SC07:SDSC07

From Education

This page contains information about the workshop scheduled for April 2-4, 2007, at the San Diego Supercomputing Center.

Contents 1 Instructors 2 Audience 3 Content 3.1 High Level 3.2 Detailed 3.3 Notes 4 Notebook 5 Schedule 6 Logistics

Instructors

• Tom Murphy and Charlie Peck, assisted by Camille Frazier, Kevin Hunter, Alex Lemann, and Kristina Wanous.

Audience

• This workshop is designed to be truly introductory in nature; no prior exposure to computational science will be assumed.
• Community college science, math, and computer science teachers and students.
• Community college technology coordinators.
• High school science, math, and computer science teachers and students.
• High school technology coordinators.
• Many know Java, enough know C. There may be a modest influx of faculty and students with a bioinformatics interest.
• Do we have a final breakdown by discipline and level?

Content

High Level

• 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. Taxonomy of High Performance Computing, aka Supercomputing in Plain English
2. Using MPI, the Message Passing Interface
3. Supporting High Performance Computing in a Small College Environment

• Bioinformatics Curriculum Modules

1. GROMACS
2. MPIBlast

• Environmental Science Curriculum Modules

1. Predator/Prey systems with cellular automata and system dynamics simulations

• Plus POVRay and lots more!

Detailed

• Monday Morning

1. Introductions, who we are and who they are - 1 hour
2. Workshop overview - 1 hour (Charlie, content and HPC/computational science landscape overview)
3. A first look at parallelizing a problem: the trapezoidal way (Tom, 1 hour)

• Monday Afternoon

1. Workshop Resources
   1. LittleFe overview (Charlie, 1 hour)
   2. BCCD overview w/ Life (Kristina, Tom, Camille, 2 hours)
   3. CSERD (Tom, 1 hour)
2. Survey participants about concurrent sessions

• Monday Evening

1. Open lab

• Tuesday Morning

1. Taxonomy of High Performance Computing, aka Supercomputing in Plain English (Charlie, 1 hour)
2. Using MPI (Message Passing Interface) the 6 + 1 Way (Tom, 2 hours)

• Tuesday Afternoon

1. Concurrent sessions

• Tuesday Evening

1. Open lab

• Wednesday Morning

1. GROMACS (Charlie and Kristina, 1.5 hours)
2. Predator/Prey systems with cellular automata and system dynamics simulations (Alex, 1.5 hours)

• Wednesday Afternoon

1. Concurrent sessions

• Possible topics for concurrent sessions. Almost all of these have a hands-on component. If the group desires any of these could become large group activities.

1. Continue any of the modules we started already.
2. Providing HPC resources in a small college environment. Infrastructure, funding, support, project development. (Charlie and Tom)
3. Performance analysis and improvement - application (high level) and low level (performance counters) (Charlie and Tom)
4. Beyond 6 + 1, Advanced MPI communications (Tom)
5. MPIBlast (Kristina)
6. POVRay (Kevin)
7. PDB->GROMACS->pyMol (Alex)
8. How can I parallelize my project? An overview of the different approaches to leveraging HPC resources. (Charlie and Tom)
9. How can I scale-up my project? Doing it in the small now, what are choices and issues for doing it big? (Charlie and Tom)
10. Other peoples software, finding, vetting, and incorporating open source libraries and software packages. (Charlie and Tom)

Notes

• Evening labs are unstructured. Participants are expected to continue work on earlier projects or expand on them.

Notebook

• Itemize the contents of the notebook based on the final content. This should be a list of links to the specific curriculum modules in the wiki and to on-line resources at Shodor, CSERD, etc.
• Ange will order 1" binders and dividers for all the students.
• Contents

1. section1-computational-science.pdf - from Shodor's Knowledge Tree (ready)
2. LittleFe-flier.pdf (updated with Acme name) - from where?
3. bccd-bootup.pdf - from BCCD wiki (ready)
4. Computational Science/HPC overview - from where?
5. netlogo.pdf - extracted from Section3Agent... from Shodor's Knowledge Tree (ready)
6. game of life - from BCCD wiki
7. povray - from CCG wiki
8. Tom's MPI slides -
9. predator/prey - from CCG wiki
10. GROMACS -
11. mpiBLAST -

• See WorkshpMaterials/SDSC

Schedule

• Monday - 8a-5p, 7p-9p
• Tuesday - 8a-5p, 7p-9p
• Wednesday - 8a-5p

Logistics

• The local technical contact is Julian Nitka, jnitka@ucsd.edu 858/534-5095, the lab has Dell desktops. * Ange sent the operators a list of who will be attending so they can let the team in on Saturday morning, they'll have the parking pass.
• SDSC will take care of name tags for all.