start:development:scripting_languages:java [MogonWiki]

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====== JAVA on MOGON ======

==== Memory ====

To run Java on MOGON, you need to reserve **much** more memory than you think. 

One example: Just calling ''java -version'' with a specified maximum heap size (1GB in this example), you need to sufficient memory or Java will not be able to run correctly.
<code bash>
#!/bin/bash

# for multithreaded JAVA programs it might(!) make sense to occupy a full node
#SBATCH -p short   # MOGON I 
#SBATCH -p smp     # MOGON II
#SBATCH -A zdvhpc
#SBATCH --mem=1800M

module load lang/Java

export MALLOC_ARENA_MAX=4
srun  java -Xms1G -Xmx1G -version
</code>

Note that for larger heap sizes, you just need to keep the offset large enough. To use more CPUs, instruct your program accordingly and [[:start:working_on_mogon:slurm_submit|reserve them]].

<callout type="warning" icon="true">
''export MALLOC_ARENA_MAX=4'' might be necessary to cope with the [[https://github.com/lattera/glibc/blob/master/malloc/arena.c|memory allocation in glibc arenas]].
</callout>

==== CPU ====

As Java creates additional threads for JVM maintainance (e.g. garbage collection) it is advisable to reserve an additional core for the Java overhead. I.e., if you have a single-threaded Java application, you should reserve a second CPU slot by using the ''-c 2'' option in your submission script to ''sbatch''.


==== Pointing JAVA applications to node local scratch directories ====

On our clusters all jobs are provided with a node local scratch directory: ''/localscratch/$SLURM_JOB_ID''. If a particular application does not allow this directory to be supplied on the command line, yet requires to write scratch files the ''_JAVA_OPTIONS'' allows to define the scratch directory anyway:

<code bash>
# put this in your job submission script to specify the local scratch directory
export _JAVA_OPTIONS="-Djava.io.tmpdir=/localscratch/${SLURM_JOB_ID}/"
</code>