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Authors: Williams, Jason (orcid: 000...  or Pawsey Supercomputing Resea... 

WEBINAR: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond

This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022.

Event description 

Scientists and educators...

Keywords: Short-format training, Clinical education, Continuing education, Professional development, Training, Lifelong learning, Pedagogy

WEBINAR: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond https://dresa.org.au/materials/webinar-effective-inclusive-and-scalable-training-in-the-life-sciences-clinical-education-and-beyond-52c113ff-573c-4ae8-a3f0-482c86f1818a This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022. Event description  Scientists and educators working in the life sciences must continuously acquire new knowledge and skills to stay up-to-date with the latest methods, technologies and research. Short-format training, such as webinars, workshops and bootcamps, are popular ways of quickly learning about new topics and gaining new skills. As trainers and educators, how can we ensure that short-format training is effective and inclusive for all? How can we ensure that our learners are equipped to continue learning and applying their new skills once they return to their day jobs? And how can we do this in a way that is scalable and sustainable? The Bicycle Principles assemble education theory and community experience into a framework for improving short-format training so that it is effective, inclusive and scalable. Over 30 international experts, including colleagues from the Australian BioCommons, Melbourne Genomics and other Australian and New Zealand organisations, helped develop the principles and an associated set of recommendations. Jason Williams, Assistant Director, DNA Learning Center, Cold Spring Harbor Laboratory - a leading genomics and bioinformatics educator and project lead, joins us to discuss the Principles and how they can be applied to achieve scalable and sustainable training in a range of Australian settings. This webinar is co-hosted by Australian BioCommons and Melbourne Genomics Training Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. WILLIAMS-Jason_aus-biocommons_nov-2022 (PDF): A PDF copy of the slides presented during the webinar. Materials shared elsewhere:   A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/18dub7jGeQ8 Melissa Burke (melissa@biocommons.org.au) Short-format training, Clinical education, Continuing education, Professional development, Training, Lifelong learning, Pedagogy
Professionalizing Training - Origin Stories for the Modern Researcher

Keynote Presentation for the ARDC Skills Summit 2023

This keynote presentation provides a brief outline of Jason William’s experience and an overview of the training initiatives he has been involved in. His presentation looks at what makes a good researcher and provokes thinking about modern...

Keywords: research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material

Professionalizing Training - Origin Stories for the Modern Researcher https://dresa.org.au/materials/professionalizing-training-origin-stories-for-the-modern-researcher-0198d9cf-9d8f-467e-8031-4d3a3536af63 Keynote Presentation for the ARDC Skills Summit 2023 This keynote presentation provides a brief outline of Jason William’s experience and an overview of the training initiatives he has been involved in. His presentation looks at what makes a good researcher and provokes thinking about modern researchers and the need for them to get serious bout career-spanning training. Jason also provides an overview of the Bike Principles and focuses on the first Bike Principles recommendation - Professionalize the training of short-format training instructors and instructional designers. contact@ardc.edu.au research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material
Using PennyLane on Setonix

Introduction to quantum computing

Keywords: Pawsey Supercomputing Centre, Setonix, quantum, PennyLane

Using PennyLane on Setonix https://dresa.org.au/materials/using-pennylane-on-setonix Introduction to quantum computing training@pawsey.org.au Pawsey Supercomputing Centre, Setonix, quantum, PennyLane
Pawsey: AWS Quantum 101 Using Amazon Braket

Join us as AWS Quantum Specialists introduce quantum simulators and gate-based quantum computers, before turning to more advanced topics.

Keywords: Pawsey Supercomputing Centre, AWS, quantum, HPC

Pawsey: AWS Quantum 101 Using Amazon Braket https://dresa.org.au/materials/pawsey-aws-quantum-101-using-amazon-braket Join us as AWS Quantum Specialists introduce quantum simulators and gate-based quantum computers, before turning to more advanced topics. training@pawsey.org.au Pawsey Supercomputing Centre, AWS, quantum, HPC
HIP Advanced Workshop

Additional topics presented about HIP, covering memory management, kernel optimisation, IO optimisation and porting CUDA to HIP.

Keywords: HIP, Pawsey Supercomputing Centre, supercomputing

HIP Advanced Workshop https://dresa.org.au/materials/hip-advanced-workshop Additional topics presented about HIP, covering memory management, kernel optimisation, IO optimisation and porting CUDA to HIP. training@pawsey.org.au HIP, Pawsey Supercomputing Centre, supercomputing
Managing Data using Acacia @ Pawsey

Acacia is Pawsey's "warm tier" or project storage. This object store is fully integrated with Setonix, Pawsey's main supercomputer, enabling fast transfer of data for project use.

These short videos introduce this high-speed object storage for hosting research data online.

Acacia is named...

Keywords: data, data skills, Acacia, Pawsey Supercomputing Centre, object storage, File systems

Managing Data using Acacia @ Pawsey https://dresa.org.au/materials/managing-data-using-acacia-pawsey Acacia is Pawsey's "warm tier" or project storage. This object store is fully integrated with Setonix, Pawsey's main supercomputer, enabling fast transfer of data for project use. These short videos introduce this high-speed object storage for hosting research data online. Acacia is named after Australia’s national floral emblem the Golden Wattle – Acacia pycnantha. training@pawsey.org.au data, data skills, Acacia, Pawsey Supercomputing Centre, object storage, File systems ugrad masters phd ecr researcher support professional
OpenCL

Supercomputers make use of accelerators from a variety of different hardware vendors, using devices such as multi-core CPU’s, GPU’s and even FPGA’s. OpenCL is a way for your HPC application to make effective use of heterogeneous computing devices, and to avoid code refactoring for new HPC...

Keywords: supercomputing, Pawsey Supercomputing Centre, CPUs, GPUs, OpenCL, FPGAs

Resource type: activity

OpenCL https://dresa.org.au/materials/opencl Supercomputers make use of accelerators from a variety of different hardware vendors, using devices such as multi-core CPU’s, GPU’s and even FPGA’s. OpenCL is a way for your HPC application to make effective use of heterogeneous computing devices, and to avoid code refactoring for new HPC infrastructure. training@pawsey.org.au Toby Potter supercomputing, Pawsey Supercomputing Centre, CPUs, GPUs, OpenCL, FPGAs masters ecr researcher support
AMD Profiling

The AMD profiling workshop covers the AMD suite of tools for development of HPC applications on AMD GPUs.

You will learn how to use the rocprof profiler and trace visualization tool that has long been available as part of the ROCm software suite.

You will also learn how to use the new...

Keywords: supercomputing, performance, GPUs, CPUs, AMD, HPC, ROCm

Resource type: activity

AMD Profiling https://dresa.org.au/materials/amd-profiling The AMD profiling workshop covers the AMD suite of tools for development of HPC applications on AMD GPUs. You will learn how to use the rocprof profiler and trace visualization tool that has long been available as part of the ROCm software suite. You will also learn how to use the new Omnitools - Omnitrace and Omniperf - that were introduced at the end of 2022. Omnitrace is a powerful tracing profiler for both CPU and GPU. It can collect data from a much wider range of sources and includes hardware counters and sampling approaches. Omniperf is a performance analysis tool that can help you pinpoint how your application is performing with a visual view of the memory hierarchy on the GPU as well as reporting the percentage of peak for many different measurements. training@pawsey.org.au supercomputing, performance, GPUs, CPUs, AMD, HPC, ROCm
Evaluate Application Performance using TAU and E4S

In this workshop, you learn about the Extreme-scale Scientific Software Stack and the TAU Performance System® and its interfaces to other tools and libraries. The workshop includes sample codes that illustrate the different instrumentation and measurement choices.

Topics covered include...

Keywords: supercomputing, TAU, E4S, Performance, ROCm, OpenMP

Resource type: activity

Evaluate Application Performance using TAU and E4S https://dresa.org.au/materials/evaluate-application-performance-using-tau-and-e4s In this workshop, you learn about the Extreme-scale Scientific Software Stack and the TAU Performance System® and its interfaces to other tools and libraries. The workshop includes sample codes that illustrate the different instrumentation and measurement choices. Topics covered include generating performance profiles and traces with memory utilization and headroom, I/O, and interfaces to ROCm, including ROCProfiler and ROCTracer with support for collecting hardware performance data. The workshop also covers instrumentation of OpenMP programs using OpenMP Tools Interface (OMPT), including support for target offload and measurement of a program’s memory footprint. During the session, there are hands-on activities on scalable tracing using OTF2 and visualization using the Vampir trace analysis tool. Performance data analysis using ParaProf and PerfExplorer are demonstrated using the performance data management framework (TAUdb) that includes TAU’s performance database. training@pawsey.org.au supercomputing, TAU, E4S, Performance, ROCm, OpenMP
HIP Workshop

The Heterogeneous Interface for Portability (HIP) provides a programming framework for harnessing the compute capabilities of multicore processors, such as the MI250X GPU’s on Setonix.

In this course we focus on the essentials of developing HIP applications with a focus on...

Keywords: HIP, supercomputing, Programming, GPUs, MPI, debugging

Resource type: full-course

HIP Workshop https://dresa.org.au/materials/hip-workshop The Heterogeneous Interface for Portability (HIP) provides a programming framework for harnessing the compute capabilities of multicore processors, such as the MI250X GPU’s on Setonix. In this course we focus on the essentials of developing HIP applications with a focus on supercomputing. Agenda - Introduction to HIP and high level features - How to build and run applications on Setonix with HIP and MPI - A complete line-by-line walkthrough of a HIP-enabled application - Tools and techniques for debugging and measuring the performance of HIP applications training@pawsey.org.au HIP, supercomputing, Programming, GPUs, MPI, debugging
C/C++ Refresher

The C++ programming language and its C subset is used extensively in research environments. In particular it is the language utilised in the parallel programming frameworks CUDA, HIP, and OpenCL.

This workshop is designed to equip participants with “Survival C++”, an understanding of the basic...

Keywords: supercomputing, C/C++, Programming

Resource type: activity

C/C++ Refresher https://dresa.org.au/materials/c-c-refresher The C++ programming language and its C subset is used extensively in research environments. In particular it is the language utilised in the parallel programming frameworks CUDA, HIP, and OpenCL. This workshop is designed to equip participants with “Survival C++”, an understanding of the basic syntax, how information is encoded in binary format, and how to compile and debug C++ software. training@pawsey.org.au supercomputing, C/C++, Programming