Logging into the system

The preferred way to access the Systems Biology Knowledgebase computer (sbkbase.ornl.gov) which is a Linux server, is by using a Secure shell (ssh) utility.  There are various ssh utilities available depending on the machine that you are connecting from:

  1. If you are connecting from a Linux/Unix machine make sure you have the OpenSSH client installed and use this.
  2. If you are accessing from a Mac, it comes with an installation of OpenSSH and so you just need to use the Terminal to get access to ssh command.
  3. If you are accessing from a Windows machine then there are a couple of recommended options:
    1. Install Putty SSH client and use this to connect directly to sbkbase.ornl.gov. (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
    2. Or you can install Cygwin and OpenSSH on Windows and then run ssh from within cygwin. (http://pigtail.net/LRP/printsrv/cygwin-sshd.html)

Once you have your account setup on sbkbase, have a user name assigned to you and have SSH properly set up then just go to the appropriate terminal and connect as follows

ssh <username>@sbkbase.ornl.gov

Once you are authenticated and have access to the system you will be on the Master node in your home directory. Hadoop is installed in the /opt directory. Make sure you have the following line in the .bashrc file in your home directory

export PATH=$PATH:/opt/hadoop/bin

Source the file to have hadoop binaries in your Path.

The main utility  for accessing the Hadoop system is “hadoop”. You can type this on the command line to get a list of command which the hadoop utility can run.

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