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Simple and Distributed Machine Learning
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Error trying to install mmlspark #771

Open chongjeeseng opened 4 years ago

chongjeeseng commented 4 years ago

When trying to install mmlspark, I encountered an error and googling it does not seem to yield many results.

Some Info about my setup

The stack trace:

[root@emr-header-1 user]# pyspark --packages com.microsoft.ml.spark:mmlspark_2.11:1.0.0-rc1
Python 3.7.3 (default, Mar 27 2019, 22:11:17)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
Ivy Default Cache set to: /root/.ivy2/cache
The jars for the packages stored in: /root/.ivy2/jars
:: loading settings :: url = jar:file:/opt/apps/ecm/service/spark/2.4.3-1.2.0/package/spark-2.4.3-1.2.0-bin-hadoop2.8/jars/ivy-2.4.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
com.microsoft.ml.spark#mmlspark_2.11 added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent-c9c90838-fd3d-49eb-863e-9b900f348032;1.0
        confs: [default]
        found com.microsoft.ml.spark#mmlspark_2.11;1.0.0-rc1 in spark-list
        found org.scalactic#scalactic_2.11;3.0.5 in central
        found org.scala-lang#scala-reflect;2.11.12 in local-m2-cache
        found org.scalatest#scalatest_2.11;3.0.5 in central
        found org.scala-lang.modules#scala-xml_2.11;1.0.6 in local-m2-cache
        found io.spray#spray-json_2.11;1.3.2 in central
        found com.microsoft.cntk#cntk;2.4 in central
        found org.openpnp#opencv;3.2.0-1 in central
        found com.jcraft#jsch;0.1.54 in central
        found org.apache.httpcomponents#httpclient;4.5.6 in central
        found org.apache.httpcomponents#httpcore;4.4.10 in central
        found commons-logging#commons-logging;1.2 in central
        found commons-codec#commons-codec;1.10 in local-m2-cache
        found com.microsoft.ml.lightgbm#lightgbmlib;2.3.100 in central
        found com.github.vowpalwabbit#vw-jni;8.7.0.3 in central
:: resolution report :: resolve 454ms :: artifacts dl 17ms
        :: modules in use:
        com.github.vowpalwabbit#vw-jni;8.7.0.3 from central in [default]
        com.jcraft#jsch;0.1.54 from central in [default]
        com.microsoft.cntk#cntk;2.4 from central in [default]
        com.microsoft.ml.lightgbm#lightgbmlib;2.3.100 from central in [default]
        com.microsoft.ml.spark#mmlspark_2.11;1.0.0-rc1 from spark-list in [default]
        commons-codec#commons-codec;1.10 from local-m2-cache in [default]
        commons-logging#commons-logging;1.2 from central in [default]
        io.spray#spray-json_2.11;1.3.2 from central in [default]
        org.apache.httpcomponents#httpclient;4.5.6 from central in [default]
        org.apache.httpcomponents#httpcore;4.4.10 from central in [default]
        org.openpnp#opencv;3.2.0-1 from central in [default]
        org.scala-lang#scala-reflect;2.11.12 from local-m2-cache in [default]
        org.scala-lang.modules#scala-xml_2.11;1.0.6 from local-m2-cache in [default]
        org.scalactic#scalactic_2.11;3.0.5 from central in [default]
        org.scalatest#scalatest_2.11;3.0.5 from central in [default]
        ---------------------------------------------------------------------
        |                  |            modules            ||   artifacts   |
        |       conf       | number| search|dwnlded|evicted|| number|dwnlded|
        ---------------------------------------------------------------------
        |      default     |   15  |   0   |   0   |   0   ||   15  |   0   |
        ---------------------------------------------------------------------

:: problems summary ::
:::: WARNINGS
                [NOT FOUND  ] org.scala-lang.modules#scala-xml_2.11;1.0.6!scala-xml_2.11.jar(bundle) (3ms)

        ==== local-m2-cache: tried

          file:/root/.m2/repository/org/scala-lang/modules/scala-xml_2.11/1.0.6/scala-xml_2.11-1.0.6.jar

                [NOT FOUND  ] commons-codec#commons-codec;1.10!commons-codec.jar (0ms)

        ==== local-m2-cache: tried

          file:/root/.m2/repository/commons-codec/commons-codec/1.10/commons-codec-1.10.jar

                ::::::::::::::::::::::::::::::::::::::::::::::

                ::              FAILED DOWNLOADS            ::

                :: ^ see resolution messages for details  ^ ::

                ::::::::::::::::::::::::::::::::::::::::::::::

                :: org.scala-lang.modules#scala-xml_2.11;1.0.6!scala-xml_2.11.jar(bundle)

                :: commons-codec#commons-codec;1.10!commons-codec.jar

                ::::::::::::::::::::::::::::::::::::::::::::::

:: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
Exception in thread "main" java.lang.RuntimeException: [download failed: org.scala-lang.modules#scala-xml_2.11;1.0.6!scala-xml_2.11.jar(bundle), download failed: commons-codec#commons-codec;1.10!commons-codec.jar]
        at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1308)
        at org.apache.spark.deploy.DependencyUtils$.resolveMavenDependencies(DependencyUtils.scala:54)
        at org.apache.spark.deploy.SparkSubmit.prepareSubmitEnvironment(SparkSubmit.scala:315)
        at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:143)
        at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:86)
        at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:926)
        at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:935)
        at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Traceback (most recent call last):
  File "/usr/lib/spark-current/python/pyspark/shell.py", line 38, in <module>
    SparkContext._ensure_initialized()
  File "/usr/lib/spark-current/python/pyspark/context.py", line 316, in _ensure_initialized
    SparkContext._gateway = gateway or launch_gateway(conf)
  File "/usr/lib/spark-current/python/pyspark/java_gateway.py", line 46, in launch_gateway
    return _launch_gateway(conf)
  File "/usr/lib/spark-current/python/pyspark/java_gateway.py", line 108, in _launch_gateway
    raise Exception("Java gateway process exited before sending its port number")
Exception: Java gateway process exited before sending its port number

Would gladly appreciate any pointers in tracing the issue.

welcome[bot] commented 4 years ago

👋 Thanks for opening your first issue here! If you're reporting a 🐞 bug, please make sure you include steps to reproduce it.

imatiach-msft commented 4 years ago

@chongjeeseng based on a quick online search, this may be a jupyter issue where SPARK_HOME is not set: https://github.com/jupyter/jupyter/issues/248 I haven't seen this issue before however, I will leave it open for now in case others see it as well

chongjeeseng commented 4 years ago

@chongjeeseng based on a quick online search, this may be a jupyter issue where SPARK_HOME is not set: jupyter/jupyter#248 I haven't seen this issue before however, I will leave it open for now in case others see it as well

hi @imatiach-msft thank you for replying, I have followed the link to the Jupyter issue you posted, but unfortunately it seems that the SPARK_HOME environment variable is set correctly.

Inputting the %env magic function into Jupyter yields the following information. As you can see,

SPARK_HOME is set to the value of '/usr/lib/spark-current'

'ZOO_LOG_DIR': '/mnt/disk1/log/zookeeper',
 'CONDA_SHLVL': '0',
 'JAVA_LIBRARY_PATH': '/usr/lib/hadoop-current/lib/native:/usr/lib/bigboot-current/lib:/usr/lib/hadoop-current/lib/native:/usr/lib/bigboot-current/lib:',
 'HIVE_CONF_DIR': '/etc/ecm/hive-conf',
 'SHELL': '/bin/bash',
 'ZEPPELIN_NOTEBOOK_DIR': '/mnt/disk1/zeppelin/notebooks',
 'LOGNAME': 'root',
 '_': '/opt/anaconda3/bin/jupyter',
 'HADOOP_HOME': '/usr/lib/hadoop-current',
 'YARN_PID_DIR': '/usr/lib/hadoop-current/pids',
 'USER': 'root',
 'SUDO_COMMAND': '/bin/su',
 'HADOOP_CONF_DIR': '/etc/ecm/hadoop-conf',
 'ZEPPELIN_CONF_DIR': '/etc/ecm/zeppelin-conf',
 'ZEPPELIN_HOME': '/usr/lib/zeppelin-current',
 'YARN_LOG_DIR': '/var/log/hadoop-yarn',
 'SPARK_CONF_DIR': '/etc/ecm/spark-conf',
 'PIG_HOME': '/usr/lib/pig-current',
 'OOZIE_URL': 'http://emr-header-1.cluster-41646:11000/oozie/',
 'SHLVL': '1',
 'XDG_SESSION_ID': '209',
 'OOZIE_CONFIG': '/etc/ecm/oozie-conf',
 'HISTTIMEFORMAT': '%d/%m/%y %T ',
 'HIVE_HOME': '/usr/lib/hive-current',
 'ZOOCFGDIR': '/etc/ecm/zookeeper-conf',
 'HADOOP_MAPRED_PID_DIR': '/usr/lib/hadoop-current/pids',
 'JAVA_HOME': '/usr/lib/jvm/java-1.8.0',
 'HISTSIZE': '1000',
 'BIGBOOT_HOME': '/usr/lib/bigboot-current',
 'HADOOP_CLASSPATH': '/usr/lib/hadoop-current/lib/*:/usr/lib/tez-current/*:/usr/lib/tez-current/lib/*:/etc/ecm/tez-conf:/usr/lib/hadoop-current/lib/*:/usr/lib/tez-current/*:/usr/lib/tez-current/lib/*:/etc/ecm/tez-conf:/opt/apps/extra-jars/*:/usr/lib/spark-current/yarn/spark-2.4.3-yarn-shuffle.jar:/opt/apps/extra-jars/*:/usr/lib/spark-current/yarn/spark-2.4.3-yarn-shuffle.jar',
 'SPARK_HOME': '/usr/lib/spark-current',
 'CONDA_ROOT': '/opt/anaconda3',
 'HUE_HOME': '/usr/lib/hue-current',
 'SQOOP_HOME': '/usr/lib/sqoop-current',
 'HADOOP_LOG_DIR': '/var/log/hadoop-hdfs',
 'ZOO_LOG4J_PROP': 'INFO,ROLLINGFILE',
 'HISTCONTROL': 'ignoredups',
 'SUDO_USER': 'user',
 'SUDO_GID': '1012',
 'PIG_CONF_DIR': '/etc/ecm/pig-conf',
 'HOSTNAME': 'emr-header-1.cluster-41646',
 'SUDO_UID': '1012',
 'SQOOP_CONF_DIR': '/etc/ecm/sqoop-conf',
 'LESSOPEN': '||/usr/bin/lesspipe.sh %s',
 'SPARK_LOG_DIR': '/mnt/disk1/log/spark',
 'FLOW_AGENT_HOME': '/usr/lib/flow-agent-current',
 'HADOOP_MAPRED_LOG_DIR': '/var/log/hadoop-mapred',
 'FLOW_AGENT_CONF_DIR': '/etc/ecm/flow-agent-conf',
 'LIVY_CONF_DIR': '/etc/ecm/livy-conf',
 'TEZ_HOME': '/usr/lib/tez-current',
 'SPARK_PID_DIR': '/usr/lib/spark-current/pids',
 'MAIL': '/var/spool/mail/root',
 'JVMFLAGS': ' -verbose:gc -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+UseGCLogFileRotation -XX:NumberOfGCLogFiles=5 -XX:GCLogFileSize=128M -Xloggc:/mnt/disk1/log/zookeeper/zookeeper-gc.log -javaagent:/var/lib/ecm-agent/data/jmxetric-1.0.8.jar=host=localhost,port=8649,mode=unicast,wireformat31x=true,process=ZOOKEEPER_ZOOKEEPER,config=/var/lib/ecm-agent/data/jmxetric.xml -verbose:gc -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+UseGCLogFileRotation -XX:NumberOfGCLogFiles=5 -XX:GCLogFileSize=128M -Xloggc:/mnt/disk1/log/zookeeper/zookeeper-gc.log -javaagent:/var/lib/ecm-agent/data/jmxetric-1.0.8.jar=host=localhost,port=8649,mode=unicast,wireformat31x=true,process=ZOOKEEPER_ZOOKEEPER,config=/var/lib/ecm-agent/data/jmxetric.xml',
 'USERNAME': 'root',
 'OLDPWD': '/root/airflow',
 'PWD': '/root',
 'LANG': 'en_US.UTF-8',
 'TERM': 'xterm-color',
 'PATH': '/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/opt/anaconda3/bin:/usr/lib/sqoop-current/bin:/usr/lib/spark-current/bin:/usr/lib/pig-current/bin:/usr/lib/hive-current/hcatalog/bin:/usr/lib/hive-current/bin:/usr/local/sbin:/usr/lib/sqoop-current/bin:/usr/lib/spark-current/bin:/usr/lib/pig-current/bin:/usr/lib/hive-current/hcatalog/bin:/usr/lib/hive-current/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/lib/bigboot-current/bin:/usr/lib/flow-agent-current/bin:/usr/lib/hadoop-current/bin:/usr/lib/hadoop-current/sbin:/usr/lib/oozie-current/bin:/usr/lib/hadoop-current/bin:/usr/lib/hadoop-current/sbin:/usr/local/bin/:/usr/lib/bigboot-current/bin:/usr/lib/flow-agent-current/bin:/usr/lib/hadoop-current/bin:/usr/lib/hadoop-current/sbin:/usr/lib/oozie-current/bin:/usr/lib/hadoop-current/bin:/usr/lib/hadoop-current/sbin',
 'LIVY_HOME': '/usr/lib/livy-current',
 'OOZIE_HOME': '/usr/lib/oozie-current',
 'HCAT_HOME': '/usr/lib/hive-current/hcatalog',
 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:',
 'HADOOP_PID_DIR': '/usr/lib/hadoop-current/pids',
 'TEZ_CONF_DIR': '/etc/ecm/tez-conf',
 'HOME': '/root',
 'ZOOKEEPER_HOME': '/usr/lib/zookeeper-current',
 'HUE_CONF_DIR': '/etc/ecm/hue-conf',
 'JPY_PARENT_PID': '12794',
 'CLICOLOR': '1',
 'PAGER': 'cat',
 'GIT_PAGER': 'cat',
 'MPLBACKEND': 'module://ipykernel.pylab.backend_inline',
 'PYSPARK_DRIVER_PYTHON': '/home/user/.conda/envs/test_env/bin/python',
 'PYSPARK_PYTHON': '/mnt/disk1/user/test_env/bin/python'

I think something else is causing the issue but the error does not seem to be very descriptive beyond the fact that the java process exited before sending the driver its port number.

EDIT: I would also like to note that starting a normal Pyspark session without adding the repository and mmlspark package as a config does not yield any issues.

gramhagen commented 4 years ago

In your config there are some livy parameters, are you running this using Apache Livy?

If so, to get that working I had to exclude some packages during the configuration (which was done within the notebook using configure magic)

%%configure -f
{
    "name": "mmlspark",
    "conf": {
        "spark.jars.packages": "com.microsoft.ml.spark:mmlspark_2.11:1.0.0-rc1",
        "spark.jars.repositories": "https://mmlspark.azureedge.net/maven",
        "spark.jars.excludes": "org.scala-lang:scala-reflect,org.apache.spark:spark-tags_2.11,org.scalactic:scalactic_2.11,org.scalatest:scalatest_2.11"
    }
}
John-Farseer commented 4 years ago

hello, I meet the same trouble. I have solved the problem ! you can try the follows:

pyspark --packages com.microsoft.ml.spark:mmlspark_2.11:1.0.0-rc1 --repositories=https://mmlspark.azureedge.net/maven

Hope my way works for you!!! hhhhhhhhh

John-Farseer commented 4 years ago

@chongjeeseng spirit from this URL: https://www.diycode.cc/projects/Azure/mmlspark

ronasama commented 4 years ago

I resolved this problem to specify microsoft repository. Thanks.

os.environ['PYSPARK_SUBMIT_ARGS'] = "--master yarn-client --num-executors 1 --executor-memory 1g --packages com.microsoft.ml.spark:mmlspark_2.11:1.0.0-rc3 --repositories 'https://mmlspark.azureedge.net/maven' pyspark-shell"