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**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, 2nd Ed."
(MIT Press, 1999)--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.

- 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.