SCIENTIFIC COMPUTING & VISUALIZATION (Fall 2017)
Course Number: CSCI 596
Class Number: 30280D (lecture); 30146R (discussion)
office: VHE 610; phone: (213) 821-2657; email: firstname.lastname@example.org
TA: Kuang Liu; email: email@example.com
Lecture: 3:30-4:50pm M W, THH 116
Discussion: 3:30-4:20pm F, VKC 100
Office Hour: 4:30-5:20pm F, VHE 610
HPC Office Hour: 2:30-5:00 pm T, LVL 3M
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.
W. D. Gropp, E. Lusk, and A. Skjellum, "Using MPI, 3rd Ed."
(MIT Press, 2014)--recommended
M. Woo, et al., "OpenGL Programming Guide, Version 4.5, 9th Ed."
A. Grama, A. Gupta, G. Karypis, and V. Kumar, "Introduction to Parallel Computing, 2nd Ed."
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 112 million-atom reactive molecular dynamics simulation to study
high-temperature oxidation of a silicon-carbide nanoparticle on 786,432 IBM Blue Gene/Q cores.
- 8/21 (M): The class begins.
- 8/25 (F): Particle-simulation demo in virtual reality (Oculus Rift and HTC Vive) platforms
at 4:30 pm in VHE 611.
- 8/25 (F): Please register by the end of Friday, so that HPC computing accounts
can be requested for all students in time for the first assignment.
- 8/29 (T): Seminar on
The convergence of machine learning, big data, and supercomputing
by Prof. Jeremy Kepner (MIT Lincoln Lab) at 10:30 am in EEB248.
- 8/29 (T): Your HPC account is ready. You should be able to log in to hpc-login3.usc.edu
using your USC ID and password. Please use the directory named as your ID under
the class directory, /home/rcf-proj/an2. Please strictly follow the guidline in the lecture pages on
how to use USC HPC cluster.
- 9/4 (M): No class; have a nice Labor Day.
- 9/6 (W): Special office hour for assignment 1 at 5:00pm in VHE 610.
- 9/6 (W): Please utilize CSCI596 on Piazza for discussions.
- 9/8 (F): HPC workshops: (1) guidance for new users (9:30-10:15 am, VPD 107);
(2) introduction to Linux, PBS and HPC (10:30 am-12:30 pm, VPD 107);
(3) introduction to HPC and cluster computing (1:30-3:30 pm, VPD 106);
- 9/8 (F): See
Friday night experiments by Andre Geim.
- 9/13 (W): See
quantum entanglement into space.
- 9/13 (W): Fun research on Santa Monica beach: Salt and sand.
- 9/15 (F): NASA Cassini grand finale.
- 9/15 (F): Watch
Second genesis: the quest for life beyond Earth.
- 9/15 (F): Office-hour discussion on assignment 2 at 4:30 pm in VHE 610.
- 9/18 (M): (1) Lecture on parallel computation of pi +
(2) Special information session by Dr. Lijun Zhang (Caltech/NASA-IPAC).
- 9/18 (M): See Chronology of computation of pi,
and Alexander Yee's program running on
Shigeru Kondo's homemade computer;
Yee's program uses Ramanujan's series (thank you, Muye, for pointing it out), also
watch The Man Who Knew Infinity if you have a chance.
- 9/18 (M): See a lecture note on recursive evaluation of a series.
- 9/20 (W): See Hyesuk's divide-&-conquer kinetic Monte Carlo paper
for an example of scalability analysis; see also
A. Slepoy et al., A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks,
J. Chem. Phys., 128, 205101 ('08).
- 9/22 (F): Final project logistics discussion--please attend.
- 9/22 (F): See the syllabus of CSCI 699 (Extreme-scale Quantum Simulations) in Spring 2018.
- 9/22 (F): Watch DIY orchestra (computational music)
by Prof. Ge Wang (Stanford).
- 9/22 (F): Office-hour discussion on assignment 3 at 4:30 pm in VHE 610.
- 11/27 (M), 11/29 (W), 12/1 (F): Final project presentations.
- 12/13 (W): Final project report due.