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Biomedical Research Computing

In 2017, the BDI formed a partnership with the Wellcome Centre for Human Genetics (WHG) to provide a unified Biomedical Research Computing (BMRC) platform to manage large-scale, data-driven research computing.

BMRC is the pre-eminent facility at Oxford University for this type of research and it supports researchers from more than a dozen departments who all contribute to the continued growth of the facility.

An introduction to the BMRC and access with charging information can be found below. A full description of the system and information for other users (for example, those outside the BDI) can be found on the Medical Sciences Division website at this address: https://www.medsci.ox.ac.uk/support-services/teams/bmrc.

To contact the BMRC team for all support, advice and information email us at bmrc-help@medsci.ox.ac.uk.

 

OVERVIEW OF MAIN FACILITIES

As of May 2019, BMRC offers nearly 7000 cluster compute cores, 60 cluster GPU cards, 10PB raw high-performance (Spectrum Scale) storage and 8PB raw lower-grade storage for data acquisition and archiving. We encourage all BDI and WHG researchers to use our platforms and offer training and workshops to help get people started. BMRC maintains an extensive set of >300 applications that researchers can use, confident that they are compiled and installed correctly.

In addition, we run an OpenStack cloud with 1200 cores and 40 GPUs backed by 300TB extreme performance NVMe Ceph and we are starting to encourage research groups to migrate to this platform.

BMRC also runs a smaller high-compliance secure VDI/cloud platform, a test-and-dev OpenStack cloud and a small oVirt VM platform. We are also exploring new storage platforms ranging from ultra-fast NVMe-over-fabric to bulk S3-compatible object storage. All these platforms are linked on our 100g Ethernet and EDR InfiniBand networks.

 

CHARGING MODEL

BMRC is developing simple comprehensive cost recovery model to ensure its sustainability and to allow for upgrades and hardware replacement. As this becomes operative it will be available on the BMRC section  of the Medical Sciences Division website.

For members of BDI the cluster compute costs are charged by shares in the scheduler share-tree policy. In January 2019 the cost of a share was £100 per year and groups typically require between 10 and 100 shares depending on their compute needs. However, we can also help to deliver specialist computing needs by allowing direct investment in our shared facility.

Storage costs are charged back to research grants either in advance or retrospectively on a six-monthly cycle. In January 2019 the charge for high-performance storage was £35 per usable terabyte per six months. We also have a low-grade tier of storage suitable for holding old data, and in January 2019 the charge for this storage was £10.60 per usable terabyte per six months.

BMRC staff are happy to give advice and estimate realistic costings for researchers when they are writing grant applications.

 

ACKNOWLEDGEMENTS

BMRC is supported by multiple funding streams. It is important that these sources of funding are properly acknowledged in all publications arising from the use of BMRC facilities. We also need authors to email us (at bmrc-help@medsci.ox.ac.uk) with the references for all publications as soon as they appear. We now have to report back regularly on research impact to our funders and maintaining an accurate central record is essential.

For papers with no WHG authors, where the computing costs have been charged back to the individual research groups, we need the following in the funding/acknowledgements section:

"Computation used the Oxford Biomedical Research Computing (BMRC) facility, a joint development between the Wellcome Centre for Human Genetics and the Big Data Institute supported by Health Data Research UK and the NIHR Oxford Biomedical Research Centre. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health."

For papers with WHG authors (which, of course, includes STRUBI) you should comply with the Wellcome Trust's Open Access Policy (https://www.well.ox.ac.uk/internal/policies-procedures/open-access-policy). The compute costs for these publications will have been covered by the Core award, and we need the following in the funding/acknowledgements section:

"Computation used the Oxford Biomedical Research Computing (BMRC) facility, a joint development between the Wellcome Centre for Human Genetics and the Big Data Institute supported by Health Data Research UK and the NIHR Oxford Biomedical Research Centre. Financial support was provided by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health."

Please remember that if there are NIHR-funded authors, the affiliation should appear in the affiliation/address section of the paper: "NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU."