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University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
eResearch UCT
Anthony Beitz
Director UCT eResearch
www.eresearch.uct.ac.za
12 May 2015
21st century research discovery through advanced computing and ICT
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Agenda
1. Introduction to eResearch2. eResearch @UCT3. Examples of eResearch at UCT4. Accessible capabilities & infrastructure
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Emergence of Research Methodologies
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
What is eResearch?
eResearch is 21st century research discovery through the application of advanced computing and IT
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
It is transformational research:
Second image courtesy of Dr. Govinda Poudel, with permission.Third image courtesy of Electronic Visualization Laboratory & Dept. of Psychiatry, UIC, with permission. Photo by Philip Chan, Monash Uni.
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
It is accelerated research:
Brains of ~100 study subjects (controls, pre-symptomatic and Huntington’s Disease sufferers) visualised at once!
Data: N. Georgiou-Karistianis (Monash Uni.) Visualisation: Y. Benovitski (Monash Uni.)
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
MRI Scanner
Collect
GPU Cluster
Compute
CAVE2TM
Comprehend
eResearch version of a microscope
Dat
a Pl
atfor
m –
Col
lect
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Research Data Commons
Communicate
Virtual Lab
Collaborate
eResearch version of a microscope
Compute
Collect
Comprehend
Dat
a Pl
atfor
m –
Col
lect
Dat
a Pl
atfor
m –
Col
lect
Dat
a Pl
atfor
m –
Col
lect
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Research Data Deluge
Data generation rates:
• Next Generation Sequencer > 200 TB / year
• Direct electron detectors > 350 TB / year (equivalent to synchrotron beamlines)
• Large Hadron Collider 15 PB / year
• Square Kilometer Array 0.3-1.5 EB / year
Laboratory based
Large facilities
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Research Acceleration & TransformationIMPLICATIONS
Need to grow access to infrastructure, capability and tools
Pace and scale increasing
• Technology is accelerating the pace and scale of research
• Large-scale data requires more structured approach data management approach
KEY CHANGES
Expert guidance and training to leverage new approaches
New tools and methodologies
• New and more powerful instruments
• Digital recognition of text, speech and imagery
• Crowdsourcing and citizen science
Swift capability to establish and support collaborations
Internationalisation
• Research funding is increasingly based on strong international collaborations
• Internationalisation is introducing new complexities in health, ecology and economy (epidemics, climate change, Global Fin. Crisis)Slide courtesy of Nathan Bailey & Lisa March (iSimplify)
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
“Scholarly practices across an astounding wide range of disciplines have become profoundly and irrevocably changed by the application of advanced information technology. This collection of new and emergent scholarly practices was first widely recognized in the science and engineering disciplines….humanities continue to showcase some of the most creative and transformative examples of the use of information technology to create new scholarship.”
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
http://www.canberra.edu.au/research/ucresearch/e-research
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Transforming research practice
• Unsuccessful structure solution of PlyC structure
• However, raw data archived in MyTardis, the Monash bioscience research data repository
• New technological advancements in 2010 and easy access to the archival data led to the PlyC structure being solved
Monash’s Dr. Sheena McGowan (under the direction of Prof. James Whisstock and Assoc. Prof. Ashley Buckle)
PlyC
http://www.quantumdiaries.org/
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
About Researchers• Research is about “doing things we don’t know how to do”
They work in an interpretive mode– Characteristics include: an iterative process; open-ended; and
thrive on ambiguity – Service providers try to remove ambiguity = breakdown in
communication and understanding
• Their requirements and goals will change over time, and very likely won’t be well known at the start
• Generally more loyal to their research community than their institution
• May require an ICT capability for only a short period of time• Very resourceful and driven by research outcomes
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Creative Solutions• Solutions are not always
“designed/engineered” – they are often “grown” via an iterative process
• If researchers engage all the way along the iterative process -- they will very likely engage at the end
• The research challenges are unique and therefore the solutions are often “unique” - no one size fits all
Slide courtesy of Prof. Paul Bonnington (Monash Uni)
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Engaging with Researchers• It’s basically about the relationship and demonstrating that
you are listening and delivering ongoing value• Never push solutions or technologies• Partner with Researchers and go on the journey of the
unknown together• Solutions should be led and owned by the Researcher
– Agile methodologies and mindsets lend themselves to this outcome
• Work in with their community• Reduce the barriers• The three T’s of an innovation environment: Talent,
Technology and Tolerance (for ambiguity and risk)
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
eResearch @ UCT
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
History of UCT eResearchBegan with UCT’s ICT Services’ (ICTS) Executive Director, Sakkie Janse van Rensburg, searching for a better way to support researchers2009: UCT ICTS staff trained in HPC2010: Built 1st cluster and visited Australia to investigate eResearch2011: HPC-trained staff focused on researchers, UCT researcher appointed to work with ICTS2013: Best-of-breed eResearch model identified, global search2014/Q1: Core partnerships and eResearch working group formed2014/Q2: Business case developed, buy-in by UCT’s Senior Leadership Group attained, initial eResearch team formed2014/Q3: Strategic plan developed2014/Q4: Interim director appointed2015/Q1: Governance established
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
eResearch Responsibilities
LegendA – AccountableC - ConsultedI – Informed
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
eResearch Centre
Research Office• Advocacy• Collaboration
ICTS• Data Storage• Compute• Cloud• Networks
DVC-Research• Leadership• Governance• Strategy• Resourcing
The Library• Research visibility &
discovery• Research data
management
Faculties• Various capabilities
Researchers
Core capability partnerships
Capability delivery
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT eResearch partners with research groups to accelerate and transform research, connecting them to the most appropriate hardware, software and services to sustain that capability
Collect Compute Comprehend
Collaborate Communicate Customise
Creating a world-class environment for 21st century discovery
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
As a partner and broker UCT eResearch will connect researchers with world-class expertise and facilities (local or external) in:
• Collection and management of research data
• Modelling, simulation and data processing through HPC
• Comprehension of big data through visualisation and data science techniques
• Promotion of collaborative research through virtual labs and cloud resources
• Dissemination of research outcomes (including data and workflows)
• Development of customised research software, hardware and services
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Resource Limits• Requirements for advanced ICT
research infrastructure are huge and growing
• Advice and fundamental infrastructure are freely available
• For needs beyond fundamental infrastructure, UCT researchers engage early with the eResearch Centre to estimate required funding and to incorporate it into a grant
Imag: permabit.com/data-affordability-gap/
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT eResearch does not want to try to be the ultimate Swiss army knife for researchers
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Target Structure for UCT’s eResearch Centre
eResearch Centre Steering
Committee
Directorate
Researcher Liaisons
Research Infrastructure
Projects
Fledgling Research
Technology Platforms
Virtual Labs & Collaborative Environments
Human Capital Development
DVC-R Exec. Dir. Research Office
NB: The lines are not indicative of line reporting
Exec. Dir. ICTS University Librarian
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Functions• Directorate
– Strategy, leadership, facilitate organisational change, comms and admin
• Researcher Liaisons– Act as brokers between researchers and capability providers
• Research infrastructure projects– Plan & execute research infrastructure projects
• Fledgling Research Technology Platforms– Provide skilled resources, specialised infrastructure and relevant training
• Virtual research labs & collaborative environments– Provide interim support for virtual research labs and collaborative envs
• Human Capital Development– Co-ordinate staff and researcher training in new research cyberinfrastructure
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Examples of eResearch at UCT
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Examples of eResearch at UCT
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
SKA - answering some of science’s biggest questions
• One of the largest scientific projects ever undertaken to answer questions such as:
• What is dark energy?
• Was Einstein right about gravity?
• Is there life elsewhere in the universe?
• eResearch is supporting storage, compute, development of new visualisation tool
• Exascale arriving soon…
www.skatelescope.org
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Enabling South African CERN researchers to partner with their international colleagues
• CERN made up of a massive globally dispersed community of researchers
• Successful international research collaborations are dependent on a good video conferencing experience
• South African researchers had a poor experience
• UCT eResearch connected CERN with national service providers to bring video conferencing up to an good level
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
• Key research projects e.g. SKA and space geodesy
• Use of HPC facilities have tripled in the past year
• 300 researchers across campus assisted by HPC
• 33 citations (and counting)
Image: Stephen Williams Photography
High Performance Computing
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Facility Support: Olympus Virtual Microscope
The old: slide boxes
The new: Olympus VS120 Microscope
eResearch:
• Worked with the UCT’s Clinical Lab Services department to set up the servers and the database
• Configured the system for various access scenarios including student, departmental and public access
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Facility Support: Centre for Imaging and AnalysisProvides the instrumental resources and expertise for structural analysis in all disciplines.
acquisition processing interpretation dissemination
Workflow:
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Facility Support:
• Nikon fluorescent microscope for live cell imaging
• eResearch supported storage, remote data analysis and collaboration
Clinical Research Centre Molecular and Cell Biology Tissue Culture Facility
• Clinical, laboratory and data management systems needed to pass an FDA or EMA audit.
• Software and computational requirements met by eResearch
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Human Heredity and Health in Africa
• First Pan African Bioinformatics Network in Africa: H3ABioNet & H3Africa Consortium
• UCT eResearch Centre, in collaboration with Information and Communication Technology Services (ICTS) and the Computational Biology Group, will be developing a data storage archive solution
• The data will include genomic data and access will be controlled according to internationally accepted standards.
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Accessible capabilities & infrastructure
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Current capabilities & infrastructure
• Training– HPC (beginner & advanced levels)– Software carpentry (Python,R, Git, ..)
• Research data storage• High Performance Computing• Virtual machines and databases• Project Managers, BAs, Devs, … for research projects
(through cost recovery)• Assistance in research grant proposals (research
infrastructure)
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
IT Infrastructure in Support of Research
Ashley [email protected]
Saturday 15 April 2023
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT Core Network & Data Centres
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT Bandwidth
• 1.2 Gbps International on WACS• 10 Gbps Local via SANREN
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT High Performance Computing (HPC)
1. Hex Cluster Nodes• Dell C6145 x 9 = 18 nodes• 4 sockets with 16 cores each• 1152 cores• 2.2TB RAM
2. HPC Cluster Nodes• HPBL460c x 19 = 19 nodes• 8 – 12 cores each• 176 cores• 648 GB RAM
Mellanox Infiniband 6036 SX Interconnect
Dell C6145 compute Node
HP BL460C compute Nodes
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT High Performance Computing (HPC)
3. GPU Nodes• SuperMicro M2090 x 3 = 3 nodes• 4 sockets with 16 cores each• Nvidia TeslaM2090 & K40M (9856 GPU
cores) • 36 CPU cores• 192 GB RAM
4. High Memory Nodes• Dell R820 x 2 = 2 nodes• 8 – 12 cores each• 176 cores• 648 GB RAM
Dell C6145 & R820 compute Nodes
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT HPC Storage
1. /home• 2 TB Storage (NFS)
2. /scratch (old)• 21 TB Storage (NFS)
3. /scratch (high speed)• 92 TB (BGFS)
BackBlaze Storage Pod
Dell MD3060 Storage unit
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT Research Data Storage
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT Research Data Storage Benefits:
• Highly discounted for research – R3450 per TB or R34 500 per 10 TB• Once-off payment• Data is backup & replicated to UFS & UWC data centres• Access your data from anywhere in the world• Collect & store data from your instruments directly to the central research data store.• Contact: - [email protected]
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Coming capabilities and infrastructure
• New visualisation tool & platform• Federated access• New data centre• New compute cluster – 1000+ cores• Training in data science, research data
management (in league with the Library)• African Research Cloud (ARC)
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
…in summary
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
Monash eResearch Centre• eResearch is 21st century research discovery through the application of advanced
computing and IT
• UCT eResearch partners with research groups to accelerate and transform research, connecting them to the most appropriate hardware, software and services to sustain that capability
UCT eResearchAdvanced computing and IT for accelerating and transforming research
Collect Compute Comprehend
Collaborate Communicate Customise
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
See: http://www.eresearch.ac.za
eResearch AfricaUniversity of Western Cape
9-13 November 2015
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
The Team Anthony Beitz (Director)
Timothy Carr
Jenny Dixon (Admin)
Piet Helm
Heine de Jager
Andrew Lewis
Chris Mtshengu
Adrianna Pinska
Jason van Rooyen
Ashley Rustin
Natalie Simon
University of Cape Town
Overview for IT Managers – 12 May 2015UCT eResearch
UCT eResearch
Email: [email protected]: www.eresearch.uct.ac.zaPhone: +27 (76) 595 9616