Announcing XSEDE Campus Champion at Harvey Mudd College

893,000 SUs (Service Units = wallclock runtime multiplied by the number of cores) on several supercomputer facilities are now available to our researchers, faculty and students free of charge. In our ongoing efforts to provide a spectrum of high-performance computing resources to our community, CIS has signed up to participate in the XSEDE Campus Champion program and received almost 900 thousand SUs from national supercomputing centers. The SUs can be used to test various scientific applications that our faculty and students run for their research projects or for their classes. The Campus Champion at HMC will help install, set up, and test research applications on different facilities and provide any necessary on-campus support for using the XSEDE resources. The Campus Champion at Harvey Mudd is the Scientific Computing Specialist, Dr. Jeho Park at CIS.

What is XSEDE?

The Extreme Science and Engineering Discovery Environment (XSEDE) is the most advanced, powerful, and robust collection of integrated advanced digital resources and services in the world. It is a single virtual system that scientists can use to interactively share computing resources, data, and expertise. Scientists and engineers around the world use these resources and services—things like supercomputers, collections of data, and new tools—to make us all healthier, safer, and better off. XSEDE, and the experts who lead the program, will make these resources easier to use and help more people use them. Click here for more information.

What does the XSEDE Campus Champion Program do for Harvey Mudd?

The Campus Champion Program at HMC will serve as a:

  • Source of local, regional and national high-performance computing and cyberinfrastructure information on our campus
  • Source of information regarding XSEDE resources and services that will benefit research and education on our campus
  • Source of start-up accounts on your campus to quickly get researchers and educators using their allocations of time on XSEDE resources, and
  • Conduit for the campus high-performance computing needs, requirements and challenges, with direct access to XSEDE staff.

With the XSEDE Campus Champion allocations, HMC can now offer easy access to various supercomputers so that our researchers can test their applications and experience the benefits of using the supercomputers. Once the applications are tested, the Campus Champion will help the researchers get a “Startup” allocation (up to 200,000 SUs) which may be used up by the researchers (or the research team) for a year. If the research project needs more time and allocations, the PI(s) of the project will then be helped to apply for a “Research” allocation that is usually a multi-year allocation with a substantially larger amount of SUs than the Startup allocation. All these resources are provided to the researchers with free of charge by the NSF-funded XSEDE program. The Campus Champion at HMC is the local person who can help our researchers take the opportunity more easily. So please feel free to stop Jeho in a hallway and ask about the XSEDE Campus Champion Program. You are also welcome to contact our Helpdesk ( for any inquiries about the XSEDE resources.


Essential MATLAB Seminar for Beginners and Refreshers

CIS will hold two MATLAB seminar sessions for MATLAB beginners and refreshers this week. Please come join us to learn something new and refresh your memory on your journey to mastering MATLAB.


  • Session 1: 4:15 pm – 5:15 pm on Thursday, September 20, 2012
  • Session 2: 11:00 am – 12:00 pm on Friday, September 21, 2012


  • Session 1: Sprague Math Seminar Room (3rd floor)
  • Session 2: Sprague Learning Studio Classroom


  • The Basics of MATLAB Computing Environment — get to know about the MATLAB desktop environment.
  • M-files — learn the basics of MATLAB scripts and functions.
  • Data Import/Export — learn how to import external data and export MATLAB data.
  • Basic Plot — draw basic 2d plots and learn simple manipulation techniques.
  • The MATLAB Editor — know how to use the MATLAB editor for easier programming.
  • Publication — learn how to comment your MATLAB codes for publication.


CIS awarded two high-end GPUs from NVIDIA

(Disclaimer: Sorry gamers. These GPUs are not for 3D gaming, but for number crunching scientific calculations!)

CIS submitted a proposal to NVIDIA’s Academic Partnership Program on the last day of May. NVIDIA quickly approved the proposal on June 11 and decided to donate us two Tesla C2075 GPUs (MSRP $2,500 per piece). Although it took a month to process the shipment at NVIDIA’s distribution center due to their high demand, it was worth the wait!

Tesla C2075 from NVIDIA

As of this writing, Tesla C2075 is the top-notch GPU available on the market for GPU computing. It has 448 CUDA cores and 6GB GDDR5 memory, which allows to pull 515 Gflops in double precision calculations and 1030 Gflops in single precision. Yup, it’s a little monster and we’ve got two of them!

CIS (Andy Davenport and Jeho Park) has been collaboratively working with Prof. Vatche Sahakian at Physics on a pilot project to prepare a new high performance GPU system on our campus. Prof. Sahakian generously offered to purchase a high-end GPU host computer. CIS is providing the NVIDIA GPUs and technical support to build a new system. Once the setup is complete, the new system will be tested and later shared with faculty and student researchers at Harvey Mudd for high-performance GPU computing experiences and tests. If you are interested in GPU computing or wish to involve in the GPU computing pilot, please contact Jeho Park at CIS for more information (or leave your comment to this post).

Useful Links:


HPC @ HMC: Survey Results

In November 2011, CIS conducted a short survey on the use of High Performance Computing (HPC) resources at Harvey Mudd College. We received 16 responses: 14 HPC users and 2 non-HPC users. We truly appreciate their time to fill out the survey. In this article, we share some of the interesting results considering the answers from those 14 HPC users.

1. Departments using HPC in research and/or teaching

First, we wished to know which departments were using HPC systems for their academic activities. Although we only had 14 responses, the result was clear. All seven departments have been involved in using HPC resources! Go Mudders! 🙂

2. The nature of the HPC use

In this question, the majority of the responders answered that they have used HPC facilities for simulation, data acquisition and analysis, and modeling. The “Other” selection includes computer animation, mathematical computation, teaching HPC and HPC research.

3. The location of the HPC facility

This result may be a bit misleading because multiple selection was allowed. One of the responders have used off-campus HPC facility and the rest have their HPC facilities in department labs or computer rooms. Four of them also have additional high-end workstations under/on their desks. The “Other” selection indicated the use of a CIS server.

4. What have you used HPC for?  All of the 14 respondents answered that they’ve used HPC resources for research and four of them have also used the resources for teaching as well (one of the four respondents teaches about HPC in class). Notice that multiple selection was also allowed for this question.

5. How do the HPC facilities you use meet your needs? Current and Future

CIS is always interested in knowing whether computing resources meet your needs now and in the future. About half of the responders thought that they have acceptable HPC systems for current and future needs. Most of the responders who chose “acceptable” for both current and future have relatively new HPC systems (< 1 year). On the other hand, those who have HPC systems older than 3 years said that the resource might not meet their needs in the future. CIS may help find required HPC resources for those who responded this question with “unacceptable” (and “neutral”). For example, FutureGrid resources may fit to your needs as it was introduced in this news article. Please contact our Scientific Computing Specialist (or leave your comments) for any assistance in finding the right HPC resources for you.

Through this survey, we believe that we’ve gathered very useful information for our HMC community. The HPC survey is still open at When you have time, please fill out this short survey so that we know more about your needs in High Performance Computing and help you accordingly.

SuperComputing (SC11) Conference for College Educators

SuperComputing (SC) conference is the leading international conference on High Performance Computing (HPC), Networking, Storage and Analysis. This year the 24th annual SC conference (SC11) was held in Seattle, WA, in November, 2011. More than 5000 participants were gathered in one place to learn, discuss, and show off cutting-edge technologies in HPC and related areas.

Although the conference is huge in all respects, the beauty of the SC conference is in its specialized sub-community conferences. One of the sub-community conferences called Education Program is very well organized to suit to college educators who teach HPC and Scientific Computing. The main focus of the Education Program is to learn and share better ways of teaching HPC and Scientific Computing (or Computational Sciences) tools to undergraduate faculty and students.

Jeho Park (Scientific Computing Specialist) at CIS attended the SC11 conference, and learned many good practices on HPC education and made relevant connections on behalf of our HMC community. A few of the takeaways worth mentioning are Bootable Cluster CD (BCCD), LittleFe Project, and FutureGrid Project.

BCCD is a turn key solution to build a Beowulf style cluster on the fly. The BCCD boot image comes with a complete parallel computing environment such as network setup, libraries, compilers, benchmarks and applications needed to teach HPC to undergraduate faculty and students. So to teach distributed and parallel computing, you just need BCCD and a couple of networked workstations or a computer with a multicore processor(s). BCCD even runs in virtual machine (VM) environments. This mean that you may boot multiple BCCD VMs on different cores and emulate the cluster environment right in front of your audience. CIS will be testing BCCD on our High Performance Workstations during the winter break. For more information, please visit

LittleFe Build OutLittleFe is an interesting project funded in part by Intel (until this year) to build a portable (< 50 lb) six-node cluster with a relatively small amount of money (< $3,000). The LittleFe portable cluster is a simple and easy way to build a hardware and software resource for teaching  parallel processing speedup, efficiency, and load balancing. CIS will keep an eye on their call for applications for 2012 LittleFe grants. If you are interested in being involved in this project at HMC, please contact Jeho at CIS.

If you are looking for a more serious type of HPC resource, take a good look at the FutureGrid Project. The FutureGrid Project focuses on offering new and dedicated test-bed environments for research challenges on grid-enabled and cloud-enabled computational schemes in sciences and engineering. The FutureGrid also actively supports education and broader outreach activities:

“…. The project will advance education and training in distributed computing at academic institutions with less diverse computational resources. It will do this through the development of instructional resources that include preconfigured environments that provide students with sandboxed virtual clusters….”

So it sounds like the FutureGrid is waiting for your innovative ideas to exploit their new experimental testbed for your research and teaching on HPC, scientific computing, parallel computing, distributed computing and cloud computing. Harvey Mudd College is especially good fit for FutureGrid in terms of its scope. So we encourage faculty members to look at the FutureGrid website and feel free to contact CIS for any assistance to apply for FutureGrid instances.

The next SC12 conference will be held in Salt Lake City, Utah on November 10, 2012.

Using Livescribe Smartpen as a Lab Notebook Device

As noted in Elizabeth’s blog post, Educational Technology and Media Services group has been sponsoring the pilot using the Livescribe pen as a lab notebook device. In this follow-up post, we share feedback from one of the pilot participants. We also introduce various sharing practices of the Livescribe notes for those who wish to try the Livescribe pen out.

Livescribe ConnectLast May 2011, Livescribe introduced Livescribe Connect as an add-on software to Livescrive Desktop. It helps share Livescribe notes easily without using their proprietary sharing method via the Livescribe online website, which was a major hurdle in sharing the Livescribe notes in the past. With current Livescribe Connect (version, there are four ways to share your Livescribe notes: Google Docs, Evernote, Facebook, and email/computer file. The table below summaries different features for different sharing methods:

Google Docs Evernote Facebook Email / File
Format Pencast PDF,
Pencast PDF,
PNG image
Embedded Flash Pencast PDF,
PNG image,
M4A audio
Downloadable Yes Yes No Yes
Searchable Text No Yes No Yes (in Livescribe Desktop)
Size Limit
for Sharing
No Yes
(25 MB – free,
50 MB – paid)
No Yes (when attached to email)

Livescribe’s Pencast PDF is a proprietary file format containing audio synced with the handwriting image in Adobe PDF. You need Adobe Reader X (version 10 or later) to interactively play the audio part of the pdf file while the image part can be viewed with any pdf viewers including Google Docs and Evernote viewer.

When uploading and sharing files via a cloud facility, the file size is an important factor to consider. Obviously, the size of the Pencast PDF file depends on the length of the audio part embedded in it. According to our tests, the Pencast PDF file takes up about 13.8 MB per one minute audio. This means that sharing Pencast PDF files on Evernote may be impractical because the upload size of one file is limited to 50 MB even with its paid premium account. But Google seems generous in allowing large PDF file upload (up to 10GB) to Google Docs. So to share a large Pencast PDF files, Google Docs would be your best bet. On the other hand, to search texts from your handwriting, Evernote is superior to Google Docs in that it offers text search feature by scanning Pencast PDFs and images.

There still exists the original (proprietary) way to share pencast files online: My Livescribe Online. Each Livescribe pen comes with 500MB online space to store and share your pencast files. Mobile device sharing is made possible through the online service. You can interactively play your pencast files on the My Livescribe space from iPhone or iPad using the Pencasts app; Android app is not yet available as of this posting.

Prof. Greg Lyzenga sent us his valuable and interesting feedback on the use of the Livescribe pen as a lab notebook device. He said, “My experience with the Livescribe was mostly pretty positive.  I found it to be pretty responsive to my writing style and the software was moderately friendly. One of the drawbacks is that you need to press pretty hard to make sure all strokes are recorded without missing or skipping.  As a result, your hand can get pretty tired after a hour of writing.  Another disadvantage as compared with an iPad or tablet is the inability to erase mistakes or use different colors.  For my personal use, I think I will prefer the iPad, even though it is a little slower in response to writing gestures.  But I will consider the Livescribe as a viable option for students who want to do electronic lab books.  For either option, pen or tablet, I am still exploring the best software and method for sharing, markup and version control. Ideally I’d like to be able to grade the notebook electronically and have my comments merged with the student’s archival copy.  I’m hoping that there is a drop box option within Sakai that will permit two-way document sharing with students so that I can do this.”

Our journey to exploit the Livescribe pen as an educational technology device will continue throughout the Fall semester. Please stay tuned for more feedback and information about the Livescribe pen from CIS.

Live Streaming of HMC Commencement 2011

On May 15th of 2011, Harvey Mudd College streamed its commencement ceremonies for the first time. With the successful collaboration of multiple teams, it went very well from the start of the preparations to the end of the event. We thank all those who worked tirelessly to make this first step as smoothly as possible.

Judy Augsburger, Senior Director of Advancement Communications, wrote about her impressions that:

I was delighted with our first livestream of commencement. The three camera shoot was well directed and the footage looked lovely. We had a total of 278 views during the ceremony, which was more than I thought we would get given that our main promotional efforts were geared towards the families of graduates, of which we had just 178.

It was rewarding for me to get a phone call at the start of the ceremony from a grandparent who was trying to access the livestream to see his grandson graduate. I talked him through some rudimentary browser features (now I know I’m not cut out for computer support services!) until he could see the ceremony. He was quite happy for the opportunity to watch his grandson get a diploma live.

A real advantage for our office of livestreaming commencement is that the video is recorded and saved in the livestream archive, and available to upload immediately. We posted it quickly to our YouTube channel and within four days it already had 481 views. We couldn’t have posted it so quickly if we had needed to go through all the footage and edit it; editing takes quite a bit of time. So we are pleased that we could provide the video quite quickly to those who couldn’t watch it live, but wanted to watch it soon after and experience some of the excitement and joy of the moment.

And about the technical aspects of the commencement live streaming prep and production, our Media Services Technician, James Sadler, reported that:

Streaming was done using and was done in standard definition. University of La Verne’s LV3TV camera and production crew were brought in to handle the three camera production and mixing. Audio was handled, as usual, by Nelson Sound and they gave the LV3TV crew a drop from their mixer board. This allowed Michael Meyka to watch over the whole production and James Sadler to make sure the streaming end of everything was up and running consistently.

The LV3TV team received a network drop coming out of the McAllister building next to the commencement site. The network connection was thoroughly tested by CIS staff members on Friday the 13th to make sure it was strong and didn’t hit any firewall issues. On the following Saturday, an actual stream was tested to verify again that everything would work properly. After trying a few different options, they decided that using a PC laptop with Wirecast 4.1 installed to send the video to was the best solution.

During the commencement, the stream went extremely smoothly with no hiccups or issues. Here are a few stats from the live stream: peak number of viewers: 77, total number of live views: 278, number of countries viewed in: 10, and replays to date (05/18/2011): ~200.

The commencement video is available on HMC’s YouTube channel.

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MATLAB Seminars for Mudders

In April, CIS offered a series of MATLAB seminars to HMC community.  There were five seminar meetings covering three different topics: basic MATLAB programming, advanced MATLAB programming and parallel processing with Parallel Processing Toolbox.

Basic MATLAB programming seminars taught by Jeho Park at CIS covered fundamental, yet essential, MATLAB programming skills for MATLAB beginners. The seminar participants enjoyed creating function m-files and supporting documents. The basic MATLAB seminar attracted many freshmen who wish to prepare themselves for the courses that require MATLAB programming skills. CIS plans to offer additional basic MATLAB seminar classes in early fall semester for those who missed the April seminar meetings. So please stay tuned.

CIS also invited the MathWorks Senior Application Engineer, Doug Eastman, to HMC campus to discuss advanced MATLAB programming topics. The MathWorks on-site seminar discussed how to make use of different MATLAB functions and memory allocation methods for a better computing performance. The presenter also introduced MATLAB parallel processing features that may lead to a significant performance improvement for some number crunching applications. The seminar was very helpful for those who seek ways to improve performance of their MATLAB codes.

For future MATLAB seminars at HMC, we welcome your suggestions for topics:

MATLAB Seminar Topic Suggestion Form

MathWorks MATLAB Seminar MathWorks MATLAB Seminar (3)



COMSOL workshop on HMC campus

A: “Dude, where’s my car? I need to drive to L.A. to attend the COMSOL workshop.”
B: “What car? And for what? Dude, did you miss the COMSOL workshop in the Learning Studio classroom last month?”
A: “Doh!” 

That’s right. CIS brought the COMSOL workshop to our campus on Friday, January 28th. It attracted a large turnout: 28 participants from Harvey Mudd (22), CMC (2), Pomona (1), CGU (1) and Keck (2). We were especially excited to see the majority of the participants were from HMC.

The workshop was led by Dr. Mina Sierou from COMSOL, Inc..  During the first half of the workshop, she covered an overview of COMSOL Multiphysics Version 4.1 by creating a simple model to explain its capabilities, basic usages and new user interface. And for the rest of the workshop, participants tried the new COMSOL 4.1 on their own laptops and asked a lot of questions they had had for a COMSOL expert.

This event was successful not only in CIS’ point of view but also in faculty participants’ perspectives. “I thought the workshop was quite effective.  …  I would recommend it to students as an time-effective way to get up to speed on the basics of COMSOL.” said Prof. David Harris from Engineering Department. We are working to offer another on-campus COMSOL workshop in Fall. So, Dude A, please stay tuned!

Visit for more information on free/non-free COMSOL seminars and training sessions.

ODE Architect in the Cloud

During Summer 2010, CIS supported three summer projects under a new faculty technology grant program, Teaching with Technology, which was a pilot run in conjunction with the Dean of Faculty’s Office.  In this article, we introduce one of the projects, ODE Architect in the Cloud, led by Dr. Robert Borrelli (PI, Mathematics Prof. Emer.) and Dr. Jeho Park (CIS, Scientific Computing Specialist). The project aimed to demonstrate the possibility of running ODE Architect in a remote virtual computing environment.

ODE Architect (ODEA) is a legacy software package that first appeared in 1998 under support of the Consortium of ODE Experiments (C*ODE*E) and the National Science Foundation.  Although it is a 12-year-old program, it’s known to provide a useful teaching environment for college level Differential Equations classes.  But, like most legacy software, it has serious incompatibility issues under modern Operating Systems.  As the ODEA package is bundled with the book, Differential Equations, which is being used in a couple of Differential Equations classes at HMC and Pomona College, the incompatibility issues are a current problem for HMC students and faculty who wish to try the software along with the text.

Prof. Borrelli, CIS , and Wiley & Sons, Inc. (the publisher of the book and the distributor of the software package) collaboratively worked to setup a virtual machine environment for the ODEA package.  CIS put the virtual machine in a cloud computing facility called CloudShare in order to provide an on-demand access to the virtual machine over the Internet.  The beauty of their service is that pre-configured virtual machines can be shared and accessed using a browser, and moreover it is free to try.  So, as a result of the project, the requirements for running the ODEA tool kit became a browser and the Internet, i.e., no more hair-pulling about incompatibility issues!

CloudShare generously offered HMC an extended number of invitations which can be used for our faculty and students during the fall semester.  Please use the form here to request an invitation from CIS to the ODE Architect in the Cloud environment.  For those who wish to try it, we encourage you to read the account setup instructions at (Their registration process is kind of tricky.)  Once you setup the CloudShare Pro trial account, you get access to the pre-configured remote virtual machine through your browser using a Java applet.  Currently the Java applet is compatible with most browsers in Windows, but only Firefox in OS X and Linux.

For all other ways to use the cloud computing environment, please refer to this QuickStart Guide and website at They have an FAQ page at, and community forum at  Again, to request an invitation to the ODE Architect in the Cloud environment, fill in the form at

Firefox browser showing ODE Architect Tool running on 32-bit Windows XP virtual machine in the Cloud.