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How to install HPC Workflow Manager client

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Vladimír Ulman edited this page Feb 14, 2023 · 17 revisions

⚠️ If after starting the HPC Workflow Manager you get error messages that include javafx terms, it's likely that you have Fiji without JavaFX. This was occasionally encountered on either macOS or Linux installations due to some license friction. In such case, you simply need to download and install Oracle JDK 8 which includes JavaFX by default or to download and install a compatible JDK distribution along with its distribution of JavaFX, and then use "No JRE" Fiji with it.

HPC Workflow Manager client is available to install through its update site.

Instructions

  • Download, install and launch Fiji,
  • go to Help › Update... › Manage update sites,
    • if there are updates listed in the "ImageJ Updater" window press Apply changes,
    • restart Fiji,
    • go to Help › Update... › Manage update sites,
  • tick HPC-ParallelTools,
  • close the window,
  • click Apply changes, and
  • restart Fiji.

If the plugin has been installed successfully the option Plugins > HPC-ParallelTools should be available.

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Short Guide Worksheets

Remote cluster

  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

  3. Download and use your own cluster

    1. Note: A small homemade cluster for testing, or when you cannot access a big HPC

  4. 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

  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

    1. List of available macro functions

  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

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