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 never be run 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
  1. Download the software:
wget https://github.com/mozack/abra2/releases/download/v2.24/abra2-2.24.jar
  1. Load a Java module:
module load biojava

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

  1. 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).