ClickHouse/spark-clickhouse-connector

Apache Arrow Error - Failed to initialize MemoryUtil

BentsiLeviav opened this issue · 4 comments

BentsiLeviav commented

When using the connector locally on macOS, a known issue with Apache Arrow is being thrown

Environment:

  • OS - MacOs - M2 (Apple Silicon)
  • Spark Version - 3.3.2
  • Connector version - 0.7.3
  • Connector artifact ID - clickhouse-spark-runtime-3.3_2.13
  • Java version - 17

Given the following simple code:

package org.example;

import org.apache.spark.sql.*;
import org.apache.spark.sql.types.DataTypes;
import org.apache.spark.sql.types.StructField;
import org.apache.spark.sql.types.StructType;

import java.util.Arrays;
import java.util.List;

public class Main {
    public static void main(String[] args) throws AnalysisException {

        String sparkJars = "**/src/main/resources/jars/clickhouse-jdbc-0.4.6-all.jar,**/src/main/resources/jars/clickhouse-spark-runtime-3.3_2.13-0.7.3.jar";

        // Create a Spark session
        SparkSession spark = SparkSession.builder()
                .appName("example")
                .master("local[*]")
                .config("spark.sql.catalog.clickhouse", "xenon.clickhouse.ClickHouseCatalog")
                .config("spark.sql.catalog.clickhouse.host", System.getenv("CLICKHOUSE_HOST") != null ? System.getenv("CLICKHOUSE_HOST") : "127.0.0.1")
                .config("spark.sql.catalog.clickhouse.protocol", "http")
                .config("spark.sql.catalog.clickhouse.http_port", System.getenv("CLICKHOUSE_HTTP_PORT") != null ? System.getenv("CLICKHOUSE_HTTP_PORT") : "8123")
                .config("spark.sql.catalog.clickhouse.user", System.getenv("CLICKHOUSE_USER") != null ? System.getenv("CLICKHOUSE_USER") : "default")
                .config("spark.sql.catalog.clickhouse.password", System.getenv("CLICKHOUSE_PASSWORD") != null ? System.getenv("CLICKHOUSE_PASSWORD") : "123456")
                .config("spark.sql.catalog.clickhouse.database", "default")
                .config("spark.jars", sparkJars)
                .getOrCreate();

        // Define the schema for the DataFrame
        StructType schema = new StructType(new StructField[]{
                DataTypes.createStructField("id", DataTypes.IntegerType, false),
        });
        List<Row> data = Arrays.asList(
                RowFactory.create(1),
                RowFactory.create(2)
        );

        // Create a DataFrame
        Dataset<Row> df = spark.createDataFrame(data, schema);

        spark.sql("use clickhouse;");
        df.createTempView("sparkView");
        spark.sql("insert into clickhouse.default.simple_table select * from sparkView");

        // Stop the Spark session
        spark.stop();
    }
}

And the ClickHouse create table statement is:

CREATE TABLE simple_table (
    id Int32 NOT NULL

) ENGINE = MergeTree()
ORDER BY id;

The result is the following exception:

Exception in thread "main" org.apache.spark.SparkException: Writing job aborted
	at org.apache.spark.sql.errors.QueryExecutionErrors$.writingJobAbortedError(QueryExecutionErrors.scala:767)
	at org.apache.spark.sql.execution.datasources.v2.V2TableWriteExec.writeWithV2(WriteToDataSourceV2Exec.scala:409)
	at org.apache.spark.sql.execution.datasources.v2.V2TableWriteExec.writeWithV2$(WriteToDataSourceV2Exec.scala:353)
	at org.apache.spark.sql.execution.datasources.v2.AppendDataExec.writeWithV2(WriteToDataSourceV2Exec.scala:244)
	at org.apache.spark.sql.execution.datasources.v2.V2ExistingTableWriteExec.run(WriteToDataSourceV2Exec.scala:332)
	at org.apache.spark.sql.execution.datasources.v2.V2ExistingTableWriteExec.run$(WriteToDataSourceV2Exec.scala:331)
	at org.apache.spark.sql.execution.datasources.v2.AppendDataExec.run(WriteToDataSourceV2Exec.scala:244)
	at org.apache.spark.sql.execution.datasources.v2.V2CommandExec.result$lzycompute(V2CommandExec.scala:43)
	at org.apache.spark.sql.execution.datasources.v2.V2CommandExec.result(V2CommandExec.scala:43)
	at org.apache.spark.sql.execution.datasources.v2.V2CommandExec.executeCollect(V2CommandExec.scala:49)
	at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.$anonfun$applyOrElse$1(QueryExecution.scala:98)
	at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$6(SQLExecution.scala:109)
	at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:169)
	at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$1(SQLExecution.scala:95)
	at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:779)
	at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:64)
	at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.applyOrElse(QueryExecution.scala:98)
	at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.applyOrElse(QueryExecution.scala:94)
	at org.apache.spark.sql.catalyst.trees.TreeNode.$anonfun$transformDownWithPruning$1(TreeNode.scala:584)
	at org.apache.spark.sql.catalyst.trees.CurrentOrigin$.withOrigin(TreeNode.scala:176)
	at org.apache.spark.sql.catalyst.trees.TreeNode.transformDownWithPruning(TreeNode.scala:584)
	at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.org$apache$spark$sql$catalyst$plans$logical$AnalysisHelper$$super$transformDownWithPruning(LogicalPlan.scala:30)
	at org.apache.spark.sql.catalyst.plans.logical.AnalysisHelper.transformDownWithPruning(AnalysisHelper.scala:267)
	at org.apache.spark.sql.catalyst.plans.logical.AnalysisHelper.transformDownWithPruning$(AnalysisHelper.scala:263)
	at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformDownWithPruning(LogicalPlan.scala:30)
	at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformDownWithPruning(LogicalPlan.scala:30)
	at org.apache.spark.sql.catalyst.trees.TreeNode.transformDown(TreeNode.scala:560)
	at org.apache.spark.sql.execution.QueryExecution.eagerlyExecuteCommands(QueryExecution.scala:94)
	at org.apache.spark.sql.execution.QueryExecution.commandExecuted$lzycompute(QueryExecution.scala:81)
	at org.apache.spark.sql.execution.QueryExecution.commandExecuted(QueryExecution.scala:79)
	at org.apache.spark.sql.Dataset.<init>(Dataset.scala:220)
	at org.apache.spark.sql.Dataset$.$anonfun$ofRows$2(Dataset.scala:100)
	at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:779)
	at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:97)
	at org.apache.spark.sql.SparkSession.$anonfun$sql$1(SparkSession.scala:622)
	at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:779)
	at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:617)
	at org.example.Main.main(Main.java:44)
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 1 in stage 0.0 failed 1 times, most recent failure: Lost task 1.0 in stage 0.0 (TID 1) (192.168.1.2 executor driver): java.lang.NoClassDefFoundError: Could not initialize class org.apache.arrow.memory.util.MemoryUtil
	at org.apache.arrow.memory.ArrowBuf.setZero(ArrowBuf.java:1161)
	at org.apache.arrow.vector.BaseFixedWidthVector.initValidityBuffer(BaseFixedWidthVector.java:216)
	at org.apache.arrow.vector.BaseFixedWidthVector.zeroVector(BaseFixedWidthVector.java:210)
	at org.apache.arrow.vector.BaseFixedWidthVector.allocateBytes(BaseFixedWidthVector.java:342)
	at org.apache.arrow.vector.BaseFixedWidthVector.allocateNew(BaseFixedWidthVector.java:309)
	at org.apache.arrow.vector.BaseFixedWidthVector.allocateNew(BaseFixedWidthVector.java:274)
	at org.apache.spark.sql.execution.arrow.ArrowWriter$.$anonfun$create$1(ArrowWriter.scala:41)
	at scala.collection.StrictOptimizedIterableOps.map(StrictOptimizedIterableOps.scala:100)
	at scala.collection.StrictOptimizedIterableOps.map$(StrictOptimizedIterableOps.scala:87)
	at scala.collection.convert.JavaCollectionWrappers$JListWrapper.map(JavaCollectionWrappers.scala:103)
	at org.apache.spark.sql.execution.arrow.ArrowWriter$.create(ArrowWriter.scala:40)
	at xenon.clickhouse.write.format.ClickHouseArrowStreamWriter.<init>(ClickHouseArrowStreamWriter.scala:33)
	at xenon.clickhouse.write.ClickHouseBatchWrite.createWriter(ClickHouseWrite.scala:74)
	at org.apache.spark.sql.execution.datasources.v2.DataWritingSparkTask$.run(WriteToDataSourceV2Exec.scala:430)
	at org.apache.spark.sql.execution.datasources.v2.V2TableWriteExec.$anonfun$writeWithV2$2(WriteToDataSourceV2Exec.scala:381)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:136)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:548)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1504)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:551)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.RuntimeException: Failed to initialize MemoryUtil. [in thread "Executor task launch worker for task 0.0 in stage 0.0 (TID 0)"]
	at org.apache.arrow.memory.util.MemoryUtil.<clinit>(MemoryUtil.java:136)
	... 23 more

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2672)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2608)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2607)
	at scala.collection.immutable.List.foreach(List.scala:333)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2607)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1182)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1182)
	at scala.Option.foreach(Option.scala:437)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1182)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2860)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2802)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2791)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:952)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2238)
	at org.apache.spark.sql.execution.datasources.v2.V2TableWriteExec.writeWithV2(WriteToDataSourceV2Exec.scala:377)
	... 36 more
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.apache.arrow.memory.util.MemoryUtil
	at org.apache.arrow.memory.ArrowBuf.setZero(ArrowBuf.java:1161)
	at org.apache.arrow.vector.BaseFixedWidthVector.initValidityBuffer(BaseFixedWidthVector.java:216)
	at org.apache.arrow.vector.BaseFixedWidthVector.zeroVector(BaseFixedWidthVector.java:210)
	at org.apache.arrow.vector.BaseFixedWidthVector.allocateBytes(BaseFixedWidthVector.java:342)
	at org.apache.arrow.vector.BaseFixedWidthVector.allocateNew(BaseFixedWidthVector.java:309)
	at org.apache.arrow.vector.BaseFixedWidthVector.allocateNew(BaseFixedWidthVector.java:274)
	at org.apache.spark.sql.execution.arrow.ArrowWriter$.$anonfun$create$1(ArrowWriter.scala:41)
	at scala.collection.StrictOptimizedIterableOps.map(StrictOptimizedIterableOps.scala:100)
	at scala.collection.StrictOptimizedIterableOps.map$(StrictOptimizedIterableOps.scala:87)
	at scala.collection.convert.JavaCollectionWrappers$JListWrapper.map(JavaCollectionWrappers.scala:103)
	at org.apache.spark.sql.execution.arrow.ArrowWriter$.create(ArrowWriter.scala:40)
	at xenon.clickhouse.write.format.ClickHouseArrowStreamWriter.<init>(ClickHouseArrowStreamWriter.scala:33)
	at xenon.clickhouse.write.ClickHouseBatchWrite.createWriter(ClickHouseWrite.scala:74)
	at org.apache.spark.sql.execution.datasources.v2.DataWritingSparkTask$.run(WriteToDataSourceV2Exec.scala:430)
	at org.apache.spark.sql.execution.datasources.v2.V2TableWriteExec.$anonfun$writeWithV2$2(WriteToDataSourceV2Exec.scala:381)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:136)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:548)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1504)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:551)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.RuntimeException: Failed to initialize MemoryUtil. [in thread "Executor task launch worker for task 0.0 in stage 0.0 (TID 0)"]
	at org.apache.arrow.memory.util.MemoryUtil.<clinit>(MemoryUtil.java:136)
	... 23 more

I already tried to set java.base/sun.nio.ch=ALL-UNNAMED as a JVM option, I didn't work.

Some references that might help:

pan3793 commented

how do you start your program, just click the "Run" button in IDEA?

BentsiLeviav commented

@pan3793
Yes, that's right. Doing it during development.
My pom.xml file is as follow:

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <groupId>org.example</groupId>
    <artifactId>ClickHouseSparkPlayground</artifactId>
    <version>1.0-SNAPSHOT</version>

    <properties>
        <maven.compiler.source>17</maven.compiler.source>
        <maven.compiler.target>17</maven.compiler.target>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <spark_binary_version></spark_binary_version>
        <scala_binary_version></scala_binary_version>
    </properties>
    <dependencies>
        <!-- https://mvnrepository.com/artifact/org.apache.spark/spark-core -->
        <dependency>
            <groupId>org.apache.spark</groupId>
            <artifactId>spark-core_2.13</artifactId>
            <version>3.3.2</version>
        </dependency>

        <dependency>
            <groupId>com.github.housepower</groupId>
            <artifactId>clickhouse-spark-runtime-3.3_2.13</artifactId>
            <version>0.7.3</version>
        </dependency>
        <!-- https://mvnrepository.com/artifact/org.apache.spark/spark-sql -->
        <dependency>
            <groupId>org.apache.spark</groupId>
            <artifactId>spark-sql_2.13</artifactId>
            <version>3.3.2</version>
        </dependency>

        <dependency>
            <groupId>com.clickhouse</groupId>
            <artifactId>clickhouse-jdbc</artifactId>
            <classifier>all</classifier>
            <version>0.4.6</version>
            <exclusions>
                <exclusion>
                    <groupId>*</groupId>
                    <artifactId>*</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
    </dependencies>

</project>
pan3793 commented

AFAIK, IDEA can not infer the Java options from pom.xml, so you MUST set it manually.

image 
-XX:+IgnoreUnrecognizedVMOptions
--add-modules=jdk.incubator.vector
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
--add-opens=java.base/java.lang.reflect=ALL-UNNAMED
--add-opens=java.base/java.io=ALL-UNNAMED
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/java.util.concurrent=ALL-UNNAMED
--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED
--add-opens=java.base/jdk.internal.ref=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
--add-opens=java.base/sun.nio.cs=ALL-UNNAMED
--add-opens=java.base/sun.security.action=ALL-UNNAMED
--add-opens=java.base/sun.util.calendar=ALL-UNNAMED
-Djdk.reflect.useDirectMethodHandle=false
-Dio.netty.tryReflectionSetAccessible=true

Well this can be achieve by Gradle,

tasks.withType(JavaExec).configureEach {
    jvmArgs = [
            "-XX:+IgnoreUnrecognizedVMOptions",
            "--add-modules=jdk.incubator.vector",
            "--add-opens=java.base/java.lang=ALL-UNNAMED",
            "--add-opens=java.base/java.lang.invoke=ALL-UNNAMED",
            "--add-opens=java.base/java.lang.reflect=ALL-UNNAMED",
            "--add-opens=java.base/java.io=ALL-UNNAMED",
            "--add-opens=java.base/java.net=ALL-UNNAMED",
            "--add-opens=java.base/java.nio=ALL-UNNAMED",
            "--add-opens=java.base/java.util=ALL-UNNAMED",
            "--add-opens=java.base/java.util.concurrent=ALL-UNNAMED",
            "--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED",
            "--add-opens=java.base/jdk.internal.ref=ALL-UNNAMED",
            "--add-opens=java.base/sun.nio.ch=ALL-UNNAMED",
            "--add-opens=java.base/sun.nio.cs=ALL-UNNAMED",
            "--add-opens=java.base/sun.security.action=ALL-UNNAMED",
            "--add-opens=java.base/sun.util.calendar=ALL-UNNAMED",
            "-Djdk.reflect.useDirectMethodHandle=false",
            "-Dio.netty.tryReflectionSetAccessible=true"
    ]
}
BentsiLeviav commented

Yes, that solved it. Thanks!