python - Connect to S3 data from PySpark

Question

I am trying to read a JSON file, from Amazon s3, to create a spark context and use it to process the data.

Spark is basically in a docker container. So putting files in docker path is also PITA. Hence pushed it to S3.

The code below explains rest of the stuff.

from pyspark import SparkContext, SparkConf
conf = SparkConf().setAppName("first")
sc = SparkContext(conf=conf)

config_dict = {"fs.s3n.awsAccessKeyId":"**",
               "fs.s3n.awsSecretAccessKey":"**"}

bucket = "nonamecpp"
prefix = "dataset.json"
filename = "s3n://{}/{}".format(bucket, prefix)
rdd = sc.hadoopFile(filename,
                    'org.apache.hadoop.mapred.TextInputFormat',
                    'org.apache.hadoop.io.Text',
                    'org.apache.hadoop.io.LongWritable',
                    conf=config_dict)

I get the following error -

Py4JJavaError                             Traceback (most recent call last)
<ipython-input-2-b94543fb0e8e> in <module>()
      9                     'org.apache.hadoop.io.Text',
     10                     'org.apache.hadoop.io.LongWritable',
---> 11                     conf=config_dict)
     12 

/usr/local/spark/python/pyspark/context.pyc in hadoopFile(self, path, inputFormatClass, keyClass, valueClass, keyConverter, valueConverter, conf, batchSize)
    558         jrdd = self._jvm.PythonRDD.hadoopFile(self._jsc, path, inputFormatClass, keyClass,
    559                                               valueClass, keyConverter, valueConverter,
--> 560                                               jconf, batchSize)
    561         return RDD(jrdd, self)
    562 

/usr/local/lib/python2.7/dist-packages/py4j/java_gateway.pyc in __call__(self, *args)
    536         answer = self.gateway_client.send_command(command)
    537         return_value = get_return_value(answer, self.gateway_client,
--> 538                 self.target_id, self.name)
    539 
    540         for temp_arg in temp_args:

/usr/local/lib/python2.7/dist-packages/py4j/protocol.pyc in get_return_value(answer, gateway_client, target_id, name)
    298                 raise Py4JJavaError(
    299                     'An error occurred while calling {0}{1}{2}.
'.
--> 300                     format(target_id, '.', name), value)
    301             else:
    302                 raise Py4JError(

Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.hadoopFile.
: java.lang.IllegalArgumentException: AWS Access Key ID and Secret Access Key must be specified as the username or password (respectively) of a s3n URL, or by setting the fs.s3n.awsAccessKeyId or fs.s3n.awsSecretAccessKey properties (respectively).
    at org.apache.hadoop.fs.s3.S3Credentials.initialize(S3Credentials.java:70)
    at org.apache.hadoop.fs.s3native.Jets3tNativeFileSystemStore.initialize(Jets3tNativeFileSystemStore.java:73)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:190)
    at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:103)
    at org.apache.hadoop.fs.s3native.$Proxy20.initialize(Unknown Source)
    at org.apache.hadoop.fs.s3native.NativeS3FileSystem.initialize(NativeS3FileSystem.java:272)
    at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2397)
    at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:89)
    at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2431)
    at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2413)
    at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:368)
    at org.apache.hadoop.fs.Path.getFileSystem(Path.java:296)
    at org.apache.hadoop.mapred.FileInputFormat.singleThreadedListStatus(FileInputFormat.java:256)
    at org.apache.hadoop.mapred.FileInputFormat.listStatus(FileInputFormat.java:228)
    at org.apache.hadoop.mapred.FileInputFormat.getSplits(FileInputFormat.java:304)
    at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:201)
    at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:205)
    at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203)
    at scala.Option.getOrElse(Option.scala:120)
    at org.apache.spark.rdd.RDD.partitions(RDD.scala:203)
    at org.apache.spark.rdd.MappedRDD.getPartitions(MappedRDD.scala:28)
    at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:205)
    at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203)
    at scala.Option.getOrElse(Option.scala:120)
    at org.apache.spark.rdd.RDD.partitions(RDD.scala:203)
    at org.apache.spark.rdd.RDD.take(RDD.scala:1060)
    at org.apache.spark.rdd.RDD.first(RDD.scala:1093)
    at org.apache.spark.api.python.SerDeUtil$.pairRDDToPython(SerDeUtil.scala:202)
    at org.apache.spark.api.python.PythonRDD$.hadoopFile(PythonRDD.scala:543)
    at org.apache.spark.api.python.PythonRDD.hadoopFile(PythonRDD.scala)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:231)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:379)
    at py4j.Gateway.invoke(Gateway.java:259)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:133)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:207)
    at java.lang.Thread.run(Thread.java:744)

I have clearly provided aswSecretAccessKey and awsAccessId. Whats going wrong?

Answer 1

I've solved adding --packages org.apache.hadoop:hadoop-aws:2.7.1 into spark-submit command.

It will download all hadoop missing packages that will allow you to execute spark jobs with S3.

Then in your job you need to set your AWS credentials like:

sc._jsc.hadoopConfiguration().set("fs.s3n.awsAccessKeyId", aws_id)
sc._jsc.hadoopConfiguration().set("fs.s3n.awsSecretAccessKey", aws_key)

Other option about setting your credentials is define them into spark/conf/spark-env:

#!/usr/bin/env bash
AWS_ACCESS_KEY_ID='xxxx'
AWS_SECRET_ACCESS_KEY='xxxx'

SPARK_WORKER_CORES=1 # to set the number of cores to use on this machine
SPARK_WORKER_MEMORY=1g # to set how much total memory workers have to give executors (e.g. 1000m, 2g)
SPARK_EXECUTOR_INSTANCES=10 #, to set the number of worker processes per node

More info:

• How to Run PySpark on AWS
• AWS Credentials