Tag Archives: Research Stories

VISIONET on R@CMon (Update)

Back in early 2014, the R@CMon team assisted SBI Australia to deploy the VISIONET (Visualizing Transcriptomic Profiles Integrated with Overlapping Transcription Factor Networks) visualisation web service on the Monash node of the NeCTAR Research Cloud. Since then, VISIONET has been further enhanced to support more complex transcription factor network topologies. To date, VISIONET has been published in two papers.

Nim, H.T., Boyd, S.E., and Rosenthal, N.A. (2014). Systems approaches in integrative cardiac biology: Illustrations from cardiac heterocellular signalling studies. Progress in Biophysics and Molecular Biology 117, 69-77.

Nim, H.T., Furtado, M.E., Costa, M.W., Rosenthal, N.A, Kitano, H., and Boyd, S.E.. (2015). VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery. BMC Bioinformatics.

The R@CMon team will continue supporting SBI Australia with its plan to further develop the VISIONET web service this year.

Stock Price Impact Models Study on R@CMon Phase 2 (Update)

A mere six months ago Paul Lajbcygier and his research group used R@CMon Phase 2 “specialist kit” for processing and analysing higher frequency stock data, as part of their stock price impact models study. Since then, they’ve been running extraction queries continuously and recently published a paper highlighting their latest findings while acknowledging the NeCTAR Research Cloud infrastructure.

Lajbcygier, P., Sojka, J. (2015). The Viability of Alternative Indexation when including all Costs”, International Review of Financial Analysis

The group will continue to use the high-memory instance on R@CMon Phase 2 as they progress their research pipeline and the R@CMon team will continue to support them on their journey.

“I expect that over the coming months we will fully utilise the generous resources on the Monash node of the NeCTAR  Research Cloud as we extend our research into this cutting edge and exciting data intensive topic.”

Associate Professor Paul Lajbcygier
Faculty of Business and Economics
Department of Accounting and Finance
Department of Banking and Finance
Monash University

Rail Network Catastrophe Analysis on R@CMon

Monash University, through the Institute of Railway Technology (IRT), has been working on a research project with Vale S.A., a Brazilian multinational metals and mining corporation and one of the largest logistical operators in Brazil, to continuously monitor and assess the health of the Carajás Railroad Passenger Train (EFC) mixed-use rail network in Northern Brazil. This project will identify locations that produce “significant dynamic responses” with the aim for proactive maintenance to prevent catastrophic rail failure. As a part of this project, IRT researchers have been involved in (a) the analysis of the collected data and (b) the establishment of a database with visualisation capabilities that allows for the interrogation of the analysed data.
irt-vale-vis-01

GPU-powered DataMap analysis and visualisation on R@CMon.

Researchers use the DataMap analysis software for data interrogation and visualisation. DataMap is a Windows-based client-server tool that integrates data from various measurements and recording systems into a geographical map. Traditionally they have the software running on a commodity laptop with a dedicated GPU connecting to their database server. To scale to larger models, conduct more rigorous analysis and visualisation, as well as support remote collaboration, the system of tools needed to go beyond the laptop.
The R@CMon team supported IRT in deploying the software on the NeCTAR Research Cloud. The deployed instance runs on the Monash-licensed Windows flavours with GPU-passthrough to support DataMap’s DirectX requirements.
irt-vale-vis-02

GPU-powered DataMap analysis and visualisation on R@CMon.

Through the Research Cloud IRT researchers and Vale S.A. counterparts are able to collaborate for modelling, analysis and results using remote access to the GPU-enabled virtual machines.
“The assistance of R@CMon in providing virtual machines that have GPU support, has been instrumental in facilitating global collaboration between staff located at Vale S.A. (Brazil) and Monash University (Australia).”
Dr. Paul Reichl
Senior Research Engineer and Data Scientist
Institute of Railway Technology

3D Stellar Hydrodynamics Volume Rendering on R@CMon Phase 2

Simon Campbell, Research Fellow from the Faculty of Science, Monash University has been running large-scale 3D stellar hydrodynamics parallel calculations on the Magnus super computing facility at iVEC and Raijin, the national peak facility at NCI. These calculations aim to improve 1D modelling of the core helium burning (CHeB) phase of stars using a novel multi-dimensional fluid dynamics approach. The improved models will have significant impact on many fields of astronomy and astrophysics such as stellar population synthesis, galactic chemical evolution and interpretation of extragalactic objects.

The parallel calculations generate raw data dumps (heavy data) containing several scalar variables, which are pre-processed and converted into HDF5. A custom script is used to extract the metadata (light data) into XDMF format, a standard format used by HPC codes and recognised by various scientific visualisation applications like ParaView and VisIt. The stellar data are loaded into VisIt and visualised using volume rendering. Initial volume renderings were done on a modest dual core laptop using just low resolution models (200 x 200 x 100, 106 zones). It’s been identified that applying the same visualisation workflow on high resolution models (400 x 200 x 200, 107 zones and above), would require a parallel (MPI) build of VisIt running on a higher performance machine.

Snapshot of turbulent convection deep inside the core of a star, volume-rendered using parallel VisIt.

Snapshot of turbulent convection deep inside the core of a star that has a mass 8 times that of the Sun. Colours indicate gas moving at different velocities. Volume rendered in parallel using VisIt + MPI.

R@CMon Phase 2 to the rescue! The timely release of R@CMon Phase 2 provided the required computational grunt to perform these high resolution volume renderings. The new specialist kit in this release includes hypervisors housing 1TB of memory. The R@CMon team allocated a share (~50%, ~460GB of memory) on one of these high memory hypervisors to do the high resolution volume renderings. Persistent storage on R@CMon Phase 2 is also provided on the computational instance for ingestion of data from the supercomputing facilities and generation of processing and rendering results. VisIt has been rebuilt on the high-memory instance, this time with MPI capabilities and XDMF support.

Initial parallel volume rendering using 24 processes shows a ~10x speed-up. Medium (400 x 200 x 200, 107 zones) and high-resolution (800 x 400 x 400, 108 zones) plots are now being generated using the high-memory instance seamlessly, and an even higher resolution (1536 x 1024 x 1024, 109 zones) simulation is currently running on Magnus. The resulting datasets from this simulation, which are expected to be several hundred gigabytes in size, will then be put in the same parallel volume rendering workflow.

Stock Price Impact Models Study on R@CMon Phase 2

Paul Lajbcygier, Associate Professor from the Faculty of Business and Economics, Monash University is studying one of the important changes that affects the cost of trading in financial markets. This change relates to the effects of trading to prices, known as “price impact”, which is brought by wide propagation of algorithmic and high frequency trading and augmented by technological and computational advances. Professor Lajbcygier’s group has recently published new results supported by R@CMon infrastructure and application migration activities, providing new insights into the trading behaviour of so-called “Flash Boys“.

This study uses datasets licensed from Sirca and represents stocks in the S&P/ASX 200 index from year range 2000 to 2014. These datasets are pre-processed using Pentaho and later ingested into relational databases for detailed analysis using advanced queries. Two NeCTAR instances on R@CMon have been used initially in the early stages of the study. One of the instances is used as the processing engine where Pentaho and Microsoft Visual Studio 2012 are installed for pre-processing and post-processing tasks. The second instance is configured as the database server where the extraction queries are executed. Persistent volume storage is used to store reference datasets, pre-processed input files and extracted results. A VicNode merit application for research data storage allocation has been submitted to support the computational access to the preprocessed data supporting the analysis workflow running on the NeCTAR Research Cloud.

Ingestion of pre-processed data into the database running on the high-memory instance, for analysis.

Ingestion of pre-processed data into the database running on the high-memory instance, for analysis.

Initially econometric analyses were done on just the lowest two groups of stocks in the S&P/ASX 200 index. Some performance hiccups were encountered when processing higher frequency groups in the index – some of the extraction queries, which require a significant amount of memory, would not complete when run on the exponentially higher stock groups. The release of R@CMon Phase 2 provided the analysis workflow the capability to attack the higher stock groups using a high-memory instance, instantiated on the new “specialist” kit. Parallel extraction queries are now running on this instance (close to 100% utilisation) to traverse the remaining stock groups from year range 2000 to 2014.

A recent paper by Manh Pham, Huu Nhan Duong and Paul Lajbcygier, entitled, “A Comparison of the Forecasting Ability of Immediate Price Impact Models” has been accepted for the “1st Conference on Recent Developments in Financial Econometrics and Applications”. This paper highlights the results of the examination of the lowest two groups of the S&P/ASX 200 index, i.e., just the initial results. Future research and publications include examination of the upper group of the index based on the latest reference data as they come available and analysis of other price impact models.

This is an excellent example of novel research empowered by specialist infrastructure, and a clear win for a build-it-yourself cloud (you can’t get a 920GB instance from AWS). The researchers are able to use existing and well-understood computational methods, i.e., relational databases, but at much greater capacity than normally available. This has the effect of speeding up initial exploratory work and discovery. Future work may investigate the use of contemporary data-intensive frameworks such as Hadoop + Hive for even larger analyses.

This article can also be found, published created commons here 1.