HIGH PERFORMANCE COMPUTING AND SIMULATIONS (Fall 2016)
Course Number: CSCI 653
Section: 30070D (lecture), 30071R (discussion)
office: VHE 610; phone: (213) 821-2657; email: firstname.lastname@example.org
Lecture: 3:30-4:50pm M W, SGM 601
Discussion: 3:30-4:20pm F, KAP 146
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 (CSCI 503 or equivalent) +
3D graphics (CSCI 580 or equivalent).
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.
W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling,
Numerical Recipes, 3rd Ed. (Cambridge Univ. Press, 2007)
--books available online
Fortran 77, and
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.
Visualization of divide-conquer-recombine based simulation of
photoexcitated electron-hole pairs in organic solar cells.
- 8/22 (M): Class begins.
- 8/22 (M): If you have not computed at the
USC Center for High Performance Computing (HPC)
before, please sign up for one of the
HPC new user meetings.
- 8/22 (M): Please see the CSCI 653 course sheet.
- 8/24 (W): See IPAM workshop on
understanding many-particle systems with machine learning.
- 8/26 (F): Please see lecture slides at
Argonne Training Program on Extreme-Scale Computing.
- 8/27 (Sa): I have requested HPC accounts for all registered students.
Please allow a week or so before the HPC team processes the request.
- 9/7 (W): Paper discussion on fast Coulombic solvers (Arnold '13)
and lecture on multiple time stepping.
- 9/7 (W): Screening of
Code: Debugging the Gender Gap at 7 pm in SCA 108, School of Cinematic Art.
- 9/8 (Th): Discussion on "build-it-yourself Raspberry cluster" at 4:30 pm in VHE 611.
- 9/8 (Th):
IBM debuts Power8 chip with NVLink.
- 9/9 (F): Lecture/discussion on "using HPC cluster" and "minimal parallel computing basics" in the class.
- 9/12 (M): Discussion on
ATPESC16: (1) scalable MPI
and (2) scalable I/O.
- 9/14 (W): Lecture on parallel molecular dynamics.
- 9/16 (F): Discussion on your paper outline topics.
- 9/19 (M): Lecture on divide-and-conquer parallelism.
- 9/21 (W): Lecture on hypercube quicksort.
- 9/23 (F): 3:30 pm: discussion on final project topics in KAP 146; 4:30 pm: discussion session for HW 2 in VHE 610.
- 9/25 (Su): SoCal Data Science Conference.
- 9/26 (M): Lecture on MD machines and Shaw's MD algorithm.
- 9/26 (M): Discussion session for HW 2 at 5:00 pm in VHE 610.
- 9/26 (M)-9/30 (F): UCLA-IPAM workshop on
Machine Learning Meets Many-Particle Problems
- 9/28 (W): Lecture on hybrid MPI+OpenMP programming.
- 9/28 (W): Last-minute discussion for HW 2 at 5:00 pm in VHE 610; please email me your submission by 11:59 pm today.
- 9/29 (Th): Seminar on
hierarchical locality and parallel programming in the extreme scale era
by Prof. Tarek A. El-Ghazawi (George Washington Univ.) at 4:00 pm in OHE 100D.
- 9/30 (F): Special lecture on "using molecular dynamics and density functional theory to study the causes of cancer"
Prof. Richard Clark (Waseda Univ.).
- 9/30 (F): See
Prof. Tarek A. El-Ghazawi's TV interview about TaihuLight.
- 10/3 (M): Lecture on quantum dynamics.
- 10/5 (W): Lecture on multiresolution methods.
- 10/6 (Th): Seminar on
software challenges for extreme scale systems, or how to play the end-game for Moore's law
by Prof. Vivek Sarkar (Rice Univ.) at 4:00 pm in OHE 100D.
- 10/10 (M) - 10/17 (M): HPC cluster is down for upgrade.
- 10/10 (M): Lecture on advanced multiresolution methods.
- 10/12 (W): Lecture on hybrid multiscale simulations (1).
- 10/13 (Th): Seminar on "scientific visualization research at ARL"
by Dr. Simon Su (Army Research Lab.) at 3:00 pm in EEB 248.
- 10/13 (Th): Seminar on
toward extreme-scale manycore architectures
by Prof. Josep Torrellas (UIUC) at 4:00 pm in OHE 100D.
- 10/14 (F): Paper discussion on graph-based O(N) quantum mechanics (Niklasson '16).
- 10/17 (M): Lecture on hybrid multiscale simulations (2).
- 10/17 (M): Seminar on
LCLS: the world's first X-ray laser
by Dr. David Fritz (Stanford Univ.) at 4:15 pm in SSL 150.
- 10/19 (W): Lecture on load balancing.
- 10/21 (F): Discussion session for HW 3 at 4:30 pm in VHE 610.
- 10/24 (M): Lecture on optimizing parallel MD.
- 10/24 (M): Discussion session for HW 3 at 5:00 pm in VHE 610.
- 10/26 (W): Lecture on GPU programming using CUDA.
- 10/26 (W): See a formal definition of scalable algorithms in
Scalable Algorithms for Data and Network Analysis
by Prof. Shang-Hua Teng.
- 10/28 (F): Paper discussion on load balancing N-body simulations (Pearce '14).
- 10/31 (M): Lecture on MPI+CUDA programming.
- 11/2 (W): Lecture on MPI+CUDA quantum dynamics.
- 11/4 (F): HPC tour, please sign in at the reception of the 3434 Grand building at 3:20 pm sharp;
see access to 3434 Grand.
Also, do not forget to bring your student photo ID.
- 11/7 (M): Lecture on Intel Xeon Phi and other new architectures.
- 11/7 (M): Discussion session for HW 4 at 5:00 pm in VHE 610.
- 11/9 (W): Lecture on scientific visualization.
- 11/9 (W): Discussion session for HW 4 at 5:00 pm in VHE 610.
- 11/11 (F): Paper discussion on graph data analytics (Marinari '07; Sandhu '15; Changpinyo '16)
and load balancing on GPUs (Chen '10).
- 11/14 (M): Lecture on animating quantum dynamics and massive dataset visualization.
- 11/16 (W): Lecture on scientific data mining.
- 11/18 (F): Paper discussion on new architectures (Fu '16, Aji '16)
and scientific data analytics (Lake '15; Zlateski '16).
- 11/18 (F): Discussion session for HW 5 at 4:30 pm in VHE 610.
- 11/18 (F): Two Ming Hsieh research awards to CSCI 653 classmates: Congratulations,
Brandon and Erick.
- 11/21 (M): Lecture on accelerated dynamics and cloud computing.
- 11/28 (M), 11/30 (W), 12/2 (F): Final project presentations;
paper discussion and
final presentation sign-up sheets.
- 12/14 (W): Final project report due.