High-Performance Computing at Vassar

Posted on March 13, 2018 by

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?
-Students
-Faculty
-Non-Faculty Researchers
-Administrative Staff

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.

Early Spring Workshop Series 2017

Posted on February 3, 2017 by Baynard Bailey

iBooks Author Workshop

Friday Feb 3rd 2:00 pm Main Library Electronic Classroom 160

iBooks Author is a free program that allows anyone to create digital books with illustrations, audio, and interactive glossaries. iBooks can be shared or sold via Apple’s iBooks Store and viewed on any Apple device, or exported to other formats. Hands-on workshop led by Steve Taylor of Academic Computing Services. Open to the campus.

Final Cut Pro X

Wednesday Feb 8th 3:30 Library Electronic Classroom 160

Interested in learning editing video or recording a narrated presentation? Come to this hands-on workshop where you will learn to use Apple’s professional but easy to use video editing software. Led by Baynard Bailey and Amy Laughlin of Academic Computing Services. Open to the campus.

Setting Up a WordPress Site

Wednesday Feb 15th 3:30 Library Electronic Classroom 160

WordPress is an open source digital publishing platform that is great for building quick and easy websites for orgs, portfolios, research and more. Led by George Witteman of VC++. Open to the campus.

An Introduction to Linux: World’s Best OS!

Wednesday Feb 22nd 3:30 Sci Vis Lab, Bridge Building

Linux is a free and open-source operating system used in all sorts of devices. Come and learn about the Bootloader, the Kernel, Daemons and the Shell! Discover
why Linux runs most of the internet and how it is the one of the most reliable and secure OS’s available. Install it on your own machine! Led by special guest Stefan Crain of The Jahnel Group.

How to Photograph your Artwork

Friday March 3rd 2:00 Taylor Hall 328

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. Led by Amy Laughlin of Academic Computing Services. Open to the campus. Contact: amlaughlin@vassar.edu

Poster Making

Wednesday March 8th 3:30 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. Learn about campus printing resources. Open to the campus

Computing Workshops Fall 2016

Posted on November 1, 2016 by Baynard Bailey

WordPress 101

Wednesday Oct 26 3:30 GIS Lab
WordPress is an open source digital publishing platform t
hat is great for building quick and easy websites for orgs, portfolios, research and more. Led by George Witteman of VC++ and Academic Computing Services.

High Performance Computing & Amazon Web Services

Friday Nov 4 2:00 Sci Vis Lab

Come and learn about the “why” and “how” of high performance computing and the resources available at Vassar. Specific topics will include an overview of the field of HPC, and an introduction to Amazon Web Services. Led by Academic Computing Services’ Chris Gahn.

Intro to HTML and CSS

Wednesday Nov 9 3:30 -Web Design 101 – I Sci Vis Lab, Bridge Building

Sometimes Tumblr, Squarespace or WordPress just won’t do it! George Witteman of VC++ will walk you through the beginning steps of hand coding a website.

Game Design 101

Wednesday Nov 16 3:30 Sci Vis Lab, Bridge Building

Ever want to get a taste of making a video game? Thinking of an alternative to another boring paper? Learn the basics of game design by hacking pong! Tom Lum of Indiebrew will lead a hands-on workshop on simple game programming using Love2D.

3D Printing Open House

Wednesday Nov 30 3:30 Library Electronic Classroom 160

Curious about 3D Printing? Come to our open house where we’ll discuss and visit campus resources for 3D Printing. Hosted by Amy Laughlin of Academic Computing Services.

Sound Editing with Audacity

Wednesday Dec 7 3:30 Library Electronic Classroom 160

Interested in podcasting? Perhaps have an interview you need to edit? Come to this workshop and learn tips on making good recordings and the basics of editing sound files with Audacity. Led by Baynard Bailey of Academic Computing Services.

Make Better Videos with Your Phone or Computer (Free!) – Vimeo Video School

Posted on October 28, 2015 by Baynard Bailey

Impressed by Vimeo’s Video School

by Baynard Bailey

I am a long time fan of Vimeo and I’ve used it to share video for a bunch of Vassar projects over the years. (FTR those who don’t know, Vimeo is “a video-sharing community for original creative work and the people who create it”.) I was excited to see that Vimeo has launched a series of videos under the heading of “Vimeo Video School“. The series is really well done, practical, and even entertaining. I have watched and sent out links to a lot of instructional videos over the years and I have to say, this series is as good or better than anything I’ve ever seen (in the genre). Here’s an example from the series “Mastering Mobile Video“:

In addition to the Mobile Video Series (which by the way totally vindicates my ire when I see people shooting their video in portrait mode) they also have these series of lessons:

Video School Lessons

Introducing Windows Movie Maker
For PC people who are new to video editing, this free series is a friendly introduction to Windows Video Maker.

iMovie for Mac
Mac-friendly folk: edit videos without the stress. Easily master iMovie essentials in this free Video School series

Final Cut Pro X
Kick your video editing up a notch (or three) with our premium series focusing on the ins and outs of Final Cut Pro X for Mac. BAM.

Adobe Premier
Brush up on the basics and learn the finer points of Adobe Premiere in this free Video School series.

This is a fun series and makes good use of technology we have in hand or on campus.

Laser Scanning Reveals Cathedral’s Mysteries

Posted on June 25, 2015 by Amy Laughlin

WATCH: Tech-savvy art historian Andrew Tallon uses lasers to unlock the builders’ secrets behind the construction of the National Cathedral in Washington, D.C.

National Geographic Article

ACS Collaborates with ART 386 students and faculty on “first-of-its-kind exhibition.”

Posted on June 8, 2015 by Amy Laughlin

Amitabha Buddha, Central Tibet, 19th century; pigment on cloth; 38 1/2 x 25 1/2 in.; The Rubin Museum of Art, New York, F1997.6.3.

ART 386, Embodying Compassion in Buddhist Art: A Curatorial Training Seminar was taught by Karen Lucic during Fall semester, 2014. The purpose of the class was to give students the opportunity to research and curate an exhibition at the Frances Lehman Loeb Art Center. During the summer of 2014, Professor Lucic contacted me to discuss creating a website for her students to use as a repository for their research and eventually this site would become a companion site to the final exhibition in April, 2015. Over the course of the Fall semester, students wrote and compiled content for the site and they worked closely with ACS to design and populate the site.

From ART 386 Syllabus:

Each student will be responsible for the digital content and interpretation of 2-3 works in the exhibition. The instructor will assign the objects to each student, based on her/his experience and preparation. These student contributions will be posted on the exhibition application and/or website. (60% of grade.)

Students will work in teams to produce additional resources for the exhibition: gallery guide, interactive maps, guide to web resources, etc. Students in the team will also give feedback on other team members’ work before submission (20% of grade.)

From ART 386 Assignment Sheet:

The purpose of this assignment is to create digital educational content for the exhibition. Always remember who your audience is: visitors to the exhibition, or online users, who might not know much—or anything—about the topic. What you write, and your choice of materials should be based on your assessment of what will enhance their experience and understanding of the exhibition. Texts should be concise and to the point. Other materials should be short but engaging.

For each work you have been assigned:

1) Write an interpretative text (no more than 100 words) for app/website

2) Select one comparative image (must be open access and high resolution); include full caption of comparative image

3) Write a text (no more than 100 words) explaining the comparison

4) Select an audio file, if possible, that enhances the work (no more than two minutes). Examples: chanting, singing, mantra recitation, etc.

5) Select a video file, if possible, that enhances understanding of the work (no more than 2 minutes). Examples: practitioners circumambulating, prostrating, spinning prayer wheels, making sand mandalas, offering incense, etc.

6) If there are no appropriate audio or video files, choose another comparative image.

7) Compile a list of unfamiliar terms from your texts, with definitions

8) Map your work, at least by country. With some works (Putuoshan, Nachi, etc.), it may be possible to be more precise about locations.

9) Record your written contributions.

While students were working to create the content for the site, ACS student employee Bryce Daniel worked on building a wireframe for the WordPress site. Professor Lucic also collaborated with Duke University students to design an App for the exhibition. The App hosted audio files recored and edited by ACS Consultant, Baynard Bailey. These recordings, narrated by both students and Professor Lucic, include short commentaries describing individual pieces in the exhibit, as well as a pronunciation guide for a glossary of terms.

The Embodying Compassion WordPress site is a comprehensive online exhibit reference guide, containing audio, video, images, interactive hotspot maps, and extensive research, curated by ART 386 students. This project proved to be a excellent example of how students, faculty, and ACS consultants collaborate to produce educational materials for the classroom and public audience.

Links:

Embodying Compassion Website

The Frances Lehman Loeb Art Center: Embodying Compassion is a first-of-its-kind exhibition celebrating one of the most important figures in Buddhist art, April 23-June 28, 2015

Get the App

The Bamboo® Graphic Input Tablet

Posted on January 13, 2015 by Steve Taylor

Do you ever need to draw or write free-hand on your computer, but doing it with a mouse is too awkward and you don’t want to buy an iPad or any other tablet computer? You may be happy with a graphic input tablet, like the Bamboo® Connect Pen, which Vassar faculty members can borrow from ACS.

A graphic input tablet is a device on which you can draw with a stylus— it doesn’t have its own display, but you see the results of your drawing on your computer screen. It’s essentially like using a mouse, but one that you can control as well as you can control a pen.

While using any software that allows you to draw free-hand— Photoshop, Powerpoint, and many others— you can draw diagrams or write equations. The Bamboo Connect tablet is made by Wacom, which is known for its large tablets that are favored by graphic designers. The Bamboo Connect is just 11″ x 7″, with a 5.8″ x 3.6″ drawing area.

Here’s a demonstration and review:

If you’d like to try it out, contact your ACS liaison.

GIS Tools for Teaching and Research

Posted on October 8, 2014 by Baynard Bailey

by Baynard Bailey

Anthropology Professor April Beisaw is a very active user of GIS (Geographic Information Systems) and other technologies in her research and in her classroom. ACS recently produced a video featuring Professor Beisaw employing mobile mapping devices in the field (devices she was able to purchase via the Frances D. Fergusson Technology Exploration Fund). Using the GPS mobile mapping device makes it easy to collect data that can then be imported/loaded into GIS to make nice maps. The video features April Beisaw using mobile mapping devices for field research.

Professor Beisaw continues to be a dynamic user and an advocate for using various GIS (Geographic Information Systems) technologies in her classroom. Last year she asked that QGIS be added to the base image for public computers on campus. I didn’t know about QGIS until April pointed it out to me. QGIS is a free and open source tool that empowers users to “create, edit, visualize, analyze and publish geospatial information”. It is also cross-platform, so that means you can use it on your Mac, Windows or Linux machine. (As an educator, I really appreciate it when software is free and cross platform!) Not too long ago, April gave a little demo in her office showing me and a couple Economics professors how to import maps into QGIS and how to get started creating your own customized maps. It seemed like a great tool for teaching and research, although there is a bit of a learning curve.

All of these maps were made with free QGIS:

I should also mention that Vassar has a GIS lab (using ArcGIS) in Ely Hall 114 and that GIS is available on the SciVis Lab machines. Vassar GIS users can also arrange a consultation with Stephanie LaRose, who is a GIS specialist that comes to campus a couple days a week. If faculty or students are interested in pursuing any of these technologies or resources and would like help, please contact Academic Computing Services by emailing acs@vassar.edu.

Prezi

Posted on April 9, 2013 by Steve Taylor

by Steve Taylor

Prezi is a tool for creating presentations, just as Powerpoint and Keynote are, but with some interesting differences. Since its creation in 2009, it’s been seen more and more in conferences.

Metaphors
One way in which Prezi differs from earlier presentation tools is its metaphor. Both Powerpoint and Keynote use the metaphor of a series of individual slides that can be shown in a predetermined sequence, just as 35mm slides would be shown with a carousel projector.

In Prezi’s metaphor, the creator arranges materials on an infinitely large canvas and— as I think of it— uses a video camera to pan and zoom through those materials. That can be done on the fly or the creator can pre-record a series of pans and zooms. The resulting presentation maintains the spatial relationships among the various materials.

It’s On the Web
Although they can be downloaded, “Prezis” are assembled on the web, through your browser, and can be presented via your browser as well. They can be shared with the general public or with a select group of colleagues (or members of a class.) You can even collaborate with others on the creation of your Prezi, which makes it a great vehicle for group projects.

Good and Bad Uses
I’ve seen great uses of Prezi and uses that make no sense at all— unfortunately, quite a few of the latter. If your presentation materials consist of a series of bullet-point lists, quotations, graphics, etc. that have no particular spatial relationship to each other, then there’s no particular reason to lay them out side by side and pan from one to another. But if there are spatial relationships— such as in a complex chart, diagram or map— then Prezi may be the perfect tool.

Here are a few examples of great uses for Prezi. You can pan and zoom on your own, or click the Play button to step through a pre-recorded tour.

“Classification of Organisms,” created by Robert Kappus, will lead you systematically through a complex chart. The chart is circular, and the zoomed-in labels and graphics are aligned along radii of the circle, but that poses no problem, as the pre-recorded tour can not only pan and zoom, but rotate the view as well.

The “Physical Features of Africa Quiz” Prezi, created by Emily Thompson, will give you a tour through the major mountain ranges of Africa. Maps tend to be difficult things to project in a classroom, because the amount of detail means that labels often are too small to see from a distance. Prezi is a great vehicle for showing detailed maps, because of the extreme levels of zooming it can support.

One of my favorite uses of Prezi is to explore different details of a complex work of art. Here’s one that I created, providing a tour through some of the details of the painting Garden of Earthly Delights, by Hieronymus Bosch. An instructor can present a series of details from a work like this, without losing the context of each detail.

A number of people have realized that Prezi can be a good tool for creating a concept map— a diagram that shows relationships among various concepts. Here’s an example of a Globalization concept map, created by Dennis Carnduff.

Go to the Prezi website to explore other materials that various people have made public, to get more ideas on how it can be used.

Licensing
Prezi offers three levels of licensing:

Public, which is free, provides you with 100 MB of storage, but requires you to make your creations public.
Enjoy, which costs $59/year, provides 500 MB storage and allows you to make your creations private.
Pro, which costs $159/year, provides 2GB storage.

However, students and teachers— anyone with an “edu” email address— can get the Enjoy level of license for free.

Prezi U
The website also provides a gateway to “Prezi U,” a community of educators who share ideas about using Prezi in their teaching.

Taxonomy of Learning Environments

Posted on November 20, 2012 by Steve Taylor

by Steve Taylor
There’s been a great deal of talk in higher-education circles over the past year, about the perils and possibilities of online learning. Often that talk has been in the context of MOOCs or Coursera, but there are many variations of online learning and I often find that two people discussing the topic have fairly different things in mind. Here then is a taxonomy that we can use to get a little closer to understanding each other.

Classroom Learning (also called Face-to-Face Learning)
This type of course serves to anchor one end of the spectrum of remoteness in learning environments. It refers to the traditional environment, in which matriculated students and their instructor meet in real space, on a frequent basis— usually two or three times per week. Readings and homework assignments exist on paper.

Enhanced Classroom Learning
As in traditional classroom learning, matriculated students and their instructor meet in real space on a frequent basis, but some of their course materials— and more significantly their course activities— reside on the web. Students may be expected to contribute to online discussions or blogs, collaborate online with classmates on group projects, or take quizzes or exams online.

Blended Learning (or Hybrid) Courses
In this type of environment, matriculated students conduct a majority of their learning online, but meet face-to-face with their class a few times throughout the term of the course. This is essentially a distance-learning approach, with some added checks, giving instructors an opportunity to confirm that students are on track, and possibly to administer an exam in a proctored setting. Blended learning courses are often offered for adult learners in rural areas, who have to drive a long distance to campus.

Distance Learning
In a distance-learning environment, matriculated students take an entire course— or sometimes an entire degree program— online. Many universities offer distance-learning programs for students who would not be able to accommodate the schedule and location of traditional courses. Many public universities, with their commitment to educating the diverse populations of their states, have had distance learning programs for years, and many large, private universities have such programs as well.

Massive Online Open Course (MOOC)
MOOCs started to become prominent in late 2011 or early 2012. They exist entirely online and, unlike the other learning environments mentioned, they do not require learners to be matriculated in any particular institution. They are generally free of charge, but offer no credits. Because there is generally no instructor interaction involved, an individual MOOC may have thousands or even tens of thousands of students.

A number of universities have endorsed and supported their faculty members who wish to design MOOCs. Their motivations at this point seem to be a desire to “push their brand” into a larger population and, to some extent, a desire to provide a public service to that population.

Traditional, residential colleges like Vassar have been providing enhanced classroom learning experiences for many years, but most are just beginning to consider whether it makes sense for them to offer courses with reduced face-to-face time.

Techademia

Academic Computing Services at Vassar College

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