Parallel Macro

Introduction

This is a project that enables Fiji users to parallelize their Macro scripts. Fiji is a distribution of ImageJ.

It is a sibbling project to the OpenMPI Ops.

This project must be used along with HPC Workflow Manager that provides a GUI. The links to it are given below.
Fasttrack: Follow these instructions to install it from a Fiji update site.

Important links

• The Short Guide on how to install and use the project HPC Workflow Manager
• The official web page about this whole project
• Wiki page of the project on imagej.net
• The source code along with manual installation instructions for it.

Reporting issues

I'm sure issues will come across :(
Please, tell us here.

Building and Installing

Prerequisites

Before building and installing this package you must:

• Have access to an HPC cluster.
• Make sure that Open MPI is installed (or available as a module) on the cluster.
• Although you can compile Parallel Macro locally, it is best to do so on the remote cluster. In this case make sure that Java 8 and Maven are also installed (or available as a module) on the remote cluster.

Installation Steps

• 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 of Fiji on a directory in which you have all access rights. Fiji is now installed.:

  • unzip fiji-linux64.zip

⚠️ 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.

• Clone this repository:

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

• 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.

Parallel Macro should now be ready to be used with HPC Workflow Manager.