Using MOOSE with NiCE

This page is in the process of being rewritten, so some sections might seem incomplete/weird!

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[Category:MOOSE]
The capabilities in this document are brand new and while we assert that they work, that may not be the case on all systems for all users. Problems should be reported directly to the NiCE team by sending an email to the project list, niceproject-development <at> lists.sourceforge.net, or following the instructions to report bugs at niceproject.sourceforge.net.</at>

This document is designed to outline the basic steps of setting up and using the MOOSE plug-ins in NiCE. NiCE currently supports four MOOSE-based applications: MARMOT, BISON, RELAP-7 and RAVEN. Although this tutorial was created with BISON in mind, the steps for using NiCE with MARMOT, RELAP-7 and RAVEN are the same.

There are two different tasks for the input generation and launching of MOOSE products within NiCE:

• MOOSE Model Builder - Generates a set of input files necessary to launch a MARMOT, BISON, RELAP-7 or RAVEN job.
• MOOSE Launcher - Initiates the MARMOT, BISON, RELAP-7 or RAVEN codes to run on a local or remote system using the files generated from the MOOSE Model Builder.

Table of Contents

• This page is in the process of being rewritten, so some sections might seem incomplete/weird!
• Installation and Configuration
  • Prerequisites
• Creating Input
• Launching a MOOSE job
  • Selecting the MOOSE product
  • Selecting the input file(s) and MOOSE executable
  • Setting parallel execution (optional)
  • Launching RELAP-7
• Visualizing Output

Installation and Configuration

Follow the instructions in the Getting NiCE article to download and install the latest version of NiCE on your system.

Prerequisites

You should have the MOOSE environment installed, either your local or remote machine. Instructions for getting MOOSE installed can be found here.

Additionally, you should have MARMOT, BISON, RELAP-7 and RAVEN compiled and ready to run.

Generating MOOSE-specific input files in NiCE requires YAML files to be prepared ahead of time. Due to export control restrictions, we cannot provide these files for you here; you will have to generate them yourself, or request them from the

To generate YAML files yourself, navigate to the directory of a MOOSE product (MARMOT, BISON, RELAP-7 or RAVEN) and execute the command:

./moose_product-opt --yaml > moose_product.yaml

replacing moose_product with a directory name (i.e. bison, marmot, relap7 or raven). As an example, to generate a BISON YAML file, you would use the following command in the /trunk/bison directory:

./bison-opt --yaml > bison.yaml

This will generate a bison.yaml file in your working directory.

Open the moose_product.yaml file and and check if it starts with:

**START YAML FILE**

and/or ends with:

**END YAML FILE**

If these two lines are in the file, remove them, because they are not valid YAML.

Repeat these steps for each MOOSE product you would like to use in NiCE. Create a directory named MOOSE in your local file system in one of the following directories:

On Linux, use: /home/<user>/ICEFiles/default/

On Mac OS X, use: /Users/<user>/ICEFiles/default/

On Windows, use: C:\Users\<user>\ICEFiles\default\

Place the all of the MOOSE YAML files you generated in the MOOSE directory before launching NiCE. If you have never launched NiCE on your system before, you will also have to create the /ICEFiles/default directory as well.

Creating Input

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Launching a MOOSE job

Once you've generated appropriate input files, launching a MOOSE job is a relatively simple task.

To get started, click the green "+" button once more to create a new NiCE Item. Select MOOSE Launcher from the menu and click OK.

A form will appear in the main NiCE workbench area. This form contains the information necessary for launching a MOOSE problem.

Selecting the MOOSE product

The first piece of necessary information is to specify which MOOSE-based application you'd like to run. From the list of Available Executables, select a MOOSE application, and immediately apply it by clicking the save button.

Selecting the input file(s) and MOOSE executable

If you are using an input file that was created elsewhere, it must be in your /ICEFiles/default/ directory prior to creating the MOOSE Launcher Item, or you will need to import it.

To import a file if it is not in your directory, click File > Import File... and choose the file that you want to import. It will then appear in the list of input files in the MOOSE launcher. You can also use NiCE's import icon.

From the Input File drop-down menu, select an appropriate RELAP-7 file. If you created your own input file in the previous step using the MOOSE Model Builder, this file should appear in the list of available files.

Next, specify which executable you will use to read the file. Here, we are using a RELAP-7 file, so we want to select the RELAP-7 executable.

The next step is to specify on which machine your MOOSE code will be run, either locally or remotely. A list of hosts used at ORNL is displayed by default, however, additional hosts can be added by clicking the "+" button to the right of the Hosts table.

When adding hosts, set the Execution Path to the trunk directory of the machine's MOOSE installation. For example, if I'm launching BISON on a machine with the follow structure:

/home/user/trunk/bison/bison-opt

I would set the execution path in NiCE to be:

/home/user/trunk

If you are launching on a remote machine, also be sure that you have appropriate privileges for the exeuction path.

Setting parallel execution (optional)

Optionally, if you'd like to take advantage of parallel processing, you may specify the number of MPI process and/or Intel Thread Building Block (TBB) threads.

To use multiple MPI processes, change the marked field to an integer value anywhere between 1 and 10000. Note that mpirun must be specified in the host machine's PATH variable. If you choose not to change this field, the default value of 1 MPI process is used.

To use multiple TBB threads, change the marked field to an integer value anywhere between 1 and 256. Note that the host machine must have Intel TBB support. If you choose not to change this field, the default value of 1 TBB thread is used.

Launching RELAP-7

Once the input file and host is specified, apply your settings by clicking the floppy disk button located in the upper-left corner of the NiCE workbench, which is the Save button.

If you make any subsequent changes to the RELAP-7 Launcher form, you will have to re-apply them by saving the form in the same way.

Lastly, use the Process menu in the upper right-hand corner; select the Launch the Job task from the drop-down menu and click the Go! button. Depending on your host machine's configuration, you may be prompted for login credentials.

Visualizing Output

This section requires VisIt 2.8, which may or may not be released at press time. Contact the NiCE team if you need a pre-release copy.

The output produced by a RELAP-7 job can be visually analyzed in NiCE by utilizing the Visualization perspective. Select Window > Perspective > Other... from the menu bar at the top of the NiCE workbench. From the resulting dialog, select Visualization and press OK.

An empty Visualization perspective will replace the existing NiCE perspective in the workbench.

Rendering in NiCE's Visualization perspective is executed through a connection to the external visualization software application, VisIt. To establish this connection, click Launch VisIt near the upper-right corner of the NiCE workbench.

A dialog for connecting to VisIt will appear. This dialog allows the user to start a new instance of VisIt on their local machine or a remote machine. The dialog additionally allows the user to connect to an already running instance of VisIt. Select a connection option and enter the appropriate parameters before clicking "OK".

If the connection to VisIt is successful, a Visualization Editor will be opened in the main workbench area. Click the Open File button from the Visualization File Viewer in the right-hand column of the workbench.

A dialog for exploring the local file system will appear. Navigate to and select the .e file produced by the RELAP-7 job execution. (Note: This may require adjusting the file extension filter in the dialog to get the file to appear.) After dismissing the file dialog, ensure that the file is selected in the Visualization File Viewer. Click the Add Plot button in the Plot Viewer on the left-hand side of the workbench.

A dialog for selecting plots to add to the Plot Viewer will appear. Check any number of plots to add and click OK.

To display a plot in the Visualization Editor, select the plot in the Plot Viewer. Click and drag on the image to manipulate its orientation.