HIGH PERFORMANCE COMPUTING AND SIMULATIONS (Fall 2022)
Course Number: CSCI 653
Section: 30398D (lecture), 30399R (discussion)
Instructor:
Aiichiro Nakano;
office: VHE 610; phone: (213) 821-2657; email: anakano@usc.edu
Lecture: 3:30-4:50pm M W, WPH 102
Discussion: 3:30-4:20pm F, KAP 158
Office Hours: 4:30-5:20pm F, VHE 610
Prerequisites:
(1) CSCI 596 (Scientific Computing and Visualization); or
(2) basic knowledge of numerical methods (CSCI 501, PHYS 516 or equivalent) +
parallel computing (EE 451 or equivalent) +
3D graphics (CSCI 580 or equivalent).
Textbooks:
D. Frenkel and B. Smit,
Understanding Molecular Simulation: From Algorithms to Applications, 2nd Ed.
(Academic Press, 2001)--recommended
A. Grama, A. Gupta, G. Karypis, and V. Kumar,
Introduction to Parallel Computing, 2nd Ed.
(Addison-Wesley, 2003)--recommended
D. L. Chopp,
Introduction to High Performance Scientific Computing
(SIAM, 2019) -- recommended
W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling,
Numerical Recipes, 3rd Ed. (Cambridge Univ. Press, 2007)
--books available online
(C and
Fortran 90)
Course Description
Provide students with advanced techniques that are common to high performance computer simulations
in science and engineering. Scalable algorithms for both deterministic and stochastic simulations
of particles and continuum will be implemented on massively parallel and
distributed computing platforms, and the simulation datasets will be visualized and analyzed
in immersive and interactive virtual environment. For details, please see
course information sheet.
Visualization of divide-conquer-recombine based simulation of
photoexcitated electron-hole pairs in organic solar cells.
Announcements
- 8/22 (M): Class begins.
- 8/26 (F): CARC computing accounts
will be requested for students registered in the first week.
- 8/26 (F): Special guest, Dr. Antonina Nazarova (USC-QCB),
speaking about computational drug screening and journal cover images.
- 8/26 (F): CARC accounts have been requested for all students.
- 8/31 (W): A final-project publication by Antonina
tweeted.
- 8/31 (W): A new book published:
Simulation with Python, R. Li and A. Nakano (APress, 2022); special visit by Rongpeng Li.
- 9/2 (F): Please look at fast multipole method (FMM) papers in the
reading list for potential discussions.
- 9/2 (F): Assignment 1 due at 11:59 pm.
- 9/5 (M): Labor Day; no class.
- 9/7 (W): Partial results of assignment 1;
let's use it to brainstorm to explore synergy among these exciting projects.
- 9/7 (W): Special guest, Hikaru Ibayashi
(USC), to discuss neural-network molecular dynamics.
- 9/9 (F): Inaugural CS Ph.D. social, Dijkstra's and Dissertations,
at 4-6 pm in RTH 526 (food and beverage served) organized by Taufeq;
register
by 9/8 (Th).
- 9/12 (M): See
Deep learning and physics by A. Tanaka et al. (Springer, 2021).
- 9/12 (M): Special office hour to discuss assignment 2 at 5 pm in VHE 610.
- 9/12 (M): Assignment 2 due.
- 9/20 (T) - 11/8 (T): Weekly online training on
AI-driven science on supercomputers offered by Argonne National Laboratory.
- 9/23 (F): CS Ph.D. social, Dijkstra's and Dissertations, at 4:30-5:20 pm in RTH 526; register
here.
- 9/23 (F): Office hour to discuss assignment 3 at 5:30 pm in VHE 610.
- 9/26 (M): Assignment 3 due.
- 10/5 (W):
Prof. Arieh Warshel interviewed by Nature Computational Science.
- 10/5 (W): See
a tale of a Caltech alumnus and
Nobel Prize in Physics 2022.
- 10/7 (F): Office hour to discuss assignment 4 at 5:15 pm in VHE 610.
- 10/10 (M): Assignment 4 due.
- 10/14 (F): Fall recess; no class.
- 10/19 (W): Special office hour to discuss assignment 5 and other topics at 5 pm in VHE 610.
- 10/21 (F): No office hour.
- 10/21 (F): Assignment 5 due.
- 10/21 (F): Seminar by Dr. Guoqing Zhou (NVIDIA) on
Deep learning of dynamically responsive chemical Hamiltonians with semiempirical quantum mechanics
in SSL 202.
- 10/28 (F): Virtual CARC tour by CARC director,
Dr. BD Kim; please use the regular lecture Zoom ID;
photo.
- 10/31 (M): Special guests, Brandon Horton and Michael Qian (Google):
photo;
note Google uses
Hilbert space-filling curve.
- 11/3 (Th): Seminar by Prof. Giorgio Parisi (2021 Nobel physics laureate) and
Prof. Marc Mezard (Univ. Bocconi Milano) on
Simulation methods for spin glasses with applications in optimization at 7 am;
see also
Information, Physics, and Computation, M. Mezard & A. Montanari (Oxford Univ. Press, 2009).
- 11/7 (M): Please create an account at
IBM Quantum before Wednesday's quantum-computing hands-on (also bring your laptop on Wednesday).
- 11/9 (W): Special office hour to discuss assignment 6 at 5 pm in VHE 610.
- 11/11 (F): Assignment 6 due.
- 11/11 (F): Veteran's Day; no class
- 11/23 (W) & 25 (F): Thanksgiving Holiday; no class.
- 12/14 (W): Final project report (GitHub repository) due.
Class Schedule
