Exploring the acceleration of the Met Office NERC Cloud model using FPGAs

The use of Field Programmable Gate Arrays (FPGAs) to accelerate computational kernels has the potential to be of great benefit to scientific codes and the HPC community in general. With the recent developments in FPGA programming technology, the ability to port kernels is becoming far more accessible. However, to gain reasonable performance from this technology it is not enough to simple transfer a code onto the FPGA, instead the algorithm must be rethought and recast in a data-flow style to suit the target architecture. In this paper we describe the porting, via HLS, of one of the most computationally intensive kernels of the Met Office NERC Cloud model (MONC), an atmospheric model used by climate and weather researchers, onto an FPGA. We describe in detail the steps taken to adapt the algorithm to make it suitable for the architecture and the impact this has on kernel performance. Using a PCIe mounted FPGA with on-board DRAM, we consider the integration on this kernel within a larger infrastructure and explore the performance characteristics of our approach in contrast to Intel CPUs that are popular in modern HPC machines, over problem sizes involving very large grids. The result of this work is an experience report detailing the challenges faced and lessons learnt in porting this complex computational kernel to FPGAs, as well as exploring the role that FPGAs can play and their fundamental limits in accelerating traditional HPC workloads.Comment: Preprint of article in proceedings, ISC High Performance 2019. Lecture Notes in Computer Science, vol 1188

Five-year follow-up of angiographic disease progression after medicine, angioplasty, or surgery

<p>Abstract</p> <p>Background</p> <p>Progression of atherosclerosis in coronary artery disease is observed through consecutive angiograms. Prognosis of this progression in patients randomized to different treatments has not been established. This study compared progression of coronary artery disease in native coronary arteries in patients undergoing surgery, angioplasty, or medical treatment.</p> <p>Methods</p> <p>Patients (611) with stable multivessel coronary artery disease and preserved ventricular function were randomly assigned to CABG, PCI, or medical treatment alone (MT). After 5-year follow-up, 392 patients (64%) underwent new angiography. Progression was considered a new stenosis of ≥ 50% in an arterial segment previously considered normal or an increased grade of previous stenosis > 20% in nontreated vessels.</p> <p>Results</p> <p>Of the 392 patients, 136 underwent CABG, 146 PCI, and 110 MT. Baseline characteristics were similar among treatment groups, except for more smokers and statin users in the MT group, more hypertensives and lower LDL-cholesterol levels in the CABG group, and more angina in the PCI group at study entry. Analysis showed greater progression in at least one native vessel in PCI patients (84%) compared with CABG (57%) and MT (74%) patients (p < 0.001). LAD coronary territory had higher progression compared with LCX and RCA (P < 0.001). PCI treatment, hypertension, male sex, and previous MI were independent risk factors for progression. No statistical difference existed between coronary events and the development of progression.</p> <p>Conclusion</p> <p>The angioplasty treatment conferred greater progression in native coronary arteries, especially in the left anterior descending territories and treated vessels. The progression was independently associated with hypertension, male sex, and previous myocardial infarction.</p

Multi-institutional and multi-disciplinary care: A successfully managed aortic dissection in the third trimester of pregnancy

Multi-disciplinary collaborative care for pregnant women with complex and emergent conditions is essential. Logistical planning, clear communication and human factor awareness are all non-clinical skills which need to be utilised in order to maximise outcomes. We describe the case of a proximal aortic dissection in the late third trimester of pregnancy diagnosed in a peripheral hospital that was transferred to a cardiothoracic centre for successful operative management 160 km away. This required the time-sensitive mobilisation and liaison of a receiving cardiothoracic, anaesthesiology and perfusionist team in conjunction with obstetric and midwifery support from an affiliated maternity hospital, as well as the national neonatal transport team. We emphasise the importance of multidisciplinary team management in complex cases and how imperative good inter-disciplinary communication is to ensure safe inter-hospital transfer. </jats:p