SC07:UTEP07

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This page contains near final information about the workshop scheduled for May 20th-26th at the University of Texas - El Paso.

Contents

Instructors

  • Paul, Dave, Charlie (Parallel/Distributed, whole week); Shawn (Chemistry, 1 day), Jeff (Biology, whole week); Ananth (Biology, 2 days); Kristina, Alex (assistants, whole week)

Audience

  • This workshop is designed to be truly introductory in nature; no prior exposure to computational science will be assumed.
  • College science, math, and computer science teachers.
  • College technology coordinators.
  • High school science, math, and computer science teachers.
  • High school technology coordinators.
  • Breakdown by discipline and level.

Content

  • LittleFe + Bootable Cluster CD + Computational Science Education Reference Desk = Acme, an inexpensive, portable platform for teaching computational science and high performance computing. Participants will learn the basics of cluster computing, both hardware and software, and see how the Acme platform can be used to teach high performance computing and computational science in a variety of educational settings.
  • High Performance Computing Curriculum Modules (1.5 days)
    • Fire
    • Bootable Cluster CD
    • Taxonomy of High Performance Computing, aka Supercomputing in Plain English
    • Using MPI, the Message Passing Interface
    • Decompostion, speedup, and efficiency of parallel scientific software
    • Supporting High Performance Computing
  • Computational Chemistry Curriculum Modules (1 day, Tuesday)
    • Overview of Computational Chemistry
    • Molecular Modeling Techniques and Applications
  • Bioinformatics Curriculum Modules (1.5 days, Wednesday and Thursday)
    • Sequence Search - BLAST, mpiBLAST, scalaBLAST
    • Clustering of Expressed Sequence Tags and in Genome Sequencing - PaCE, CAP3
    • Molecular dynamics - GROMACS, mpiGROMACS, NAMD
    • Systems Biology - CellDesigner, Systems Biology Workbench
  • Undergraduate Curriculum Development (.5 day)
    • In-situ modules
    • Standalone courses
  • Participant Projects and Presentations
    • Start on Wednesday, work in the afternoon and evening lab sessions
  • Which ones for the whole group? Which as parallel sessions? There are a number of other small group sessions we could do, e.g. performance analysis with gprof, xmpi, and performance counters, advanced MPI, analysis of gene expression, systems biology, etc. Look at the other workshop outlines for other ideas.

Materials

CDs

Download [SC07 reimbursement form.]

Notebook Sections

  • LittleFe + Bootable Cluster CD + Computational Science Education Reference Desk = Acme
    • Computational Science
    • BCCD Presentation
    • BCCD Bootup
    • CSERD
  • High Performance Computing
    • Acme
    • GalaxSee
    • Game of Life
    • Parameter Space
    • MPI Reference
    • NetLogo
  • Computational Chemistry
  • Bioinformatics

Schedule

The daily schedule is roughly 9a-12p, 2p-5p, and 7p-9p.

  • Sunday
    • Evening dinner and opening presentation 7p- 9p, Summit Hall, Miner Village
  • Monday will begin at the El Paso Natural Gas Conference Center (EPNGCC)
    • Morning 9a-12p
    • Afternoon 2p-5p
    • Evening - open lab 7p-9p
  • Tuesday will begin at the El Paso Natural Gas Conference Center (EPNGCC)
    • Morning 9a-12p
    • Afternoon 2p-5p: Overview of Computational Chemistry (Lecture and Lab); Molecular Modeling Techniques and Applications (Lecture and Lab)
    • Evening - open lab 7p-9p
  • Wednesday will begin at the El Paso Natural Gas Conference Center (EPNGCC)
    • Morning - 9a-12p: Introduction to Bioinformatics & Computational Biology, BLAST, Parallel BLAST. (Includes a 30 minutes break and discussion.)
    • Afternoon - 2p-5p: Large-scale sequence analysis & applications, Clustering, Assembly, PaCE, CAP3. (Includes a 30 minutes break and discussion.)
    • Evening - free time
  • Thursday will begin at the El Paso Natural Gas Conference Center (EPNGCC)
    • Morning 9a-12p
    • Afternoon - 2p-5p concurrent sessions and presentation preparation
    • Evening - 7p-9p Dinner at Paco Wongs Restaurant
  • Friday will begin at the El Paso Natural Gas Conference Center (EPNGCC)
    • Morning - 9a- 12p presentation preparation
    • Afternoon - 2p-5p presentations

Logistics

  • Between 25 and 30 participants.
  • Housing, on-site if possible, for participants and instructors. Being able to walk between housing and the lab is really nice, particularly for the instructors.
  • Software to install/test beforehand in labs - BCCD, Netlogo, Java

Chemistry Software (in addition to WebMO/Gaussian-MOPAC-Tinker on bobsced), ALL FREE downloads: ACD ChemSketch 10.0 Freeware: http://www.acdlabs.com/download/chemsk.html BioRad KnowItAll Academic Edition: http://www.knowitall.com/academic/welcome.html Adobe Shockwave: http://www.adobe.com/shockwave/download/download.cgi Netlogo: http://ccl.northwestern.edu/netlogo/download.shtml Molecular Workbench Volume 1.3; http://mw.concord.org/modeler/index.html

  • Notebook contents, timetable for Krell to do reproduction.

Questions and Open Items

  • Put time estimates on each of the major chunks under Content.
  • Make a complete list of the possible small group sessions.
  • As the Content is stabilized put pointers to the curriculum modules in the appropriate places.
  • About 30 registered (as of Apr 16), can't hold much more than that.
  • Presentation by local person about HPC resources, access, tools, etc. Pat will follow-up.
  • When do we need to have PDFs to Krell for the notebooks? May 9 is preferred, May 11 ok

Presentations

Marco Gallo

  • UTEP
  • (Conflict with time, turned in separately)

Don Costello

  • University of Nebraska-Lincoln
  • Combinatorics problem – look at groups testing problem from a parallel standpoint.

Philip Smith & Yazeed Hiyari

  • Texas Tech
  • MPI Problem database, to build up a set of examples for an MPI course
  • Started with an example of parallelizing a midpoint quadrature rule
  • Eventual goal to have database of examples.

Jesus Pando

  • DePaul University
  • HPC in the Physics curriculum
  • Physics 300 (after intro mech, E&M, modern) introduces numerics, http://math.bu.edu/odes, ODE course starting with models, look at each diffeq numerically, analytically , graphically.
  • Course is required before any upper level physics course. All upper division classes have numerical work built into the curriculum.
  • Examples – ODE course covers Lorentz System
  • Problem - to put in HPC we have to drop something, limited access to release time to implement change, problems with reliability of open source systems, commercial implementations are expensive.

Michelle Joseph

  • Experimentation Phobic Control and Financial Circumvention via Computational Modeling
  • UTEP
  • middle, secondary, over-crowded colleges - seminar series
  • allow teachers to design, conduct, and analyze experiments before risking live experiments

Emmanuel Ncheuguim

Jose Hurtado

  • UTEP
  • Geology
  • Curriculum changes in geology
    • undergraduates currently have little in programming
    • getting worse as state is mandating that school decrease core curriculum component
    • Limited geophysics, more basic math and physics
  • Possible changes
    • Approach skills from a computational approach
      • computational component in geodynamics course
      • HPC modules in remote sensing and digital image processing course
    • better understanding of concepts
    • more experience with computing
    • better preparation fro graduate school and industry

Rebecca Reiss

  • New Mexico Tech
  • Project, Get $$$$$$$$$$
  • Currently planning for a HHMI undergraduate education grant
  • integration of life sciences with other disciplines including quantitative studies
  • recent acquisition of high throughput DNA sequencer
  • Use of bioinformatics tools (Geysir)
  • Curriculum change
    • Science 101
      • Computer Simulations in Math, Physics, Chemistry, and Biology
    • Biophysics
    • Expand Bioinformatics
  • Faculty Development and Outreach
    • MS in science teaching for certified teachers
      • MST course in HPC and HTS

Sarala Arunagiri

  • UTEP
  • Parallel and Distributed Computing Courses
    • BCCD provides a method of looking at examples in architecture courses to prepare students for P&DC course

Erin Hodgess

  • University of Houston Downtown
  • Computer and Mathematical Sciences
  • Statistical Computing (new course)
    • Use R with BCCD
    • Implement Gromacs

Art Duval

  • UTEP
  • Math
  • Combinatorics
  • Having students do experimentations computationally to support understanding of combinatorics relations

Ming-Ying Leung, Raul Cruz-Cano, Clemente Aguilar

  • UTEP
  • Bioinformatics
  • Getting HPC into undergraduate bioinformatics course
  • Current program is masters level only, no undergrad degree in bioinformatics
  • Want to have a course at undergad level, introduced in Spring 2004 (Special topics in Math)
    • Math, CS, Statistics students
    • original course outline overly ambitious
    • Too much biology for Math and CS students
    • Parallel programming might be more interesting to these students in math and CS, but could stick with bioinformatics examples

Kevin Livingstone

  • Trinity College
  • introducing computational and modeling in the introductory biology sequence
  • HHMI grant for cross disciplinary integration
    • Bio faculty have sat through intro disciplinary courses in other disciplines and vice versa
    • Calculus for modeling
  • Looking to create more computation based assignments in each biology module
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