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dedup_job java.lang.UnsatisfiedLinkError

Open syedhasnainrazashah opened this issue 1 year ago • 3 comments

Hello I am getting this error while running dedup_job.

I am able to run sample_job and Korean_job but when I get this error in dedup_job.

I am using conda env, spark 3.0.1 with hadoop 2.7 with java SDK 8 on Windows. My system variables are set properly.

Need help

Kindly add a deduplication job for the Korean dataset.

py4j.protocol.Py4JJavaError: An error occurred while calling o52.partitions.
: java.lang.UnsatisfiedLinkError: org.apache.hadoop.io.nativeio.NativeIO$POSIX.stat(Ljava/lang/String;)Lorg/apache/hadoop/io/nativeio/NativeIO$POSIX$Stat;
        at org.apache.hadoop.io.nativeio.NativeIO$POSIX.stat(Native Method)
        at org.apache.hadoop.io.nativeio.NativeIO$POSIX.getStat(NativeIO.java:608)
        at org.apache.hadoop.fs.RawLocalFileSystem$DeprecatedRawLocalFileStatus.loadPermissionInfoByNativeIO(RawLocalFileSystem.java:934)
        at org.apache.hadoop.fs.RawLocalFileSystem$DeprecatedRawLocalFileStatus.loadPermissionInfo(RawLocalFileSystem.java:848)
        at org.apache.hadoop.fs.RawLocalFileSystem$DeprecatedRawLocalFileStatus.getPermission(RawLocalFileSystem.java:816)
        at org.apache.hadoop.fs.LocatedFileStatus.<init>(LocatedFileStatus.java:52)
        at org.apache.hadoop.fs.FileSystem$4.next(FileSystem.java:2199)
        at org.apache.hadoop.fs.FileSystem$4.next(FileSystem.java:2179)
        at org.apache.hadoop.mapred.FileInputFormat.singleThreadedListStatus(FileInputFormat.java:287)
        at org.apache.hadoop.mapred.FileInputFormat.listStatus(FileInputFormat.java:244)
        at org.apache.hadoop.mapred.FileInputFormat.getSplits(FileInputFormat.java:332)
        at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:205)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:49)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.api.python.PythonRDD.getPartitions(PythonRDD.scala:55)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:49)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.ShuffleDependency.<init>(Dependency.scala:101)
        at org.apache.spark.rdd.ShuffledRDD.getDependencies(ShuffledRDD.scala:87)
        at org.apache.spark.rdd.RDD.$anonfun$dependencies$2(RDD.scala:264)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.dependencies(RDD.scala:260)
        at org.apache.spark.rdd.ShuffledRDD.getPreferredLocations(ShuffledRDD.scala:98)
        at org.apache.spark.rdd.RDD.$anonfun$preferredLocations$2(RDD.scala:324)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.preferredLocations(RDD.scala:324)
        at org.apache.spark.scheduler.DAGScheduler.getPreferredLocsInternal(DAGScheduler.scala:2529)
        at org.apache.spark.scheduler.DAGScheduler.getPreferredLocs(DAGScheduler.scala:2503)
        at org.apache.spark.SparkContext.getPreferredLocs(SparkContext.scala:1898)
        at org.apache.spark.rdd.DefaultPartitionCoalescer$PartitionLocations.$anonfun$getAllPrefLocs$1(CoalescedRDD.scala:198)
        at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
        at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
        at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
        at org.apache.spark.rdd.DefaultPartitionCoalescer$PartitionLocations.getAllPrefLocs(CoalescedRDD.scala:197)
        at org.apache.spark.rdd.DefaultPartitionCoalescer$PartitionLocations.<init>(CoalescedRDD.scala:190)
        at org.apache.spark.rdd.DefaultPartitionCoalescer.coalesce(CoalescedRDD.scala:391)
        at org.apache.spark.rdd.CoalescedRDD.getPartitions(CoalescedRDD.scala:90)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:49)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.api.python.PythonRDD.getPartitions(PythonRDD.scala:55)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.api.java.JavaRDDLike.partitions(JavaRDDLike.scala:61)
        at org.apache.spark.api.java.JavaRDDLike.partitions$(JavaRDDLike.scala:61)
        at org.apache.spark.api.java.AbstractJavaRDDLike.partitions(JavaRDDLike.scala:45)
        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:748)

syedhasnainrazashah avatar Apr 01 '24 06:04 syedhasnainrazashah

Can you share more info regarding your errors? There needs some more context.

Taekyoon avatar Apr 01 '24 06:04 Taekyoon

I run this command with default parameters in dedup_job.yaml on test_korean_jsonl_data

python bin/sparkapp.py dedup_job --config_path=./configs/dedup_job.yaml

Missing Python executable 'C:\Users\master\anaconda3\envs\dps\python', defaulting to 'C:\Users\master\anaconda3\envs\dps\Lib\site-packages\pyspark\bin\..' for SPARK_HOME environment variable. Please install Python or specify the correct 
Python executable in PYSPARK_DRIVER_PYTHON or PYSPARK_PYTHON environment variable to detect SPARK_HOME safely.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Traceback (most recent call last):
  File "D:\UST\semester 3\Field Research\LLM\dps\bin\sparkapp.py", line 15, in <module>
    dps.spark.run()
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\dps\spark\run.py", line 11, in run
    fire.Fire(
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\fire\core.py", line 138, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\fire\core.py", line 463, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\fire\core.py", line 672, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\dps\spark\jobs\dedup_job.py", line 80, in dedup_job
    .reduceByKey(lambda x, y: x + y)
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\pyspark\rdd.py", line 1893, in reduceByKey
    return self.combineByKey(lambda x: x, func, func, numPartitions, partitionFunc)
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\pyspark\rdd.py", line 2138, in combineByKey
    numPartitions = self._defaultReducePartitions()
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\pyspark\rdd.py", line 2583, in _defaultReducePartitions
    return self.getNumPartitions()
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\pyspark\rdd.py", line 2937, in getNumPartitions
    return self._prev_jrdd.partitions().size()
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\py4j\java_gateway.py", line 1321, in __call__
    return_value = get_return_value(
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\pyspark\sql\utils.py", line 111, in deco
    return f(*a, **kw)
  File "C:\Users\master\anaconda3\envs\dps\lib\site-packages\py4j\protocol.py", line 326, in get_return_value
    raise Py4JJavaError(
py4j.protocol.Py4JJavaError: An error occurred while calling o52.partitions.
: java.lang.UnsatisfiedLinkError: org.apache.hadoop.io.nativeio.NativeIO$POSIX.stat(Ljava/lang/String;)Lorg/apache/hadoop/io/nativeio/NativeIO$POSIX$Stat;
        at org.apache.hadoop.io.nativeio.NativeIO$POSIX.stat(Native Method)
        at org.apache.hadoop.io.nativeio.NativeIO$POSIX.getStat(NativeIO.java:608)
        at org.apache.hadoop.fs.RawLocalFileSystem$DeprecatedRawLocalFileStatus.loadPermissionInfoByNativeIO(RawLocalFileSystem.java:934)
        at org.apache.hadoop.fs.RawLocalFileSystem$DeprecatedRawLocalFileStatus.loadPermissionInfo(RawLocalFileSystem.java:848)
        at org.apache.hadoop.fs.RawLocalFileSystem$DeprecatedRawLocalFileStatus.getPermission(RawLocalFileSystem.java:816)
        at org.apache.hadoop.fs.LocatedFileStatus.<init>(LocatedFileStatus.java:52)
        at org.apache.hadoop.fs.FileSystem$4.next(FileSystem.java:2199)
        at org.apache.hadoop.fs.FileSystem$4.next(FileSystem.java:2179)
        at org.apache.hadoop.mapred.FileInputFormat.singleThreadedListStatus(FileInputFormat.java:287)
        at org.apache.hadoop.mapred.FileInputFormat.listStatus(FileInputFormat.java:244)
        at org.apache.hadoop.mapred.FileInputFormat.getSplits(FileInputFormat.java:332)
        at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:205)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:49)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.api.python.PythonRDD.getPartitions(PythonRDD.scala:55)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:49)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.ShuffleDependency.<init>(Dependency.scala:101)
        at org.apache.spark.rdd.ShuffledRDD.getDependencies(ShuffledRDD.scala:87)
        at org.apache.spark.rdd.RDD.$anonfun$dependencies$2(RDD.scala:264)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.dependencies(RDD.scala:260)
        at org.apache.spark.rdd.ShuffledRDD.getPreferredLocations(ShuffledRDD.scala:98)
        at org.apache.spark.rdd.RDD.$anonfun$preferredLocations$2(RDD.scala:324)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.preferredLocations(RDD.scala:324)
        at org.apache.spark.scheduler.DAGScheduler.getPreferredLocsInternal(DAGScheduler.scala:2529)
        at org.apache.spark.scheduler.DAGScheduler.getPreferredLocs(DAGScheduler.scala:2503)
        at org.apache.spark.SparkContext.getPreferredLocs(SparkContext.scala:1898)
        at org.apache.spark.rdd.DefaultPartitionCoalescer$PartitionLocations.$anonfun$getAllPrefLocs$1(CoalescedRDD.scala:198)
        at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
        at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
        at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
        at org.apache.spark.rdd.DefaultPartitionCoalescer$PartitionLocations.getAllPrefLocs(CoalescedRDD.scala:197)
        at org.apache.spark.rdd.DefaultPartitionCoalescer$PartitionLocations.<init>(CoalescedRDD.scala:190)
        at org.apache.spark.rdd.DefaultPartitionCoalescer.coalesce(CoalescedRDD.scala:391)
        at org.apache.spark.rdd.CoalescedRDD.getPartitions(CoalescedRDD.scala:90)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:49)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.api.python.PythonRDD.getPartitions(PythonRDD.scala:55)
        at org.apache.spark.rdd.RDD.$anonfun$partitions$2(RDD.scala:300)
        at scala.Option.getOrElse(Option.scala:189)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:296)
        at org.apache.spark.api.java.JavaRDDLike.partitions(JavaRDDLike.scala:61)
        at org.apache.spark.api.java.JavaRDDLike.partitions$(JavaRDDLike.scala:61)
        at org.apache.spark.api.java.AbstractJavaRDDLike.partitions(JavaRDDLike.scala:45)
        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:748)

syedhasnainrazashah avatar Apr 01 '24 06:04 syedhasnainrazashah

This is a spark environment issue. You need to simple test to run spark on your local environment first.

Taekyoon avatar Apr 01 '24 06:04 Taekyoon