Prof. Bill Daub Awarded XSEDE Research Allocation

Harvey Mudd College’s computational chemistry lab has been awarded supercomputing resources to support two senior thesis studies on density functional theory (DFT) calculations applied to ketal and ortho ester Claisen rearrangements. The award (165K core hours + 2 TB disk space) is worth about $8,000 for the first year and renewable based on the needs and progress.

Chemistry Professor Bill Daub was awarded startup allocations from the Extreme Science and Engineering Discovery Environment (XSEDE) in 2016 and his students (Gabriel Phun ‘18 and Kareesa Kron ‘18) used the allocations for their summer research, producing a significant amount of results. One of his students, Gabriel Phun ‘18 told us the story of his summer research.

Based on the results, Prof. Daub (PI) and CIS’ Dr. Jeho Park (Co-PI) worked together and requested a substantial amount of computing time from two supercomputer centers (San Diego Supercomputing Center and Texas Advanced Computing Center). The proposal went through a competitive process, designed in a similar fashion to the NSF peer-review system. The committee notified us of its approval on December 15, 2017. The new research allocation, which is good until the end of 2018, will provide enough computing power for the students’ senior thesis studies. Unlike the startup allocations, which have some limitations like the project term being only one year, the research computing allocations can be renewed after the first year and more computing time may be added as needed based on the project progress. If you would like to know more about supercomputer resources through XSEDE, please contact Jeho Park at

[Some useful links]

HMC Scientific Computing Workshop Series for Spring 2015

With the finals around the corner and the summer break soon to follow, we will wrap up the HMC Scientific Computing Workshop Series for Spring 2015 with these three popular workshops:

  • Essential MATLAB for Beginners (FULL)
    April 30th at 5:30 pm to 7:00 pm in Aviation Room at Hoch-Shanahan Dining Commons
  • R for Statistical Computing
    May 7th at 5:30 pm to 7:00 pm in Aviation Room at Hoch-Shanahan Dining Commons
  • Advanced MATLAB (for summer math/research students)
    May 21st at 12:00 pm to 1:30 pm in Aviation Room at Hoch-Shanahan Dining Commons

All these workshops are digital badge-earning opportunities. All participants who finish their required work in and out of the workshop will be awarded a digital badge through HMC CIS Digital Badge program. For more information about digital badges, please see

Seats are limited. So if you are interested, please register at

Essential MATLAB for Beginners will cover the following topics:

  • Basics of MATLAB Desktop — get to know about the MATLAB computing environment.
  • Scripts and Functions — learn the basics of MATLAB scripts and functions and their differences.
  • Data Import/Export — learn how to import external data and export MATLAB data for other applications.
  • Basic Plots — draw basic 2d plots and learn the simple manipulation techniques.
  • MATLAB Editor — know how to use the MATLAB editor for programming, debugging and publishing your MATLAB codes.

For the R for Statistical Computing workshop, you will learn:

  • How to make use of RStudio IDE.
  • How to work with Data (1): data types and objects.
  • How to create plots: simple plotting methods.
  • How to work with Data (2): Student’s t tests (two-sample and one-sample) and normality test.

We will continue on the Advanced MATLAB workshop to learn:

  • Advanced data structures: cells, structures, data types, and memory usage.
  • Data import/export: tips and tricks to handle data import and export.
  • Advanced use of functions: subfunctions, nested functions, anonymous functions, and function handles.
  • Debugger and profiler: ways to debug and profile MATLAB functions.
  • Performance considerations: memory allocation, vectorization, and parallelization.
  • GUI using GUIDE: A quick introduction to MATLAB GUI Development Environment (only when time permits).

Any questions? Contact Jeho Park at

A Big Data Day Workshop at Harvey Mudd College

Harvey Mudd Scientific Computing Seminar Series: XSEDE HPC Workshop on Big Data

BigData_2267x1146_trasparentWe are pleased to announce a one-day Big Data workshop on Tuesday, April 7, 2015 from 8 am to 2 pm on the Harvey Mudd campus (Shanahan 2461). The workshop will be led by Pittsburgh Supercomputing Center and the Scientific Computing Specialist at Harvey Mudd will be the on-site TA for local participants. This workshop will focus on topics such as Hadoop and Spark. If you are unable to attend the whole workshop due to your class schedule, I would recommend you the first two sessions to learn the basics of Big Data and do some hands-on programming using Java.

The workshop registration is required for the hands-on part. Please register at The registration requires an XSEDE account which you can obtain from

* Workshop Agenda *
8:00 am: Welcome
8:30 am: Intro to Big Data
9:15 am: Hadoop
10:00 am: Lunch break
11:00 am: Hadoop (cont)
11:30 am: Exercises
12:15 pm: Spark
1:15 pm: Exercise 2
2:00 pm: Adjourn
(All times given are PST)

Due to demand, this workshop will be telecast to several satellite sites. This workshop is NOT available via a webcast.

Please feel free to let me know if you have any questions. I hope to see you at the workshop. Thanks!

Jeho Park, Ph.D.
Scientific Computing Specialist, HMC
909) 607-9023

Mathematica Seminar at Harvey Mudd College

wolfram-mathematica-10We are pleased to announce that a Mathematica seminar will be held on our campus (Aviation Room in Hoch-Shanahan) on Tuesday, February 24th, 2015 from noon to 1 pm. Please come join us to learn more about new Mathematica 10 features that can help your job done more easily and efficiently. Seats are limited, so please register for the seminar. Here’s the details:

Wolfram Technologies in Education and Research

February 24, 2015
12:00-1:00, including Q&A
Harvey Mudd College: Aviation Room in Hoch-Shanahan Dining Commons

This talk illustrates capabilities in Mathematica 10 and other Wolfram technologies that are directly applicable for use in teaching and research on campus. Topics of these technical talks include:

  • Enter calculations in everyday English, or using the flexible Wolfram Language
  • Visualize data, functions, surfaces, and more in 2D or 3D
  • Store and share documents locally or in the Wolfram Cloud
  • Use the Predictive Interface to get suggestions for the next useful calculation or function options
  • Access trillions of bits of on-demand data
  • Use semantic import to enrich your data using Wolfram curated data
  • Easily turn static examples into mouse-driven, dynamic applications
  • Access 10,000 free course-ready applications
  • Utilize the Wolfram Language’s wide scope of built-in functions, or create your own
  • Get deep support for specialized areas including machine learning, time series, image processing, parallelization, and control systems, with no add-ons required

Current users will benefit from seeing the many improvements and new features of Mathematica 10 and Wolfram Alpha Pro, but prior knowledge of the Wolfram Language is not required. All attendees will receive an electronic copy of the examples, which can be adapted to individual projects.




HMC Scientific Computing Workshop and Digital Badge

We are pleased to announce the HMC Scientific Computing Workshop schedule in October.  The workshops will be held on Wednesdays from 5:30 pm to 7 pm in Aviation Room in Hoch-Shanahan Dining Commons.

  • October 8th: Essential MATLAB for Beginners — Learn the basics of MATLAB programming and plotting through hands-on examples of simple script m-file and function m-file.
  • October 15th: Advanced MATLAB — Learn more about MATLAB’s advanced programming skills: data structures, advanced use of functions, debugging and profiling, and parallel computing techniques.
  • October 22nd: R for Statistical Computing — Know R for statistical data analysis and graphs.
  • October 29th: OpenMP Multithreaded Programming — an easy way to parallelize and speed up your iterative calculations on multi-core machines.

All these workshops are digital badge-earning opportunities. All participants who finish their required work in and out of the workshop will be awarded a digital badge through CIS Digital Badge Pilot program. For more information about digital badges, please see

HMC Scientific Computing Digital Badges

Please reserve your seat by signing up at


OK Glass, shoot a laser beam!

Google GlassHave you tried it on?

Glass is Google’s wearable computer that sits on your right ear and displays its contents through a tiny prism projector screen over your right eye. (duh)

During this summer break, CIS had a test-out event of a Google Glass loaned from the Claremont Library for two weeks. Soon after the announcement for the event, several people (six faculty, seven staff, and six students) with exceptional curiosity jumped right in. At Harvey Mudd, we like scientific experiments. So in this case, the hypothesis to accept (or otherwise sadly reject) was “Google Glass helps teaching and learning (in a way).” (Hey Google, isn’t Harvey Mudd a perfect place for testing such an emerging technology in higher ed? Contact us if you want to donate a Google Glass or two. ;))

Anyway, those 18 enthusiastic experimentalists came back with their personal opinions after trying Glass out for two to three hours. Two common responses were “It’s cool!” and, interestingly, “It made my head and eyes hurt.” A group of MyCS students tried it for a scavenger hunt using Glass apps like Word Lens for a group of teachers and reported that it went really well–this was actually a great use case for Glass in an educational setting. In addition, a couple of faculty members noted that the usefulness in teaching and learning would be dependent on the Glassware you use.

In fact, the default functions of Glass are pretty basic: google something, take a photo, record a video, get directions to, and send a message to, etc. But my 13-year-old son’s first command for Glass was “OK Glass, shoot a laser beam!” Unfortunately (and fortunately to me) it didn’t shoot a laser beam on me. It, however, could’ve done that if he had installed a Glass app doing it (at least on its screen). And it could’ve been educational (in a way) like showing how to calculate the power density of different laser beams depending on parameters like the beam diameter and the distance from the object. So as our faculty members noted in their feedback, with the right Glassware, it may be useful for education in near future.

P.S. We couldn’t accept or reject the hypothesis due to the small sample size. Google, we are eager to do more experiments and you know what to do. 😉

Scientific Computing Seminars: MATLAB, Parallel Computing, and GPU Computing

CIS is very excited to announce the post-spring break events specially hand-picked for you. We have three scientific computing seminars lined up for the week of March 24th and April 1st. If you are interested, please pick one or two (or even all three) and register online to reserve your seat. Please find the details below:

MathWorks MATLAB Seminar:
Wednesday, March 26th from 12:45 pm to 3:30 pm in Sprague Learning Studio Classroom
Register online at

Title: Programming with MATLAB
Topics covered will include:
•    Basics of the MATLAB programming language
•    Automating with scripts
•    Building robust, maintainable functions
•    Tools for efficient program development
•    Using objects and authoring classes in MATLAB

Parallel Computing Seminar:
Thursday, March 27th from 12:00 pm to 1:00 pm in Sprague Learning Studio Classroom
Register online at

Title: Parallel Computing with MPI (Message Passing Interface)
Topics covered will include:
•    Basics of Parallel Processing
•    Ways to make your program run (much) faster
•    Hands-on examples of MPI

XSEDE HPC Monthly Workshop on OpenACC GPU Programming:
Tuesday, April 1st from 8:00 am to 2 pm in Sprague Learning Studio Classroom
Register online at

Title: OpenACC* GPU Programming
Topics covered will include:
•   Parallel Computing and Accelerators
•   Intro to OpenACC
•   Using OpenACC with CUDA Libraries
•   Advanced OpenACC and OpenMP 4.0

*OpenACC is the accepted standard using compiler directives to allow quick development of GPU capable codes using standard languages and compilers. It has been used with great success to accelerate real applications within very short development periods. This workshop assumes knowledge of either C or Fortran programming.

XSEDE HPC Workshop on MPI at Harvey Mudd College

Harvey Mudd College will be participating in Pittsburgh Supercomputing Center’s XSEDE HPC Workshop about MPI (Message Passing Interface) as a remote site. MPI is a message passing library standard that can be used to parallelize your serial C/Fortran program and algorithm to exploit multi-node, multi-core clusters (or supercomputers) for enhanced performance and/or accuracy. If you are interested in learning MPI, please register for the workshop through XSEDE and come join us in the Learning Studio Classroom on Wednesday, December 4th and Thursday, December 5th.

This is a two-day intensive workshop through which you can learn from the basics to more advanced skills of MPI programming.

The tentative agenda given below is subject to change.

Wednesday, December 4
All times given are PST

  • 08:00 Welcome
  • 08:15 Computing Environment
  • 09:00 Intro to Parallel Computing
  • 10:00 Lunch break
  • 11:00 Introduction to MPI
  • 12:30 Introductory Exercises
  • 01:30 Scalable Programming: Laplace code
  • 02:00 Adjourn/Laplace Exercises

Thursday, December 5
All times given are PST

  • 08:00 Laplace Exercises
  • 09:00 Laplace Solution
  • 09:30 Lunch break
  • 10:30 Advanced MPI
  • 11:30 Outro to Parallel Computing
  • 12:30 MPI Debugging and Profiling
  • 01:30 Adjourn

Please visit the workshop page for more information:

For more information about other XSEDE HPC trainings, please visit the course calendar page at

For any questions, please contact Jeho Park (x79023 or email at CIS

XSEDE HPC Workshop about OpenACC GPU Computing

[Online Registration for Harvey Mudd College is open at]

Harvey Mudd College will be participating in Pittsburgh Supercomputing Center’s XSEDE HPC Workshop about OpenACC. If you are interested in learning GPU programming with OpenACC, please register for the workshop through XSEDE and come join us in Learning Studio Classroom on Tuesday, November 5th. OpenACC is a GPU (Graphics Processor Unit) programming standard for C and Fortran. Using accelerators such as GPUs is a great way to substantially reduce the computational time of computationally-expensive numerical algorithms such as dense linear algebra problems and FFT. And OpenACC is an easy way to enable GPU computing blocks in your program.

(If your schedule is too tight to commit yourselves for the whole five-hour workshop, you can register for the workshop and just participate in the sections for “Intro to OpenACC” from 9:15 am to 10:00 am and/or from 11 am to 1 pm to get an idea how you can use OpenACC for your program.)

Continue reading “XSEDE HPC Workshop about OpenACC GPU Computing”

MathWorks MATLAB Seminar at HMC for The Claremont Colleges

matlab_logo_smallWe are excited to announce a free half-day MathWork Seminar at Harvey Mudd College for The Claremont Colleges. Please join us on Friday, March 8th from noon to 4:00 pm in Math Seminar Room on the 3rd floor of Sprague. A light lunch will be provided. Seats are limited, so please register online at Details below.

Technical Computing with MATLAB at Harvey Mudd College

—Register now—
Register at

Presenter: Saket Kharsikar, Application Engineer
12:00 p.m. – 12:30 a.m. Registration and Lunch
12:30 p.m. – 1:15 p.m. What’s new in 2012b?

Highlights include:
• New MATLAB Desktop
• Packaging and Installing MATLAB Apps
• Redesigning help
• Import tool enhancements for text files

1:15 p.m. – 1:40 p.m. Break

1:40 p.m. – 3:40 p.m. Mathematical Modeling with MATLAB
Mathematical models are critical to understanding and accurately simulating the behavior of complex systems. They enable important tasks such as forecasting system behavior for various “what if” scenarios, characterizing system response, and designing control systems.

This session will show how you can use MATLAB products for mathematical modeling tasks, including:

• Developing models using data fitting and first-principle modeling techniques
• Optimizing the accuracy of mathematical models
• Simulating models and post-processing the results
• Documenting and sharing models

You will also learn about different approaches you can use to develop models, including developing models programmatically using the MATLAB language, deriving closed-form analytical equations using symbolic computation, and leveraging prebuilt graphical tools for specific modeling tasks such as curve and surface fitting.

Q&A 3:40 p.m. -4:00 p.m.

—Register now—
Register at