💬 Java applications do not typically require special installation.
💡 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
💬 In this example we’ll install and run the Java application ABRA2.
/projappldirectory 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 $USER mkdir abra2 cd abra2
module load biojava
💡 If you get error messages or warnings about the Java version, try loading another Java module.
java -jar abra2-2.24.jar
💡 If you are not in the same directory as the .jar file, you need to include the full path to the file, e.g.
java -jar /projappl/<project>/$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
💬 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).