How to install Parallel Macro

Introduction

This worksheet will help you install the remote part of the Parallel Macro and then OpenMPI Ops.

If you are using Linux or Mac you will need to use the terminal to connect to the remote HPC cluster. If you are using Windows please download, install and use putty to connect to the cluster.

You need to use your username and password, or username and certificate with it's password, to connect to the cluster. If you are not sure, please contact the administrator of the HPC cluster.

The Salomon supercomputer is used as an example of a remote HPC cluster in this guide.

Prerequisites on the remote cluster

• One of the following supported schedulers must be available on the cluster:
  • PBS Professional
  • Slurm Workload Manager
  • IBM Spectrum LSF
• Bash or compatible shell.
• SSH must be available.
• Open MPI must be available and installed.

Download and install Fiji on the remote-cluster

Execute the following commands after connecting to the remote cluster:

Download the official Linux version of Fiji on the remote cluster using wget:

wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip

Extract the downloaded archive:

unzip fiji-linux64.zip

Build and install Parallel Macro on the remote cluster

git clone https://github.com/fiji-hpc/parallel-macro.git

cd parallel-macro

⚠️ Names of Environment Modules might be different on your cluster. They may use lower case names, for example module load maven. Type module avail to list all available modules on your cluster. Any Apache Maven version compatible with JDK 8 is acceptable for the installation.

Make sure that the Java Development Kit (JDK) 8 and Apache Maven are available in your cluster by trying the following:

• javac -version if a message with a version number in the 1.8 series is displayed, then JDK 8 is installed.
  • If the version is not in the 1.8 series or the command is not found, then try to load a Java module (in the 1.8 series) on your cluster, for example module load Java/1.8.0_202.
• mvn -version if a message with any version number is displayed, then Maven is installed.
  • If this command is not found, try loading the default Apache Maven module on your cluster with the module load Maven command. If there is no available module, try to install Apache Maven manually.

Run the following script which will build and install Parallel Macro in the Fiji located in your remote cluster home directory:

bash build.sh

ℹ️ If you are not using your home directory for the installation, you have to provide the full path of Fiji to the build script. For example, bash build.sh /mnt/shared/Fiji.app.

How to install OpenMPI Ops on the same remote Fiji

git clone https://github.com/fiji-hpc/scijava-parallel-mpi

cd scijava-parallel-mpi

Execute the build script which will automatically compile and copy the resulting jar file in the jars directory of Fiji.

bash build.sh

Parallel Macro page

For updated information you may also check the read me file on the Parallel Macro project page.

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