SCIENTIFIC COMPUTING & VISUALIZATION (Fall 2014)

Course Number: CSCI 596
Class Number: 30280D
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
Discussion board: Google group link
Lecture: 3:30-4:50pm M W, SOS B46
Office Hours: Nakano: 3:30-4:50pm F (VHE 610); Tran: 8:30-9:30am F (VHE 611)
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.
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.

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

Announcements

• 8/25/14 (M): The class begins.
• 9/3/14 (W): See information on the JSPS postdoctoral fellowship in Japan; brought by a special guest, Dr. Naoto Umezawa at the National Institute for Materials Science in Japan.
• 9/15/14 (M): Professor Naomi Levine is looking for a CS student (MS or PhD) to assist in the development of a novel marine ecosystem model. This model will be used to investigate the impact of climate change on marine ecosystems. The ultimate goal is for this model to be incorporated into a global Earth Systems Model to improve future climate predictions. The student must be proficient in FORTAN and MATLAB. Specific tasks will include translating existing code from MATLAB to FORTAN, parallelizing the code, interfacing with HPCC, and increasing the efficiency of the code.
• 9/15/14 (M): Special lecture on spatially heterogeneous dynamic plankton model by Professor Naomi Levine.
• 9/15/14 (M): Please read the assignment submission guideline by John Tran.
• 9/17/14 (W): Special lecture on adiabatic quantum computing and D-Wave by John Tran.
• 9/19/14 (F): Discussion session for assignment 1 at 3:30pm in VHE 610.
• 9/19/14 (F): HPC workshop on Linux/Unix.
• 9/22/14 (M): Seminar on Understanding nanomaterials: in-situ imaging, measurements, and manipulation in the electron microscope by Dr. Eli Sutter (Brookhaven Nat'l Lab.).
• 9/24/14 (W): See the paper on the first sublinear-scaling density-functional-theory algorithm by R. Baer et al.
• 9/26/14 (F): HPC workshop on HPC cluster computing.
• 9/26/14 (F): Discussion session for assignment 2 at 3:30pm in VHE 610.
• 10/3/14 (F): Discussion session for assignment 3 at 3:30pm in VHE 610.
• 10/8/14 (W): For the final project, team efforts are encouraged with the condition that the role of each team member is clearly delineated in the final-project report--please utilize the discussion board for team building.
• 10/8/14 (W): Please see the Data Incubator fellowship opportunity.
• 10/13/14 (M): Special lecture on MapReduce and Hadoop by John Tran.
• 10/15/14 (W): HPC tour, please be 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. Group photo.
• 10/15/14 (W): From Maureen Dougherty (USC-HPC director): "You can use HPC compute nodes to run Hadoop/MapReduce by following the instructions on any head node under /usr/usc/hadoop/default/README.USC. John Mehringer has been working with several groups to get this working."
• 10/29/14 (W): Special discussion session for assignment 4 at 5:00pm in VHE 610.
• 11/6/14 (Th): Seminar on From atoms to systems - bridging of theory to applications by Dr. Sadasivan Shankar (Intel/Harvard Univ.).
• 11/7/14 (F): Discussion session for assignment 5/6 at 3:30pm in VHE 610.
• 11/10/14 (M): Seminar on Thermoelectric materials by Dr. David Singh (Oak Ridge Nat'l Lab.).
• 11/14/14 (F): Discussion session for assignment 6 at 3:30pm in VHE 610.
• 12/1/14 (M): Final-project presentations, Part 1 at 3:30 pm in SOS B46.
• 12/3/14 (W): Final-project presentations, Part 2 at 3:30 pm in SOS B46.