/ciml-summer-institute-2022

Repository for the CIML 2022 Summer Institute training materials.

Primary LanguageJupyter NotebookGNU General Public License v3.0GPL-3.0

ciml-summer-institute-2022

Website: https://na.eventscloud.com/website/35357/home/

Interactive Videos

  • Recorded sessions can be found here
  • A full catalog of all our trainings at SDSC can be found here.

Contents:

Description:

This repository contains all the presentations and training material used for the CIML Summer Institute. To work with the material, remember to CLONE this repo.

Agenda:

All times are in Pacific time.

Preparation Day (Wednesday, 06/22/22)

TIME (Pacific time) TOPIC PRESENTER
9:00 AM - 9:20 AM 1.1 Welcome & Orientation Mary Thomas
9:20 AM – 9:50 AM 1.2 Access, Accounts, Login, Environment, Expanse User Portal Mary Thomas
9:50 AM – 10:10 AM 1.3 Running Jupyter Notebooks on Expanse Marty Kandes
10:10 AM – 10:30 AM Q&A, Wrap-up All

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HPC & Parallel Concepts (Monday, 06/27/22)

TIME (Pacific time) TOPIC PRESENTER
8:00 AM – 8:05 AM 2.1 Quick Welcome Mary Thomas
8:05 AM – 9:05 AM 2.2 Introduction HPC/Cyberinfrastructure Robert Sinkovits
9:05 AM – 10:05 AM 2.3 CPU Computing - Hardware, Architecture, Software, Running Jobs Mary Thomas
10:05 AM – 11:35 AM 2.4 Data Management and File Systems Marty Kandes
11:35 AM – 12:05 PM Break/Lunch
12:05 PM – 1:50 PM 2.5 GPU Computing - Hardware architecture and software infrastructure Andreas Goetz
12:05 PM – 1:50 PM Q&A, Wrap-up All

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Scalable Machine Learning (Tuesday, 06/28/22)

TIME (Pacific time) TOPIC PRESENTER
8:00 AM – 8:05 AM 3.1 Quick Welcome Mary Thomas
8:05 AM – 9:15 AM 3.2 Introduction to Singularity: Containers for Scientific and
High-Performance Computing		 Marty Kandes
9:15 AM – 11:00 AM 3.3 CONDA Environments and Jupyter Notebook on Expanse: Scalable & Reproducible Data Exploration and ML Peter Rose
11:00 AM – 11:30 AM Break/ Lunch
11:30 AM – 11:45 AM 3.4 Machine Learning (ML) Overview
Session was skipped, but resources are still availabe		 Mai Nguyen
11:45 AM – 12:15 PM 3.5 R on HPC Demo Paul Rodriguez
12:15 PM – 2:15 PM 3.6 Spark Mai Nguyen

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Deep Learning (Wednesday, 06/29/22)

TIME (Pacific time) TOPIC PRESENTER
8:00 AM – 8:05 AM 4.1 Quick Welcome Mary Thomas
8:05 AM – 9:05 AM 4.2 Intro to NN/CNN Paul Rodriguez
9:05 AM – 10:05 AM 4.3 Deep Learning Paul Rodriguez
10:05 AM – 10:50 AM 4.4 Deep Learning Layers and Models Mai Nguyen
10:55 AM – 11:25 AM Break/Lunch
11:25 AM – 12:25 PM 4.5 Deep Learning Transfer Learning Mai Nguyen
12:25 PM – 1:25 PM 4.6 Deep Learning – Other topics Paul Rodriguez
1:25 PM – 2:00 PM Q&A, wrap-up

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CIML Instructors

Name Title Contact
Andreas Goetz, Ph.D. Research Scientist, Principal Investigator awgoetz at ucsd.edu
Marty Kandes Ph.D. Computational and Data Science Research Specialist mkandes at ucsd.edu
Mai Nguyen Ph.D. Lead for Data Analytics mhnguyen at ucsd.edu
Paul Rodriguez Ph.D. Computational Data Scientist p4rodriguez at ucsd.edu
Peter Rose Ph.D. Director for Structural Bioinformatics Laboratory pwrose at ucsd.edu
Robert Sinkovits Ph.D. Director of Education and Training rssinkovits at ucsd.edu
Mary Thomas Ph.D. Director of CIML, Computational Data Scientist, HPC Trainer mpthomas at ucsd.edu

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