This is a custom Confluence template that is intended to be re-used in the creation of workshops presented by ARCC on the Wiki. All of the content in these sections is intended to be replaced by the author of the workshop. The first step in this style guide is to ensure that the the page is in wide mode to maximize the real estate for content when possible. The Title of the Page should be the same as the Title of the workshop and this section should include a quick intro to the topic, why it’s important for ARCC users, and what users should expect to get out of this workshop. Next should be a Table of Contents macro in vertical format. The Table is intended to be used as an agenda section for presenter mode as well as navigation for non-presenting viewing so that users can find the documentation and navigate to what they need to brush up on. Finally, at the end of each section, there should be a divider to indicate the separation of “slides”In the applications module in this tutorial the interactive applications were mentioned as available, but there are some nuances to getting them started and working for your use case. On this module we will go over getting the interactive desktop, MATLAB, and Paraview interactive applications working. Jupyter Notebooks will be covered in another workshop.
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Headers and Sections
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Code Examples
Two Column Tables are nice ways to separate content/ Background info along with a code example on the same “Slide”. Please notice the table width. This should stop scroll bars from appearing
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Bullets are nice to include for distinct points
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yep
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they
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sure
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Please use the "code snippet" in the + button when creating code examples. Also please do not go
past the width of the table. This is to prevent scroll bars appearing
This is the Max number of code lines to show on an example |
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Straight Code - No context
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Limit to 16 lines in the example.
This is the end |
Same Thing With Images
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Two Column Tables are nice ways to separate content/ Background info along with an image example on the same “Slide”. Please notice the table width. This should stop scroll bars from appearing
Bullets are nice to include for distinct points
yep
they
sure
are
This is 14 lines
Alternatively No Table
Finally The End
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Link to Previous sub-module or Home Module
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Interactive Desktop
Open OnDemand’s interactive desktop application enables users to use the MedicineBow HPC system as if it were a regular desktop computer that many are used to rather than a command line interface (CLI). However, since MedicineBow is a Linux based system, so is the interactive desktop and may not be as familiar as a Windows or Mac desktop. On MedicineBow, the Xfce desktop environment is used to facilitate this functionality.
Before you use the interactive desktop be prepared that it will prompt you for:
Project/Account
Number of hours
Desktop Configuration for your CPU and RAM requirements
GPU requirements
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Configuring the Desktop
In this simple example we configure the desktop with:
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Launching the Desktop
When launching the desktop, it will not open immediatley. What is happening is that the system is allocating the hardware needed and then submitting a job to a compute node to run. Once it is ready, you will see a green bar that says it’s running. To actually launch the desktop, you have to click the Launch button on the bottom of the box  |
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Exploring the Desktop
Once launched, the desktop appears in the browser window, with familiar apps in the bottom menu bar like:
Some GUI applications can be launched in this desktop or manage files, etc. |  |
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MATLAB
Launching MATLAB is as similar process, the options are a little different where version of the software is one of them and the CPU and RAM options can be manually selected instead of a drop down.
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Parallel Computing in MATLAB
If you’ve used Matlab before, you’ll be familiar with the window you see after launching. However, In order to use the parallel functionality of MATLAB, you have to set your environment.
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Also, be aware if you are running parallel, that by default, Matlab restricts you to 12 worker threads, so you’d need to override this if you needed by setting the poolobj = parapool (’local’, 24); |
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ParaView
Once again the process of launching the Paraview GUI is similar, but with different options:
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Using Paraview
Once the application is launched, you will see the application running in your browser window.
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Managing Interactive Sessions
It is a good practice to keep the number of interactive sessions you are working on in check. As each of these are using resources on MedicineBow, if you have many open sessions that are idle, you will be preventing other users from using them. You can free up those resources by cancelling your sessions using the “Cancel” button |
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Next Steps
Previous | Workshop Home |
Use the following link to provide feedback on this training: https://forms.gle/92CJWwULQdqL4hjm8 or use the QR code below.
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