Several Java Development Kits are installed in /usr/local/Java. Older versions are available for applications that require them. The latest version of java is symlinked to /usr/local/java.

module load java/1.8.0_92

This will set the appropriate JAVA_HOME, PATH and LD_LIBRARY_PATH environment variables.

You may run a jar file directly using the -jar flag:

java [options] -jar jarfile

All java-based applications can utilize these options.

Including these options will configure the amount of memory required to run the java-based application. [size] can be defined in kilobytes (e.g. 5k), megabytes (10m), or gigabytes (8g).

• -Xms[size] set initial heap size
• -Xmx[size] set maximum heap size
• -Xss[size] set thread stack size

It is very common to include -Xmx4g with calls to java. This requires that 4GB of memory is available to the java instance.

Java-based applications will very often require a scratch space for creating temporary files during execution. By default, this is set to /tmp. Unfortunately, many genomic java applications require much more scratch space than is available in /tmp. Worse, running multiple instances of java on a single node may fill up /tmp. In this case, including the option

• -Djava.io.tmpdir=[TMPDIR]

will configure java to use [TMPDIR] as a scratch space. Typically, this can be set to /lscratch/$SLURM_JOB_ID:

java -Djava.io.tmpdir=/lscratch/$SLURM_JOB_ID -jar jarfile

Please see information on allocting lscratch here.

Some java applications fail to run under batch conditions because an X11 display is not available, or no keyboard is detected, even though the command should run in batch or in the background. For these situations, running java in so-called "headless" mode may allow batch runs:

java -Djava.awt.headless=true -jar jarfile

For more information about how to configure java-based applications, type

java --help

at the prompt, or go to http://www.oracle.com/technetwork/java.

By default, the Java virtual machine (JVM) will calculate the available number of CPUs at runtime. This default behaviour can easily consume most of the available CPUs. In most cases, you should use the following option to limit the number of threads the JVM will use for garbage collection:

• -XX:ParallelGCThreads=2

The Server VM is intended for long-running Java applications. It is optimized and tuned to maximize peak operating speed. For long running Java processes, it is recommended to use the following option:

• -server

Biowulf compute nodes are behind a firewall and must be configured to use proxy servers to access the internet. This configuration is not respected by default within the Java environment. Set the flag -Djava.net.useSystemProxies to true to access the internet from within Java.

java -Djava.net.useSystemProxies=true -jar jarfile

In many instances, you can set an environment variable to the same effect.

export JAVA_TOOL_OPTIONS="-Djava.net.useSystemProxies=true"