Hi Moon and al,
I have a standalone cluster with one master, one worker. I submit jobs
through zeppelin. master, worker, and zeppelin run in a separate container.
My zeppelin-env.sh:
# spark home
export SPARK_HOME=/usr/local/spark
# set hadoop conf dir
export HADOOP_CONF_DIR=/opt/hadoop-2.7.3/etc/hadoop
# set options to pass spark-submit command
export SPARK_SUBMIT_OPTIONS="--packages com.databricks:spark-csv_2.11:1.5.0
--deploy-mode cluster"
# worker memory
export ZEPPELIN_JAVA_OPTS="-Dspark.driver.memory=7g
-Dspark.submit.deployMode=cluster"
# master
export MASTER="spark://<master>:7077"
My notebook code is very simple. It read csv and write it again in
directory /data previously created:
%spark.pyspark
def read_input(fin):
'''
Read input file from filesystem and return dataframe
'''
df = sqlContext.read.load(fin, format='com.databricks.spark.csv',
mode='PERMISSIVE', header='false', inferSchema='true')
return df
def write_output(df, fout):
'''
Write dataframe to filesystem
'''
df.write.mode('overwrite').format('com.databricks.spark.csv').options(delimiter=',',
header='true').save(fout)
data_in = '/data/01.csv'
data_out = '/data/02.csv'
df = read_input(data_in)
newdf = del_columns(df)
write_output(newdf, data_out)
I used --deploy-mode to *cluster* so that the driver is run in the worker
in order to read the CSV in the /data directory and not in zeppelin. When
running the notebook it complains that
/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar is
missing:
org.apache.zeppelin.interpreter.InterpreterException: Ivy Default Cache set
to: /root/.ivy2/cache The jars for the packages stored in: /root/.ivy2/jars
:: loading settings :: url =
jar:file:/opt/spark-2.1.0/jars/ivy-2.4.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
com.databricks#spark-csv_2.11 added as a dependency :: resolving
dependencies :: org.apache.spark#spark-submit-parent;1.0 confs: [default]
found com.databricks#spark-csv_2.11;1.5.0 in central found
org.apache.commons#commons-csv;1.1 in central found
com.univocity#univocity-parsers;1.5.1 in central :: resolution report ::
resolve 310ms :: artifacts dl 6ms :: modules in use:
com.databricks#spark-csv_2.11;1.5.0 from central in [default]
com.univocity#univocity-parsers;1.5.1 from central in [default]
org.apache.commons#commons-csv;1.1 from central in [default]
--------------------------------------------------------------------- | |
modules || artifacts | | conf | number| search|dwnlded|evicted||
number|dwnlded|
--------------------------------------------------------------------- |
default | 3 | 0 | 0 | 0 || 3 | 0 |
--------------------------------------------------------------------- ::
retrieving :: org.apache.spark#spark-submit-parent confs: [default] 0
artifacts copied, 3 already retrieved (0kB/8ms) Running Spark using the
REST application submission protocol. SLF4J: Class path contains multiple
SLF4J bindings. SLF4J: Found binding in
[jar:file:/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in
[jar:file:/opt/zeppelin-0.7.1/lib/interpreter/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in
[jar:file:/opt/hadoop-2.7.3/share/hadoop/common/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
explanation. SLF4J: Actual binding is of type
[org.slf4j.impl.Log4jLoggerFactory] Warning: Master endpoint
spark://spark-drone-master-sofiane.autoetl.svc.cluster.local:7077 was not a
REST server. Falling back to legacy submission gateway instead. Ivy Default
Cache set to: /root/.ivy2/cache The jars for the packages stored in:
/root/.ivy2/jars com.databricks#spark-csv_2.11 added as a dependency ::
resolving dependencies :: org.apache.spark#spark-submit-parent;1.0 confs:
[default] found com.databricks#spark-csv_2.11;1.5.0 in central found
org.apache.commons#commons-csv;1.1 in central found
com.univocity#univocity-parsers;1.5.1 in central :: resolution report ::
resolve 69ms :: artifacts dl 5ms :: modules in use:
com.databricks#spark-csv_2.11;1.5.0 from central in [default]
com.univocity#univocity-parsers;1.5.1 from central in [default]
org.apache.commons#commons-csv;1.1 from central in [default]
--------------------------------------------------------------------- | |
modules || artifacts | | conf | number| search|dwnlded|evicted||
number|dwnlded|
--------------------------------------------------------------------- |
default | 3 | 0 | 0 | 0 || 3 | 0 |
--------------------------------------------------------------------- ::
retrieving :: org.apache.spark#spark-submit-parent confs: [default] 0
artifacts copied, 3 already retrieved (0kB/4ms)
java.nio.file.NoSuchFileException:
/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar at
sun.nio.fs.UnixException.translateToIOException(UnixException.java:86) at
sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
So, what I did next is copy the
/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar
in the worker container and restarted the interpreter and run the notebook.
It doesn't complain anymore about the zeppelin-spark_2.11-0.7.1.jar, but I
got another exception in the notebook related to the
RemoteInterpreterManagedProcess:
org.apache.zeppelin.interpreter.InterpreterException: Ivy Default Cache set
to: /root/.ivy2/cache The jars for the packages stored in: /root/.ivy2/jars
:: loading settings :: url =
jar:file:/opt/spark-2.1.0/jars/ivy-2.4.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
com.databricks#spark-csv_2.11 added as a dependency :: resolving
dependencies :: org.apache.spark#spark-submit-parent;1.0 confs: [default]
found com.databricks#spark-csv_2.11;1.5.0 in central found
org.apache.commons#commons-csv;1.1 in central found
com.univocity#univocity-parsers;1.5.1 in central :: resolution report ::
resolve 277ms :: artifacts dl 7ms :: modules in use:
com.databricks#spark-csv_2.11;1.5.0 from central in [default]
com.univocity#univocity-parsers;1.5.1 from central in [default]
org.apache.commons#commons-csv;1.1 from central in [default]
--------------------------------------------------------------------- | |
modules || artifacts | | conf | number| search|dwnlded|evicted||
number|dwnlded|
--------------------------------------------------------------------- |
default | 3 | 0 | 0 | 0 || 3 | 0 |
--------------------------------------------------------------------- ::
retrieving :: org.apache.spark#spark-submit-parent confs: [default] 0
artifacts copied, 3 already retrieved (0kB/8ms) Running Spark using the
REST application submission protocol. SLF4J: Class path contains multiple
SLF4J bindings. SLF4J: Found binding in
[jar:file:/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in
[jar:file:/opt/zeppelin-0.7.1/lib/interpreter/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in
[jar:file:/opt/hadoop-2.7.3/share/hadoop/common/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
explanation. SLF4J: Actual binding is of type
[org.slf4j.impl.Log4jLoggerFactory] Warning: Master endpoint
spark://spark-drone-master-sofiane.autoetl.svc.cluster.local:7077 was not a
REST server. Falling back to legacy submission gateway instead. Ivy Default
Cache set to: /root/.ivy2/cache The jars for the packages stored in:
/root/.ivy2/jars com.databricks#spark-csv_2.11 added as a dependency ::
resolving dependencies :: org.apache.spark#spark-submit-parent;1.0 confs:
[default] found com.databricks#spark-csv_2.11;1.5.0 in central found
org.apache.commons#commons-csv;1.1 in central found
com.univocity#univocity-parsers;1.5.1 in central :: resolution report ::
resolve 66ms :: artifacts dl 5ms :: modules in use:
com.databricks#spark-csv_2.11;1.5.0 from central in [default]
com.univocity#univocity-parsers;1.5.1 from central in [default]
org.apache.commons#commons-csv;1.1 from central in [default]
--------------------------------------------------------------------- | |
modules || artifacts | | conf | number| search|dwnlded|evicted||
number|dwnlded|
--------------------------------------------------------------------- |
default | 3 | 0 | 0 | 0 || 3 | 0 |
--------------------------------------------------------------------- ::
retrieving :: org.apache.spark#spark-submit-parent confs: [default] 0
artifacts copied, 3 already retrieved (0kB/4ms) at
org.apache.zeppelin.interpreter.remote.RemoteInterpreterManagedProcess.start(RemoteInterpreterManagedProcess.java:143)
at
org.apache.zeppelin.interpreter.remote.RemoteInterpreterProcess.reference(RemoteInterpreterProcess.java:73)
at
org.apache.zeppelin.interpreter.remote.RemoteInterpreter.open(RemoteInterpreter.java:258)
at
org.apache.zeppelin.interpreter.remote.RemoteInterpreter.getFormType(RemoteInterpreter.java:423)
at
org.apache.zeppelin.interpreter.LazyOpenInterpreter.getFormType(LazyOpenInterpreter.java:106)
at org.apache.zeppelin.notebook.Paragraph.jobRun(Paragraph.java:387) at
org.apache.zeppelin.scheduler.Job.run(Job.java:175) at
org.apache.zeppelin.scheduler.RemoteScheduler$JobRunner.run(RemoteScheduler.java:329)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266) at
java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at
java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
In the Spark jobs I see a
org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer running, and
the stderr logs complains about missing log4j.properties:
Launch Command: "/usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java" "-cp"
"/opt/zeppelin-0.7.1/interpreter/spark/*:/opt/zeppelin-0.7.1/lib/interpreter/*:/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar:/usr/local/spark/conf/:/usr/local/spark/jars/*:/opt/hadoop-2.7.3/etc/hadoop:/opt/hadoop-2.7.3/etc/hadoop/*:/opt/hadoop-2.7.3/share/hadoop/common/lib/*:/opt/hadoop-2.7.3/share/hadoop/common/*:/opt/hadoop-2.7.3/share/hadoop/hdfs/*:/opt/hadoop-2.7.3/share/hadoop/hdfs/lib/*:/opt/hadoop-2.7.3/share/hadoop/hdfs/*:/opt/hadoop-2.7.3/share/hadoop/yarn/lib/*:/opt/hadoop-2.7.3/share/hadoop/yarn/*:/opt/hadoop-2.7.3/share/hadoop/mapreduce/lib/*:/opt/hadoop-2.7.3/share/hadoop/mapreduce/*:/opt/hadoop-2.7.3/share/hadoop/tools/lib/*"
"-Xmx1024M"
"-Dspark.jars=file:/root/.ivy2/jars/com.databricks_spark-csv_2.11-1.5.0.jar,file:/root/.ivy2/jars/org.apache.commons_commons-csv-1.1.jar,file:/root/.ivy2/jars/com.univocity_univocity-parsers-1.5.1.jar,file:/root/.ivy2/jars/com.databricks_spark-csv_2.11-1.5.0.jar,file:/root/.ivy2/jars/org.apache.commons_commons-csv-1.1.jar,file:/root/.ivy2/jars/com.univocity_univocity-parsers-1.5.1.jar,file:/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar"
"-Dspark.driver.supervise=false" "-Dspark.driver.extraJavaOptions=
-Dfile.encoding=UTF-8
-Dlog4j.configuration=file:///opt/zeppelin-0.7.1/conf/log4j.properties
-Dzeppelin.log.file=/opt/zeppelin-0.7.1/logs/zeppelin-interpreter-spark--zeppelin-sofiane-1-zyfya.log"
"-Dspark.app.name=org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer"
"-Dspark.submit.deployMode=cluster"
"-Dspark.master=spark://spark-drone-master-sofiane.autoetl.svc.cluster.local:7077"
"-Dspark.driver.extraClassPath=::/opt/zeppelin-0.7.1/interpreter/spark/*:/opt/zeppelin-0.7.1/lib/interpreter/*::/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar"
"-Dspark.rpc.askTimeout=10s" "-Dfile.encoding=UTF-8"
"-Dlog4j.configuration=file:///opt/zeppelin-0.7.1/conf/log4j.properties"
"-Dzeppelin.log.file=/opt/zeppelin-0.7.1/logs/zeppelin-interpreter-spark--zeppelin-sofiane-1-zyfya.log"
"org.apache.spark.deploy.worker.DriverWrapper"
"spark://Worker@172.30.102.7:41417"
"/usr/local/spark/work/driver-20170503115405-0036/zeppelin-spark_2.11-0.7.1.jar"
"org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer"
"46151"
========================================
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in
[jar:file:/opt/zeppelin-0.7.1/interpreter/spark/zeppelin-spark_2.11-0.7.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in
[jar:file:/usr/local/spark/jars/slf4j-log4j12-1.7.16.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
log4j:ERROR Could not read configuration file from URL
[file:/opt/zeppelin-0.7.1/conf/log4j.properties].
java.io.FileNotFoundException:
/opt/zeppelin-0.7.1/conf/log4j.properties (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.<init>(FileInputStream.java:138)
at java.io.FileInputStream.<init>(FileInputStream.java:93)
at
sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90)
at
sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188)
at
org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:557)
at
org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
at org.apache.log4j.LogManager.<clinit>(LogManager.java:127)
at
org.slf4j.impl.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:64)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:285)
at
org.apache.commons.logging.impl.SLF4JLogFactory.getInstance(SLF4JLogFactory.java:155)
at
org.apache.commons.logging.impl.SLF4JLogFactory.getInstance(SLF4JLogFactory.java:132)
at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:685)
at
org.apache.hadoop.security.UserGroupInformation.<clinit>(UserGroupInformation.java:85)
at
org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2373)
at
org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2373)
at scala.Option.getOrElse(Option.scala:121)
at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2373)
at org.apache.spark.SecurityManager.<init>(SecurityManager.scala:221)
at
org.apache.spark.deploy.worker.DriverWrapper$.main(DriverWrapper.scala:42)
at
org.apache.spark.deploy.worker.DriverWrapper.main(DriverWrapper.scala)
log4j:ERROR Ignoring configuration file
[file:/opt/zeppelin-0.7.1/conf/log4j.properties].
log4j:WARN No appenders could be found for logger
(org.apache.hadoop.metrics2.lib.MutableMetricsFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
17/05/03 11:54:06 INFO SecurityManager: Changing view acls to: root
17/05/03 11:54:06 INFO SecurityManager: Changing modify acls to: root
17/05/03 11:54:06 INFO SecurityManager: Changing view acls groups to:
17/05/03 11:54:06 INFO SecurityManager: Changing modify acls groups to:
17/05/03 11:54:06 INFO SecurityManager: SecurityManager:
authentication disabled; ui acls disabled; users with view
permissions: Set(root); groups with view permissions: Set(); users
with modify permissions: Set(root); groups with modify permissions:
Set()
17/05/03 11:54:07 INFO Utils: Successfully started service 'Driver' on
port 39770.
17/05/03 11:54:07 INFO WorkerWatcher: Connecting to worker
spark://Worker@172.30.102.7:41417
17/05/03 11:54:07 INFO TransportClientFactory: Successfully created
connection to /172.30.102.7:41417 after 27 ms (0 ms spent in
bootstraps)
17/05/03 11:54:07 INFO WorkerWatcher: Successfully connected to
spark://Worker@172.30.102.7:41417
17/05/03 11:54:07 INFO RemoteInterpreterServer: Starting remote
interpreter server on port 46151
The process never finishes, so I got to kill it...
What's going on? Anything wrong with my configuration?
Any help appreciated. I am struggling since a week.
