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RCC News: July 2015

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Barrine outage

UQ's High Performance Computer (Barrine) will be closed down for up to two weeks, starting from Wednesday, 1 July 2015, for reconfiguration work. This is as per previous notifications sent to Barrine users. 
Barrine is being reconfigured with a new batch server and without the Panasas storage subsystem. Removing these (commercially) licensed components will allow us to operate Barrine for the remainder of 2015, and possibly into 2016, extending its life significantly.
Read the Barrine webpage to find out what Barrine users should do with their jobs, files and data during the shutdown period. 

RCC to take ownership of FlashLite next week

RCC will take ownership of FlashLite, a new data intensive High Performance Computer, within a week.  Over the next three weeks RCC will perform setup and configuration of the cluster and its storage, and perform tuning and testing before releasing it in late July.

FlashLite is an exciting addition to RCC's HPC infrastructure, providing high performance modelling capability coupled with very large main memory and input/output (IO). Please contact us ( to discuss whether FlashLite is a good platform for your research.
More FlashLite info

FlashLite user training rescheduled

FlashLite user training scheduled for 1 July 2015 has been postponed due to a delay in acceptance testing of FlashLite by the vendor and UQ.
Those who registered for the 1 July session will automatically be granted a place in the rescheduled session, the date and room for which have yet to be confirmed. RCC will update you with these details as soon as they have been confirmed. 

If you haven't already done so, please email to register for the FlashLite training session.

Upcoming new resource: the Euramoo virtual cluster 

RCC, in collaboration with QCIF and eRSA, is building a new  computer cluster called Euramoo.
Built on the NeCTAR cloud, Euramoo is optimised for multiple serial jobs as opposed to large parallel ones. However, it will also support small message passing (MPI) and OpenMP type programs with low bandwidth requirements. It is ideally suited to large parameter sweep or ensemble applications.

Euramoo will offer a very flexible platform because you can augment RCC's NeCTAR allocation with your own. It will also operate with the Nimrod parameter sweep and workflow tools, providing a powerful high-level environment to augment other systems.
RCC expects Euramoo will be ready for use by late July. 

Want to be an early adopter?

If you are keen to be a FlashLite and/or Euramoo early adopter, please contact:

NCI training for UQ HPC users NCI logo

RCC has organised for the NCI (National Computational Infrastructure) user services team to visit UQ to run training sessions for UQ HPC users across two full days on 29 and 30 June.

On 29 June, learn how to use Raijin, a high-performance, distributed-memory cluster computer. This introductory session will also describe the basics of NCI access, policies, and the merit allocation schemes. This will be useful for potential users, and could also be useful background information for established users. We remind users that time allocated by the National Merit Allocation committee can be augmented by dedicated UQ and QCIF allocations.

On 30 June, an advanced course will focus on parallel programming and performance on Raijin. See the NCI website for the questions you need to address before registering for this session. 

Please email to register for either session (places are still available), and for assistance with merit applications. 

Join our Kepler workshop 

RCC is hosting a workshop on the Kepler Scientific Workflow System and its applications on Tuesday, 14 July, 9am–4:30pm.

The workshop will focus on three main areas:
  1. A generic introduction course to the Kepler system.
  2. Use cases from different disciplines and research areas, including users’ first-hand experience with Kepler.
  3. Technical details in deploying and developing scientific workflows.
Speakers include: 
  • Ilkay Altintas, Director for the Center of Excellence in Workflows for Data Science at the San Diego Supercomputer Center (SDSC), University of California, San Diego
  • Siddeswara Guru, TERN (Terrestrial Ecosystem Research Network) Data Integration and Synthesis Coordinator at The University of Queensland
  • Matthew Watts, a computer programmer and systems analyst working for Prof Hugh Possingham at The Ecology Centre, University of Queensland.
Please email Minh Dinh ( to register your interest in this Kepler workshop, or if you have any queries.

Senator commends UQ open data collection at national showcase

Senator Scott Ryan at the ANDS Showcase
A UQ Major Open Data Collection was commended by Senator Scott Ryan (pictured) at the ANDS Showcase in Canberra on 19 June.
The UQ project, led by QCIF/RCC’s Belinda Weaver, developed an online platform to make genotypic and phenotypic information about Australian wheat breeds available for search and download ( These data form part of the global Wheat Information System.
Senator Ryan said: “These collections range from the very broad… to the very focused, like the University of Queensland’s Australian Wheat Collection, which provides a centralised access point for Australian wheat breeders and researchers.”
Australian Wheat was one of more than 30 internationally significant collections that have been fully described and made openly available by Australian research institutions through the MODC initiative. This includes another UQ major open data project, Flint Collection: Sharing Indigenous Languages.  
As well as featuring Senator Ryan, Chief Scientist, Prof Ian Chubb also attended the ANDS Showcase.

Harvard and Stanford speakers at UQ Winter School in Math & Computational BiologyJohn Quackenbush

The range of speakers at this year's UQ-hosted, RCC-sponsored Winter School in Mathematical and Computational Biology, is arguably the event's best yet.

Speakers include Prof John Quackenbush (pictured) from the Harvard School of Public Health and Dana-Farber Cancer Institute, and Assoc-Prof Stephen Montgomery from Genome Informatics, Department of Pathology, Stanford University — not to mention RCC Director Prof David Abramson speaking on big data, statistics and applications!

The Winter School will be held from 6–10 July on UQ's St Lucia Campus. Check out the full programPlease register.

RCC lets them eat cake at Mozilla Global Sprint

RCC hosted Brisbane’s first entry in the annual Mozilla Science Lab Global Sprint for two days in early June. 

The RCC/QCIF’s Belinda Weaver organised the Brisbane sprint as part of RCC outreach.

The sprint is a hackathon to build projects that benefit open science. The first, in 2014, involved more than 100 people in 22 cities worldwide. This year, 30 cities took part. Sites keep in touch globally via a continuous video conference.
Belinda and her team worked on ‘Library Carpentry’ – a version of Software Carpentry aimed specifically at Australian librarians, and based on work being done by James Baker of the British Library. She was joined by Helen Morgan from the UQ Library and Thea Koutsoukis, who teaches coding to primary school children, During the sprint, they:
  • hosted Google hangouts to consult librarians about course content
  • analysed survey responses to Belinda’s Library Carpentry: Building Blocks survey
  • developed a course outline based on librarians’ feedback
  • investigated OpenRefine as a data clean-up tool
  • tested a container environment for training that lets users run the Unix shell and Python within a Web browser (useful for librarians who lack access to command line tools).
Also involved were Dr Nick Hamilton from the IMB/RCC who worked on coding (and took photos), and Mitch Stanton-Cook and Tom Robinson from Scott Beatson’s Lab in UQ’s School of Chemistry and Molecular Biosciences. Mitch and Tom worked on a bioinformatics project and gave helpful advice to the Library Carpentry team.

The highlight of the RCC-hosted ‘sprint’ was the pistachio and pomegranate cake that Belinda made. Its picture was retweeted and favourited many times on Twitter, and earned Brisbane a ‘BEST.SITE.EVER’ tweet from @MozillaScienceLab.

L–R: Belinda Weaver and Thea Koutsoukis are joined virtually by Mozilla Global Sprinters in Auckland, Melbourne, and Vancouver.

Thea Koutsoukis, Belinda Weaver and Helen Morgan.
L–R: Thea Koutsoukis, Belinda Weaver and Helen Morgan.

Tom Robinson and Mitch Stanton-Cook.
L–R: Tom Robinson and Mitch Stanton-Cook.

Brisbane's Mozilla Global Sprint cake

Belinda Weaver's pistachio and pomegranate cake stole the show. All photos were taken by Dr Nick Hamilton, RCC/IMB.

RCC Director rides for MS

Through participating in a charity 100km bike ride on Sunday,  21 June, RCC Director Prof David Abramson has raised more than $2,700 to support people living with multiple sclerosis. 

David rode in the 25th anniversary of the Enerflex MS Brissie to the Bay event, from Brisbane's South Bank to Wellington Point and back. 

At the time of writing, David had raised $2,758. The event overall aims to raise $1.6m, and is thus far only about $76,000 from its target.

It's not too late to support David's efforts and the multiple sclerosis charity. Visit his fundraising webpage to donate.

L–R: RCC's David Abramson with QCIF CEO Rob Cook after their 100km charity bike ride for multiple sclerosis.
people and technology

What's On

NCI-run training for UQ HPC users, 29–30 June, UQ St Lucia. More info
Statistics for Frightened Bio-Researchers, 29 June, 13 July & 27 July, IMB. More info
Software carpentry workshop, 2–3 July, UQ St Lucia. More info
UQ Winter School in Mathematical & Computational Biology, 6–10 July, UQ St Lucia. More info
Kepler workshop, 14 July, UQ St Lucia. More info
FlashLite half-day workshop, date TBC, UQ St Lucia. More info
Dr Nick's Image Clinic, most Monday mornings, for IMB researchers and held, by Dr Nick Hamilton, at IMB.
SC15, The International Conference for HPC, Networking, Storage & Analysis, 15–20 Nov, Austin, Texas. More info
Coming soon...
RCC's semester two seminar program. Check @RCCUQ for more info.

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