1. Introduction to SeqWare
  2. Installation
  3. Getting Started
  4. SeqWare Pipeline
  5. SeqWare MetaDB
  6. SeqWare Portal
  7. SeqWare Web Service
  8. SeqWare Query Engine
  9. Glossary
  10. Frequently Asked Questions
  11. APIs
  12. Source Code
  13. Plugins
  14. Modules
  15. Advanced Topics
    1. Installing the Oozie client.
    2. Configuring the Oozie client
    3. Commands to query Oozie:
    4. Terminating an oozie job:
    5. Restarting a terminated Oozie job
    6. Resuming a suspended Oozie job

Monitoring Oozie

Installing the Oozie client.

  1. Add the cdh4 repository (detailed cdh4 guide is here:http://www.cloudera.com/content/cloudera/en/documentation/cdh4/v4-5-0/CDH4-Installation-Guide/cdh4ig_topic_4.html) to your sources list (/etc/apt/sources.list.d/cloudera.list)
    deb [arch=amd64] http://archive.cloudera.com/cdh4/ubuntu/precise/amd64/cdh precise-cdh4 contrib
    deb-src http://archive.cloudera.com/cdh4/ubuntu/precise/amd64/cdh precise-cdh4 contrib
  2. Install the oozie client:
    sudo apt-get update
    sudo apt-get install oozie-client

Configuring the Oozie client

  1. Add oozie host and timezone to ~/.bashrc:
    export OOZIE_URL="http://localhost:11000/oozie"
  2. Source your bashrc file:
    source ~/.bashrc
  3. Test your configuration:
    user@localhost:~$ oozie admin -version
    Oozie server build version: 3.3.2-cdh4.5.0

Commands to query Oozie:

  1. List top 100 jobs:
    user@localhost:~$ oozie jobs
  2. List top 5 (or any other specific number) jobs:
    user@localhost:~$ oozie jobs -len 5
  3. Get detailed information on an oozie job:
    user@localhost:~$ oozie job -info <OOZIE_JOB_ID> [-verbose]
  4. Get detailed information on an oozie action:
    user@localhost:~$ oozie job -info <OOZIE_ACTION_ID>
  5. Get the log for an oozie job:
    user@localhost:~$ oozie job -log <OOZIE_JOB_ID>

Terminating an oozie job:

First, use get the job ID by finding it in the list from oozie jobs or the details of oozie job -info <OOZIE_JOB_ID>. Then kill the job:

user@localhost:~$ oozie job -kill <OOZIE_JOB_ID>

Restarting a terminated Oozie job

  1. You will need a “job.properties” file which is used to configure the job when it resumes. If you don’t have one, you can create one. Here is an example:
    oozie.wf.application.path=<OOZIE APP PATH, eg: hdfs://localhost:18020/user/someUser/seqware_workflow/oozie-da66ddd3-1f1b-4441-8f04-658db9a8644a>

    Note: The host and port numbers shown assume that you are running SeqWare in a VirtualBox instance, with the port forwarding configured. See here for more details. If you are not connecting to SeqWare running inside a local virtual machine, you may want to adjust these values.

  2. Re-run the oozie job using the properties file:
    user@localhost:~$ oozie job -rerun <OOZIE_JOB_ID> -config job.properties

Resuming a suspended Oozie job

  1. It’s probably a good idea to first try to determine why the job was suspended. You can chekc the log, or the job info:
    user@localhost:~$ oozie job -info <OOZIE_JOB_ID> [-verbose]


    user@localhost:~$ oozie job -log <OOZIE_JOB_ID>
  2. Resume the oozie job:
    user@localhost:~$ oozie job -resume <OOZIE_JOB_ID>