Introduction to Scientific Visualization with VisIt
Instructor: Amit Chourasia, San Diego Supercomputer Center, UCSD
Duration: 3 - 4 hours
Pre-requisites: None, but must complete tutorial requirements noted below.
Recordings for tutorial on Jun 10, 2019
Audio only recording
Running visit on Comet
Documentation for VisIt on Comet
Run VisIt in batch on Comet
Comet host profile for VisIt-3.0.x
Comet host profile for VisIt-2.12.x
Comet host profile for VisIt-2.9.x
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Users can interactively visualize and analyze data ranging in scale from small (<10 core) desktop-sized projects to large (>100,000 core) leadership-class computing facility simulation campaigns. Users can quickly generate visualizations, animate them through time, manipulate them with a variety of operators and mathematical expressions, and save the resulting images and animations for presentations.
This hands-on tutorial is fairly intense, you must complete this section to gain most out of it. Don't wait till last minute to complete these steps.
Computer with recent Operating system (tablets, netbooks are not sufficient for this tutorial).
Mouse with scroll wheel (laptop track pads are very cumbersome for 3d navigation, your fingers will tire out on track pad)
VisIt software: Download and install Version 3.0 from https://wci.llnl.gov/simulation/computer-codes/visit/executables.
- Do not try to compile the software unless you are adventurous and know what your are doing. Still be prepared to spend at least one full day if everything work out perfectly on your system.
Mac users: In case the official VisIt 3.0 DMG does not open, you may download the binary from here (~278 MB), unzip then move it to your /Applications folder.
- Start VisIt to make sure it works correctly. This will also create the preference folders that are needed in later steps. Grant VisIt application permission to accept incoming/outgoing connections when prompted, if not granted VisIt won't be able to perform remote visualization on HPC clusters.
Download VisIt host profile for Comet: visit3.0.x-comet-host-profile.zip.
Unzip it, then move the xml files (not the unzipped folder) to following location. These locations are not created unless VisIt is started once.
Linux and Mac: ~/.visit/hosts/
Download sample data: visit_data_files.tar.gz. Unzip it to your desktop
Webcast attendees must test their computer setup by visiting https://zoom.us/test
Tip for webcast attendees
Since VisIt software requires fairly large screen space, having the webcast
displayed on a different monitor than the one you will use for working during the hands-on portions will be very helpful.
Who may skip this tutorial?
All beginners are welcome to attend the tutorial, however consider the following
If you don't anticipate working with mesh based data or don't know what mesh based data is than this tutorial may not provide you substantial practical benefits.
If you are an intermediate user of VisIt software, there are only a few nuggets in this tutorial that may be of some value.
Visualization is largely understood and used as an excellent communication tool by researchers. This narrow view often keeps scientists from fully using and developing their visualization skillset. This tutorial will provide a "from the ground up" understanding of visualization and its utility in error diagnostic and exploration of data for scientific insight. When used effectively visualization can provide a complementary and effective toolset for data analysis, which is one of the
most challenging problems in computational domains. In this tutorial we plan to bridge these gaps by providing end users with fundamental visualization concepts, execution tools, customization and usage examples.
The tutorial comprises of four closely related sessions as follows:
Visualization fundamentals: Lecture - Assay of standard techniques and their utility (45 min)
Introduction to VisIt software - Perform basic tasks in VisIt (Hands-on, 40mins)
Perform sophisticated tasks with VisIt (Hands-on, 40 mins)
Remote visualization with VisIt on Comet cluster at SDSC (Hands-on, 20 mins, Training accounts will be provided)
Getting further help with VisIt
Excellent manuals and guides are available at https://wci.llnl.gov/simulation/computer-codes/visit/manuals
Getting Data into Visit: is an extremely useful manual that provides receipes in C, Fortran and other languages for data translation into formats that VisIt supports.
You can search or send specific questions to the VisIt's user mailing list. The mail list is vibrant, welcoming and supportive. Hat tip to developers!
If using XSEDE resources, you may request support by emailing at firstname.lastname@example.org
If using SDSC resources, you may request support by emailing email@example.com
After consulting for over a decade on visualization with researchers around the country. It was evident that training the researchers was a more scalable approach as it allowed deeper collaboration and independence for researchers to continue doing things themselves when my consulting ended. Softwares like VisIt have matured, are well supported and are now easy enough for most researchers to adopt.
To this effect, I started offering the tutorial to a more broader audience rather than keeping it limited to my collaborators. Now this tutorial has been offered numerous times, it has been very well attended (to my pleasant surprise) with attendees spanning ranks from Professors, HPC Managers/Staff, Post-docs, Graduate and undergrad students as well as Industry professionals. I have also witnessed people attend this tutorial out of pure curiosity. Based on strong feedback
I have learned that the tutorial is quite engaging with plenty of useful and practical exercises. One of the tutorial had over 100 attendees in 7 time zones around the world.