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From Michał Wesołowski (Jira) <j...@apache.org>
Subject [jira] [Created] (SPARK-29574) spark with user provided hadoop doesn't work on kubernetes
Date Wed, 23 Oct 2019 15:29:00 GMT
Michał Wesołowski created SPARK-29574:
-----------------------------------------

             Summary: spark with user provided hadoop doesn't work on kubernetes
                 Key: SPARK-29574
                 URL: https://issues.apache.org/jira/browse/SPARK-29574
             Project: Spark
          Issue Type: Bug
          Components: Kubernetes
    Affects Versions: 2.4.4
            Reporter: Michał Wesołowski


When spark-submit is run with image built with "hadoop free" spark and user provided hadoop
it fails on kubernetes (hadoop libraries are not on spark's classpath). 

I downloaded spark [Pre-built with user-provided Apache Hadoop|https://www-us.apache.org/dist/spark/spark-2.4.4/spark-2.4.4-bin-without-hadoop.tgz]. 

I created docker image with usage of [docker-image-tool.sh|[https://github.com/apache/spark/blob/master/bin/docker-image-tool.sh]]. 

 

Based on this image (2.4.4-without-hadoop)

I created another one with Dockerfile
{code:java}
FROM spark-py:2.4.4-without-hadoop
ENV SPARK_HOME=/opt/spark/
# This is needed for newer kubernetes versions
ADD https://repo1.maven.org/maven2/io/fabric8/kubernetes-client/4.6.1/kubernetes-client-4.6.1.jar
$SPARK_HOME/jars
COPY spark-env.sh /opt/spark/conf/spark-env.sh
RUN chmod +x /opt/spark/conf/spark-env.sh
RUN wget -qO- https://www-eu.apache.org/dist/hadoop/common/hadoop-3.2.1/hadoop-3.2.1.tar.gz
| tar xz  -C /opt/
ENV HADOOP_HOME=/opt/hadoop-3.2.1
ENV PATH=${HADOOP_HOME}/bin:${PATH}

{code}
Contents of spark-env.sh:
{code:java}
#!/usr/bin/env bash
export SPARK_DIST_CLASSPATH=$(hadoop classpath):$HADOOP_HOME/share/hadoop/tools/lib/*
export LD_LIBRARY_PATH=$HADOOP_HOME/lib/native
{code}
spark-submit run with image crated this way fails since spark-env.sh is overwritten by [volume
created when pod starts|https://github.com/apache/spark/blob/master/resource-managers/kubernetes/core/src/main/scala/org/apache/spark/deploy/k8s/submit/KubernetesClientApplication.scala#L108]

As quick workaround I tried to modify [entrypoint script|https://github.com/apache/spark/blob/ea8b5df47476fe66b63bd7f7bcd15acfb80bde78/resource-managers/kubernetes/docker/src/main/dockerfiles/spark/entrypoint.sh]
to run spark-env.sh during startup and moving spark-env.sh to a different directory. 
 Driver starts without issues in this setup however, evethough SPARK_DIST_CLASSPATH is set
executor is constantly failing:
{code:java}
PS C:\Sandbox\projekty\roboticdrive-analytics\components\docker-images\spark-rda> kubectl
logs rda-script-1571835692837-exec-12
++ id -u
+ myuid=0
++ id -g
+ mygid=0
+ set +e
++ getent passwd 0
+ uidentry=root:x:0:0:root:/root:/bin/ash
+ set -e
+ '[' -z root:x:0:0:root:/root:/bin/ash ']'
+ source /opt/spark-env.sh
+++ hadoop classpath
++ export 'SPARK_DIST_CLASSPATH=/opt/hadoop-3.2.1/etc/hadoop:/opt/hadoop-3.2.1/share/hadoop/common/lib/*:/opt/hadoop-3.2.1/share/hadoop/common/*:/opt/hadoop-3.2.1/share/hadoop/hdfs:/opt/hadoop-3.2.1/share/hadoop/hdfs/lib/*:/opt/hadoop-3.2.1/share/hadoop/hdfs/*:/opt/hadoop-3.2.1/share/hadoop/mapreduce/lib/*:/opt/hadoop-3.2.1/share/hadoop/mapreduce/*:/opt/hadoop-3.2.1/share/hadoo++
SPARK_DIST_CLASSPATH='/opt/hadoop-3.2.1/etc/hadoop:/opt/hadoop-3.2.1/share/hadoop/common/lib/*:/opt/hadoop-3.2.1/share/hadoop/common/*:/opt/hadoop-3.2.1/share/hadoop/hdfs:/opt/hadoop-3.2.1/share/hadoop/hdfs/lib/*:/opt/hadoop-3.2.1/share/hadoop/hdfs/*:/opt/hadoop-3.2.1/share/hadoop/mapreduce/lib/*:/opt/hadoop-3.2.1/share/hadoop/mapreduce/*:/opt/hadoop-3.2.1/share/hadoop/yarn:/opt/hadoop-3.2.1/share/hadoop/yarn/lib/*:/opt/hadoop-3.2.1/share/hadoop/yarn/*:/opt/hadoop-3.2.1/share/hadoop/tools/lib/*'
++ export LD_LIBRARY_PATH=/opt/hadoop-3.2.1/lib/native
++ LD_LIBRARY_PATH=/opt/hadoop-3.2.1/lib/native
++ echo 'SPARK_DIST_CLASSPATH=/opt/hadoop-3.2.1/etc/hadoop:/opt/hadoop-3.2.1/share/hadoop/common/lib/*:/opt/hadoop-3.2.1/share/hadoop/common/*:/opt/hadoop-3.2.1/share/hadoop/hdfs:/opt/hadoop-3.2.1/share/hadoop/hdfs/lib/*:/opt/hadoop-3.2.1/share/hadoop/hdfs/*:/opt/hadoop-3.2.1/share/hadoop/mapreduce/lib/*:/opt/hadoop-3.2.1/share/hadoop/mapreduce/*:/opt/hadoop-3.2.1/share/hadoop/yarn:/opt/hadoop-3.2.1/share/hadoop/yarn/lib/*:/opt/hadoop-3.2.1/share/hadoop/yarn/*:/opt/hadoop-3.2.1/share/hadoop/tools/lib/*'
SPARK_DIST_CLASSPATH=/opt/hadoop-3.2.1/etc/hadoop:/opt/hadoop-3.2.1/share/hadoop/common/lib/*:/opt/hadoop-3.2.1/share/hadoop/common/*:/opt/hadoop-3.2.1/share/hadoop/hdfs:/opt/hadoop-3.2.1/share/hadoop/hdfs/lib/*:/opt/hadoop-3.2.1/share/hadoop/hdfs/*:/opt/hadoop-3.2.1/share/hadoop/mapreduce/lib/*:/opt/hadoop-3.2.1/share/hadoop/mapreduce/*:/opt/hadoop-3.2.1/share/hadoop/yarn:/opt/hadoop-3.2.1/share/hadoop/yarn/lib/*:/opt/hadoop-3.2.1/share/hadoop/yarn/*:/opt/hadoop-3.2.1/share/hadoop/tools/lib/*
++ echo LD_LIBRARY_PATH=/opt/hadoop-3.2.1/lib/native
+ SPARK_K8S_CMD=executor
LD_LIBRARY_PATH=/opt/hadoop-3.2.1/lib/native
+ case "$SPARK_K8S_CMD" in
+ shift 1
+ SPARK_CLASSPATH=':/opt/spark//jars/*'
+ env
+ sed 's/[^=]*=\(.*\)/\1/g'
+ sort -t_ -k4 -n
+ grep SPARK_JAVA_OPT_
+ readarray -t SPARK_EXECUTOR_JAVA_OPTS
+ '[' -n '' ']'
+ '[' -n '' ']'
+ PYSPARK_ARGS=
+ '[' -n '' ']'
+ R_ARGS=
+ '[' -n '' ']'
+ '[' '' == 2 ']'
+ '[' '' == 3 ']'
+ case "$SPARK_K8S_CMD" in
+ CMD=(${JAVA_HOME}/bin/java "${SPARK_EXECUTOR_JAVA_OPTS[@]}" -Xms$SPARK_EXECUTOR_MEMORY -Xmx$SPARK_EXECUTOR_MEMORY
-cp "$SPARK_CLASSPATH" org.apache.spark.executor.CoarseGrainedExecutorBackend --driver-url
$SPARK_DRIVER_URL --executor-id $SPARK_EXECUTOR_ID --cores $SPARK_EXECUTOR_CORES --app-id
$SPARK_APPLICATION_ID --hostname $SPARK_EXECUTOR_POD_IP)
+ exec /sbin/tini -s -- /usr/lib/jvm/java-1.8-openjdk/bin/java -Xms3g -Xmx3g -cp ':/opt/spark//jars/*'
org.apache.spark.executor.CoarseGrainedExecutorBackend --driver-url spark://CoarseGrainedScheduler@rda-script-1571835692837-driver-svc.default.svc:7078
--executor-id 12 --cores 1 --app-id spark-33382c27389c4b289d79c06d5f631819 --hostname 10.244.2.24
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/hadoop/fs/FSDataInputStream
        at org.apache.spark.executor.CoarseGrainedExecutorBackend$.run(CoarseGrainedExecutorBackend.scala:186)
        at org.apache.spark.executor.CoarseGrainedExecutorBackend$.main(CoarseGrainedExecutorBackend.scala:281)
        at org.apache.spark.executor.CoarseGrainedExecutorBackend.main(CoarseGrainedExecutorBackend.scala)
Caused by: java.lang.ClassNotFoundException: org.apache.hadoop.fs.FSDataInputStream
        at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 3 more
{code}



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