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Triquetrum/Kepler

This page is a work in progress.

The goal of this page is to illustrate how to use Kepler Scientific Workflow System Actors in Triquetrum.

Note that the Kepler Scientific Workflow System is not the same as the Kepler release of Eclipse. In this page, the term Kepler is used to mean the Kepler Scientific Workflow System.

Kepler

The Kepler Scientific Workflow System has actors that we would like to use in Triquetrum. In this case, we would like to use Kepler's Distributed Data-Parallel (DDP) actors.

For a brief overview of DDP, see:

The biggest issue with the integration is that Kepler's classes are not set up for OSGi. Triquetrum/Extending Triquetrum discusses how to set up the packages.

Status

As of June 7, 2016, porting the Kepler ExecutionChoice actor to Triquetrum is partially complete. The ExecutionChoice actor was chosen because it is an arbitrarily complex actor that would not be an easy port. The primary issue is that the ExecutionChoice code uses the Swing-based BasicGraphFrame code that is not present in Triquetrum. The next step would be to get the ptolemy.actor.lib.hoc.Case actor working in Triquetrum because the Case actor has internal models that need to be viewable. Right now, the UI uses ptolemy.vergil.modal.CaseGraphFrame and CaseGraphTableau, which use BasicGraphFrame, which is not present in Triquetrum because Triquetrum does not use the Swing-based viewer. After that, the next step would be to refactor ExecutionChoice to follow the Case example where the UI is in ptolemy.vergil.modal.CaseGraphFrame and CaseGraphTableau.

The current work is in checked in to a repository, see Triquetrum/Kepler Triquetrum Repository.

Kepler Installation

  1. See Kepler and Eclipse for how to download and configure Kepler. To get the DDP work, we use the biokepler configuration, so:
  mkdir kepler
  cd kepler
  svn co https://code.kepler-project.org/code/kepler/trunk/modules/build-area
  cd build-area/
  ant change-to -Dsuite=biokepler  
  ant clean-cache
  ant eclipse
  1. Import the Kepler projects into a new workspace that is not the same as where Triquetrum is set up
  2. Create a Kepler Run configuration an run it:
  • project: biokepler
  • main class: org.kepler.Kepler

Kepler Fails to start: ProvKAREntryHandler$Factory

If, during startup, we get this message:

java.lang.ClassNotFoundException: org.kepler.kar.handlers.ProvKAREntryHandler$Factory
  at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
  at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

The solution is to select use the biokepler project, not the kepler project.

Run the DDP demo

Kepler will start up. Close the splash window and under Components, double click on DDP and then wordcount-execution-choice.xml. Below is a screen shot of the initial Kepler window:

KeplerMainDDPWordCount.png

The wordcount demo has multiple ways of counting words. The default way is to use Unix commands.

Below is a run that counts words using Unix commands:

KeplerWorkflowSystemLocalExecution.png

To use the other ways of counting words, double click on the Word Count actor and change the Choice parameter.

Our first goal is to get Kepler running and count words using Unix commands.

Resources