HIGH PERFORMANCE COMPUTING AND SIMULATIONS (Fall 2019)
Course Number: CSCI 653
Section: 30398D (lecture), 30399R (discussion)
office: VHE 610; phone: (213) 821-2657; email: firstname.lastname@example.org
Lecture: 3:30-4:50pm M W, LVL 13
Discussion: 3:30-4:20pm F, VPD 106
Office Hours: 4:30-5:20pm F, VHE 610
(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).
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.
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
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.
- 8/26 (M): Class begins--discussion of logistics.
- 8/28 (W): Introductory lecture;
AI for science townhall (agenda of Argonne townhall) and
UCLA-IPAM program on
Machine learning for physics and the physics of learning.
- 8/29 (Th): ACM tech talk on
A new golden age for computer architecture by Prof. David Patterson (UC Berkeley).
- 8/30 (F): Discussion of HW1.
- 9/2 (M): Labor day, no class.
- 9/3 (T): Piazza forum
was created; please use it to discuss with your classmates.
- 9/4/ (W): Lecture on molecular dynamics (MD).
- 9/6 (F): Seminar on
Population annealing: massively parallel Monte Carlo simulations and efficient estimation of the density of states
by Dr. Lev Barash (HSE Tikhonov Moscow Institute of Electronics and Mathematics).
- 9/6 (F): See DARPA FastNIC program:
What scientific breakthroughs will be enabled by 100x increase in network speed?
- 9/6 (F): Discussion of HW1--partial results;
QXMD GitHub repository
and "quantum computational science" by Lindsay Bassman.
- 9/9 (M): Lecture on spatiotemporal multiresolution MD.
- 9/9 (M): US Department of Energy (DOE) established
Artificial Intelligence and Technology Office (AITO).
- 9/9 (M): See the level of mathematics used in
Deep Learning, I. Goodfellow, et al. (MIT Press, 2016).
- 9/11 (W): Lecture on fast multipole method (FMM) algorithm and code; discussion of HW2.
- 9/13 (F): 3:30 pm: getting started with parallel computing in VPD 106;
4:30 pm: discussion session for HW 2 in VHE 610.
- 9/16 (M): Lecture on parallel MD.
- 9/17 (T): NVIDIA Webinar on
Accelerating quantum chemistry simulations with AI at 11 am.
- 9/18 (W): Lecture on divide-&-conquer (DC) parallelization.
- 9/20 (F): Self-study: running MPI programs at the Center for High-Performance Computing (HPC)--
no classroom meeting due to the football game.
- 9/23 (M): Lecture and team building on "quantum parallel scientific computing:
quantum programming, quantum compilation and
quantum circuit" by Lindsay Bassman.
- 9/25 (W): Hypercube-quicksort programming using MPI.
- 9/26 (Th): 4:30 pm: special discussion session for HW 3 & office hour in VHE 610.
- 9/27 (F): Discussion of "your" papers.
- 9/27 (F): See
lecture slides at the IPAM workshop on "From Passive to Active: Generative and Reinforcement Learning with Physics".
- 9/30 (M): Lecture on hybrid MPI+OpenMP parallel MD.
- 10/1(T)-2(W): XSEDE training on
big data: analytics & machine learning at USC; please register
- 10/2 (W): Lecture on parallel quantum dynamics (QD), fast Fourier transform (FFT) and multiresolution methods (wavelets).
- 10/4 (F): Logistics of HW4 (wavelet image compression).
- 10/7 (M): Parallel (asynchronous) MPI+OpenMP programming of wavelet image compression.
- 10/9 (W): Lecture on advanced multiresolution methods.
- 10/11 (F): Research topics on MD + paper-topic discussion.
- 10/11 (F): 4:30 pm: discussion session for HW 4 in VHE 610.
- 10/14 (M): Lecture on multiscale simulations.
- 10/16 (W): Lecture on load balancing, including O(N) spectral method based on Krylov-subspace iteration.
- 10/18 (F): Fall recess, no class.
- 10/21 (M): Lecture on optimizing parallel MD.
- 10/23 (W): Lecture on graphics processing unit (GPU) programming using CUDA and hybrid MPI+OpenMP+CUDA programming.
- 10/25 (F): Parallel QD programming using MPI.
- 10/28 (M): Triple-decker MPI+OpenMP+CUDA QD programming (1).
- 10/28 (M): Seminar on
The road to quantum supremacy by Dr. Daniel Sank (Google) at 4:15 pm in MCB 101.
- 10/30 (W): Triple-decker MPI+OpenMP+CUDA QD programming (2); paper discussion.
- 10/31 (Th): Seminar on
Robots in space: how AI and machine learning are revolutionizing space exploration
by Dr. Masahiro Ono (JPL) at 2 pm in SAL 101.
- 11/1 (F): Final-project logistics; paper discussion.
- 11/1 (F): 4:30 pm: discussion session for HW 5 in VHE 610.
- 11/1 (F): See
DOE readies multibillion-dollar AI push in Sience, October 31 issue.
- 11/4 (M): HPC tour, please sign in at the reception of the 3434 Grand building at 3:45 pm sharp;
see access to 3434 Grand.
Also, do not forget to bring your student photo ID, which is required to enter the building for security;
this is jointly with MASC 575 (basics of atomistic simulations of materials) students and will be
led by Prof. Ken-ichi Nomura.
- 11/6 (W): scientific virtual reality (VR) demo by Ankit Mishra;
see B. Horton et al., Game-Engine-Assisted Research platform for Scientific computing (GEARS) in virtual reality,
SoftwareX 9, 112 (2019) and
A. Mishra et al, Materials genome software framework: scalable parallel simulation, virtual reality visualization and machine learning,
in Proc. CSC'19, p. 125.
- 11/8 (F): Lecture on OpenMP target offload; paper discussion.
- 11/8 (F): 4:30 pm: discussion session for HW 5 in VHE 610.
- 11/11 (M): Lecture on scientific Grid computing; paper discussion.
- 11/13 (W): Lecture on scientific data mining and machine learning; paper discussion.
- 11/14 (Th): Seminar on
Energy-efficient integrated photonics for high-performance computing and beyond
by Dr. Di Liang (Hewlett Packard) at 11:00 am in EEB 248.
- 11/15 (F): Final-project and paper discussions.
- 11/18 (M): Lecture on Monte Carlo (MC); paper discussion.
- 11/20 (W): Lecture on scientific visualization; paper discussion.
- 11/22 (F): (1) paper discussions conclude; (2) final-project topic due.
- 11/25 (M): Special lectures: (1) Dr. Manaschai Kunaseth (ThaiSC) on
scalable parallel MD and news from SC19; and
(2) Dr. Pankaj Rajak (Argonne) on simulation + learning.
- 11/27 (W), 11/29 (F): Thanksgiving holidays, no class.
- 12/2 (M): Final GitHub-repository preparation (no regular class);
fill at least the name (team), title & abstract.
- 12/4 (W), 12/6 (F): Final project presentation using the repository.
- 12/18 (W): Final project report (GitHub repository) due.