Difference between revisions of "Triquetrum/Kepler"

Latest revision as of 10:23, 8 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.

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:

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.

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

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 a new workspace that is not the same as 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.

Resources

Triquetrum/Kepler Triquetrum Repository - The current effort to use Kepler actors in Triquetrum. (Start here)
Triquetrum/Kepler Feature - How the Triquetrum/Kepler Triquetrum Repository was created
Triquetrum/Kepler Tree Shaking - a first attempt at including all of the classes that were used by Kepler at run time.
Bug 84: Test out integrating Kepler code into Triquetrum: Use DDP/Hadoop as driver.
Triquetrum/Extending Triquetrum

@@ Line 14: / Line 14: @@
 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 ===
+== 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 ==
 # 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
@@ Line 23: / Line 28: @@
     ant clean-cache
     ant eclipse
-# Import the Kepler projects into the same workspace as to where Triquetrum is set up
+# Import the Kepler projects into a new workspace that is not the same as 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$Factory ====
+=== Kepler Fails to start: ProvKAREntryHandler$Factory ===
 If, during startup, we get this message:
@@ Line 51: / Line 56: @@
 Our first goal is to get Kepler running and count words using Unix commands.
-== Creating a new Kepler Bundle ==
-See [[Triquetrum/Extending_Triquetrum#Creating_an_actor_bundle | Creating an actor bundle]].
-# Create the plug-in,
-## In Eclipse: File -> New Plug-in Project
-## In the dialog, set the Project Name: to org.kepler.triquetrum.ddpDemo
-## Click Finish
-# In the org.kepler.triquetrum.ddpDemo package, update MANIFEST.MF:
-<pre>
-Import-Package: org.apache.commons.lang;version="2.6.0",
-  org.osgi.framework;version="1.8.0",
-  org.ptolemy.classloading;version="11.0.0",
-  org.ptolemy.classloading.osgi;version="11.0.0",
-  org.ptolemy.commons;version="11.0.0",
-  ptolemy.actor;version="11.0.0",
-  ptolemy.actor.gui;version="11.0.0",
-  ptolemy.data;version="11.0.0",
-  ptolemy.data.expr;version="11.0.0",
-  ptolemy.data.type;version="11.0.0",
-  ptolemy.kernel;version="11.0.0",
-  ptolemy.kernel.util;version="11.0.0",
-  ptolemy.moml;version="11.0.0",
-  ptolemy.util;version="11.0.0"
-Export-Package: org.kepler;version="1.0.0"
-</pre>
-# Create the p2.inf file (See [[Triquetrum/Extending_Triquetrum#Creating_an_actor_bundle | Creating an actor bundle]])
-## Open the org.eclipse.triquetrum.workflow.actor.plot project, click on META-INF, highlight the p2.inf file and select copy
-## In the org.kepler.triquetrum.ddpDemo project click on META-INF and paste
-## The p2.inf file will be created.
-== What Kepler classes are necessary? ==
-The next step is to determine what Kepler classes are necessary.
-The demo primarily uses [http://www.biokepler.org/userguide#execchoice  org.kepler.ddp.actor.ExecutionChoice], which is a composite actor that contains submodels that implement the different ways the actor can be executed.
-The -verbose option of the java command will report what classes are loaded.
-Unfortunately, it seems that adding -verbose to the run configuration in Eclipse does not report the Kepler classes that are loaded, so we use the command line
-To run the model without the UI from the command line
- cd kepler/build_area
- ant run -Dworkflow=../ddp/workflows/demos/wordcount-execution-choice.xml
-Edit kepler/build-area/src/org/kepler/build/Run.java and insert the following into the runSuite() method:
-  java.createJvmarg().setLine("-verbose");
-Compile the build system:
-  ant -f kepler-tasks.xml
-Run the model and save the output to a file:
-  ant run -v -Dworkflow=../ddp/workflows/demos/wordcount-execution-choice.xml >& /tmp/run.txt
-To see how many org.kepler classes are loaded (the sed command converts any inner classes that have $ in their name to the parent class, so org.kepler.util.sql.Table$IndexType becomes org.kepler.util.sql.Table)
- grep 'Loaded' /tmp/run.txt | grep org.kepler | awk '{print $3}' | sed 's/\$.*\//' | sort | uniq |  sed 's@\.@/@g' | awk '{print $1 ".java"}' > /tmp/files
-'''FIXME''': Kepler classes should not be in org.kepler because the Kepler project does not have the kepler.org domain name.
-The above returns 188 files.  Not all of these classes will be necessary at runtime when running the model, but the important thing here is to make a guess at what classes are necessary.
-The script below, when run in the kepler directory, will create a tar file with all the .java files:
-<pre>
-#!/bin/sh
-if [ ! -d files ]; then
-   mkdir files
-fi
-files=`cat /tmp/files`
-for file in $files
-do
-    srcs=`ls -1d */src`
-    for src in $srcs
-    do
-      	if [ -f $src/$file ]; then
-            (cd $src; tar -cf - $file) | (cd files; tar -xvf -)
-            break;
-	fi
-    done
-done
-(cd files; tar -cf ../files.tar .)
-ls -l files.tar
-</pre>
-Place the above in a file called kepler/findKeplerFiles.
-Run the script with:
-  cd kepler
-  sh ./findKeplerFiles
-Create copies of the files in the org.kepler.triquetrum.ddpDemo module (your pathname will vary)
-  cat files.tar | (cd ~/src/workspaceTriq04Mar/org.kepler.triquetrum.ddpDemo/src; tar -xf -)
-'''FIXME''' This is really wrong because we are creating one bundle for all the Kepler files used by one demo.  A better way would create multiple bundles for the various Kepler modules.
-== Tracking Down Dependencies ==
-Right click on the org.kepler.triquetrum.ddpDemo project and select refresh.  In the Problems tab, there will be many compilation problems. Below are the problems we saw and the solutions:
-=== _controller cannot be resolved in KeplerGraphFrame ===
-The error is:
-  Description	Resource	Path	Location	Type
-  _controller cannot be resolved to a variable	KeplerGraphFrame.java	/org.kepler.triquetrum.ddpDemo/src/org/kepler/gui	line 245	Java Problem
-KeplerGraphFrame extends ptolemy.vergil.actor.ActorGraphFrame. Triquetrum does not use ActorGraphFrame
-The solution is to remove org.kepler.triquetrum.ddpDemo/src/org/kepler/gui/KeplerGraphFrame.java
-=== _debugging cannot be resolved in ExecutionChoiceDirector ===
-The error is:
-  Description	Resource	Path	Location	Type
-  _debugging cannot be resolved to a variable	ExecutionChoiceDirector.java	/org.kepler.triquetrum.ddpDemo/src/org/kepler/ddp/actor	line 101	Java Problem
-The problem is that ExecutionChoiceDirector extends CaseDirector, which is not found.
-Looking at the errors in the imports, we see we need Case and Refinement as well:
-The solution is to copy over these files:
- (cd $PTII; tar -cf - ptolemy/actor/lib/hoc/{Case,CaseDirector,Refinement}.java) | (cd ~/src/workspaceTriq04Mar/org.kepler.triquetrum.ddpDemo/src/; tar -xvf -)
 == Resources ==
+* [[Triquetrum/Kepler Triquetrum Repository]] - The current effort to use Kepler actors in Triquetrum. (Start here)
+* [[Triquetrum/Kepler Feature]] - How the [[Triquetrum/Kepler Triquetrum Repository]] was created
+* [[Triquetrum/Kepler Tree Shaking]] - a first attempt at including all of the classes that were used by Kepler at run time.
 * [https://github.com/eclipse/triquetrum/issues/84 Bug 84: Test out integrating Kepler code into Triquetrum: Use DDP/Hadoop as driver.]
 * [[Triquetrum/Extending Triquetrum]]
+[[Category:Triquetrum]]

Notice: this Wiki will be going read only early in 2024 and edits will no longer be possible. Please see: https://gitlab.eclipse.org/eclipsefdn/helpdesk/-/wikis/Wiki-shutdown-plan for the plan.

Difference between revisions of "Triquetrum/Kepler"

Latest revision as of 10:23, 8 June 2016

Contents

Kepler

Status

Kepler Installation

Kepler Fails to start: ProvKAREntryHandler$Factory

Run the DDP demo

Resources

Breadcrumbs

Notice: this Wiki will be going read only early in 2024 and edits will no longer be possible. Please see: https://gitlab.eclipse.org/eclipsefdn/helpdesk/-/wikis/Wiki-shutdown-plan for the plan.

Difference between revisions of "Triquetrum/Kepler"

Latest revision as of 10:23, 8 June 2016

Contents

Kepler

Status

Kepler Installation

Kepler Fails to start: ProvKAREntryHandler$Factory

Run the DDP demo

Resources