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Difference between revisions of "Triquetrum/Kepler"
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=== Kepler Installation === | === Kepler Installation === | ||
| − | # See [https://kepler-project.org/developers/reference/kepler-and-eclipse Kepler and Eclipse] for how to download and configure Kepler. | + | # See [https://kepler-project.org/developers/reference/kepler-and-eclipse 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 | ||
| + | # Import the Kepler projects into the same workspace as to where Triquetrum is set up | ||
| + | # 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 === | === Run the DDP demo === | ||
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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: | 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: | ||
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Our first goal is to get Kepler running and count words using Unix commands. | Our first goal is to get Kepler running and count words using Unix commands. | ||
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== Resources == | == Resources == | ||
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* [https://github.com/eclipse/triquetrum/issues/84 Bug 84: Test out integrating Kepler code into Triquetrum: Use DDP/Hadoop as driver.] | * [https://github.com/eclipse/triquetrum/issues/84 Bug 84: Test out integrating Kepler code into Triquetrum: Use DDP/Hadoop as driver.] | ||
* [[Triquetrum/Extending Triquetrum]] | * [[Triquetrum/Extending Triquetrum]] | ||
Revision as of 16:17, 1 June 2016
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.
Contents
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:
- Ilkay Altintas, Daniel Crawl, Jianwu Wang. A Distributed Data-Parallel Execution Framework in the Kepler Scientific Workflow System. October 16, 2015. Presented at the Eleventh Biennial Ptolemy Miniconference, Berkeley.
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.
Kepler Installation
- 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
- Import the Kepler projects into the same workspace as to where Triquetrum is set up
- 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:
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:
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.