Schedule

Graduate Student Talk (first 15 minutes) - Md Shihab Shahriar - Harnessing High-Performance Computing in Drug Discovery

Readings:

• Why Parallel Computing?, Parallel and High Performance Computing, Yuliana Zamora, Robert Robey

Readings:

• Introduction, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson

Optional Reading:

• [Supercomputers: The Amazing Race] - Gordon Bell

In class participation is required!

Readings:

• HPC Architecture 1, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson
• Commodity Clusters, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson

Readings:

• Benchmarking, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson
• The Essential Resource Management, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson
• Batch Schedulers:Bringing Order to Chaos, Parallel and High Performance Computing, Yuliana Zamora, Robert Robey

Readings:

• The Essential OpenMP, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson
• OpenMP that Performs, Parallel and High Performance Computing, Yuliana Zamora, Robert Robey

Supplemental Reading:

• Multicore and GPU Programming, Shared-Memory Programming: OpenMP, Gerassimos Barlas
• OpenMP, Parallel Programming, Bertil Schmidt, Jorge Gonzalez-Martinez, Christian Hundt and Moritz Schlarb

Access granted to all CS455 students to lakeshore.acer.uic.edu, you must be on UIC network or using VPN to access. Test access before Tuesday class.

Professor Zhiling Lan will lecture on GPU Architecture and CUDA.

Guest lecture by Yuliana Zamora of NVIDIA and co-author of our textbook Parallel and High Performance Computing with Robert Robey.

Readings:

• The Essential MPI, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson
• MPI: The Parallel Backbone, Parallel and High Performance Computing, Yuliana Zamora, Robert Robey

Supplemental Reading:

• Message Passing Interface, Parallel Programming, Bertil Schmidt, Jorge Gonzalez-Martinez, Christian Hundt and Moritz Schlarba

Job submission script examples for PBS Pro and Slurm.

Readings:

• Parallel Algorithms, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson
• Parallel Algorithms and Patterns, Parallel and High Performance Computing, Yuliana Zamora, Robert Robey
• Debugging, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson

ALCF research scientist and UIC PhD graduate Victor Mateevitsi will lecture on Visualization.

Readings:

• Visualization, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson

Supplemental Reading:

• Overview of Visualization, Visualization Handbook (Editors: Charles D. Hansen and Chris R. Johnson), William J. Schroeder and Kenneth M. Martin

Readings:

• Performance Monitoring, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson
• Checkpointing, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson

Readings:

• Next Steps and Beyond, High Performance Computing Thomas Sterling, Maciej Brodowicz, Matthew Anderson

• Shambhawi Sharma - Accelerating Genome Sequencing With HPC
• Idunnuoluwa Adeniji - High-Performance Computing Applications in Cosmological Simulations
• Karim El Husseini - From Petaflops to Energy Solutions
• Yihe (Jordan) Zhang - HPC has Transformed Financial Services
• Sabyasachi Behera - HPC in Weather Prediction

• Eddie Federmeyer - HPC and Astrophysics
• Rohan Salvi - Utilizing HPC for Environmental Modeling
• Niccolo Brembilla - HPC in Earthquake Simulation
• Siddhant Agarwal - High-Performance Computing in Molecular Dynamics-based Drug Discovery
• Armaan Ashfaque - High-Performance Computing for Lattice Quantum Chromodynamics

• Krish Patel - Exploring High Performance Computing in Numerical Weather Prediction and Climate Modeling
• Wesley Kwiecinski - HPC and its Role in CERN’S ATLAS Experiment
• Jiaxin Lu - HPC in Finance
• Siva Rama Krishnan Valady Karthi - High-Performance Computing for Multi-Omics Integration in Personalized Medicine
• Maksym Turkot - High-Performance Computing in Precision Medicine

• Sudha Sree Yerramsetty - Accelerating Genome Sequencing With HPC
• Jayanth Mohan - Accelerating Material Science using HPC and AI
• Anh Nguyen- High Performance Computing for Protein Language Models
• Brian Rosca - HPC and Modern Cryptography: The Race Against Quantumbrian
• Vikram Harikrishnan - HPC for Nuclear Stockpile Stewardship