National Computational Infrastructure

NCI

Video Gallery

  • NCI’s data and compute expertise have played an integral role in a recently launched website that provides easy access to a wide range of environmental data covering the entire country. The data covers measurements from precipitation and river flows to tree cover and bushfire intensity.

    The website can overlay data from several different satellites on top of a map of Australia, showing variability across the country and how that has changed over the past 16 years. At the start of every year, the previous year’s data will be added to the site, providing up to date coverage of key environmental variables.

    See the website: http://wenfo.org/aus-env/#/

  • Chloe Jian Ma of Mellanox Technologies and NCI’s Manager of HPC Systems and Cloud Services Dr Muhammad Atif present “Chasing The Rainbow” at the 2016 OpenStack Summit in Austin, Texas.

    In this presentation, NCI and Mellanox join hands to discuss the various approaches experimented to construct a high-performance cloud, comparison of the pros and cons of each of the approaches, preliminary performance results, and the role of high-speed network for enhancing cloud performance and efficiency.

     

  • NCI’s HPC Systems Administrator Andrew Howard presents “Pursuit of High-Performance in OpenStack Clouds”.

    NCI has created platforms which combine the flexibility of OpenStack Cloud provisioning with both high speed Ethernet and high performance InfiniBand fabrics to deliver a union of compute and I/O which challenges traditional HPC performance.

  • Modelled topography of the eastern Australian highlands since 150 million years ago. The model is based on a coupled plate tectonic-mantle convection model run on the Australian high performance computer Raijin (http://nci.org.au/systems-services/na…). The model shows that the time-dependent interaction of plate motion with mantle downwellings and upwellings accounts for the broad pattern of margin uplift phases. Initial dynamic uplift of 400-600 m from 120-80 Ma was driven by the eastward motion of eastern Australia’s margin away from the sinking eastern Gondwana slab, followed by tectonic quiescence to about 60 Ma in the south (Snowy Mountains). Renewed uplift of ~700 m in the Snowy Mountains is propelled by the gradual motion of the margin over the edge of the large Pacific mantle upwelling. In contrast the northernmost portion of the highlands records continuous uplift from 120 Ma to present-day totalling about 800 m. The northern highlands experienced a continuous history of dynamic uplift, first due to the end of subduction to the east of Australia, then due to moving over a large passive mantle upwelling. In contrast, the southern highlands started interacting with the edge of the large Pacific mantle upwelling ~40-50 million years later, resulting in a two-phase uplift history. Our results are in agreement with published uplift models derived from river profiles and the Cretaceous sediment influx into the Ceduna sub-basin offshore southeast Australia, reflecting the fundamental link between dynamic uplift, fluvial erosion and depositional pulses in basins distal to passive margin highlands.

  • A fascinating look at how the Canberra landscape has changed over the last three decades.

    This video contains 108 images of the Canberra region taken by the USGS/NASA Landsat satellites between 1987 and 2014.

    The video highlights green vegetation on the ground so differences between seasons and rainy periods stand-out. Look out for the impact of the 2003 bushfire.

  • Andrew Howard, HPC Systems Administrator at NCI, presents Project InfiniCloud.

    InfiniCloud is an application platform which combines the high speed InfiniBand communications capabilities of High Performance Computing (HPC) with the flexibility of an Openstack Cloud deployment.

     

  • HPC Systems and Cloud Services Manager Dr Muhammad Atif presents ‘Implementation of a high performance scientific cloud backed by Dell hardware’ at the Dell booth during SC14.

  • Cloud Services Manager Joseph Antony speaks about NCI’s Lustre infrastructure at the Lustre Developer Conference in September 2013.

  • NCI Cloud Services Manager Joseph Antony discusses the future of supercomputing at the 2013 Supercomputing Conference in Denver.

  • … and you thought HPC virtualisation was never going to happen.

    In this video from from the Dell booth at SC13, Rich Brueckner from insideHPC moderates a panel on the topic of HPC Virtualization.

    Panelist include:
    Brad Dispensa, University of California, San Francisco
    Jim Wilgenbush, Florida State University
    Paul Calleja, Cambridge University
    Brett Zimmerman, University of Oklahoma
    Joseph Antony, NCI

    “HPC clusters have become a cornerstone for many scientific fields including some we’d never expected, such as biology. Virtualization is essential to a vast new era of systems and has (with some hype) given birth to ‘The Cloud’. The two are not necessarily incompatible and work is being done to bring benefits that enterprise users of virtualization enjoy to the HPC arena where — despite years of experience — we still battle with the challenge that large scale computing presents. This panel will challenge old notions, update you on current activities and provoke a debate about what’s needed for the future.”

  • SC13: Showcasing Australian HPC

    In November 2013 representatives from Australian High Performance Computing centres attended SC13 in Denver, Colorado.

    Hosting a booth that features daily ‘Tim Tam Talks’ and iconic Aussie giveaways the Australian HPC booth brings local expertise to the world stage.

    This video showcases scientific visualisations and world-class research taking place at the following organisations:
    NCI
    iVEC
    VLSCI
    V3 Alliance
    MASSIVE
    LaTrobe University
    RMIT
    CAS, Swinburne
    CSIRO

  • NCI in Australia powers research with PBS Pro on the Raijin supercomputer

    This video, filmed at SC13 in Denver is an interview by Rich Brueckner from InsideHPC.

    NCI Director Professot Lindsay Botten and Associate Director Allan Williams describe the mission of their nationwide research organization and how they use Altair PBS Pro to manage job workloads on the 1 Petaflop Raijin supercomputer.

  • Data recall — Demonstration of NCI tape library

    In conjunction with short term and persistent disk storage, NCI has three Spectra Logic T950 libraries, the largest having eight frames — as seen in this video. There are 33 drives in the eight frame library with each drive able to recall up to 140MB/second.

    The storage system consists of multiple tape libraries using LTO-5 media (1.5-3.0 TB each), packed into groups of ten tapes per TeraPack.  With 952 TeraPack slots, this library is capable of holding 9520 tapes, storing between 13.9 uncompressed and 28.5 compressed Petabytes of data. Each tape is up to 850m in length, with a thickness of 6.4µ.

    The time taken for the system to deliver data after a user request can vary. Although communication to the library is instantaneous, recall time is dependent upon the location of the robot that retrieves tapes, availability of a free tape drive, and the location of the data stored on the 800m plus length of tape. i.e. if the data requested is stored toward the end of a tape, the drive must spool through the length before being able to access the target data. Typically, this delivery occurs between 30 seconds to a few minutes.

  • Simulation of 2004 Boxing Day tsunami – Patong beach

    The 2004 Indian Ocean earthquake occurred off the west coast of Sumatra, Indonesia.

    The quake triggered a series of devastating tsunamis along the coast of most of the landmasses bordering the Indian Ocean, inundating coastal communities with waves up to 30 meters.

    This simulation shows the tsunami hitting Patong Beach, one of the worst affected areas of Phuket, Thailand.

    The underlying model used to generate the scenario is the ANUGA hydrodynamic model which is a free and open source software tool, suitable for predicting the consequences of hydrological disasters such as riverine flooding, storm surges and tsunamis.

    More information about the software is available: http://en.wikipedia.org/wiki/ANUGA_Hydro

    Scientific visualisation by NCI VizLab’s Drew Whitehouse.

  • Jet driven feedback in galaxy formation

    These four movies, from simulations by Wagner et al. (2012), show the density (D density.mov and Dprimed density.mov) and velocity (D vclouds.mov and Dprimed vclouds.mov) of the jet and interstellar medium as a powerful (10 to the power of 38 Watt) jet forces its way through a field of dense inhomogeneous clouds, embedded in the hot interstellar medium, surrounding the nucleus of an active galaxy containing a black hole. These movies are made from slices through the mid-plane of a 3D volume.

    The jet is launched from the environs of the black hole and forces its way through the clouds driving them out from the galactic nucleus. At the same time the jet is deflected in different directions by the clouds and in both cases inflates a large spherical bubble in the interstellar medium. This is an important effect since before this work had been done, it had been assumed that jets would not have a significant influence on the entire interstellar medium of the galaxy.

    Click here to read the full publication

  • The visible male project

    This video was created by NCI Vizlab’s Ajay Limaye using data from the Visible Human Project.

    The Project is an effort to create a detailed data set of cross-sectional photographs of the human body, in order to facilitate anatomy visualisation applications. A male and a female cadaver were cut into thin slices which were then photographed and digitized. This video shows the males head.

    The male cadaver, a 38-year-old Texas murderer who was executed by lethal injection, was encased and frozen in a gelatin and water mixture in order to stabilize the specimen for cutting. The specimen was then “cut” in the axial plane at 1 millimeter intervals. Each of the resulting 1,871 “slices” were photographed in both analog and digital, yielding 15 gigabytes of data.

    The project is run by the U.S. National Library of Medicine (NLM) under the direction of Michael J. Ackerman. Planning began in 1989; the data set of the male was completed in November 1994 and the one of the female in November 1995.

    http://www.nlm.nih.gov/research/visible/

  • Visible Human Project

    This video was created by NCI Vizlab’s Ajay Limaye using data from the Visible Human Project.

    The Project is an effort to create a detailed data set of cross-sectional photographs of the human body, in order to facilitate anatomy visualisation applications. A male and a female cadaver were cut into thin slices which were then photographed and digitized. This video shows the males leg.

    The male cadaver, a 38-year-old Texas murderer who was executed by lethal injection, was encased and frozen in a gelatin and water mixture in order to stabilize the specimen for cutting. The specimen was then “cut” in the axial plane at 1 millimeter intervals. Each of the resulting 1,871 “slices” were photographed in both analog and digital, yielding 15 gigabytes of data.

    The project is run by the U.S. National Library of Medicine (NLM) under the direction of Michael J. Ackerman. Planning began in 1989; the data set of the male was completed in November 1994 and the one of the female in November 1995.

    http://www.nlm.nih.gov/research/visible/

  • Hypothetical Inundation Model

    This inundation model was developed as part of the Catastrophic Disasters Working Group activity in 2005 by the Attorney Generals Department and Geoscience Australia for the then Australian Emergency Management Committee.

    The event is entirely hypothetical and was put in place for discussion of response to catastrophic scenarios only.

    The underlying model used to generate the scenario is the ANUGA hydrodynamic model which is a free and open source software tool, suitable for predicting the consequences of hydrological disasters such as riverine flooding, storm surges and tsunamis.

    More information about the software is available: http://en.wikipedia.org/wiki/ANUGA_Hydro

    Scientific visualisation by NCI VizLab’s Drew Whitehouse.

  • Development of a mouse lung

    Morphogenesis is the biological process that causes an organ to develop its shape.

    Many developmentally important genes are proposed to influence branching morphogenesis, but without bespoke methods to accurately quantify the complex spatial data sets that describe it, scientists had have no way of objectively assessing their individual contributions to this process.

    This scientific visualisation by NCI Vizlab’s Ajay Limaye shows a developing mouse lung. The study ‘Spatial mapping and quantification of developmental branching morphogenesis’ was carried out by Kieran Short, Mark Hodson and Ian Smyth.

    Their technical advance provides a crucial resource that will enable rigorous characterisation of the genetic and environmental factors that regulate this essential and evolutionarily conserved developmental mechanism.

    Read the full article in the January 2013 issue of Development:http://bit.ly/176HbQF

  • Sea Urchin Fossil

    The object of the imaging study was to non-invasively dissect the jaw and tooth structure
    from the sediment and to re-assemble the different structures of the jaw in order to
    improve understanding of the mechanical function of the structure and of the
    evolution of modern sea urchins.

    Scientific visualisation by NCI VizLab’s Ajay Limaye using Drishti software, based on research by Stuart R. Stock, Feinberg School of Medicine Northwestern University Chicago; Graham R. Davis, QMUL; and Andrew B. Smith, Natural History Museum London.

  • Whale cochlear fossil

    This scientific visualisation of a whale cochlear fossil was created by Ajay Limaye from NCI Vizlab using Drishti software.

    The dataset for this clip was provided by Professor Tim Senden from the ANU Department of Applied Mathematics.

    http://physics.anu.edu.au/people/prof…

    Drishti is a Volume Exploration and Presentation Tool supported by the National eResearch Collaboration Tools and Research (NeCTAR) project.

  • Digital Rock

    Innovation combining supercomputing with high-resolution 3D scanning of oil-bearing rocks, such as the Mt Gambier sandstone shown in this clip, won Digitalcore the 2012 Rio Tinto Eureka Prize for Commercialisation of Innovation.

    Until countries develop sustainable green energy supplies, oil and gas are required to power our daily activities. To improve the mining of these finite resources, Digitalcore devised technology that illustrates how oil and gas flow through different rocks, in turn enabling more effective extraction of these hydrocarbons from the earth.

    This scientific visualisation is by Ajay Limaye, NCI Vizlab.

    Digitalcore was formed in 2009 and includes Dr Victor Pantano as Chief Executive Officer, Professor Mark Knackstedt as Chief Technology Officer, Professor Tim Senden and Dr Adrian Sheppard from the Research School of Physics and Engineering at the ANU, and Professor Val Pinczewski and Associate Professor Christoph Arns from the School of Petroleum Engineering at UNSW.

    Read more about the project here: http://eureka.australianmuseum.net.au/E5AEB3F0-95D5-11E1-BC26005056B06558?DISPLAYENTRY=true

    Drishti is a Volume Exploration and Presentation Tool supported by the National eResearch Collaboration Tools and Research (NeCTAR) project.

  • Starburst-driven galactic wind

    Starburst galaxies are galaxies that are observed to be forming stars at an unusually fast rate.

    This clip shows simulated formation of the filaments observed in starburst galaxies such as M82. The combined power from supernovae in the starburst at the galaxy’s centre drives out a fast, hot wind from the galactic disk. Cool, dense gas is swept into this wind forming filaments than can be seen at ionized wavelengths.

    In this visualisation, only gas from the cloudy galactic disk is seen. The top left quadrant shows the filaments of ionized hydrogen forming in one hemisphere of a galaxy over a period of 4 million years. As the hot wind forms in the galaxy’s centre, gas from these clouds are entrained into the wind. The top right and bottom left quadrants show the temperature and density respectively of this gas on a log10 scale.

    While the hot wind that creates the filaments is tenuous and has temperatures of the order of 10 million degrees Kelvin, the filamentary material is dense and relatively cool at 10,000 K. The bottom right quadrant shows the magnitude of the velocity of the filamentary gas. The gas accelerates as it is drawn into the outflow and reaches speeds of up to 800 km/s.

    Scientific visualisation by Drew Whitehouse, NCI Vizlab from research carried out by Professor Geoff Bicknell: http://www.mso.anu.edu.au/~geoff/ and Dr Jackie Cooper.

  • Rain patterns near Darwin

    This animation shows the results from high-resolution simulations of convective clouds near Darwin, Australia. The simulation is of a period during a major international field experiment: The Tropical Warm Pool International Cloud Experiment (TWP-ICE), which was held in January-February 2006. The simulations use the Weather Research and Forecasting (WRF) model and represent the atmosphere using a series of nested grids; the highest resolution grid has a horizontal grid spacing of 417 m. The simulations were performed at the National Computational Infrastructure (NCI) Facility in Canberra.

    These particular simulations are reported in a new paper that appeared in the peer-reviewed journal Monthly Weather Review in 2013. This study describes new methods to compare cloud model simulations to radar observations. The work shows that many aspects of the simulated convection are realistic and agree with the observations, but it also better quantified some of the errors in the depth and intensity of the simulated thunderstorms.

    These simulations, along with many others, are being used by the ARC Centre of Excellence for Climate System Science researchers to understand the processes controlling the diurnal cycle of deep convection in the tropics, and the mechanisms by which clouds become organised into long-lived propagating systems. This work should lead to improved representation of clouds and thunderstorms in weather prediction and climate models.

    Scientific visualisation by Stuart Ramsden NCI Vizlab.

    Read the full paper:

    Caine, Simon, Todd P. Lane, Peter T. May, Christian Jakob, Steven T. Siems, Michael J. Manton, James Pinto, 2013: Statistical Assessment of Tropical Convection-Permitting Model Simulations Using a Cell-Tracking Algorithm. Mon. Wea. Rev., 141, 557–581.

    http://dx.doi.org/10.1175/MWR-D-11-00…

  • Dolicho: the tiny teak saviour

    In south-east Asia, teak is the most widely grown and economically important native forest plantation species and is the source of most commercial wood products.

    Ever since this tree was identified as an important timber species, its commercial development in plantations in the Indian region has been severely hindered by outbreaks of the moth Hyblaea puera (Cramer) (Lepidoptera: Hyblaeidae), a ‘teak defoliator’ whose caterpillar strips the tree of leaves.

    The most serious impact of defoliation is the reduction of volume increment, and H. puera can cause losses of up to 44% of the potential harvest.

    To reduce this impact, biological control through the use of natural enemies was introduced. One focus of this research was the assessment of local parasites.

    Until 1996, one species of wasp, Sympiesis, was still undescribed. It was found to be the most promising of the parasites, attacking the first and second instar larvae.

    This visualisation is of the wasp Sympiesis dolichogaster (Family Eulophidae). Only 2mm in length, this tiny creature can bring over 30% of the moths population under control.

    Scientific visualisation by Ajay Limaye NCI Vizlab using Drishti. Image courtesy of John LaSalle.

    Read the full paper,  A new species of Sympiesis (Hymenoptera: Eulophidae) parasitic on the teak defoliator Hyblaea puera (Lepidoptera: Hyblaeidae) in India, here:

    http://journals.cambridge.org/download.php?file=%2FBER%2FBER86_01%2FS0007485300052226a.pdf&code=50081d31f2e1846c5eecd461067b11c3

    Drishti is a Volume Exploration and Presentation Tool supported by the National eResearch Collaboration Tools and Research (NeCTAR) project.

  • The path of earthquakes through the Earth’s inner core

    This video shows the effect of seismic ray-paths caused by large earthquakes on the Earth’s inner core. The recordings were taken on globally distributed seismic stations.

    Dr Hrvoje Tkalčić is a Fellow in Seismology in the ANU Research School of Earth Sciences. He is engaged in a further proliferation of seismic instruments and data in Australia, which will establish a solid basis for studying Earth’s structure, as well as seismic sources more generally.

    For more information, see: http://rses.anu.edu.au/~hrvoje/

    This visualisation of Dr Tkalčić’s research was done by Rhys Hawkins from NCI Vizlab.

    This clip combines research cited in the following papers:

    Tkalcic H., B. Romanowicz and N. Houy, Constraints on D” structure using PKP(AB-DF), PKP(BC-DF) and PcP-P travel time data from broadband records, Geophys. J. Int. 149(3), 599-616, 2002.

    Tkalcic, H., Large variations in travel times of mantle-sensitive seismic waves
    from the South Sandwich Islands: Is the Earth’s inner core a conglomerate of
    anisotropic domains?, Geophys. Res. Lett., 37, L14312, doi:10.1029/2010GL043841,
    2010.

    Tkalcic, H., Structure and dynamics of the Earth’s inner core, solicited review
    paper in preparation for Reviews in Geophysics, 2013.

  • Eddies in the Southern Ocean

    The ocean is constantly in motion, flowing in general patterns known as currents. When the water spins away from these currents, an eddy is created.

    Eddies abound in the Southern Ocean. This clip shows the absolute field from a year in the Southern Ocean. The large jets spawn a number of eddies which propagate around for months at a time, before being reabsorbed by the jets.

    Despite their small size, these eddies are very significant to the climate of the Southern Ocean. For example, eddies partially control the total ocean circulation around Antarctica, the temporal response of the circulation to change (such as global warming) and the flux of heat towards Antarctica.

    Simulations performed by Isa Rosso, Andreas Klocker and Andy Hogg at The Australian National University Supercomputing Facility using the Ocean General Circulation Model MITgcm.

    Visualisation by Stuart Ramsden, NCI Vizlab.

  • A tour of the global ocean

    This visualisation shows the evolution of sea surface temperatures over a three year period.

    The research was conducted by Paul Spence, Matthew England, Andy Hogg, Marshall Ward and Stephen Griffies for the ARC Centre of Excellence for Climate System Science.

    Scientific visualisation by Stuart Ramsden, NCI VizLab.

  • Airspace structures in mice

    In developing treatments for the airway disease cystic fibrosis, researchers from Adelaide’s Women’s and Children’s Hospital needed to develop a new approach for non-invasive detection of airway health and disease in live mouse models.

    Working with the Monash Centre for Synchrotron Science, they coupled phase-contrast synchrotron X-ray imaging with software written by VizLab’s Ajay Limaye, and a high-resolution, non-invasive image of a mouse was created.

    These images clearly show the morphology and structure of nasal and lung airways and the middle ear in mice, using two- and three-dimensional representations.

    Parsons DW, Morgan KS, Donnelley M, Fouras A, Crosbie J, Williams I, Boucher R, Uesugi K, Yagi N, and Siu KKW (2008), “High Resolution Visualisation of Airspace Structures in Intact Mice Via Synchrotron Phase Contrast X-ray Imaging (PCXI)”, J. Anat., 213 (2), 217-27.

    DOI: 10.1111/j.1469-7580.2008.00950.x

    The full paper is available:

    http://onlinelibrary.wiley.com/doi/10…

    Drishti is a Volume Exploration and Presentation Tool supported by the National eResearch Collaboration Tools and Research (NeCTAR) project.

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