Short Guide

Welcome

This short guide has been designed as a series of worksheets.

The worksheets will show you how to configure and use both:

• Fiji on the remote cluster (a system of several computers that will process your macros in parallel),
• Fiji on your local computer (a laptop or workstation computer),
• how to develop a parallelized macro or Jython script,
• and (optionally) how it can be made to be reporting its progress.

You want to take exactly one option from the Remote cluster section, or none if you are already set up.

You probably want to follow the worksheets in order in the Local computer section.

Ask for help

This is a difficult topic. Parallelization and/or its realization is known to be very hard. On the email(s) below we offer assistance, which is, however, naturally limited by our own experience and time availability.
🆘 📧 vladimir.ulman at vsb.cz

Leave feedback and wishes, Report issues

Issues are likely to come across :(
Please tell us here or on the email(s) above.

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The Short Guide

The HPC Workflow Manager suite consists of a GUI-enabled local Fiji client, and of a Fiji, tailored with the Parallel Macro and OpenMPI Ops, installed on the remote side. The guide starts by setting up the server/cluster side first.

Remote cluster

Choose exactly one of the options, or none if you're already set up.

If you have access to a cluster/supercomputer and want to use it:

1. Comfortably install cluster-side tools
2. Manually install cluster-side tools
   1. Note: The cluster-side tools are technically the Parallel Macro and OpenMPI Ops

Otherwise, obtaining your own testbed:

1. Download and use your own cluster

   1. Note: Gets you a small homemade cluster

2. Building from scratch your own cluster and configuring it

   1. Note: You will learn and understand everything that's behind the scenes
   2. Additional Useful Information

Local computer

First time here? Please, follow the worksheets in order for the best experience.

1. How to install HPC Workflow Manager client

2. How to set up the paradigm for Parallel Macro

3. Using HPC Workflow Manager to start a new macro job

4. Monitoring progress, output and error reporting

5. How to write a parallel macro

6. How to write a parallel macro part 2

7. How to use the progress reporting functions

8. Demonstration of a real parallel macro

9. Running OpenMPI Ops though HPC Workflow Manager

More Information

1. The official web pages about this HPC Parallel Tools

2. Cheatsheet and a poster about the tool 📋

3. Tutorial video 📺 from I2K conference 2022 workshop series

4. Troubleshooting instructions 🐛 🔨

5. Progress Logs (Details about the file format of the logs.)