CSE 260 Homework #1

Due Tuesday 10/1/08 in class

Worth 10 points

1. Tell me about yourself. At what stage are you in your graduate studies? What are your research interests? Are you contemplating using parallel compuation in your research or for your job?

   Are there any aspects of your technical background that you'd like to tell me about, or that you'd like to develop further?

   What would you like to get out of the course? Do you have a research project in mind? Are you interested in using the Cell BE, a GPU, or are you interested in MPI programming? Are you looking for a lab partner? How do you feel about your programming and teamwork skills? Would you like to improve them? Do you feel you could teach these skills to others? Does anything else come to mind?
   

2. Browse the web and read about an application that has previously been implemented on a parallel computer. Provide a writeup that describes the application, including prior results and their significance. If any special tools were used to develop the application, discuss them as necessary.

   Report on available information that addresses the following points.

   1. What is the application and its significance?
   2. What equations are being solved, and what are the algorithms used to solve them?
   3. What hardware does the application run on, and what levels of parallelism are employed typically?
      1. How well does the application scale?
      2. What are the bottlenecks or other limitations and how did the developers attempt to deal with them?
      3. Are there any outstanding performance bottlenecks or limitations that the code developers plan to address in the future?
   4. What programming tools, libraries, or compilers were used?
   5. Does the application produce large amounts of data? If so, are the management, access, and manipulation of the data considered a technical challenge?
   6. Is the application still in use? Are there applications that solve the same problem? Is there any competition? Is the software a commercial product?
   7. How widely (was) is the application used? Does it have a wiki or a user's group?

   Submitting your assignment

   Turn in hard copy in class, but post a URL in the Assignment # 1 Conference of the course web board pointing to your responses for part (2). (If you would rather only turn in part I to me, just submit part 2 on-line.) Your document should be in HTML, PDF, or text format.

   Suggestions for places to look for applications.

   • NAMD, a parallel molecular dynamics code.
   • http://www.cs.ucsd.edu/groups/hpcl/scg/mcellk, MCell-K, a parallel cell microphysiology simulator based on the MCell simulator.
   • www.qcmethod.com The Quasicontinuum (QC) method, a mixed continuum and atomistic approach for simulating the mechanical response of polycrystalline materials at zero temperature.
   • SuperLU, a general purpose library for the direct solution of large, sparse, non-symmetric systems of linear equations on high performance machines.
   • NWChem computational chemistry package.
   • ENZO Cosmology code

   Here are some web sites describing applications

   • Southern California, Earthquake Center
   • SCEC Community Modeling Environment
   • Weather Research and Forecasting (WRF) Model
   • Theoretical Computational Seismology
   • Computational Infrastructure for Geodynamics
   • Applied Numerical Algorithms Group (ANAG), Lawrence Berkeley Laboratory.
   • Center for Computational Sciences and Engineering (CCSE) Lawrence Berkeley Laboratory. Also see Parallel Structured Adaptive Mesh Refinement, esp HyperClaw
   • Center for Applied Scientific Computing (CASC), LLNL.
   • Environmental Molecular Sciences Lab, Pacific Northwestern Research Laboratory.
   • Theoretical and Computational Biophysics group (Beckman Institute)
   • Inter*ctive Supercomputing is a company that produces Star-P, a parallel Matlab system. See their success stories for a list of applications