.GDBRDD.compute(GDBRDD.scala:22)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:123)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1889)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
    at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:365)
    at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
    at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3389)
    at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2550)
    at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2550)
    at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3370)
    at org.apache.spark.sql.execution.SQLExecution$$anonfun$withNewExecutionId$1.apply(SQLExecution.scala:78)
    at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:125)
    at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:73)
    at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3369)
    at org.apache.spark.sql.Dataset.head(Dataset.scala:2550)
    at org.apache.spark.sql.Dataset.take(Dataset.scala:2764)
    at org.apache.spark.sql.Dataset.getRows(Dataset.scala:254)
    at org.apache.spark.sql.Dataset.showString(Dataset.scala:291)
    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:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:238)
    at java.lang.Thread.run(Thread.java:748)
Caused by: com.amazonaws.AmazonClientException: Unable to load AWS credentials from any provider in the chain
    at com.amazonaws.auth.AWSCredentialsProviderChain.getCredentials(AWSCredentialsProviderChain.java:117)
    at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:3521)
    at com.amazonaws.services.s3.AmazonS3Client.headBucket(AmazonS3Client.java:1031)
    at com.amazonaws.services.s3.AmazonS3Client.doesBucketExist(AmazonS3Client.java:994)
    at org.apache.hadoop.fs.s3a.S3AFileSystem.initialize(S3AFileSystem.java:297)
    at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2669)
    at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:94)
    at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2703)
    at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2685)
    at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:373)
    at org.apache.hadoop.fs.Path.getFileSystem(Path.java:295)
    at com.esri.gdb.GDBIndex$.apply(GDBIndex.scala:130)
    at com.esri.gdb.GDBRDD.compute(GDBRDD.scala:22)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:123)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    ... 1 more
mraad commented 4 years ago

Have yet to try this off S3 - will test it - looks like there is an issue with AWS credentials. Unable to load AWS credentials from any provider in the chain Have to track it down

cdibble commented 4 years ago

Thanks for getting back to me. I am very interested in seeing that functionality- please let me know if there is anything else I can provide based on my experience. Cheers!

mraad commented 4 years ago

Thanks for your patience, still trying to debug this, can replicate the problem, trying to find a solution.

mraad commented 1 year ago

Tried it on MinIO using:

export PACKAGES="${PACKAGES:+$PACKAGES,}org.apache.hadoop:hadoop-aws:3.3.1"

--conf spark.hadoop.fs.s3a.access.key="minioadmin" \ --conf spark.hadoop.fs.s3a.secret.key="minioadmin" \ --conf spark.hadoop.fs.s3a.endpoint=http://localhost:9000 \ --conf spark.hadoop.fs.s3a.impl=org.apache.hadoop.fs.s3a.S3AFileSystem \ --conf spark.hadoop.fs.s3a.path.style.access=true \ --conf spark.hadoop.fs.s3a.connection.ssl.enabled=false \ --conf spark.jars.packages="${PACKAGES}" \