Explain how to run OpenMPI jobs with Java

The starter documentation is helpful. It would be good to explain how to compile OpenMPI since the default installation may not have all features a user may want. As an example to run a Java application, the following is required after setting up a cluster with SLURM on Ubuntu 20.04.

sudo apt-get install openjdk-11-jdk build-essential
wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.2.tar.gz
tar -xf openmpi-4.1.2.tar.gz
cd openmpi-4.1.2
./configure --prefix=$HOME/openmpi-4.1.2-install --enable-mpi-java --enable-mpi-fortran \
 --with-ofi=/opt/amazon/efa --disable-man-pages
make
make install
cd ..
wget https://download.java.net/openjdk/jdk11/ri/openjdk-11+28_linux-x64_bin.tar.gz
tar -xf openjdk-11+28_linux-x64_bin.tar.gz

Since the home directory is shared to the compute nodes, but software installed using the package manager, apt in this case is not, run time dependencies need to be placed in the home directory or some other shared directory or an AMI created - in this case, the extra required dependency OpenJDK 11 is downloaded directly. To run an example java program, first compile an example program on the head node

cd openmpi-4.1.2/examples
$HOME/openmpi-4.1.2-install/bin/mpijavac Hello.java

then create a SLURM submission script, in this case

nano submit.sh

then place the following in submit.sh:

#!/bin/bash
#SBATCH --job-name=HelloJava
#SBATCH --ntasks=2
#SBATCH --ntasks-per-node=1
#SBATCH --output=%x_%j.out

/home/ubuntu/ompi-install/bin/mpirun -np 2 /home/ubuntu/jdk-11/bin/java Hello

then submit the job

sbatch submit.sh

Further notes

This builds on https://github.com/aws/aws-parallelcluster/wiki/OpenMPI-Install-from-Source-and-Uninstall which is a little outdated at present.
A related issue on building OpenMPI.
EFA installation instructions do not discuss building OpenMPI from source.

awsdocs / aws-parallelcluster-user-guide

Explain how to run OpenMPI jobs with Java #66

Further notes