java.md

---

layout: default
title: Installing Java applications
parent: 9. Installing own software
grand_parent: Part 2
nav_order: 6
has_children: false
has_toc: false
permalink: /hands-on/installing/installing_hands-on_java.html

---

Installing Java applications (on Puhti)

💬 Java applications do not typically require special installation.

• You just need to download the distribution package, typically a .jar file.

💡 Compute nodes do not have a default Java installation, so you need to load a suitable Java module.

You can check the available modules with the command:

module spider java

💬 Despite their name, modules named biojava are just normal Java installations, which can be used with any software, not just bio applications.

☝🏻 Some java applications fail to run on the login nodes. Try running them using sinteractive instead (or by opening a compute node shell in the Puhti web interface).

‼️ Naturally, computationally heavy tasks should be never ran on the login nodes.

💡 The compute nodes have very limited /tmp space. If you have to set the temporary file location for a Java application, you can use:

export _JAVA_OPTIONS=-Djava.io.tmpdir=/path/to/tmp  # replace with the actual path 

Example: Installing ABRA2

💬 In this example we'll install and run the Java application ABRA2.

1. Create a personal folder (if not done already) under your project's /projappl directory and move there. Then create (and move to) a new directory for the installation:

   cd /projappl/<project>  # replace <project> with your CSC project, e.g. project_2001234
   mkdir -p $USER
   cd $USER
   mkdir abra2
   cd abra2
   

2. Download the software:

   wget https://github.com/mozack/abra2/releases/download/v2.24/abra2-2.24.jar
   

3. Load a Java module:

   module load biojava
   

   💡 If you get error messages or warnings about the Java version, try loading another Java module.

4. Run the application:

   java -jar abra2-2.24.jar
   

   💡 If you are not in the same directory as the .jar file, you need to include the full path to the file, e.g.

   java -jar /projappl/<project>/$USER/abra2/abra2-2.24.jar  # replace <project> with your CSC project, e.g. project_2001234, and ensure that the path corresponds to the true path
   

Example 2: Java application with a shell wrapper script

💬 Some Java applications come with shell scripts that are used to launch them instead of calling Java directly. See the documentation of each software for details.

💡 One example of such an application is BEAST:

sinteractive --account <project>  # replace <project> with your CSC project, e.g. project_2001234
module load beast
beast -help

☝🏻 BEAST will fail to run on the login nodes. Try running it in an interactive session instead (using sinteractive or a compute node shell in the Puhti web interface).