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 https://www.mathworks.com/hmc2014

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 http://www.formstack.com/forms/hmc-seminar_registration_spring2014

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 https://portal.xsede.org/course-calendar/-/training-user/class/163

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: https://www.psc.edu/index.php/training/xsede-hpc-workshop-december-2013

For more information about other XSEDE HPC trainings, please visit the course calendar page at https://portal.xsede.org/course-calendar

For any questions, please contact Jeho Park (x79023 or email jepark@hmc.edu) at CIS

XSEDE HPC Workshop about OpenACC GPU Computing

[Online Registration for Harvey Mudd College is open at https://portal.xsede.org/course-calendar/-/training-user/class/152/session/271.]

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.)

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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 http://www.mathworks.com/HMC2013. Details below.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Technical Computing with MATLAB at Harvey Mudd College
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

—Register now—
Register at http://www.mathworks.com/HMC2013

—Agenda—
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 http://www.mathworks.com/HMC2013

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 (helpdesk@hmc.edu) for any inquiries about the XSEDE resources.

Links:

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.

When:

  • 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

Where:

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

Agenda:

  • 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 http://www.formstack.com/forms/hmc-hpc_survey_f2011. 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 http://bccd.net/.

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 1.0.1.53964), 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,
PDF
Pencast PDF,
PDF,
PNG image
Embedded Flash Pencast PDF,
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.