A solution designed and integrated by OCF has been announced as a winner in two categories at the 2017 HPC Wire Readers’ Choice Awards.
Announced at SuperComputing 2017 in Denver, USA, the Cloud Infrastructure for Microbial Bioinformatics, (CLIMB) has won the award for ‘Best Use of HPC in Life Sciences’ and ‘Best HPC Collaboration in Academia, Government or Industry’.
CLIMB is a UK based cloud project funded by the UK’s Medical Research Council to support research by academic microbiologists. The current live system is located across the Universities of Birmingham, Cardiff and Warwick.
The Best Use of HPC in Life Sciences Award was awarded for real-time analysis of Zika genomes using CLIMB cloud computing, supported by Lenovo, OpenStack, IBM, Red Hat and Dell EMC. The Best HPC Collaboration in Academia, Government or Industry was awarded to CLIMB for the provision of resources for projects that globally impact public health, using the expertise of Lenovo, OpenStack, IBM Spectrum Scale, Red Hat, and Dell EMC.
Simon Thompson, Research Computing Specialist who built the initial CLIMB pilot system comments, “We are delighted that CLIMB’s achievements have been recognised by the HPC Wire Readers’ Choice Awards. CLIMB is one of the most complex environments we’ve had to build, learning a lot of new technologies. We were able to work with our contacts at OCF, IBM and Lenovo to help us build such a successful HPC platform.”
CLIMB is one of the first multi-site OpenStack deployments in the UK dedicated to supporting the needs of research computing and remains the only truly federated academic research cloud operating in the UK. A fourth node, based at Swansea, is currently under development and due for launch later in 2017.
Since building the CLIMB cloud, the research partnership has expanded to include the Universities of Bath and Leicester as well as the BBSRC funded Quadram Institute. It’s open to all microbial researchers in the UK and has even been used to support training courses in the Gambia and Vietnam. Currently, CLIMB supports over 200 research groups from across academia, government and healthcare.
One recent project using the CLIMB infrastructure was research into the Zika virus. Professor Nick Loman, Professor of Microbial Genomics and Bioinformatics at the University of Birmingham (and CLIMB Fellow), says, “Genome sequencing can generate rapid insights into the scale and patterns-of-spread of important epidemics. When Zika struck the Americas, we were able to respond rapidly by deploying portable sequencing to affected areas, generating sequence data in days. Comparative genome sequence analysis requires significant computation and storage requirements.
The new system provides rapid, on-demand computation to speed up the analysis. We can instantly access hundreds of CPUs, thousands of gigabytes of RAM and tens of terabytes of storage. This means we can keep pace with the rapid data generation, and quickly release important new findings to the scientific and public health community in order to assist epidemic response efforts.”
The use of mobile field labs and cloud computing resources followed on from previous work with Ebola. As part of the CLIMB offering, researchers are able to access toolsets developed by other institutions including GVL (Melbourne University) and EDGE bioinformatics (Los Alamos).
With over 7,500 vCPU cores of processing power, the CLIMB system represents the largest single system designed specifically for microbiologists in the world. The CLIMB infrastructure runs OpenStack and is physically located across four University sites and is made up of Lenovo SystemX servers with either 512GB or 3TB of RAM and up to 192 cores, enabling researchers to request huge amounts of computing resource on the fly.
Storage is provided by IBM StorWise with IBM Spectrum Scale and Red Hat Ceph running on Dell servers. The pilot service for CLIMB was developed at the University of Birmingham with the architecture subsequently replicated at the other sites.
The CLIMB system was designed, and is led on a technical side by Tom Connor (Cardiff), Simon Thompson and Nick Loman (Birmingham). The system itself sits within a wider project, led by Mark Pallen (Quadram) and Sam Sheppard (Bath) that includes the provision of refurbished bioinformatics space, training courses and three research fellowships.
We look forward to continuing our support with the CLIMB project in the future. More details on the CLIMB project can be found at http://www.climb.ac.uk/.