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ciml-summer-institute-2021

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 PST.

Preparation Day (Fri, 06/18/21)

TIME (PST) TOPIC PRESENTER
9:00 AM - 9:20 AM 1.1. Welcome & Orientation Mary Thomas
9:20 AM – 9:50 AM 1.2. Accounts, Login, Environment, Running Jobs Mary Thomas
9:50 AM – 10:10 AM 1.3. Running Secure Jupyter Notebooks on Expanse Mary Thomas & Marty Kandes
10:10 AM – 10:30 AM 1.4. Installing your own miniconda & creating conda environments Peter Rose
10:30 AM – 10:50 AM 1.5. Interactive Services Using the Expanse User Portal Subha Sivagnanam & Marty Kandes
10:50 AM – 11:00 AM Q&A, Wrap-up all

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Cyberinfrastructure & HPC (Tues, 06/22/21)

TIME (PST) TOPIC PRESENTER
8:00 AM - 9:00 AM 2.1 Welcome, Orientation, & Introductions Mary Thomas
9:00 AM – 9:40 AM 2.2 Introduction HPC/Cyberinfrastructure Robert Sinkovits
9:40 AM – 10:20 AM 2.3 CPU Computing - Hardware, architecture, and software infrastructure Mary Thomas
10:20 AM – 11:00 AM 2.4 GPU Computing - Hardware architecture and software infrastructure Andreas Goetz
11:00 AM – 11:45 AM Break/Lunch
11:45 PM – 12:25 PM 2.5 Data Management and File Systems Manu Shantharam
12:25 PM – 1:05 PM 2.6 Introduction to Singularity: Containers for Scientific and High-Performance Computing Marty Kandes
1:05 PM – 1:35 PM 2.7 Reproducibility in Science and Machine Learning Peter Rose
1:35 PM – 2:00 PM. Q&A, Wrap-up

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Scalable Machine Learning (Weds, 06/23/21)

TIME (PST) TOPIC PRESENTER
8:00 AM – 8:30 AM 3.1 Machine Learning (ML) Overview Mai Nguyen
8:30 AM – 9:15 AM 3.2 R on High-Performance Computing (HPC) Paul Rodriguez
9:15 AM – 9:30 AM Break
9:30 AM – 10:45 AM. 3.3 Spark Mai Nguyen
10:45 AM – 11:45 AM Break/Lunch
11:45 AM – 12:30 PM 3.4 Intro to NN/CNN Paul Rodriguez
12:15 AM – 12:30 AM Break/Lunch
12:30 PM – 1:45 PM 3.5 Deep Learning Mai Nguyen
1:45 PM – 2:00 PM 3.6 Q&A, Wrap-up

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Machine Learning Hands-on (Thurs, 06/24/21)

TIME (PST) TOPIC PRESENTER
8:00 AM - 9:15 AM 4.1 Writing and Sharing Computational Analyses in Jupyter Notebooks Peter Rose
9:15 AM – 9:30 AM Break
9:30 AM – 10:00 AM 4.2 Spark Hands-on Mai Nguyen &
Paul Rodriguez
10:00 AM - 10:30 AM 4.3 Continue Spark Hands-on Hands-on Mai Nguyen &
Paul Rodriguez
10:30 AM - 11:00 AM 4.4 Deep Learning Hands-on Mai Nguyen &
Paul Rodriguez
11:00 AM – 12:00 PM Break/Lunch
12:00 PM – 1:00 PM 4.5 Deep Learning Transfer Learning Hands-on Mai Nguyen &
Paul Rodriguez
11:00 PM – 1:45 PM 4.6 Deep Sequence Learning Hands-on Mai Nguyen &
Paul Rodriguez
1:45 PM – 2:00 PM Q&A, Wrap-up

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Instructors

NAME TITLE ORG
Andy Goetz Director - Computational Chemistry Laboratory (bio) SDSC
Marty Kandes Computational and Data Science Research Specialist (bio) SDSC
Mai Nguyen Lead - Data Analytics (bio) SDSC
Paul Rodriguez Research Programmer (bio) SDSC
Peter Rose Director - Structural Bioinformatics Laboratory (bio) SDSC
Bob Sinkovits Director for Scientific Computing Applications (bio) SDSC
Manu Shantharam TITLE (bio) SDSC
Subha Sivagnanam TITLE (bio) SDSC
Mahidhar Tatineni Director of User Services (bio) SDSC
Mary Thomas Computational Data Scientist, Lead - HPC Training (bio) SDSC
Cindy Wong Computational and Data Science Research Specialist (bio) SDSC
Nicole Wolter Computational and Data Science Research Specialist (bio) SDSC

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