The second publication in the ACS Technology White Paper series is on the topic of high-performance computing, or “HPC.”Written by Academic Computing Consultant for the Sciences Chris Gahn, it explains how researchers— often in the sciences, but not always— are turning from expensive lab computers to powerful remote computers for their number crunching.
Academic Computing Services (ACS) is embarking on a new initiative to share the best of our thinking on various academic technology topics with the Vassar faculty. Our Technology White Papers will be brief, informal reports on technologies that we think you’ll find interesting. Each will explain what the technology is, what its potential benefits are, how it’s currently being used in higher education, and how you can get started with it.
Our inaugural white paper, researched and reported by Senior Academic Computing Consultant Baynard Bailey, is on the topic of digital storytelling. Possible future topics include high performance computing, virtual reality, and microcredentials, or digital badging. Please let us know if these efforts are useful for you, and if there are particular topics that you’d like us to address.
Director, Academic Computing Services
The Audio Nook
ACS has worked with User Services to install an “audio nook” in the Design Studio. Located in the north wing of the main library, this is a DIY audio recording station. It’s a great place to make a quick recording.
The Snowball cardioid microphone does a great job picking up the speech of the narrator at the same time ignoring background noise. You don’t have to talk very loud, you just need to be close. Listen for yourself!
There are two moveable sound baffle panels which dampen background noise and also provide a degree of privacy while you record.
Here’s another angle featuring Digital Media Consultant Jaineel Doshi ’20.
The Design Studio staff sits at the design studio service desk and can provide help you if you need it.
Other Campus Sound Resources
Chicago Hall Audio Studio
If you need more sound isolation or more privacy, you can arrange to use the Chicago Hall Audio Studio. The space provides more sound isolation and professional quality recording capacity. To arrange to use the space, please email Academic Computing Services email@example.com.
Zoom H1 Recorders can be signed out from Media Resources. ACS maintains a classroom set of recorders that can be used for class projects. These are perfect for field recordings. Contact firstname.lastname@example.org for individual borrowing or email@example.com for class projects or training.
Audacity is a free program that can be downloaded and installed on Windows or Macs. It is installed on all the Design Studio and Library Electronic Classroom machines. If you need help, please ask a design studio student employee or email Baynard Bailey firstname.lastname@example.org
Adobe’s Audition is a “comprehensive toolset that includes multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content.” Audition is also installed in the Design Studio and the Electronic Classroom.
Savvy Research with Zotero
Learn how to use Zotero to automatically grab citations from web content, organize your research with tags and keywords, collaborate for group work, and configure bibliography exports for print and web tools. Please RSVP to email@example.com.
Video Editing: Final Cut Pro X
02/08 Friday 1:00 pm, Main Library Electronic Classroom 160
Interested in learning video editing or recording a narrated presentation? Come to this hands-on workshop where you will learn to use Apple’s powerful but easy to use video editing software. Led by Baynard Bailey of Academic Computing Services, organized by DiSSCo. Please rsvp to firstname.lastname@example.org (suggested but not required).
Video Editing: Adobe Premiere Pro
Interested in learning to edit video with a powerful and popular software suite? Come to this hands-on workshop where you will learn to use Adobe Premiere Pro. Led by Baynard Bailey of Academic Computing Services, organized by DiSSCo. Please rsvp to email@example.com (suggested but not required).
Intro. to Python
A hands-on intro to this popular scripting language. Led by Academic Computing Services’ Chris Gahn, organized by DiSSCo. Please rsvp to firstname.lastname@example.org (suggested but not required).
Intro. to R and Data Visualization
Basic overview of using R and RStudio for statistical analysis and data visualization. This workshop covers the practice of using R; it does not teach statistical concepts.Led by Carolyn Moritz, Digital Technologies Librarian. Please RSVP to email@example.com (suggested but not required)
Intro to Digital Drawing
Interested in drawing digitally or in VR? We will provide a brief overview of digital drawing options on mobile tablets, peripherals and in VR. Try out a number of different devices. Led by Amy Laughlin and Baynard Bailey of Academic Computing Services, organized by DiSSCo. Please rsvp to firstname.lastname@example.org (suggested but not required).
High-Performance Computing (Cancelled)
03/01 Friday 1:00 pm, Sci Viz Lab, Bridge Building
03/29 Friday 2:00 pm, Collaboration Studio, Main Library
Advanced follow-up to the fall E-Sewing workshop: Have fun making wearable tech with LilyPads and learn to use and program Arduino boards to bring your tech crafts to life. Those who have completed e-sewing projects at the library are encouraged to bring them for this workshop; however, all are welcome! Led by Carolyn Moritz, Digital Technologies Librarian. RSVP to email@example.com (suggested but not required).
Photographing Your Artwork
Need to put together your senior portfolio? Want to submit work to galleries or other exhibition calls for entry? Come to this workshop and learn how to photograph 2D and 3D artwork. Organized by DiSSCo, Led by Amy Laughlin of Academic Computing Services. Please rsvp to firstname.lastname@example.org (suggested but not required).
Intro. to GIS and Spatial Mapping
Need a custom map for a project or assignment? Interested in analyzing patterns, processes, and relationships between different features or phenomena across a geographic area? Geospatial mapping has applications in almost any discipline. Come to this hands-on workshop to make a custom map and learn about the tools and resources available for your own mapping project. Led by Neil Curri, GIS Academic Computing Consultant and Adjunct Instructor. (Image: Mariah Caballero, Biology & Geography ’19)
Introduction to Audio Recording
04/17 Wednesday 3:30 pm, Collaboration Studio, Main Library
Planning to record voice or music and you have never done it before? Come to this hands-on workshop where we’ll practice making recordings with Zoom recorders. We’ll also go over campus resources for audio production and visit the audio studio in Chicago Hall. Led by Baynard Bailey of Academic Computing Services, organized by DiSSCo. Please rsvp to email@example.com (suggested but not required).
Introduction to Audio Editing
Interested in podcasting? Perhaps you have an interview you need to edit? Come to this hands-on workshop and learn about campus resources, tips on making good recordings and the basics of editing sound files with Audacity (and a brief overview of Audition, Garageband and Hindenberg). Led by Baynard Bailey of Academic Computing Services, organized by DiSSCo. Please rsvp to firstname.lastname@example.org (suggested but not required).
05/08 Wednesday 3:00 pm, Collaboration Studio, Main Library
Explore first-hand the potential VR and 360 video have to offer on our various interactive VR devices and 360 video viewers. Brainstorm and discuss ways this can impact teaching and learning. Or just come to relax and have fun!
Technology Workshops – Fall 2018 Flier – post October Break
Intro to Video Editing with Premiere Pro
Interested in learning editing video or recording a narrated presentation?
Come to this hands-on workshop where you will learn to use Adobe Premiere Pro. Led by Baynard Bailey of Academic Computing Services. Please rsvp to email@example.com (suggested but not required).
Intro to Linux
11/07 Wednesday 3:30 pm, Sci Vis Lab, Bridge Building
Linux is a free and open-source operating system with superior security and performance to MacOS and Windows. Come learn how to get started exploring the Linux world on your very own laptop, or use one of our computers. Learn about the many “flavors” of Linux, how to use the terminal (command-line), and how to install and update software from a package manager. Led by Chris Gahn of Academic Computing Services. Please rsvp to firstname.lastname@example.org (suggested but not required).
Poster Making and Basic Design
11/16 Friday 2:00 pm Library Electronic Classroom 160
Need a poster for an academic conference? Want to print a giant poster for your event? Come to this hands-on workshop, learn basic design and how to use Adobe Illustrator to lay out a poster. Led by Baynard Bailey of Academic Computing Services. Please rsvp to email@example.com (suggested but not required).
Photographing and Documenting your Artwork
11/28 Wednesday 3:30 Taylor 104
Need to put together your senior portfolio? Want to submit work to galleries or other exhibition calls for entry? Come to this workshop and learn how to document your artwork and to do basic Photoshop editing. Led by Amy Laughlin of Academic Computing Services. Please rsvp to firstname.lastname@example.org (suggested but not required).
12/07 Friday 2:00-4:00 pm Collaboration Studio, Main Library
Interested in 360 video or experiencing Virtual Reality? We’ll have an Oculus Rift and a Playstation VR setup, as well as several 360 video viewers. Come try these devices out and discuss how they might impact education. Organized by Academic Computing Services and the Library.
In support of the Environmental Studies focus on the Casparkill Watershed, we recorded a flight above the Casparkill Creek, from its source to its mouth in the Hudson River, a distance of about 10 miles. The course was covered by 6 separate flights, as shown below. We also flew a course over the Casparkill’s biggest tributary, the Fonteyn Kill.
Click on a red or green line segment to see a drone video of the corresponding section of the Casperkill Creek, flown north to south. (Click on the yellow line segment to see a drone video of the Fonteyn Kill.)
The Eucharistic Dove, one of only a few left in existence, is found behind glass in the Frances Lehman Loeb Art Center, making it a difficult piece to investigate closely. Academic Computing Services students, Dylan MacDonald, Zechariah Lee, and Sufyan Abbasi, under the guidance of Amy Laughlin and Professor Andrew Tallon, were put to the task of producing a 3D model that preserves the texture of the Dove for closer inspection.
The model was produced using a technique called photogrammetry, which is the process of stitching together a 3D model based on a sequence of images. The technique combines novel application of computer vision with classical projection mapping that produces stunning results. The software used was Agisoft Photoscan, an industry standard photogrammetry software that allows users to stitch together an orbit of still photos into a 3D model, like so:
As a proof of concept, we began with trying to model a candlestick, donated to us by Professor Tallon, which had similar properties as the Eucharistic Dove in size and luster. Due to the reflective surface of the candlestick, we found that using a green screen was out of the question since the shades of green were reflecting off of the object and projected onto the model. After trying different techniques, we discovered that shooting with a white background in the Loeb photo studio proved to be the best way to eliminate any unwanted reflections in our model.
Once we took photos of all angles of the Dove (over 200 pictures total), we used Adobe Photoshop to mask out the backgrounds and loaded the images into Photoscan. There, a second masking process was done to tell the software the bounds of the object to be generated.
Once Photoscan was finished processing the files, we were left with a .obj file that formed the 3D model of the Dove, a .tif file that dictated the texture, (shown below) and a .mta file that maps the texture to the 3D model.
Next, we loaded the model into Blender, an open source 3D modeling software. Here, we made edits to the generated 3D model, such as filling in the bottom area of the Dove where photos were not available.
Finally, the model was ready to be published on SketchFab, an online publishing platform for 3D models, which allows users to manipulate the model in 3D space and view the model in virtual reality.
From start to end, the process took about a semester for the initial research and testing, and half a semester for photographing the Dove and making edits to the model. Dylan and Zech worked on masking the Dove in Photoshop and Photoscan and generating the 3D model in Photoscan, and Sufyan worked with Blender to make the edits to the model.
We hope that you enjoy the Dove as much as we enjoyed producing the model. If you have a project idea involving 3D modeling and need some help, please contact Amy Laughlin in Academic Computing Services in CIS.
I wish I had known this years ago when I ran the Media Cloisters! It turns out you can connect multiple USB inputs and outputs on Macs. This is great if you want to team-edit video or record two people at once. You’ll need two USB headsets for this to work.
Getting Two USB Headsets to Work:
This is built-in functionality for Mac OSX. Plug in both headphones, then open Audio Midi setup from /Applications/Utilities.
Click the plus in the lower left corner and choose “Create Multi-Output Device.”
Check the checkboxes beside both headphones.
If you want to rename your new virtual device, you can double click the new entry in the list on the left and give it a name like “Both headphones.”
In System Preferences, you can now set the output to go to your new Multi-Output Device.
Setting up Two USB Headphones Mics
A similar arrangement will work to create two USB inputs. Create an aggregate device for the USB headsets.
Check the appropriate boxes.
To record in Audacity onto two separate channels, choose “(Stereo) Recording Channels” as your input:
What is HPC?
Have you ever tried to run some code or perform some data analysis on your personal computer, and it ended up taking several hours or even days to finish? Frequently, we interact with data sets or projects that are simply too taxing for a single computer (even a very powerful one) to complete. This happens very frequently in a variety of fields across disciplines. High-Performance Computing (or HPC as it is known) is a field in technology concerned with providing advanced computing resources to researchers in order to speed up their data processing or modeling projects. Typically, these computing resources take the form of what is known as a computing “cluster”, which is really just a fancy name for a large number of computers that are all connected together and process data in unison.
Who can benefit from HPC?
HPC at Vassar (on-campus)
Here at Vassar, we have a computing cluster named “Junior” that was built in 2010. Junior has been used by many faculty and students over the years to run countless analyses and simulations for coursework and research in the Sciences and Humanities. The big advantage of using a system like Junior is that it has what’s called a job scheduler program installed. In Junior’s case, the scheduler program is called SLURM. Slurm enables users to submit the code or analysis that they want to run, and then the system will automatically load the required packages and software to complete the job, and output it into a user-specified format. This means that a user can submit a job that might take the system several days to finish, and then go and work on something else while awaiting the results, confident that work is being performed by the automated processes on the computer the whole time.
HPC at Vassar (off-campus/remote)
Here at Vassar, we have access to off-campus HPC resources as well:
- Through an agreement with the NSF-supported XSEDE system (The Extreme Science and Engineering Discovery Environment), Vassar researchers are able to apply for computing allocations on a variety of cluster environments that provide abundant libraries of packages, software, compilers, and user interfaces. The best part – It’s completely 100% free for Vassar! Your tax dollars are hard at work creating and maintaining this extensive network of HPC resources for use by all researchers.
- Vassar has an agreement with Amazon Web Services (or AWS) to provide for Virtual computing environments hosted in Amazon’s many data centers around the country. While we do pay by the hour for resources through AWS, the scalability and versatility afforded to us through this system are incredibly useful. Computing environments can be built and made accessible to the end-user very quickly and easily by administrators on campus.
- We are exploring additional resources such as Google Cloud, Microsoft Azure, products from IBM, and partnerships with other colleges and universities with more robust computing infrastructure. We are also looking into avenues for the upgrade and/or replacement of Junior.
HPC Projects & Initiatives at Vassar
Many faculty at Vassar have been involved in using HPC in the course of their research and teaching. Courses and projects in Biology, Chemistry, Cognitive Science, Computer Science, Mathematics, and Physics & Astronomy all make use of Junior and other HPC resources for course work and projects.
Just a few of the specific HPC projects underway or already completed include:
- Chemistry Molecular research by Franco Caruso and Miriam Rossi which utilized Materials Studio in a cluster environment and has resulted in the publication of two successful journal submissions with a third in progress.
- Biology research on viruses and bacteria using QIIME and other genetic analysis tools on both the local cluster and in AWS by David Esteban.
- Deep learning research and course work using GPU-enhanced computational systems in the cloud by Joshua de Leeuw.
- Computational Quantum Chemistry research by Leah I. Bendavid on XSEDE.
Find out More!
If you’re interested in learning more about HPC, or getting in touch with other people at Vassar who are using HPC resources, please email Chris Gahn, the ACS Consultant for the Sciences.
Making Posters at Vassar Presentation (link requires VC gmail login)
You can use any software you like to create posters or fliers. The most common applications used are Adobe Illustrator and MS Powerpoint. The goal is to create a .pdf that can be shared with the printer. Adobe Illustrator is available in the library electronic classroom and the 24 hour space of the library (AKA DMZ).
Here are some ACS created tutorials for creating academic posters with Adobe Illustrator:
- Graphic Design Tutorial (12 minutes)
- Illustrator Tutorial (25 minutes)
- Exporting Tutorial (4 minutes)
Print jobs smaller 11″x17″ or smaller go to the Copy Center, and can be picked up at the post office counter in college center.
Print jobs larger than 11″x17″ go to Media Resources, which is in the basement of the College Center. Further details and to submit a print job please visit https://servicedesk.vassar.edu/catalog_items/307242-poster-request
If you would like to arrange training for faculty or classes, please email email@example.com
If you are hosting a poster event or poster session, please contact campus activities to reserve their foam boards and/or easels: firstname.lastname@example.org
I’ve helped many classes create posters for academic purposes. Here are various poster sets created by students I’ve trained (some links require VC login):
- Ford Symposium Posters from 2012
- Ford Symposium from 2013
- WMST 241 2012
- French 235
- WMST 241 2012
- French 345
- MEDS 310 Fall 2017
For a list of upcoming public workshops keep an eye the events listed in our Moodle site or visit http://pages.vassar.edu/dissco/events/