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RCC News: June 2015

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Welcome to RCC News!

This is the first of our regular new-look e-newsletters. Through this we'll keep you up-to-date with new seminars and training sessions, and anything else that's happening in the Research Computing Centre (RCC) that's new and could be of interest to you. 

RCC team
The RCC team

New FlashLite HPC coming soon

As of 18 March 2015, the contract for the purchase of FlashLite was finalised and the purchase order was raised, and is currently being installed. 

FlashLite, a new High Performance Computer for Australian researchers, was funded by an ARC LIEF grant and built by HPC specialist XENON Systems. It has been designed to support data intensive science, and incorporates special features to allow researchers to process very large amounts of data.

We anticipate a multi-month delivery period due to the specialised nature of some of the components. 

A further acceptance testing period and configuration will also be necessary. At this time, and not withstanding any major delays, we expect FlashLite will be in place and operating by late June and users to be able to login by early July 2015.

We will be sending 
details on how to apply for a FlashLite account. RCC Director David Abramson will run some information sessions to help you decide if FlashLite is right for your research problems.

FlashLite Fact Sheet

XENON's Werner Scholz and RCC Director Prof David Abramson
On Wednesday, 27 May, XENON Chief Technology Officer Werner Scholz (left) and RCC Director Prof David Abramson visited FlashLite's new base in Brisbane. 

FlashLite in the national media

News about FlashLite was syndicated across Fairfax Media's metropolitan newspaper websites, including The Age, Sydney Morning HeraldBrisbane Times, Canberra Times and WA Today

The news of FlashLite's imminent arrival also featured on IT media sites ZDNet and ITWire, and in technology business reports Communications Day and the Rust Report

Barrine fights on!

In response to user feedback, Barrine will continue to operate at least until the end of 2015. To do this, however, the Barrine cluster must be reconfigured in mid-2015. 

The emphasis of this extension to its useful life is for multi-node (MPI) codes. A limited suite of software applications will be available. RCC will alert users regarding any interruptions to the Barrine service.

More info about making the transition from Barrine HPC

RCC seeks UQ researchers to test "virtual" cluster

RCC is currently developing a cluster-in-the-cloud which will provide additional computational resources to UQ researchers. Specifically, it will assist those who are transitioning from the current high performance cluster on campus, Barrine.

These cloud-based resources (built on NeCTAR QRIScloud) will be well suited to single CPU/small memory footprint jobs, typically in the vicinity of 8CPUs.  Whilst this virtual cluster is smaller than Barrine is (in available cores, node memory and attached storage), and has less inter-node communication bandwidth, it will augment existing facilities, including the National Compute Infrastructure (NCI) and RCC's new computer, FlashLite. It can also be scaled elastically in the future.

We are seeking current or former Barrine users who would like to test the suitability of using a virtual cluster resource in their work. If you are interested, please email:

RCC employee awarded fellowship

Marlies Hankel

RCC/QCIF eResearch Analyst Dr Marlies Hankel (pictured left) was awarded a UQ Promoting Women Fellowship last year, which she is undertaking this year. 

The fellowship aims to support more women in reaching higher level positions. It provides funding for time release for one semester to allow the applicant to focus on a specific project. 

Marlies’ application was based on her 50% employment with RCC/QCIF (she also works with the Australian Institute for Bioengineering and Nanotechnology), and to be released from her RCC/QCIF duties to write up a current research project for publication in August/September this year. 

Her research project is titled: ‘Advanced anode and cathode materials for lithium ion batteries’. She is using computational modelling to investigate the lithium uptake in several novel porous carbon membranes and assess their suitability as lithium ion battery anode materials.

Discussing genomes over lunch

The second RCC Genomic Postdoc Engagement Lunch, run by RCC/IMB's Dr Nick Hamilton, was held on Friday, 8 May. These monthly lunches are a great way for early-career genomics researchers to share ideas in an informal setting. 

RCC Genomic Postdoc Engagement Lunch
L-R: Cheong-Xin Chan, Lauren Walsh, Ben Woodcroft, Mike Imelfort and Tim Lamberton at the 2nd RCC Genomics Postdoc Engagement Lunch (not shown, Selene Fernandez Valverde.)

RCC and ITEE sponsor UQ students to visit Uni of California, San Diego 

The RCC and ITEE sponsored three UQ undergraduate students to visit the University of California, San Diego earlier this year for a two-month stay.

Alexia Lee and Zinta Flodine undertook project work within the University's Temporal Dynamics of Learning Center (TDLC), and Troy Smith worked within the San Diego Supercomputer Center

The students were sponsored as part of the Queensland Undergraduate Research Projects Abroad (QURPA) program. RCC and ITEE (UQ's School of IT & Electrical Engineering) launched QURPA in 2013, for UQ IT students to travel to international research institutions for a period of eight weeks to integrate into research groups as team members.

Students Alexia and Zinta wrote the following trip report (please note that iRat is a rat animat robot), and Troy's trip report is further below. 

The iRat project
Alexia Lee and Zinta Flodine

Travelling to San Diego as undergraduate researchers was an invaluable experience, both in terms of furthering personal/professional development and the iRat project.

Our current work focuses on giving the iRat social behaviours, making it a more effective tool for social interaction studies. I worked on a program that uses computer vision to enable the iRat to follow a rat. This trip has shifted my perspective on many issues, including why interdisciplinary work is critical, what constitutes a good robot and why embodied agents are necessary. 

My purpose in San Diego was to gain tools for analysing rat-iRat interactions by involvement in running experiments and collaboration with the expertise of the Chiba lab. The experience further exposed me to research culture and enabled me to interact with and learn from a diverse range of scientists within TDLC and UCSD.

We would both like to thank you [RCC and ITEE] for providing us with this valuable opportunity.

UQ students Zinta Flodine and Alexia Lee meet TDLC's Dr Deborah Forster

Zinta Flodine (purple jumper) and Alexia Lee (blue shirt) meet TDLC's Dr Deborah Forster (centre) and the robot RUBI at the TDLC annual research meeting.

Earth sciences applications
Troy Smith

For my QURPA placement, I spent two months working at the San Diego Supercomputer Center at the University of California, San Diego, with Yifeng Cui as my mentor, to use supercomputers in earth sciences applications in the form of two projects. 

The first project entailed working on earthquake forward modelling code developed at SDSC, which uses GPU code and custom IO libraries to predict the effects of earthquakes, then output the data from the model into a strain tensor for use in engineering. 

The key achievement from this project was in implementing attenuation effects into the existing model to account for changes in energy in the seismic waves propagating through the earth.  

The second project was to install the Monash-developed geodynamic program Underworld onto the [supercomputer] Gordon cluster and perform benchmarking tests to evaluate how it performs on larger clusters. The tests were run on up to 128 nodes, or 2048 cores, significantly higher than previous published performance tests.  The code was very efficient until more than 64 nodes were used, after which, the performance improvements effectively flattened out.

There was also still time to enjoy southern California. The housing for the duration of the program was at the International House, which featured a vibrant community of local and international students. It was rare to find anyone who didn’t understand a second language, or anyone who didn’t show genuine interest in research work. 

The social life is very active, with regular language tables and region-themed events put on by I-House, and other social activities organised by international students and visiting scholars. This included Superbowl parties on campus, museum trips, movies in the San Diego region and camping trips further afield, the highlight of which was a road trip to the spectacular Yosemite National Park.

Overall, the time at UCSD was a great learning experience for coding, HPC and collaborating with other disciplines, supported by a great social community outside of the lab. The next trip to San Diego can’t come soon enough.

UQ student Troy Smith in California's Yosemite National Park with fellow International House students
UQ student Troy Smith (back left) in California's Yosemite National Park with fellow students from the University of California, San Diego 
International House.

people and technology

What's On

Hands-on HPC session for UQ staff/students, 29 May, UQ St Lucia Campus. Email
Dr Nick's Image Clinic, most Monday mornings, for IMB researchers and held, by Dr Nick Hamilton, at IMB.
Mozilla Science Global Sprint, 4–5 June, global. Register | More info
Statistics for Frightened Bio-Researchers, 29 June, 13 July & 27 July, IMB. More info
NCI-run training for UQ HPC users, 29 June, UQ St Lucia. More info
FlashLite half-day workshop, 1 July, UQ St Lucia. 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
SC15, The International Conference for HPC, Networking, Storage & Analysis, 15–20 Nov, Austin, Texas. More info

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