I am trying to replicate what was done in this article Loading Big SAS files
What I am doing is starting up a jupyter notebook and running the code below. I keep getting a Java load error and I can't figure out why.
Spark Version:2.4.6
Scala Version:2.12.2
Java Version:1.8.0_261
import findspark
findspark.init()
from pyspark.sql.session import SparkSession
spark = SparkSession.builder.\
config("spark.jars.packages","saurfang:spark-sas7bdat:2.0.0-s_2.11")\
.enableHiveSupport().getOrCreate()
df=spark.read.format('com.github.saurfang.sas.spark')\
.load(r'D:\IvyDB\opprcd\opprcd2019.sas7bdat')
Error I always get is below
Py4JJavaError: An error occurred while calling o163.load.
: java.util.concurrent.TimeoutException: Timed out after 60 sec while reading file metadata, file might be corrupt. (Change timeout with 'metadataTimeout' paramater)
at com.github.saurfang.sas.spark.SasRelation.inferSchema(SasRelation.scala:189)
at com.github.saurfang.sas.spark.SasRelation.(SasRelation.scala:62)
at com.github.saurfang.sas.spark.SasRelation$.apply(SasRelation.scala:43)
at com.github.saurfang.sas.spark.DefaultSource.createRelation(DefaultSource.scala:209)
at com.github.saurfang.sas.spark.DefaultSource.createRelation(DefaultSource.scala:42)
at com.github.saurfang.sas.spark.DefaultSource.createRelation(DefaultSource.scala:27)
at org.apache.spark.sql.execution.datasources.DataSource.resolveRelation(DataSource.scala:341)
at org.apache.spark.sql.DataFrameReader.loadV1Source(DataFrameReader.scala:239)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:227)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:174)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
In our case, we were able to fix this issue by adding Parso library into pyspark. Parso is one of the requirements in Spark SAS Data Source.
Related
I am a newbie in pyspark, While trying to read parquet file through pyspark I get the below error. I have tried various things like reinstallation of jre and jdk, updating environment variables. Matching winutils.exe but nothing seems to work.
Error: **
An error occurred while calling o60.load.
: java.lang.UnsatisfiedLinkError: org.apache.hadoop.io.nativeio.NativeIO$Windows.access0(Ljava/lang/String;I)Z
at org.apache.hadoop.io.nativeio.NativeIO$Windows.access0(Native Method)
at org.apache.hadoop.io.nativeio.NativeIO$Windows.access(NativeIO.java:793)
at org.apache.hadoop.fs.FileUtil.canRead(FileUtil.java:1215)
at org.apache.hadoop.fs.FileUtil.list(FileUtil.java:1420)
at org.apache.hadoop.fs.RawLocalFileSystem.listStatus(RawLocalFileSystem.java:601)
at org.apache.hadoop.fs.FileSystem.listStatus(FileSystem.java:1972)
at org.apache.hadoop.fs.FileSystem.listStatus(FileSystem.java:2014)
at org.apache.hadoop.fs.ChecksumFileSystem.listStatus(ChecksumFileSystem.java:761)
at org.apache.spark.util.HadoopFSUtils$.listLeafFiles(HadoopFSUtils.scala:225)
at org.apache.spark.util.HadoopFSUtils$.$anonfun$parallelListLeafFilesInternal$1(HadoopFSUtils.scala:95)
at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:286)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at scala.collection.TraversableLike.map(TraversableLike.scala:286)
at scala.collection.TraversableLike.map$(TraversableLike.scala:279)
at scala.collection.AbstractTraversable.map(Traversable.scala:108)
at org.apache.spark.util.HadoopFSUtils$.parallelListLeafFilesInternal(HadoopFSUtils.scala:85)
at org.apache.spark.util.HadoopFSUtils$.parallelListLeafFiles(HadoopFSUtils.scala:69)
at org.apache.spark.sql.execution.datasources.InMemoryFileIndex$.bulkListLeafFiles(InMemoryFileIndex.scala:158)
at org.apache.spark.sql.execution.datasources.InMemoryFileIndex.listLeafFiles(InMemoryFileIndex.scala:131)
at org.apache.spark.sql.execution.datasources.InMemoryFileIndex.refresh0(InMemoryFileIndex.scala:94)
at org.apache.spark.sql.execution.datasources.InMemoryFileIndex.<init>(InMemoryFileIndex.scala:66)
at org.apache.spark.sql.execution.datasources.DataSource.createInMemoryFileIndex(DataSource.scala:565)
at org.apache.spark.sql.execution.datasources.DataSource.resolveRelation(DataSource.scala:409)
at org.apache.spark.sql.DataFrameReader.loadV1Source(DataFrameReader.scala:274)
at org.apache.spark.sql.DataFrameReader.$anonfun$load$3(DataFrameReader.scala:245)
at scala.Option.getOrElse(Option.scala:189)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:245)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:188)
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.ClientServerConnection.waitForCommands(ClientServerConnection.java:182)
at py4j.ClientServerConnection.run(ClientServerConnection.java:106)
at java.lang.Thread.run(Thread.java:750)
**
Edit - code is quite simple:-
python
import pyspark.sql.functions as F
import pandas as pd
from pyspark.sql import SparkSession
from pyspark.sql.types import TimestampType
from pyspark.sql.utils import AnalysisException
spark = SparkSession.builder.getOrCreate()
path = "C:\\ProgramData\\MyData"
df = spark.read.format("parquet").option("header",True).load(str(path))
I am using spark-3.2.1-bin-hadoop3.2. Python version is 3.10.
Solution:- Copy winutils from link and try one by one version and check which version is working. Ideally the version matching with Pyspark version should work but different version worked in my case.
Please help out if you get any clue.
I'm trying to read xlsx to PySpark and tried with multiple ways to import the library of Spark-excel but I still get errors while reading xlsx file.
I'm using Spark with standalone mode on my Mac.
My code:
# spark configuration
spark_path = "/spark/spark-3.0.1-bin-hadoop2.7"
findspark.init(spark_path)
spark = SparkSession.builder.master("local").appName("Word Count").config("--packages com.crealytics:spark-excel_2.12:0.13.7").getOrCreate()
data_location = "bank_transactions.xlsx"
df = spark.read.format("com.crealytics.spark.excel").load(data_location)
I got the following error:
Py4JJavaError: An error occurred while calling o37.load.
: java.lang.NoClassDefFoundError: scala/Product$class
at com.crealytics.spark.excel.Utils$MapIncluding.<init>(Utils.scala:9)
at com.crealytics.spark.excel.WorkbookReader$.<init>(WorkbookReader.scala:31)
at com.crealytics.spark.excel.WorkbookReader$.<clinit>(WorkbookReader.scala)
at com.crealytics.spark.excel.DefaultSource.createRelation(DefaultSource.scala:28)
at com.crealytics.spark.excel.DefaultSource.createRelation(DefaultSource.scala:18)
at com.crealytics.spark.excel.DefaultSource.createRelation(DefaultSource.scala:12)
at org.apache.spark.sql.execution.datasources.DataSource.resolveRelation(DataSource.scala:344)
at org.apache.spark.sql.DataFrameReader.loadV1Source(DataFrameReader.scala:297)
at org.apache.spark.sql.DataFrameReader.$anonfun$load$2(DataFrameReader.scala:286)
at scala.Option.getOrElse(Option.scala:189)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:286)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:232)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.base/java.lang.Thread.run(Thread.java:832)
Caused by: java.lang.ClassNotFoundException: scala.Product$class
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:602)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
... 23 more
Solutions:
Download proper spark-excel library, for me it's:
https://mvnrepository.com/artifact/com.crealytics/spark-excel_2.12/0.13.7
Create directory spark_jars in the SPARK_HOME then store the spark-excel package in spark_jars directory
Add the spark_jars to spark.executor.extraClassPath of Spark session:
findspark.init(spark_path)
spark = SparkSession.builder.master("local") \
.appName("Word Count") \
.config("spark.jars.packages","com.crealytics:spark-excel_2.12:0.13.7") \
.getOrCreate()
spark
I'm using HDP sandbox 3.1 and performing NLTK on 50K files using spark2 Interpreter and Zeppelin Notebook.
It's a single node setup.
I've given 12GB RAM to Guest System and 6CPUs.
In spark, I'm reading all 50K files in a single RDD Operation, but at 63% my process hangs, and then it leads to ERROR.
Now which Values in Spark and YARN I've to set, so Spark can work in full throttle.
Edit: Each file size is around 3KB
Following is the log when Error occurred
Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.collectAndServe.
: org.apache.spark.SparkException: Job 0 cancelled because SparkContext was shut down
at org.apache.spark.scheduler.DAGScheduler$$anonfun$cleanUpAfterSchedulerStop$1.apply(DAGScheduler.scala:837)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$cleanUpAfterSchedulerStop$1.apply(DAGScheduler.scala:835)
at scala.collection.mutable.HashSet.foreach(HashSet.scala:78)
at org.apache.spark.scheduler.DAGScheduler.cleanUpAfterSchedulerStop(DAGScheduler.scala:835)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onStop(DAGScheduler.scala:1848)
at org.apache.spark.util.EventLoop.stop(EventLoop.scala:83)
at org.apache.spark.scheduler.DAGScheduler.stop(DAGScheduler.scala:1761)
at org.apache.spark.SparkContext$$anonfun$stop$8.apply$mcV$sp(SparkContext.scala:1931)
at org.apache.spark.util.Utils$.tryLogNonFatalError(Utils.scala:1361)
at org.apache.spark.SparkContext.stop(SparkContext.scala:1930)
at org.apache.spark.SparkContext$$anon$3.run(SparkContext.scala:1876)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:642)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2034)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2055)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2074)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099)
at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:939)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
at org.apache.spark.rdd.RDD.collect(RDD.scala:938)
at org.apache.spark.api.python.PythonRDD$.collectAndServe(PythonRDD.scala:162)
at org.apache.spark.api.python.PythonRDD.collectAndServe(PythonRDD.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 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)
(<class 'py4j.protocol.Py4JJavaError'>, Py4JJavaError(u'An error occurred while calling z:org.apache.spark.api.python.PythonRDD.collectAndServe.\n', JavaObject id=o101)
Environment: Spark 2.4.0
I have included spark-sql-kafka-0-10 jar, and it's of the same version as that of the Spark I am using.
Here's the exception:
py4j.protocol.Py4JJavaError: An error occurred while calling o38.load.
: java.lang.NoClassDefFoundError: org.apache.kafka.common.serialization.ByteArrayDeserializer
at org.apache.spark.sql.kafka010.KafkaSourceProvider$.<init>(KafkaSourceProvider.scala:487)
at org.apache.spark.sql.kafka010.KafkaSourceProvider$.<clinit>(KafkaSourceProvider.scala)
at org.apache.spark.sql.kafka010.KafkaSourceProvider.validateStreamOptions(KafkaSourceProvider.scala:414)
at org.apache.spark.sql.kafka010.KafkaSourceProvider.sourceSchema(KafkaSourceProvider.scala:66)
at org.apache.spark.sql.execution.datasources.DataSource.sourceSchema(DataSource.scala:209)
at org.apache.spark.sql.execution.datasources.DataSource.sourceInfo$lzycompute(DataSource.scala:95)
at org.apache.spark.sql.execution.datasources.DataSource.sourceInfo(DataSource.scala:95)
at org.apache.spark.sql.execution.streaming.StreamingRelation$.apply(StreamingRelation.scala:33)
at org.apache.spark.sql.streaming.DataStreamReader.load(DataStreamReader.scala:171)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:90)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:55)
at java.lang.reflect.Method.invoke(Method.java:508)
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:812)
Caused by: java.lang.ClassNotFoundException: org.apache.kafka.common.serialization.ByteArrayDeserializer
at java.net.URLClassLoader.findClass(URLClassLoader.java:610)
at java.lang.ClassLoader.loadClassHelper(ClassLoader.java:937)
at java.lang.ClassLoader.loadClass(ClassLoader.java:882)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:343)
at java.lang.ClassLoader.loadClass(ClassLoader.java:865)
... 20 more
I didn't have kafka-clients jar in my classpath. Adding it fixes the missing class exception
Starting the spark-shell with the packages option will work too:
spark-shell --packages org.apache.spark:spark-sql-kafka-0-10_2.11:2.4.0
I have a Hive UDF written in java and I am trying to use it in pyspark 2.0.0. below are the steps
1. Copy the jar file to EMR
2. started a pyspark job like below
pyspark --jars ip-udf-0.0.1-SNAPSHOT-jar-with-dependencies-latest.jar
3. used the below code access the UDF
from pyspark.sql import SparkSession
from pyspark.sql import HiveContext
sc = spark.sparkContext
sqlContext = HiveContext(sc)
sqlContext.sql("create temporary function ip_map as 'com.mediaiq.hive.IPMappingUDF'")
I get the below error:
py4j.protocol.Py4JJavaError: An error occurred while calling o43.sql.
: java.lang.NoSuchMethodError:
org.apache.hadoop.hive.conf.HiveConf.getTimeVar(Lorg/apache/hadoop/hive/conf/HiveConf$ConfVars;Ljava/util/concurrent/TimeUnit;)J
at
org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.(RetryingMetaStoreClient.java:76)
at
org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:132)
at
org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:104)
at
org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:98)
at
org.apache.hadoop.hive.ql.metadata.Hive.createMetaStoreClient(Hive.java:2453)
at org.apache.hadoop.hive.ql.metadata.Hive.getMSC(Hive.java:2465) at
org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:340)
at
org.apache.spark.sql.hive.client.HiveClientImpl.(HiveClientImpl.scala:189)
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
org.apache.spark.sql.hive.client.IsolatedClientLoader.createClient(IsolatedClientLoader.scala:258)
at
org.apache.spark.sql.hive.HiveUtils$.newClientForMetadata(HiveUtils.scala:359)
at
org.apache.spark.sql.hive.HiveUtils$.newClientForMetadata(HiveUtils.scala:263)
at
org.apache.spark.sql.hive.HiveSharedState.metadataHive$lzycompute(HiveSharedState.scala:39)
at
org.apache.spark.sql.hive.HiveSharedState.metadataHive(HiveSharedState.scala:38)
at
org.apache.spark.sql.hive.HiveSharedState.externalCatalog$lzycompute(HiveSharedState.scala:46)
at
org.apache.spark.sql.hive.HiveSharedState.externalCatalog(HiveSharedState.scala:45)
at
org.apache.spark.sql.hive.HiveSessionState.catalog$lzycompute(HiveSessionState.scala:50)
at
org.apache.spark.sql.hive.HiveSessionState.catalog(HiveSessionState.scala:48)
at
org.apache.spark.sql.hive.HiveSessionState$$anon$1.(HiveSessionState.scala:63)
at
org.apache.spark.sql.hive.HiveSessionState.analyzer$lzycompute(HiveSessionState.scala:63)
at
org.apache.spark.sql.hive.HiveSessionState.analyzer(HiveSessionState.scala:62)
at
org.apache.spark.sql.execution.QueryExecution.assertAnalyzed(QueryExecution.scala:49)
at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:64) at
org.apache.spark.sql.SparkSession.sql(SparkSession.scala:582) 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:237) 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:745)
You may have built your UDF with a different version of Hive. Be sure to specify the same version of Hive in your pom.xml used to build the jar containing the UDF. See this previous answer, for example.