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Authors: Coddington, Paul (orcid: 00...  or Bretaudeau, Anthony (orcid:...  or Cytowski, Maciej (orcid: 00...  or Pawsey Supercomputing Resea... 

WEBINAR: Where to go when your bioinformatics outgrows your compute

This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.

Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute...

Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing

WEBINAR: Where to go when your bioinformatics outgrows your compute https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute-7a5a0ff8-8f4f-4fd0-af20-a88d515a6554 This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021. Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.  We also describe bioinformatics and computing support services available to Australian researchers.  This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney. 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. Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar. Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/hNTbngSc-W0 Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WORKSHOP: Refining genome annotations with Apollo

This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.

Workshop description 

Genome annotation is crucial to defining the function of genomic sequences. This process...

Keywords: Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation

WORKSHOP: Refining genome annotations with Apollo https://dresa.org.au/materials/workshop-refining-genome-annotations-with-apollo-d8f95fb3-7dc4-40e0-87d5-e7a4b2ceaf16 This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021. Workshop description  Genome annotation is crucial to defining the function of genomic sequences. This process typically involves a round of automated annotation followed by manual curation. Manual curation allows you to visualise your annotations so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is typically performed collaboratively as part of a team effort. Apollo is a popular tool for facilitating real-time collaborative, manual curation and genome annotation editing. In this workshop we will learn how to use Apollo to refine genome annotations using example data from an E. coli strain. We’ll focus on the basics like getting data into Apollo, viewing evidence tracks, editing and adding structural and functional annotation, visualising the results and collaborating on genome annotations. This workshop made use of a training instance of  the new Australian Apollo Service. This service enables Australian-based research groups and consortia to access Apollo and host genome assembly and supporting evidence files for free. This service has been made possible by The Australian BioCommons and partners at QCIF and Pawsey. To learn more about the Australian Apollo Service you can watch the Australian Apollo Launch Webinar. This workshop was presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) . The Australian Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons as well as Queensland Government RICF funding. The training materials presented in this workshop were developed by Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet for the Galaxy Training Network. Helena and Anthony are part of the Gallantries project which is supported by Erasmus Programme of the European Union. 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. Schedule (PDF): A breakdown of the topics and timings for the workshop 2021 Apollo Training Intro (PPTX and PDF): Slides used to introduce the Australian Apollo Service Augustus.gff3 (gff3): E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia. Blastp_vs_swissprot.gff3: E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia. Materials shared elsewhere: This workshop is based on the tutorial ‘Refining genome annotations with Apollo’ which was developed for the Galaxy Training Network. Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet, Erasmus Programme, 2021 Refining Genome Annotations with Apollo (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html Online; accessed Wed Dec 15 2021 See also: Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012 Melissa Burke (melissa@biocommons.org.au) Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation
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
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: OpenCL, supercomputing, CPUs, GPUs, FPGAs, HPC

OpenCL https://dresa.org.au/materials/opencl-3eabb316-794d-4f46-959a-725be3ae1bde 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. Topics covered in this course are : - Introduction to OpenCL - How to build and run applications on Setonix with OpenCL and MPI - Matrix multiplication with OpenCL – fully explained line by line - How to debug OpenCL applications and kernels - Measure performance with OpenCL Events and open source tools - Memory management - Coarse and fine-grained shared memory - Strategies for building optimised OpenCL kernels - Optimise IO performance with asynchronous operations training@pawsey.org.au OpenCL, supercomputing, CPUs, GPUs, FPGAs, HPC
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
WORKSHOP: Refining genome annotations with Apollo

This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.

Workshop description

Genome annotation is crucial to defining the function of genomic sequences. This...

Keywords: Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation

WORKSHOP: Refining genome annotations with Apollo https://dresa.org.au/materials/workshop-refining-genome-annotations-with-apollo This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021. **Workshop description** Genome annotation is crucial to defining the function of genomic sequences. This process typically involves a round of automated annotation followed by manual curation. Manual curation allows you to visualise your annotations so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is typically performed collaboratively as part of a team effort. Apollo is a popular tool for facilitating real-time collaborative, manual curation and genome annotation editing. In this workshop we will learn how to use Apollo to refine genome annotations using example data from an E. coli strain. We’ll focus on the basics like getting data into Apollo, viewing evidence tracks, editing and adding structural and functional annotation, visualising the results and collaborating on genome annotations. This workshop made use of a training instance of  the new Australian Apollo Service. This service enables Australian-based research groups and consortia to access Apollo and host genome assembly and supporting evidence files for free. This service has been made possible by The Australian BioCommons and partners at QCIF and Pawsey. To learn more about the Australian Apollo Service you can watch the Australian Apollo Launch Webinar. This workshop was presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) . The Australian Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons as well as Queensland Government RICF funding. The training materials presented in this workshop were developed by Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet for the Galaxy Training Network. Helena and Anthony are part of the Gallantries project which is supported by Erasmus Programme of the European Union. 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. - Schedule (PDF): A breakdown of the topics and timings for the workshop - 2021 Apollo Training Intro (PPTX and PDF): Slides used to introduce the Australian Apollo Service - Augustus.gff3 (gff3): E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia. - Blastp_vs_swissprot.gff3: E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia. **Materials shared elsewhere:** This workshop is based on the tutorial ‘Refining genome annotations with Apollo’ which was developed for the Galaxy Training Network. Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet, Erasmus Programme, 2021 Refining Genome Annotations with Apollo (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html Online; accessed Wed Dec 15 2021 See also: Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012 Melissa Burke (melissa@biocommons.org.au) Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation
WEBINAR: Where to go when your bioinformatics outgrows your compute

This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.

Bioinformatics analyses are often complex, requiring multiple software tools and specialised...

Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing

WEBINAR: Where to go when your bioinformatics outgrows your compute https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021. Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.  We also describe bioinformatics and computing support services available to Australian researchers.  This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney. 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. - Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar - Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar. **Materials shared elsewhere:** A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/hNTbngSc-W0 Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing