Author Archives: Steve Quenette

2nd place in the SC21 Indy Student Cluster Competition

Six Monash University students have taken 2nd prize in the SuperComputing 2021 Indy Student Cluster Competition (IndySCC).

The IndySCC is a 48 hour contest where students run a range of benchmarking software (this year – HPL and HPCG), well established scientific applications (Gromacs, John The Ripper) and a mystery program (Devito), whilst also keeping power consumption to under 1.1KW. That’s right – even the most advanced digital research infrastructure has meaningful Net Zero aspirations!

The six students – the Student Cluster Team – are part of an undergraduate team called Deep Neuron. Deep Neuron itself is part of a larger group of Engineering Teams that offer a range of extra-curricular activities. DeepNeuron is focused on improving the world through the combination of Artificial Intelligence (AI) and High-Performance Computing (HPC).

“The experience of participating in such a well known competition and the opportunity to collaborate with different students and experts allowed us to learn valuable skills outside of our classroom. We feel privileged and would like to thank all the support from DeepNeuron, supervisors and the faculty”

Yusuke Miyashita, HPC Lead, Deep Neuron

This achievement is even more impressive given that the students have never physically met each other due to covid restrictions. Earlier this year, the students also entered the Asia Supercomputing Community 2021 virtual Student Cluster Competition (ASC21 SCC), where they won the Application Innovation Award (shared with Tsinghua University) for the fastest time for the Mystery Application. That team was led by Emily Trau, who also works as a casual at MeRC.

“Despite the COVID lockdown, the students from Monash University’s Deep Neuron have hit well above their weight, winning significant prizes in two prestigious International Student Cluster Competitions. Well done to all involved”

Simon Michnowicz, Monash HPC team

All teams in the competition were tasked with configuring a resource made available to them on the Chameleon Cloud for each benchmark. Chameleon is similar to the Nectar Research Cloud, in that it provides Infrastructure as a Service to researchers. However Chameleon focus is experiments in edge, cloud and HPC (experiments on the infrastructure itself). The Research Cloud focus is being a resource for, and the instigator of collaboration for all research disciplines. Where Chameleon and the Research Cloud and Monash are particularly similar is being the test bed for new hardware and software technologies pertinent to digital research infrastructure. For example, MASSIVE and Monash’s own MonARCH HPC are built on the Research Cloud.

It is formally the end of the competition. What a journey! You all did an excellent job and we are impressed by how smart, hard-working and dedicated all the teams were. You all deserve a round of applause”

IndySCC21 Chairs Aroua Gharbi and Darshan Sarojini

JohntheRipper cracking passwords

GROMACS simulation of a model membrane

Monash University Joins OpenInfra Foundation as Associate Member

In research, building on the shoulders of others has long meant referencing the contributions of past papers. However, increasingly research-led data & (and the focus here…) tools are more impactful contributions. 

To this end, and after nearly a decade in the making, the eResearch Centre has joined the Open Infrastructure Foundation as an associate member. See the announcement here.

Universities are living laboratories for research-driven infrastructure. They require perpetual & bespoke computing at scale, which when combined, are the killer app for #opensource infrastructure, the associated communities and their practices. 

“Monash University has long believed in the power of using open source solutions to provide infrastructure for research, so it is with great pleasure that we formalize our long relationship and welcome them as a new associate member.”

Thierry Carrez, vice president of engineering at the OpenInfra Foundation, partnership announcement

Over the last decade open data and open source software have established legal entities (foundations) to ensure priorities, quality and sustainability of the data/tool are managed at commercial / real-world levels. Our partnership Open Infrastructure Foundation helps our researchers access tools for their own digital instruments that are in-turn produced, curated and maintained at the rate of global cloud development (across all industries). In this regard we’re amongst a pioneering set of institutions including CERN, Boston University and others. We give back by ensuring our research workloads are driving the community and infrastructure, pushing new technologies and expectations through the ecosystem.

“Open source and in particular the OpenInfra ecosystem is the language by which we craft HPC, highly sensitive, cloud and research data instruments at scale in a way that is closer to research needs, and with access mechanisms that is closer to research practice. We look forward to continued sharing of learnings with the community and pioneering of digital research infrastructure.”

Steve Quenette, Deputy Director of the Monash eResearch Centre, partnership announcement

To provide some indication of impact – 0.5 billion users (including our ~1000 research CIs) using 1.8m servers / 8.4m virtual machines and 4.5m public IP addresses benefit every contribution made by the global community. (From 2020 survey, which is certainly under-reported)

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

Monash University, NVIDIA and ARDC partner to explore the offloading of security in collaborative research applications

Collaboration in the research sector (universities) has an impact on infrastructure that is a microcosm for the future Internet. 

Why is this? Researchers are increasingly connected, increasingly participating in grand challenge problems, and increasingly reliant on technology. Problem solving for big global challenges, as distinct from fundamental research, can involve large-scale human-related data, which is sensitive and sometimes commercial-in-confidence. Researchers are rewarded to be first to discovery. One way to accelerate discovery is to be the “first to market” with disruptive technology. That is, develop the foundational research discovery tool (think software or instrument that provides the unique lens to see the solution, a “21st century microscope” so to speak). If we think of research communities as instrument designers and builders, they must then build the scientific applications that span the Internet (across local infrastructure, public cloud and edge devices). 

What is an example 21st century microscope for a mission-based problem? To prove the effectiveness of an experimental machine learning based algorithm running on an NVIDIA Jetson-connected edge device controlling a building’s battery. It’s informed by bleeding-edge economics theory, participates in a microgrid of power generators (e.g. solar), storage and consumers (buildings) at the scale of a small city, and is itself connected to the local power grid. Through the Smart Energy City project within the Net Zero Initiative we are doing just that.

A tension is observed between mission-based endeavours involving researchers from any number of organisations, and the responsibility for data governance, which ultimately resides with each researcher’s organisation. Contemporary best practices in technological and process controls adds more work to researchers and technology alike, potentially slowing research down. And yet cyber threats are an exponential reality. It cannot be ignored. How do we make it safe and easy for researchers to explore and develop instruments in this ecosystem? How do we create an environment that scales to any number of research missions? 

What is the technological and process approach that enables a globe’s worth of individual research contributions to mission-based problems that will also scale with the evolving cyber landscape?

In February, NVIDIA, Monash University’s eResearch Centre, Monash University’s Cyber Risk & Resilience team and the Australian Research Data Commons (ARDC), commenced a partnership to explore the role DPUs play in this microcosm. Monash now hosts ten NVIDIA BlueField-2 DPUs residing in its Research Cloud, essentially a private cloud, which itself forms part of the ARDC Nectar Research Cloud, Australia’s federated research cloud, which is funded through the National Collaborative Research Infrastructure Strategy (NCRIS). The partnership is to explore the paradigm of off-loading (what is ultimately) micro-segmentation onto DPUs, thus removing the burden of increased security from CPUs, GPUs and top-of-rack / top-of-organisation security appliances. Concurrently Monash is exploring a range of contemporary appliances, microsegmentation software and automations of research data governance.

Steve Quenette, Deputy Director of the Monash eResearch Centre and lead of this project states:

“Micro-segmenting per-research application would ultimately enable specific datasets to be controlled tightly (more appropriately firewalled) and actively & deeply monitored, as the data traverses a researcher’s computer, edge devices, safe havens, storage, clouds and HPC. We’re exploring the idea that the boundaries of data governance are micro-segmented, not the organisation or infrastructures. By offloading technology and processes to achieve security, the shadow-cost of security (as felt by the researcher, e.g. application hardening and lost processing time) is minimised, whilst increasing the transparency and controls of each organisation’s SOC. It is a win-win to all parties involved.”

Dan Maslin, Monash University Chief Information Security Officer:

“As we continue to push the boundaries of research technology, it’s important that we explore new and innovative ways that utilise bleeding edge technology to protect both our research data and underpinning infrastructure. This partnership and the exploratory use of DPUs is exciting for both Monash University and the industry more broadly.”

Carmel Walsh, Director eResearch Infrastructure & Service, ARDC:

“To support research at a national and international level requires investment in leading edge technology. The ARDC is excited to partner with the Monash eResearch Centre and NVIDIA to explore how to apply DPUs to research computing and how to scale this technology nationally to provide our Australian researchers with the competitive advantage.”

This is an example of the emerging evolution in security technology to security everywhere or distributed security. By shifting the security function as orthogonal to the application (including the operating system), the data centre (Monash in this case) can affect it’s own chosen depth introspection and enforcement, at the same rate that clouds and applications are growing.

“The transformation of the data center into the new unit of computing demands zero-trust security models that monitor all data center transactions in real time,” said Ami Badani, Vice President of Marketing at NVIDIA. “NVIDIA is collaborating with Monash University on pioneering cybersecurity breakthroughs powered by the NVIDIA Morpheus AI cybersecurity framework, which uses machine learning to anticipate threats with real-time, all-packet inspection.”

We are presently forming the team involving cloud and security office staff, and performing preliminary investigations in our test cloud. We’re expecting to communicate findings incrementally over the year.

Disruptive change in the clinical treatment of pancreatic cancer

Professor Jenkins’ research focuses on pancreatic cancer, an inflammation-associated cancer and the fourth most common cause of cancer death worldwide, with an extremely low 5% five-year survival rate. Typically studies look at gene expression patterns between normal pancreas and cancerous pancreas in order to identify unique signatures, which can be indicative of sensitivity or resistance to specific chemotherapeutic treatments.

“Using next generation gene sequencing, involving big instruments, big data and big computing – allows near-term disruptive change in the clinical treatment of pancreatic cancer.” Prof. Jenkins, Monash Health..

To date, gene expression studies have largely focused on samples taken from open surgical biopsy; a procedure known to be very invasive and only possible in 20% of pancreatic cancers. Prof Jenkins’ group, in collaboration with Dr Daniel Croagh from the Department of Upper Gastrointestinal and Hepatobiliary Surgery at Monash Medical Centre, recently trialled an alternative less invasive process available to nearly all pancreatic cancer patients known as endoscopic ultrasound-guided fine-needle aspirate (EUS-FNA) which uses a thin, hollow needle to collect the samples of cells from which genetic material can be extracted and analysed. The challenge then becomes to ensure gene sequencing from EUS-FNA samples is comparable to open surgical biopsy such that established analysis and treatment can be used.


Twenty-four EUS-FNA-derived genetic samples from normal and cancerous pancreas were sequenced at the MHTP Medical Genomics Facility producing a total amount of 40Gb of raw data. Those data were securely transferred onto R@CMon by the Monash Bioinformatics Platform for processing, statistical analysis and computational exploration using state-of-the-art Bioinformatics methods.

super_computer

Results thus far from this study show that data from EUS-FNA-derived samples were of high quality and also allowed the identification of gene expression signatures between normal and cancerous pancreas. Professor Jenkins’ group is now confident that EUS-FNA-derived material not only has the potential to capture nearly all of pancreatic cancer patients (compared to ~20% by surgery), but to also improve patient management and their treatment in the clinic.

“The current clinical genomics research space requires specialized high performance computational and storage infrastructure to support the processing and long term storage of those so-called “big data”. Thus R@CMon plays a major role in the discovery and development of new therapies and the improvement of Human health care in general.” Roxane Legaie, Senior Bioinformatician, Monash Bioinformatics Platform

 

R@CMon hosted Australia’s first Ceph Day

Ceph Days are a series of regular events in support of the Ceph open source community. They now occur at locations all around the world. In November, R@CMon hosted Australia’s first Ceph Day. The day hosted 70-odd guests, many of which  were from interstate and a few from overseas. There participants were from the research sector, private industry and ICT providers.  It was a fantastic culmination of Australia’s growing Ceph community.

If you don’t already know, Ceph is basically an open-source technology for software-defined cluster-based storage.  It means our storage backend is essentially infinitely scalable, and our focus can shift to the access mechanisms for data.

Check out the promo:

R@CMon has pioneered the adoption of Ceph for accessible research data storage and at mid-2013 was the first NeCTAR Research Cloud node to provide un-throttled volume storage. R@CMon has also worked closely with was InkTank and now Redhat to develop the support model for such an enterprise (see Ceph Enterprise – a disruptive period in the storage marketplace).

The day began with the Ceph Community Director – Patrick McGarry. His presentation included information about the upcoming expanded Ceph metrics platform, what the Ceph User Committee has been up to, new community infrastructure for a better contributor experience, and revised open source governance.

Undoubtedly the highlight of the day was the joint talk given by R@CMon’s very own director – Steve Quenette and technical lead – Blair Bethwaite. Here we explain Ceph in the context of the 21st century microscope – the tool each researcher creates to do modern day research. We also explain how we technically approached creating our fabric.

R@CMon announced as a Mellanox “HPC Center of Excellence”

At SuperComputing 2015 in Austin our network/fabric partner Mellanox announced R@CMon (Monash University) as a “HPC Centre of Excellence. A core goal of the HPC CoE is to drive the technological innovations required for the next generation (exascale) supercomputing, whilst also ensuring that such an exascale computer is relevant to modern research. R@CMon is a stand out pioneer at converging cloud, HPC and data, all of which are key to the “next generation”.

“We see Monash as a leader in Cloud and HPC on the Cloud with Openstack, Ceph and Lustre on our Ethernet CloudX platform.” Sudarshan Ramachandran, Regional Sales Manager, Australia & New Zealand

From a fabric innovation point of view, it has been a very productive and exciting 24months for R@CMon. By early 2014 the internal Monash University HPC system “MCC” was burst onto the Research Cloud, allowing a researcher’s own merit the be leveraged with institutional investment. It also represents a shift towards soft HPC, where the size of a HPC system changes regularly with time. Earlier this year we announced our early adoption of RoCE (RDMA over Converged Ethernet) using Mellanox technologies. The meant the same fabric used for cloud networking could also be used for HPC and data storage backplanes.  In turn MCC on the R@CMon also enabled RDMA communications, that is, real HPC performance but on an otherwise orchestrated cloud.

 

Finally at the Tokyo OpenSack summit 2015, Mellanox announced R@CMon as debuting the World’s first 100G End-to-End Cloud. This technology eases scaling and heterogeneity of performance aspects. In particular, it sets the basis for processor and storage performance for peak and converged cloud/HPC needs. Watch this space!

 

 

R@CMon Storage

Our journey towards R@CMon Storage (Storage-as-a-Service)…

In May 2013 R@CMon went live with an OpenStack cell within the NeCTAR (Australian) Research Cloud confederation. It was an innovation in its own right, targeting the commodity end of both the fundamental and translational research needs of Australia (see R@CMon IDC Spotlight – AMD & DELL). Our technical partner, Dell, has successfully applied the design pattern to many other subsequent Research Cloud nodes, and many other OpenStack based private cloud deployments both nationally and internationally. Shortly after the launch of this initial IaaS compute cell, we introduced Ceph based volume storage, becoming the first volume storage service on the Research Cloud, and in doing so, instigated a collaboration with InkTank (now Redhat). By November 2014 R@CMon launched the “Phase 2” Specialist IaaS cell, an “e”-resource motivated by research that pushes boundaries. Within this cell R@CMon added an RDMA-able interconnect to our storage and compute fabric, instigating an innovative technical collaboration with Mellanox.

Thus R@CMon is an environment to build what we call “21st Century Microscopes” – where researchers orchestrate the instruments, compute, storage, analysis and visualisation themselves, looking down and tuning this 21st century lens, using big data and big computing to make new discoveries.

And accordingly, R@CMon is an environment for innovative data services for the long-tail (if you like – more ICT like). Unashamedly – Our instances of Ceph is what we can “enterprise”, whilst each user or tenant has their own needs on file protocol, capacity and latency.

R@CMon Storage is a collection of storage access methods and underlying storage infrastructure products. Why do we present storage as both front-ends and infrastructure? Because most users want access methods – it should just work, but most microscope builders want infrastructure – it should be a building block. R@CMon Storage is also the Monash operating centre to VicNode – where we explain some of these products.

We now have a series of R@CMon Storage products and services available – ranging from infrastructure products, access methods and data management.