The Java Runtime Environment (JRE) version 1.6.0_11 is currently available cluster-wide on Palmetto. If a user needs a different version of Java, or if the Java Development Kit (JDK, which includes the JRE) is needed, that user is encouraged to download and install Java (JRE or JDK) for herself. Below is a brief overview of installing the JDK in a user’s /home directory.


The JRE is basically the Java Virtual Machine (Java VM) that provides a platform for running your Java programs. The JDK is the fully featured Software Development Kit for Java, including the JRE, compilers, and tools like JavaDoc and Java Debugger used to create and compile programs.

Usually, when you only care about running Java programs, the JRE is all you’ll need. If you are planning to do some Java programming, you will need the JDK.

Downloading the JDK

The JDK cannot be downloaded directly using the wget utility because a user must agree to Oracle’s Java license ageement when downloading. So, download the JDK using a web browser and transfer the downloaded jdk-7uXX-linux-x64.tar.gz file to your /home directory on Palmetto using scp, sftp, or FileZilla:

scp  jdk-7u45-linux-x64.tar.gz
jdk-7u45-linux-x64.tar.gz                                                             100%  132MB  57.7KB/s   38:58

Installing the JDK

The JDK is distributed in a Linux x86_64 compatible binary format, so once it has been unpacked, it is ready to use (no need to compile). However, you will need to setup your environment for using this new package by adding lines similar to the following at the end of your ~/.bashrc file:

export JAVA_HOME=/home/galen/jdk1.7.0_45
export PATH=$JAVA_HOME/bin:$PATH

Once this is done, you can log-out and log-in again or simply source your ~/.bashrc file and then you’ll be ready to begin using your new Java installation.