Glioblastoma (GBM) is a highly invasive brain tumor, whose cells infiltrate surrounding normal brain tissue beyond the lesion outlines visible in the current medical scans. These infiltrative cells are treated mainly by radiotherapy. Existing radiotherapy plans for brain tumors derive from population studies and scarcely account for patient-specific conditions. Here, we provide a Bayesian machine learning framework for the rational design of improved, personalized radiotherapy plans using mathematical modeling and patient multimodal medical scans. Our method, for the first time, integrates complementary information from high-resolution MRI scans and highly specific FET-PET metabolic maps to infer tumor cell density in GBM patients. The Bayesian framework quantifies imaging and modeling uncertainties and predicts patient-specific tumor cell density with credible intervals. The proposed methodology relies only on data acquired at a single time point and, thus, is applicable to standard clinical settings. An initial clinical population study shows that the radiotherapy plans generated from the inferred tumor cell infiltration maps spare more healthy tissue thereby reducing radiation toxicity while yielding comparable accuracy with standard radiotherapy protocols. Moreover, the inferred regions of high tumor cell densities coincide with the tumor radioresistant areas, providing guidance for personalized dose-escalation. The proposed integration of multimodal scans and mathematical modeling provides a robust, non-invasive tool to assist personalized radiotherapy design.

A fundamental understanding of how various biological traits and features provide organisms with a competitive advantage can help us improve the design of several mechanical systems. Numerical optimization can be invaluable for this purpose, by allowing us to scrutinize the evolution of specific biological adaptations. Importantly, the use of numerical optimization can help us overcome limiting constraints that restrict the evolutionary capability of biological species. Thus, we couple high-fidelity simulations of self-propelled swimmers with evolutionary optimization algorithms, to examine peculiar swimming patterns observed in a number of fish species. More specifically, we investigate the intermittent form of locomotion referred to as `burst-and-coast' swimming, which involves a few quick flicks of the fish's tail followed by a prolonged unpowered glide. This mode of swimming is believed to confer energetic benefits, in addition to several other advantages. We discover a range of intermittent-swimming patterns, the most efficient of which resembles the swimming-behaviour observed in live fish. We also discover patterns which lead to a marked increase in swimming-speed, albeit with a significant increase in energy expenditure. Notably, the use of multi-objective optimization reveals locomotion patterns that strike the perfect balance between speed and efficiency, which can be invaluable for use in robotic applications. The analyses presented may also be extended for optimal design and control of airborne vehicles. As an additional goal of the paper, we highlight the ease with which disparate codes can be coupled via the software framework used, without encumbering the user with the details of efficient parallelization.

We present simulations of blood and cancer cell separation in complex microfluidic channels with subcellular resolution, demonstrating unprecedented time to solution, performing at 65.5% of the available 39.4 PetaInstructions/s in the 18, 688 nodes of the Titan supercomputer.

We propose an adaptive Memetic Particle Swarm Optimization algorithm where local search is selected from a pool of different algorithms. The choice of local search is based on a probabilistic strategy that uses a simple metric to score the efficiency of local search. Our study investigates whether the pool size affects the memetic algorithm's performance, as well as the possible benefit of using the adaptive strategy against a baseline static one. For this purpose, we employed the memetic algorithms framework provided in the recent MEMPSODE optimization software, and tested the proposed algorithms on the Benchmarking Black Box Optimization (BBOB 2012) test suite. The obtained results lead to a series of useful conclusions.

We present unprecedented, high throughput simulations of cloud cavitation collapse on 1.6 million cores of Sequoia reaching 55% of its nominal peak performance, corresponding to 11 PFLOP/s. The destructive power of cavitation reduces the lifetime of energy critical systems such as internal combustion engines and hydraulic turbines, yet it has been harnessed for water purification and kidney lithotripsy. The present two-phase flow simulations enable the quantitative prediction of cavitation using 13 trillion grid points to resolve the collapse of 15'000 bubbles. We advance by one order of magnitude the current state-of-the-art in terms of time to solution, and by two orders the geometrical complexity of the flow. The software successfully addresses the challenges that hinder the effective solution of complex flows on contemporary supercomputers, such as limited memory bandwidth, I/O bandwidth and storage capacity. The present work redefines the frontier of high performance computing for fluid dynamics simulations.

With the increasing diversity of computing systems and the rapid performance improvement of commodity hardware, heterogeneous clusters become the dominant platform for low-cost, high-performance computing. Grid-enabled and heterogeneous implementations of MPI establish it as the de facto programming model for these environments. On the other hand, task parallelism provides a natural way for exploiting their hierarchical architecture. This hierarchy has been further extended with the advent of general-purpose GPU devices. In this paper we present the implementation of an MPI-based task library for heterogeneous and GPU clusters. The library offers an intuitive programming interface for multilevel task parallelism with transparent data management and load balancing. We discuss design and implementation issues regarding heterogeneity support and report performance results on heterogeneous cluster computing environments.

Abstract We present the development of a novel high‐performance face detection system using a neural network‐based classification algorithm and an efficient parallelization with OpenMP. We discuss the design of the system in detail along with experimental assessment. Our parallelization strategy starts with one level of threads and moves to the exploitation of nested parallel regions in order to further improve, by up to 19%, the image‐processing capability. The presented system is able to process images in real time (38 images/sec) by sustaining almost linear speedups on a system with a quad‐core processor and a particular OpenMP runtime library. Copyright © 2009 John Wiley & Sons, Ltd.

In this work we present the runtime architecture of the OMPi OpenMP compiler. OMPi is a source-to-source C translator featuring a portable, modular and extensible runtime system. It allows for OpenMP threads to map to different execution entities which range from kernel/user-level threads to processes, providing transparent support of OpenMP applications on both SMP machines and clusters of SMPs. When operating within an SMP machine, arbitrary threading libraries can be employed; currently a multitude of such libraries is available, including one which is based on portable user-level threading, for high-performance nested parallelism support. When operating on a cluster, processes are used as the execution entities and different software DSM cores can be utilized under a unified interface; the runtime system uses a hybrid approach whereby its internal bookkeeping is done through explicit message passing, while user-program shared variables are handled by the DSM core.