Slicer3:Batchmake Integration - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:42:11Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Marianna: Protected "Slicer3:Batchmake Integration" [edit=sysop:move=sysop]

2008-05-22T16:25:20Z

Protected "Slicer3:Batchmake Integration" [edit=sysop:move=sysop]

Marianna: Unprotected "Slicer3:Batchmake Integration"

2008-05-19T17:05:18Z

Unprotected "Slicer3:Batchmake Integration"

Marianna: Replacing page with ''''Note:''' We are migrating this content to the slicer.org domain - The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:Batchmake_I...'

2008-05-19T17:05:00Z

Replacing page with '<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:Batchmake_I...'

Aylward: /* To do */

2007-10-24T23:35:00Z

To do

Aylward at 15:19, 3 October 2007

2007-10-03T15:19:59Z

Aylward at 15:05, 3 October 2007

2007-10-03T15:05:48Z

Aylward: /* Introduction */

2007-10-03T14:59:27Z

Introduction

Aylward at 14:59, 3 October 2007

2007-10-03T14:59:12Z

Aylward: New page: == Introduction == * Goal: Run Slicer execution modules on multiple datasets and/or explore the parameter space of those modules using local computer resources or local GRID resources ==...

2007-10-03T14:52:52Z

New page: == Introduction == * Goal: Run Slicer execution modules on multiple datasets and/or explore the parameter space of those modules using local computer resources or local GRID resources ==...

New page

== Introduction ==

* Goal: Run Slicer execution modules on multiple datasets and/or explore the parameter space of those modules using local computer resources or local GRID resources

== Background ==

* [http://www.batchmake.org BatchMake] provides an open-source toolkit for launching a controlled sequence of applications on the local computer or a GRID.
* [http://www.cs.wisc.edu/condor Condor] is used as the open-source toolkit that provides access to GRID resource. It also provides an easy-to-install and easy-to-configure GRID implementation/network. We highly recommend it for your GRID needs.
* BatchMake and Condor work together to sequence tasks and to allocate and monitor resources and job progress.

== Status ==

=== Completed ===
# BatchMake Library
#* Distributed via Slicer3's getbuildtest2.tcl script
#** Slicer3 code location: Slicer3-lib/BatchMake
#* Default distribution does not include Condor
#** Can be installed by users
#** Changing two BatchMake variables will configure BatchMake to use Condor
# EMSegmenter BatchMake module
#* Distributed via Slicer3's getbuildtest2.tcl script
#** Slicer3 GUI Access: Filters/BatchProcessing/EMSegmenter BatchMake Module
#** Slicer3 code location: Slicer3/Applications/CLI/BatchMake
#* Applies EMSegmenter algorithm to a collection of data using local computer or GRID
# GaussianBlur BatchMake module
#* Distributed via Slicer3's getbuildtest2.tcl script
#** Slicer3 GUI Access: Filters/BatchProcessing/GaussianBlur BatchMake Module
#* Provides a simple example of how to batchmake-ify your Slicer3 modules

=== To do ==
* Provide documentation
* Determine how to deliver BatchMake's GRID monitoring tool with Slicer3
** Requires FLTK - will not be re-written into KWWidgets

← Older revision		Revision as of 17:42, 10 July 2017
Line 1:		Line 1:
−	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [~~http~~://www.slicer.org/~~slicerWiki/index.php~~/Slicer3:Batchmake_Integration here]</font></big>	+	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Batchmake_Integration here]</font></big>

← Older revision		Revision as of 17:05, 19 May 2008
Line 1:		Line 1:
−	~~== Introduction ==~~	+	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:Batchmake_Integration here]</font></big>
−
−	~~=== Goals ===~~
−
−	* Enable Slicer3 execution modules to process multiple datasets with minimal user interactions ("batch processing")
−	* Enable the exploration of the parameter spaces of Slicer3 execution modules ("parameter space evaluations")
−	* Support using local computer resources or local GRID resources for batch process and parameter space evaluations.
−
−	~~=== Summary ===~~
−
−	* BatchMake integration with Slicer3 is complete.
−	* Real-world applications (EMSegmenter) are using BatchMake from within Slicer.
−	* Examples are given on how to use BatchMake with your Slicer3 Execution Modules (GaussianBlur example).
−
−	~~== Background ==~~
−
−	* [http://www.batchmake.org BatchMake] provides an open-source toolkit for launching a controlled sequence of applications on the local computer or a GRID.
−	* [http://www.cs.wisc.edu/condor Condor] is used as the open-source toolkit that provides access to GRID resource. It also provides an easy-to-install and easy-to-configure GRID implementation/network. We highly recommend it for your GRID needs.
−	* BatchMake and Condor work together to sequence tasks and to allocate and monitor resources and job progress.
−
−	~~== Status ==~~
−
−	~~=== Completed ===~~
−	~~# BatchMake Library~~
−	~~#* Distributed via Slicer3~~'~~s getbuildtest2.tcl script~~
−	~~#** Slicer3 code location~~: ~~Slicer3-lib/BatchMake~~
−	~~#* Default distribution does not include Condor~~
−	~~#** Can be installed by users~~
−	~~#** Changing two BatchMake variables will configure BatchMake to use Condor~~
−	~~# EMSegmenter BatchMake module~~
−	~~#* Distributed via Slicer3~~'~~s getbuildtest2.tcl script~~
−	~~#** Slicer3 GUI Access: Filters/BatchProcessing/EMSegmenter BatchMake Module~~
−	~~#** Slicer3 code location: Slicer3/Applications/CLI/BatchMake~~
−	~~#* Applies EMSegmenter algorithm to a collection of data using local computer or GRID~~
−	~~# GaussianBlur BatchMake module~~
−	~~#* Distributed via Slicer3~~'~~s getbuildtest2.tcl script~~
−	~~#** Slicer3 GUI Access: Filters/BatchProcessing/GaussianBlur BatchMake Module~~
−	~~#* Provides a simple example of how to batchmake-ify your Slicer3 modules~~
−
−	~~=== To do ===~~
−	* Provide documentation
−	* Provide tutorial at AHM in January 2008
−	* Determine how to deliver BatchMake'~~s GRID monitoring tool with Slicer3~~
−	** Requires FLTK - will not be re-written into KWWidgets
−	* Consider general (no programming required) solution to ~~using BatchMake with other Slicer modules~~
−	** User browses to execution modules and specifies where wildcards should be substituted into command line
−	* Provide batch registration module
−	** Requires completion of Registration Modules (non-batch versions)
−	*** See: http://www.na-~~mic.org/Wiki/index.php/NAC_Grid_Enabled_ITK~~
−	*** See: http://www.~~na-mic~~.org/~~Wiki~~/index.php/~~ITK_Registration_Optimization~~
−
−	~~=== Related links ===~~
−
−	* http://~~wiki.na-mic.org/Wiki/index.php/Slicer3:Large_scale_experiment_control_brainstorming~~

← Older revision		Revision as of 23:35, 24 October 2007
Line 49:		Line 49:
	*** See: http://www.na-mic.org/Wiki/index.php/NAC_Grid_Enabled_ITK		*** See: http://www.na-mic.org/Wiki/index.php/NAC_Grid_Enabled_ITK
	*** See: http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization		*** See: http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization
		+
		+	=== Related links ===
		+
		+	* http://wiki.na-mic.org/Wiki/index.php/Slicer3:Large_scale_experiment_control_brainstorming

@@ Line 2: / Line 2: @@
 * Goal: Run Slicer execution modules on multiple datasets and/or explore the parameter space of those modules using local computer resources or local GRID resources
-* Summary: BatchMake, EMSegmenter BatchMake module, and GaussianBlur batchMake module (a simple example) have been integrated with Slicer3.  Documentation remains to be completed.
+* Summary: BatchMake integration with Slicer3 is complete.  Real-world applications (EMSegmenter) are using BatchMake from within Slicer.   Examples are given on how to use BatchMake with your Slicer3 Execution Modules (GaussianBlur example).
 == Background ==
@@ Line 36: / Line 36: @@
 * Consider general (no programming required) solution to using BatchMake with other Slicer modules
 ** User browses to execution modules and specifies where wildcards should be substituted into command line

@@ Line 2: / Line 2: @@
 * Goal: Run Slicer execution modules on multiple datasets and/or explore the parameter space of those modules using local computer resources or local GRID resources
-* Summary: BatchMake, EMSegmenter BatchMake module, and GaussianBlur batchMake module (simple example) have been integrated with Slicer3.  Documentation remains to be completed.
+* Summary: BatchMake, EMSegmenter BatchMake module, and GaussianBlur batchMake module (a simple example) have been integrated with Slicer3.  Documentation remains to be completed.
 == Background ==

← Older revision	Revision as of 16:25, 22 May 2008
(No difference)

@@ Line 2: / Line 2: @@
 * Goal: Run Slicer execution modules on multiple datasets and/or explore the parameter space of those modules using local computer resources or local GRID resources
 == Background ==
@@ Line 28: / Line 29: @@
 #* Provides a simple example of how to batchmake-ify your Slicer3 modules
-=== To do ==
+=== To do ===
 * Provide documentation
 * Determine how to deliver BatchMake's GRID monitoring tool with Slicer3
 ** Requires FLTK - will not be re-written into KWWidgets