HPC Workflow Manager

Introduction

This is a bundle of all the projects that are used to build the HPC Workflow Manager. That said, this is the repository to start with in order to build the whole project.

Important links

• The Short Guide on how to install and use the project
• The official web page about this whole project
• Wiki page of the project on imagej.net

Reporting issues

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

Building and installing the client part

Build and installation prerequisites

You will need the following:

• You need a computer with either Windows, Linux or macOS.
• JDK 8, the recommended JDK version is the Oracle JDK. If you do not wish to use this distribution you will need to choose one which contains JavaFX.
• JavaFX is used for the GUI, many JDK 8 distributions do not include it by default and a separate installation is necessary for example in OpenJDK.
• Maven is used to automate the building process.

Build

Open a terminal window.

Clone this project on your system.

git clone --recurse-submodules https://github.com/fiji-hpc/hpc-workflow-manager-full

Inside the cloned directory use Maven with package target to build a jar of this project.

mvn clean package

Installation

Follow the these steps to install:

• Download the latest version of Fiji from the official site for your system. Choose the correct version for your operating system.
• Extract the downloaded zip archive anywhere on your system. Fiji is now installed.
• Copy all of the generated jar files found in hpc-workflow-manager-full/target/module-assembly-bin/lib (of the cloned directory) in the plugins or jars directory of Fiji (either directory will do, there is no need to copy to both directories).

HPC Workflow Manager, the client local version, is now ready to be used.

Building and installing the server part

How to setup the remote cluster for use with HPC Workflow Manager

• If you want to use the parallel Macro and Script features please read the installation guide, and then follow the short guide to get started.
• You may also consider to use the Script (Jython) features along with the scijava-parallel-mpi project which provides parallelized common image operations.

Further information

These Fiji wiki articles were written in the past and some information may be out-of-date. However they contain relevant information on the design and motivation as well as the SPIMM workflow type which is available for use in current versions:

• Click here for an article on the Fiji wiki on the SPIMM Workflow features.
• Click here for more information on how to use the Macro parallelization features. Additionally for more information on one of the ways used to connect to the cluster (middleware):
• HEAppE Middleware which can be used for SPIMM Workflow type jobs and Macro jobs.