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Difference between revisions of "Developing MOOSE Applications with ICE"

(With CMake)
(Adding a New Kernel)
 
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=== Prerequisites ===  
 
=== Prerequisites ===  
  
To use the MOOSE support in ICE, the user will need to have MOOSE installed on their system along with any MOOSE-based application that the user would like to run (the user can simply use "moose_test" if no other application is available).
+
To use the MOOSE support in ICE, the user will need to have MOOSE installed on their system along with any MOOSE-based application that the user would like to run. The user can simply use "moose_test" as the project name if no other application is available (the example in this tutorial uses the name "animals").
  
Please note that installing MOOSE requires the user to add several packages (prerequisites) to their system. For more information on how to install MOOSE, check out the MOOSE [http://www.mooseframework.org/getting-started Getting Started] guide.
+
Please note that installing MOOSE requires the user to add several packages (prerequisites) to their system. For more information on how to install MOOSE and the prerequisites for doing so, please check out the MOOSE [http://www.mooseframework.org/getting-started Getting Started] guide.
  
To install MOOSE and create a MOOSE-based application from scratch (or clone an existing application) from within ICE itself, check out the [[Developing MOOSE Applications with ICE]] article.
+
For Mac OS X users, ICE developers also recommend installing the [http://brew.sh/ Homebrew package manager] to ensure all required packages and their dependencies are available to the user.
  
 
== Cloning MOOSE ==
 
== Cloning MOOSE ==
Line 19: Line 19:
 
[[File:Clone_moose_dev_menu_stc.png]]
 
[[File:Clone_moose_dev_menu_stc.png]]
  
This step will automatically connect to the MOOSE GitHub repository, create a local clone on the user's disk, and import the MOOSE into the 'Project Explorer.'
+
This step will automatically connect to the MOOSE GitHub repository, create a local clone on the user's disk, and import MOOSE into the "Project Explorer."
  
 
[[File:Moose_project_explorer_stc.png]]
 
[[File:Moose_project_explorer_stc.png]]
Line 30: Line 30:
 
[[File:open_git_perspective_stc_1.png]]
 
[[File:open_git_perspective_stc_1.png]]
  
Then select 'Git' from the list and click ''OK''.
+
Then select ''Git'' from the list and click ''OK''.
  
 
[[File:open_git_perspective_stc_2.png]]
 
[[File:open_git_perspective_stc_2.png]]
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A wizard will prompt the user to provide information for the Git repository they are attempting to use.
 
A wizard will prompt the user to provide information for the Git repository they are attempting to use.
  
For MOOSE, enter <tt>https://github.com/idaholab/moose</tt> into the 'URI' field and select ''Next''.
+
For MOOSE, enter <tt>https://github.com/idaholab/moose</tt> into the "URI" field and select ''Next''.
  
 
[[File:clone_wizard.png]]
 
[[File:clone_wizard.png]]
Line 58: Line 58:
 
[[File:Git_clone_progress_stc.png]]
 
[[File:Git_clone_progress_stc.png]]
  
After the clone completes, the user will be presented with a 'Git Repository' view.
+
After the clone completes, the user will be presented with a "Git Repository" view.
  
To import MOOSE into the ICE 'Project Explorer,' simply right click the MOOSE repository and select ''Import Projects''. This will present the user with the import wizard.
+
To import MOOSE into the ICE "Project Explorer," simply right click the MOOSE repository and select ''Import Projects''. This will present the user with the import wizard.
  
 
[[File:Import_git_projects_stc.png]]
 
[[File:Import_git_projects_stc.png]]
  
On the first wizard page, select ''Import using the New Project wizard'' and click ''Finish''. This will present the user with the ICE 'New Project' wizard.
+
On the first wizard page, select ''Import using the New Project wizard'' and click ''Finish''. This will present the user with the ICE "New Project" wizard.
  
 
From here, open the C/C++ tree node and select ''Makefile project with Existing Code''. Provide a valid project name and toolchain and click ''Finish.''
 
From here, open the C/C++ tree node and select ''Makefile project with Existing Code''. Provide a valid project name and toolchain and click ''Finish.''
  
MOOSE should now appear in the user's 'Project Explorer.'
+
MOOSE should now appear in the user's "Project Explorer."
  
 
[[File:import_git_proj.png]]-->
 
[[File:import_git_proj.png]]-->
  
 
== Building MOOSE ==  
 
== Building MOOSE ==  
To build MOOSE/Libmesh within ICE, open the 'Make Target' view pane by going to ''Window'' > ''Show View'' > ''Other''.
+
The [[#Cloning MOOSE|Cloning MOOSE]] step above also creates the two required build targets used to build Libmesh and MOOSE. Libmesh is required for MOOSE to build, so the user should start there.
  
[[file:Open_make_target_view_stc.png]]
+
===Building Libmesh===
 +
The "Build Libmesh" build target will appear in the "Build Targets" view pane.  
  
This will prompt the 'Show View' dialog box. From there select ''Build Target'' and click ''OK.''
+
Double clicking the "Build Libmesh" target will execute the <tt>sh update_and_rebuild_libmesh.sh</tt> script with the output streaming in the "Console" view pane.
  
[[file:Select_build_target_stc.png]]
+
[[file:Moose_build_libmesh_stc_1.png]]
  
The MOOSE project is now visible in the 'Build Target' pane. Right click on MOOSE and select ''New''.
+
Note that this process will take some time.
  
[[file:Moose_select_new_build_target_stc.png]]
+
[[file:Moose build libmesh stc-2.png]]
  
This will prompt the 'Create Build Target' dialog, shown below.
+
===Building MOOSE===
 +
Once the Libmesh build completes, the user can then execute the "Build MOOSE" target and the output should stream in the "Console" view pane.
  
Set the 'Target name' as ''Build Libmesh''.<br />
+
[[file:Cmake_build_target_stc.png]]
For Build Target: uncheck 'Same as Target name' and leave the 'Build target' field blank.<br />
+
For Build Command: uncheck 'Use builder settings' and set the command as ''sh scripts/update_and_rebuild_libmesh.sh''.<br />
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Click ''OK''.
+
  
[[file:Moose_create_build_target_stc.png]]
+
Note that this process will take some time.
  
'Build Libmesh' should now appear as a target, which upon double-clicking will execute the ''update_and_rebuild_libmesh.sh'' script with the output streaming in the 'Console' view pane.
+
[[file:Moose_build_console_output_stc.png]]
  
[[file:Moose_build_libmesh_stc_1.png]]
+
With MOOSE built, the user can start the process of creating their own MOOSE-based application. The first step, "Forking the Stork," is described below.
  
[[file:Moose build libmesh stc-2.png]]
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== Forking the Stork ==
 +
The MOOSE development team provides a GitHub repository called "stork" (located at https://github.com/idaholab/stork) that includes the base structure needed to create a new MOOSE application. So, "Forking the Stork"—as the MOOSE team coined it—implies forking this repository, changing its name to the name of the user's new MOOSE application, and cloning the contents of the repository to the user's local disk.
  
===With CMake===
+
ICE provides this functionality through a simple interface, allowing an ICE user to "Fork the Stork" in a few short steps.
  
Once this step completes, the user can create another 'Build Target' in the same manner, this time setting the 'Build target' field as ''Make All'' and setting the Build command  as ''cmake -E chdir framework make'' (feel free to add -j N to this command, where N is the number of make threads).
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First, in the main ICE menu, select ''Developer'' > ''Framework'' > ''MOOSE'' > ''Fork the Stork''.
  
[[file:Cmake_build_target_stc.png]]
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[[File:Fork_Path.png]]
  
If CMake is not installed on the user's machine, they can find the necessary files and instructions on [https://cmake.org/install/ CMake's website] or use the alternative method below. If installing CMake on Mac OS X, the user must also [http://tudat.tudelft.nl/projects/tudat/wiki/Install_on_Mac_OS_X#Step-5-Add-CMake-to-path set the path].
+
The resulting dialog will prompt the user for the name of their new MOOSE application ("animals" in this case), as well as their GitHub username and password.
  
===Without CMake===
+
[[File:fork_dialog.png]]
  
Alternatively, if CMake is not available or not preferred, the user can still build with a couple of extra steps.
+
Once the user has provided this information and clicked ''Finish'', ICE will fork the "stork" repository (located at https://github.com/idaholab/stork), rename it to the provided application name, clone it to <tt>~/ICEFiles</tt> on the user's local disk, and import it into ICE as a new C++ project in the C/C++ perspective's "Project Explorer" view pane.
  
First, right click on the MOOSE project in the 'Project Explorer' and select ''Properties''.
+
[[File:new_app.png]]
  
[[file:Moose_build_properties_stc.png]]
+
To look at a MOOSE class referenced in one of the new MOOSE application's source files, simply click the class name or the header file and click F3. ICE will take the user directly to the declaration for that MOOSE class so they can peruse and look up its method definitions.
  
In this 'Properties' dialog, select ''C/C++ Build'' and append to the 'Build directory' field with ''framework'' as shown below.
+
== Adding a New Kernel ==
  
[[file:Moose_build_properties_dialog_stc.png]]
+
The user can easily create custom Kernels with ICE once they have cloned, built, and "Forked the Stork" to produce a new MOOSE application.
  
Double clicking this Build target will execute the MOOSE build, and the output should stream in the 'Console' view pane.
+
To create a new Kernel, right click on the new MOOSE-based application project and select ''New'' > ''MOOSE Object'' > ''Kernel''.  
  
== Forking the Stork ==
+
[[File:new_kernel.png]]
The MOOSE development team provides a GitHub repository called 'stork' (located at https://github.com/idaholab/stork) that includes the base structure needed to create a new MOOSE application. So, 'Forking the Stork'—as the MOOSE team coined it—implies forking this repository, changing its name to the name of the user's new MOOSE application, and cloning the contents of the repository to the user's local disk.
+
  
ICE provides this functionality through a simple interface, allowing an ICE user to 'Fork the Stork' in a few short steps.
+
This action will prompt the user for the name of the new Kernel subclass.
  
First, in the main ICE menu, select ''Developer'' > ''Framework'' > ''MOOSE'' > ''Fork the Stork''.
+
Simply enter the desired name and click ''OK''.
  
[[File:Fork_Path.png]]
+
[[file:kernel_name_dialog.png]]
  
The resulting dialog will prompt the user for the name of their new MOOSE application ("animal" in this case), as well as their GitHub username and password.
+
ICE will automatically generate a new include and source file in <tt>include/kernel</tt> and <tt>src/kernel</tt>, respectively.
  
[[File:fork_dialog.png]]
+
These new files are the stubbed out, base implementation of a subclassed Kernel can be modified to fit the user's operation.  
  
Once the user has provided this information and clicked ''Finish'', ICE will fork the https://github.com/idaholab/stork repository, rename it to the provided application name, clone it to <tt>~/ICEFiles</tt> on the user's local disk, and import it into ICE as a new C++ project in the C/C++ perspective's 'Project Explorer' view pane.
+
[[File:kernel_source.png]]
  
[[File:new_app.png]]
+
== Building your MOOSE App ==
 +
Building the newly-created MOOSE application is simple because the "Fork the Stork" action also produced a build target (make all) for the user.
  
Additionally, the import generates a fully configured 'Build Target' in the 'Build Target' view pane and sets up the C++ Indexer to point to the new ICE/MOOSE project's include files. This is essential for facilitating code completion and MOOSE code search MOOSE application development.
+
Navigate to the "Build Target" view pane and double click on ''make all'' (the new build target).
  
 
[[File:make_target.png]]
 
[[File:make_target.png]]
  
To look at a MOOSE class referenced in one of the new MOOSE application's source files, simply click the class name or the header file and click F3. ICE will take the user directly to the declaration for that MOOSE class so they can peruse and look up its method definitions.
+
The new MOOSE application will then build, producing an application executable. Note that this will take some time.
  
== Adding a New Kernel ==
+
[[file:animals_build_console_output.png]]
  
Once you've cloned and built MOOSE, and Forked the Stork to produce a new MOOSE application ready for development, you can easily create custom Kernels with ICE. To create a new Kernel, right click on your new MOOSE-based application project and select New > MOOSE Object > Kernel.  
+
== Pushing Changes Back to GitHub ==
 +
As the user makes modifications to their project, they will want to periodically commit or "push" these changes to their GitHub repository.
  
[[File:new_kernel.png]]
+
===Git Perspective===
  
This action will display an input prompt asking for the name of your new Kernel subclass. Simply enter the name and push 'Ok'. Then ICE will automatically generate a new include and source file in include/kernel and source/kernel, respectively. The new files are the stubbed out, base implementation of a subclassed Kernel that you can then add to and modify.  
+
The first step is to open the "Git Perspective" by clicking the ''Open Perspective'' button in the upper right hand corner of ICE.
  
[[File:kernel_source.png]]
+
[[file:ICE_OpenPerspective.png]]
  
== Building your MOOSE App ==
+
Next, select ''Git'' from the resulting prompt and click ''OK''.
Building your MOOSE application is simple because the 'Fork the Stork' action produced a Make Target for you. Simply double-click that make target and you application will build, producing the application executable.  
+
  
== Pushing Changes Back to GitHub ==  
+
[[file:Open_git_perspective_stc_2.png]]
To push changes to the remote GitHub repository at https://github.com/username/animal, switch back to the Git perspective and click your applications git repository in the Git Repositories view. On the bottom right of the screen, you should see another set of tabbed views, one of them being the Git Staging view.  
+
 
 +
The user should now have the ''Git'' perspective button available on the ICE toolbar.
 +
 
 +
[[file:Git_perspective_button_stc.png]]
 +
 
 +
Click the ''Git'' perspective button to bring up the Git interface pane in the main ICE window. The user should now see the repository for their MOOSE-based application in the "Git Repositories" view pane (left), "animals" in this case.
 +
 
 +
[[file:Git_repos_view_stc.png]]
 +
 
 +
===Push Changes===
 +
 
 +
To push project changes/modifications to the remote GitHub repository, switch to the Git perspective, as above, and select the desired repository in the "Git Repositories" view pane.
 +
 
 +
The "Git Repositories" view includes a new set of tabbed views. Select the ''Git Staging'' tab to pull up the "Git Staging" view pane.
 +
 
 +
[[file:Git_commit.png]]
 +
 
 +
Drag any "Unstaged Changes" to the "Staged Changes" section.
  
[[File:git_commit.png]]
+
Provide a brief message describing the nature of the commit.
  
Click the Git Staging View and drag any Unstaged Changes to the Staged Changes section. Now provide a brief commit message and click 'Commit and Push', enter your GitHub credentials, and watch as your files are committed to the remote repository!
+
Finally, click ''Commit and Push,'' enter the GitHub credentials if/when prompted, and watch as the new files are committed to the remote repository!
  
 
== Executing Built MOOSE Application ==
 
== Executing Built MOOSE Application ==
 
Now that you've developed a new MOOSE application you need to develop input files for it and execute it to see your desired results. This is simple with ICE: just use the built in MOOSE Model Builder and MOOSE Launcher Items. Detailed instructions can be found at [[Using MOOSE with ICE]].
 
Now that you've developed a new MOOSE application you need to develop input files for it and execute it to see your desired results. This is simple with ICE: just use the built in MOOSE Model Builder and MOOSE Launcher Items. Detailed instructions can be found at [[Using MOOSE with ICE]].

Latest revision as of 10:26, 23 November 2016

Introduction

This article is designed to guide users through a typical workflow for developing MOOSE-based applications in ICE. Since ICE is built on top of the Eclipse platform, a large variety of sophisticated tools and technologies for developing scientific software can be leveraged for developing MOOSE applications.

Version control, code editing, code completion, code building, and code generation are just a few of the technologies available to MOOSE-based application developers using ICE. Additionally, after the user develops a custom MOOSE application, the usual MOOSELauncher and MOOSEModel items—along with the ICE Visualization perspective—are still at their disposal for constructing input files, launching jobs, and visualizing results.

Prerequisites

To use the MOOSE support in ICE, the user will need to have MOOSE installed on their system along with any MOOSE-based application that the user would like to run. The user can simply use "moose_test" as the project name if no other application is available (the example in this tutorial uses the name "animals").

Please note that installing MOOSE requires the user to add several packages (prerequisites) to their system. For more information on how to install MOOSE and the prerequisites for doing so, please check out the MOOSE Getting Started guide.

For Mac OS X users, ICE developers also recommend installing the Homebrew package manager to ensure all required packages and their dependencies are available to the user.

Cloning MOOSE

The latest version of ICE makes cloning MOOSE very simple.

In the main ICE window, click Developer > Framework > MOOSE > Clone Moose.

Clone moose dev menu stc.png

This step will automatically connect to the MOOSE GitHub repository, create a local clone on the user's disk, and import MOOSE into the "Project Explorer."

Moose project explorer stc.png


Building MOOSE

The Cloning MOOSE step above also creates the two required build targets used to build Libmesh and MOOSE. Libmesh is required for MOOSE to build, so the user should start there.

Building Libmesh

The "Build Libmesh" build target will appear in the "Build Targets" view pane.

Double clicking the "Build Libmesh" target will execute the sh update_and_rebuild_libmesh.sh script with the output streaming in the "Console" view pane.

Moose build libmesh stc 1.png

Note that this process will take some time.

Moose build libmesh stc-2.png

Building MOOSE

Once the Libmesh build completes, the user can then execute the "Build MOOSE" target and the output should stream in the "Console" view pane.

Cmake build target stc.png

Note that this process will take some time.

Moose build console output stc.png

With MOOSE built, the user can start the process of creating their own MOOSE-based application. The first step, "Forking the Stork," is described below.

Forking the Stork

The MOOSE development team provides a GitHub repository called "stork" (located at https://github.com/idaholab/stork) that includes the base structure needed to create a new MOOSE application. So, "Forking the Stork"—as the MOOSE team coined it—implies forking this repository, changing its name to the name of the user's new MOOSE application, and cloning the contents of the repository to the user's local disk.

ICE provides this functionality through a simple interface, allowing an ICE user to "Fork the Stork" in a few short steps.

First, in the main ICE menu, select Developer > Framework > MOOSE > Fork the Stork.

Fork Path.png

The resulting dialog will prompt the user for the name of their new MOOSE application ("animals" in this case), as well as their GitHub username and password.

Fork dialog.png

Once the user has provided this information and clicked Finish, ICE will fork the "stork" repository (located at https://github.com/idaholab/stork), rename it to the provided application name, clone it to ~/ICEFiles on the user's local disk, and import it into ICE as a new C++ project in the C/C++ perspective's "Project Explorer" view pane.

New app.png

To look at a MOOSE class referenced in one of the new MOOSE application's source files, simply click the class name or the header file and click F3. ICE will take the user directly to the declaration for that MOOSE class so they can peruse and look up its method definitions.

Adding a New Kernel

The user can easily create custom Kernels with ICE once they have cloned, built, and "Forked the Stork" to produce a new MOOSE application.

To create a new Kernel, right click on the new MOOSE-based application project and select New > MOOSE Object > Kernel.

New kernel.png

This action will prompt the user for the name of the new Kernel subclass.

Simply enter the desired name and click OK.

Kernel name dialog.png

ICE will automatically generate a new include and source file in include/kernel and src/kernel, respectively.

These new files are the stubbed out, base implementation of a subclassed Kernel can be modified to fit the user's operation.

Kernel source.png

Building your MOOSE App

Building the newly-created MOOSE application is simple because the "Fork the Stork" action also produced a build target (make all) for the user.

Navigate to the "Build Target" view pane and double click on make all (the new build target).

Make target.png

The new MOOSE application will then build, producing an application executable. Note that this will take some time.

Animals build console output.png

Pushing Changes Back to GitHub

As the user makes modifications to their project, they will want to periodically commit or "push" these changes to their GitHub repository.

Git Perspective

The first step is to open the "Git Perspective" by clicking the Open Perspective button in the upper right hand corner of ICE.

ICE OpenPerspective.png

Next, select Git from the resulting prompt and click OK.

Open git perspective stc 2.png

The user should now have the Git perspective button available on the ICE toolbar.

Git perspective button stc.png

Click the Git perspective button to bring up the Git interface pane in the main ICE window. The user should now see the repository for their MOOSE-based application in the "Git Repositories" view pane (left), "animals" in this case.

Git repos view stc.png

Push Changes

To push project changes/modifications to the remote GitHub repository, switch to the Git perspective, as above, and select the desired repository in the "Git Repositories" view pane.

The "Git Repositories" view includes a new set of tabbed views. Select the Git Staging tab to pull up the "Git Staging" view pane.

Git commit.png

Drag any "Unstaged Changes" to the "Staged Changes" section.

Provide a brief message describing the nature of the commit.

Finally, click Commit and Push, enter the GitHub credentials if/when prompted, and watch as the new files are committed to the remote repository!

Executing Built MOOSE Application

Now that you've developed a new MOOSE application you need to develop input files for it and execute it to see your desired results. This is simple with ICE: just use the built in MOOSE Model Builder and MOOSE Launcher Items. Detailed instructions can be found at Using MOOSE with ICE.

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