SCIENTIFIC COMPUTING & VISUALIZATION

SCIENTIFIC COMPUTING & VISUALIZATION (Fall 2015)

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Course Number: CSCI 596
Class Number: 30280D (lecture); 30146R (discussion)
Instructor: Aiichiro Nakano; office: VHE 610; phone: (213) 821-2657; email: anakano@usc.edu
TA: John Tran; email: jtran@isi.edu; homework submission: usc.csci596@gmail.com
Lecture: 3:30-4:50pm M W, SGM 601
Discussion: 4:30-5:30pm F, KAP 156
Office Hour: 2:00-3:00pm M, VHE 611
HPC Office Hour: 2:30-5:00 pm, T, LVL 3M by Avalon Johnson
Prerequisites: Basic knowledge of programming, data structures, linear algebra, and calculus; a nice introduction for a non-computer science student to fill the gap: Y. Patt and S. Patel, Introduction to Computing Systems: From Bits and Gates to C and beyond; T. Hey and G. Papay, The Computing Universe.
Textbooks:
W. D. Gropp, E. Lusk, and A. Skjellum, "Using MPI, 3rd Ed." (MIT Press, 2014)--recommended
M. Woo, et al., "OpenGL Programming Guide, Version 4.3, 8th Ed." (Addison-Wesley, 2013)--recommended
A. Grama, A. Gupta, G. Karypis, and V. Kumar, "Introduction to Parallel Computing, 2nd Ed." (Addison-Wesley, 2003)--recommended

Course Description
Particle and continuum simulations are used as a vehicle to learn basic elements of high performance scientific computing and visualization. Students will obtain hands-on experience in: 1) formulating a mathematical model to describe a physical phenomenon; 2) discretizing the model, which often consists of continuous differential or integral equations, into algebraic forms in order to allow numerical solution on computers; 3) designing/analyzing numerical algorithms to solve the algebraic equations efficiently on parallel computers; 4) translating the algorithms into a program; 5) performing a computer experiment by executing the program; 6) visualizing simulation data in an immersive and interactive virtual environment; and 7) managing/mining large datasets. For details, please see course information sheet.

Visualization of a billion-atom reactive molecular dynamics simulation of cavitation bubble collapse in water on 163,840 IBM Blue Gene/P cores.

Announcements

8/24/15 (M): The class begins.
8/27/15 (Th): Seminar on Strongly correlated plasmas since Bohm and Pines by Prof. Setsuo Ichimaru from University of Tokyo at 2:00 pm in EEB 248 (refreshments will be served).
8/28/15 (F): On Andre Geim's Friday night experiments.
9/1/15 (T): HPC office hours will be 2:30-5:00 pm every Tuesday in LVL 3M (basement of Leavey library).
9/2/15 (W): Special lecture on Introduction to HPC cluster computing by Avalon Johnson at USC Center for High Performance Computing (HPC).
9/3/15 (Th): Your HPC account is ready; please find your directory under /home/rcf-proj2/an2.
9/4/15 (F): Webinar on Parallel programming and optimization for Intel architecture.
9/16/15 (W): Assignment 0 results are now available.
9/18/14 (F): Special office hour for assignment 1 at 5:30pm in VHE 610.
9/25/14 (F): Special office hour for assignment 2 at 5:30pm in VHE 610.
9/28/15 (M): Please see the Data Incubator fellowship opportunity.
10/2/15 (F): Special lecture/demo on "Virtual reality as a research tool" by Erick Moen (USC); photo 1; photo 2.
10/2/15 (F): Special office hour for assignment 3 - Part I at 5:30pm in VHE 610.
10/7/15 (W): HPC tour, please sign in at the reception of the 3434 Grand building at 3:50 pm sharp; see access to 3434 Grand. Also, do not forget to bring your student photo ID; photo 1; photo 2.
10/9/15 (F): Special lecture on "Accelerating reactive molecular dynamics on GPU" by Dr. Ken-ichi Nomura (Quantlab).
10/9/15 (F): Special office hour for assignment 3 - Part II at 5:30pm in VHE 610.
10/19/15 (M): Discussion on D-Wave quantum-computer projects with John Tran at 2:00 pm in VHE 611.
10/19/15 (M): Seminar on Killing, germination and surprises with spores of bacteria of Bacillus species by Prof. Peter Setlow from University of Connecticut at 4:15 pm in SLH 102.
10/20/15 (T): Southern California Simulations in Science Conference (SCSSC 2015) at UC Santa Barbara.
10/21/15 (W): Video conference with Dr. Ken-ichi Nomura about reactive molecular dynamics on GPU, at 5:30 pm in VHE 610.
10/23/15 (F): Discussion on assignment 4 in the class.
10/26/15 (M): Special lecture on GPU-based inverse rendering with multi-objective particle swarm optimization by Koki Nagano, Thomas Collins, and Chi-An Chen (USC-ICT/ISI).
10/28/15 (W): Special office hour for assignment 4 at 5:00pm in VHE 610.
10/30/15 (F): Special lecture on "Intel Phi programming" by Patrick Small; see Intel Xeon Phi Coprocessor Developer's Quick Start Guide.
10/30/15 (F): Special office hour for assignment 4 at 5:30pm in VHE 610.
11/4/15 (W): You may respond to planned USC software carpentry workshop; please also see information on software carpentry workshops.
11/5/15 (Th): Please see data science internship and job opportunities at ConversionLogic.
11/12/15 (F): ACM News: In Memoriam: Gene Amdahl 1922-2015
11/13/15 (F): Special lecture by Dr. Akio Miyoshi (founder and CEO, inSight, Inc.).
11/13/15 (F): Deadline to discuss and agree on your final project topic with me.
11/13/15 (F): Special office hour for the last assignment 6 at 5:30pm in VHE 610.
11/20/15 (F): Special lecture by Prof. Yukari Mitsuhashi (Kobe University, Japan).
11/30/15 (M), 12/2/15 (M), 12/4/15 (F): Final project presentations.
12/11/15 (F): Final project report due.