java.lang.UnsatisfiedLinkError: com.microsoft.ml.lightgbm.lightgbmlibJNI.voidpp_handle [BUG]

SynapseML version

0.10.0

System information

• Language version: python 3.8.10
• Spark Version: 3.2.1
• Spark Platform Synapse - Databricks

So I have followed the installation instruction into databricks as per https://microsoft.github.io/SynapseML/docs/getting_started/installation/#databricks

Describe the problem

Conversion of predictions data set to numpy is resulting in unsatisfied link error java.lang.UnsatisfiedLinkError: com.microsoft.ml.lightgbm.lightgbmlibJNI.voidpp_handle

I think this is the line that is causing the error.

Now I find it hard to believe that my bit of code is particularly novel, so I cannot be the only one who is having this issue. Or I am doing something wrong.

Code to reproduce issue

from pyspark.ml.feature import VectorAssembler, StringIndexer
from pyspark.ml import Pipeline


# get col names and defintions
string_cols = [c for c, t in df.dtypes if t =='string']
string_index = [f"{s}_index" for s in string_cols]
numeric_cols = [c for c, t in df.dtypes if t !='string']
numeric_cols.remove('objective')


stringIndexer = StringIndexer(inputCols=string_cols, outputCols=string_index, handleInvalid="keep")
featurizer = VectorAssembler(inputCols=numeric_cols+string_index, outputCol="features", handleInvalid="keep")

data_pipeline = Pipeline(stages= [stringIndexer, featurizer])

data = data_pipeline.fit(df).transform(df)["objective", "features"]

# split into train and test  
train, test = data.randomSplit([0.90, 0.10], seed=1)

from synapse.ml.lightgbm import LightGBMClassifier
param = {
             'featuresCol':"features", 
            'labelCol':"objective",
            'zeroAsMissing': False,
            'objective': 'binary',
            'metric': 'binary',
            'verbosity': 0,
            'isUnbalance': True,
            'useBarrierExecutionMode':True, #fix for a known issue see details https://github.com/microsoft/SynapseML/issues/1534
            'learningRate': 0.019960206745150144,
             'posBaggingFraction': 0.741400512824773,
             'negBaggingFraction': 0.9592530174926162,
             'lambdaL1': 7.222372408024596e-07,
             'lambdaL2': 8.048479891726644e-08,
             'numLeaves': 231,
             'featureFraction': 0.7013476730404191,
             'baggingFraction': 0.9473274453520037,
             'baggingFreq': 7,
             'minDataInLeaf': 30,

        }
  

lgb_class = LightGBMClassifier(**param)
model = lgb_class.fit(train)        
predictions = model.transform(test)

import numpy as np
prediction_probability = np.array(predictions.select('probability').collect())

Other info / logs

---

Py4JJavaError Traceback (most recent call last) <command-391679> in <module> 1 import numpy as np ----> 2 f = np.array(predictions.select(‘probability’).collect())

/databricks/spark/python/pyspark/sql/dataframe.py in collect(self) 713 # Default path used in OSS Spark / for non-DF-ACL clusters: 714 with SCCallSiteSync(self._sc) as css: –> 715 sock_info = self._jdf.collectToPython() 716 return list(_load_from_socket(sock_info, BatchedSerializer(PickleSerializer()))) 717

/databricks/spark/python/lib/py4j-0.10.9.1-src.zip/py4j/java_gateway.py in call(self, *args) 1302 1303 answer = self.gateway_client.send_command(command) -> 1304 return_value = get_return_value( 1305 answer, self.gateway_client, self.target_id, self.name) 1306

/databricks/spark/python/pyspark/sql/utils.py in deco(*a, **kw) 115 def deco(*a, **kw): 116 try: –> 117 return f(*a, **kw) 118 except py4j.protocol.Py4JJavaError as e: 119 converted = convert_exception(e.java_exception)

/databricks/spark/python/lib/py4j-0.10.9.1-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name) 324 value = OUTPUT_CONVERTER[type](answer[2:], gateway_client) 325 if answer[1] == REFERENCE_TYPE: –> 326 raise Py4JJavaError( 327 “An error occurred while calling {0}{1}{2}.\n”. 328 format(target_id, “.”, name), value)

Py4JJavaError: An error occurred while calling o11576.collectToPython. : org.apache.spark.SparkException: Job aborted due to stage failure: Task 73 in stage 55.0 failed 4 times, most recent failure: Lost task 73.3 in stage 55.0 (TID 21878) (10.30.252.53 executor 32): org.apache.spark.SparkException: Failed to execute user defined function (LightGBMClassificationModel$$Lambda$7979/1876654359: (struct<type:tinyint,size:int,indices:array<int>,values:array<double>>) => struct<type:tinyint,size:int,indices:array<int>,values:array<double>>) at org.apache.spark.sql.errors.QueryExecutionErrors$.failedExecuteUserDefinedFunctionError(QueryExecutionErrors.scala:168) at org.apache.spark.sql.errors.QueryExecutionErrors.failedExecuteUserDefinedFunctionError(QueryExecutionErrors.scala) at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source) at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43) at org.apache.spark.sql.execution.WholeStageCodegenExec$$anon$1.hasNext(WholeStageCodegenExec.scala:759) at org.apache.spark.sql.execution.collect.UnsafeRowBatchUtils$.encodeUnsafeRows(UnsafeRowBatchUtils.scala:80) at org.apache.spark.sql.execution.collect.Collector.$anonfun$processFunc$1(Collector.scala:155) at org.apache.spark.scheduler.ResultTask.$anonfun$runTask$3(ResultTask.scala:75) at com.databricks.spark.util.ExecutorFrameProfiler$.record(ExecutorFrameProfiler.scala:110) at org.apache.spark.scheduler.ResultTask.$anonfun$runTask$1(ResultTask.scala:75) at com.databricks.spark.util.ExecutorFrameProfiler$.record(ExecutorFrameProfiler.scala:110) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:55) at org.apache.spark.scheduler.Task.doRunTask(Task.scala:156) at org.apache.spark.scheduler.Task.$anonfun$run$1(Task.scala:125) at com.databricks.spark.util.ExecutorFrameProfiler$.record(ExecutorFrameProfiler.scala:110) at org.apache.spark.scheduler.Task.run(Task.scala:95) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$13(Executor.scala:825) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1655) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$4(Executor.scala:828) at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23) at com.databricks.spark.util.ExecutorFrameProfiler$.record(ExecutorFrameProfiler.scala:110) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:683) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.UnsatisfiedLinkError: com.microsoft.ml.lightgbm.lightgbmlibJNI.voidpp_handle()J at com.microsoft.ml.lightgbm.lightgbmlibJNI.voidpp_handle(Native Method) at com.microsoft.ml.lightgbm.lightgbmlib.voidpp_handle(lightgbmlib.java:628) at com.microsoft.azure.synapse.ml.lightgbm.booster.BoosterHandler$.com$microsoft$azure$synapse$ml$lightgbm$booster$BoosterHandler$$createBoosterPtrFromModelString(LightGBMBooster.scala:42) at com.microsoft.azure.synapse.ml.lightgbm.booster.BoosterHandler.<init>(LightGBMBooster.scala:64) at com.microsoft.azure.synapse.ml.lightgbm.booster.LightGBMBooster.boosterHandler$lzycompute(LightGBMBooster.scala:237) at com.microsoft.azure.synapse.ml.lightgbm.booster.LightGBMBooster.boosterHandler(LightGBMBooster.scala:232) at com.microsoft.azure.synapse.ml.lightgbm.booster.LightGBMBooster.score(LightGBMBooster.scala:396) at com.microsoft.azure.synapse.ml.lightgbm.LightGBMClassificationModel.predictProbability(LightGBMClassifier.scala:178) at com.microsoft.azure.synapse.ml.lightgbm.LightGBMClassificationModel.$anonfun$transform$4(LightGBMClassifier.scala:138) … 23 more

Driver stacktrace: at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:3029) at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2976) at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2970) at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62) at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49) at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2970) at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1390) at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1390) at scala.Option.foreach(Option.scala:407) at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1390) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:3238) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:3179) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:3167) at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49) at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:1152) at org.apache.spark.SparkContext.runJobInternal(SparkContext.scala:2638) at org.apache.spark.sql.execution.collect.Collector.runSparkJobs(Collector.scala:241) at org.apache.spark.sql.execution.collect.Collector.collect(Collector.scala:276) at org.apache.spark.sql.execution.collect.Collector$.collect(Collector.scala:81) at org.apache.spark.sql.execution.collect.Collector$.collect(Collector.scala:87) at org.apache.spark.sql.execution.collect.InternalRowFormat$.collect(cachedSparkResults.scala:75) at org.apache.spark.sql.execution.collect.InternalRowFormat$.collect(cachedSparkResults.scala:62) at org.apache.spark.sql.execution.ResultCacheManager.collectResult$1(ResultCacheManager.scala:611) at org.apache.spark.sql.execution.ResultCacheManager.computeResult(ResultCacheManager.scala:618) at org.apache.spark.sql.execution.ResultCacheManager.$anonfun$getOrComputeResultInternal$1(ResultCacheManager.scala:561) at scala.Option.getOrElse(Option.scala:189) at org.apache.spark.sql.execution.ResultCacheManager.getOrComputeResultInternal(ResultCacheManager.scala:560) at org.apache.spark.sql.execution.ResultCacheManager.getOrComputeResult(ResultCacheManager.scala:457) at org.apache.spark.sql.execution.ResultCacheManager.getOrComputeResult(ResultCacheManager.scala:436) at org.apache.spark.sql.execution.SparkPlan.executeCollectResult(SparkPlan.scala:422) at org.apache.spark.sql.Dataset.$anonfun$collectToPython$1(Dataset.scala:3739) at org.apache.spark.sql.Dataset.$anonfun$withAction$1(Dataset.scala:3951) at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withCustomExecutionEnv$8(SQLExecution.scala:240) at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:388) at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withCustomExecutionEnv$1(SQLExecution.scala:187) at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:968) at org.apache.spark.sql.execution.SQLExecution$.withCustomExecutionEnv(SQLExecution.scala:142) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:338) at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3949) at org.apache.spark.sql.Dataset.collectToPython(Dataset.scala:3737) 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:380) at py4j.Gateway.invoke(Gateway.java:295) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:251) at java.lang.Thread.run(Thread.java:748) Caused by: org.apache.spark.SparkException: Failed to execute user defined function (LightGBMClassificationModel$$Lambda$7979/1876654359: (struct<type:tinyint,size:int,indices:array<int>,values:array<double>>) => struct<type:tinyint,size:int,indices:array<int>,values:array<double>>) at org.apache.spark.sql.errors.QueryExecutionErrors$.failedExecuteUserDefinedFunctionError(QueryExecutionErrors.scala:168) at org.apache.spark.sql.errors.QueryExecutionErrors.failedExecuteUserDefinedFunctionError(QueryExecutionErrors.scala) at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source) at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43) at org.apache.spark.sql.execution.WholeStageCodegenExec$$anon$1.hasNext(WholeStageCodegenExec.scala:759) at org.apache.spark.sql.execution.collect.UnsafeRowBatchUtils$.encodeUnsafeRows(UnsafeRowBatchUtils.scala:80) at org.apache.spark.sql.execution.collect.Collector.$anonfun$processFunc$1(Collector.scala:155) at org.apache.spark.scheduler.ResultTask.$anonfun$runTask$3(ResultTask.scala:75) at com.databricks.spark.util.ExecutorFrameProfiler$.record(ExecutorFrameProfiler.scala:110) at org.apache.spark.scheduler.ResultTask.$anonfun$runTask$1(ResultTask.scala:75) at com.databricks.spark.util.ExecutorFrameProfiler$.record(ExecutorFrameProfiler.scala:110) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:55) at org.apache.spark.scheduler.Task.doRunTask(Task.scala:156) at org.apache.spark.scheduler.Task.$anonfun$run$1(Task.scala:125) at com.databricks.spark.util.ExecutorFrameProfiler$.record(ExecutorFrameProfiler.scala:110) at org.apache.spark.scheduler.Task.run(Task.scala:95) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$13(Executor.scala:825) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1655) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$4(Executor.scala:828) at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23) at com.databricks.spark.util.ExecutorFrameProfiler$.record(ExecutorFrameProfiler.scala:110) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:683) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) … 1 more Caused by: java.lang.UnsatisfiedLinkError: com.microsoft.ml.lightgbm.lightgbmlibJNI.voidpp_handle()J at com.microsoft.ml.lightgbm.lightgbmlibJNI.voidpp_handle(Native Method) at com.microsoft.ml.lightgbm.lightgbmlib.voidpp_handle(lightgbmlib.java:628) at com.microsoft.azure.synapse.ml.lightgbm.booster.BoosterHandler$.com$microsoft$azure$synapse$ml$lightgbm$booster$BoosterHandler$$createBoosterPtrFromModelString(LightGBMBooster.scala:42) at com.microsoft.azure.synapse.ml.lightgbm.booster.BoosterHandler.<init>(LightGBMBooster.scala:64) at com.microsoft.azure.synapse.ml.lightgbm.booster.LightGBMBooster.boosterHandler$lzycompute(LightGBMBooster.scala:237) at com.microsoft.azure.synapse.ml.lightgbm.booster.LightGBMBooster.boosterHandler(LightGBMBooster.scala:232) at com.microsoft.azure.synapse.ml.lightgbm.booster.LightGBMBooster.score(LightGBMBooster.scala:396) at com.microsoft.azure.synapse.ml.lightgbm.LightGBMClassificationModel.predictProbability(LightGBMClassifier.scala:178) at com.microsoft.azure.synapse.ml.lightgbm.LightGBMClassificationModel.$anonfun$transform$4(LightGBMClassifier.scala:138) … 23 more

What component(s) does this bug affect?

• area/cognitive: Cognitive project
• area/core: Core project
• area/deep-learning: DeepLearning project
• area/lightgbm: Lightgbm project
• area/opencv: Opencv project
• area/vw: VW project
• area/website: Website
• area/build: Project build system
• area/notebooks: Samples under notebooks folder
• area/docker: Docker usage
• area/models: models related issue

What language(s) does this bug affect?

• language/scala: Scala source code
• language/python: Pyspark APIs
• language/r: R APIs
• language/csharp: .NET APIs
• language/new: Proposals for new client languages

What integration(s) does this bug affect?

• integrations/synapse: Azure Synapse integrations
• integrations/azureml: Azure ML integrations
• integrations/databricks: Databricks integrations

AB#1911075

[mhamilton723]

Hey @timpiperseek @martamaslankowska we cut a new version 0.10.1, please let us know if this solves your issues thanks for your patience!

[martamaslankowska]

we cut a new version 0.10.1, please let us know if this solves your issues

Hi, thanks a lot for the new version! I just checked it out and it seems to be working - so that indeed solves my problem 😊