Distributed-memory large deformation diffeomorphic 3D image registration

We present a parallel distributed-memory algorithm for large deformation diffeomorphic registration of volumetric images that produces large isochoric deformations (locally volume preserving). Image registration is a key technology in medical image analysis. Our algorithm uses a partial differential equation constrained optimal control formulation. Finding the optimal deformation map requires the solution of a highly nonlinear problem that involves pseudo-differential operators, biharmonic operators, and pure advection operators both forward and back- ward in time. A key issue is the time to solution, which poses the demand for efficient optimization methods as well as an effective utilization of high performance computing resources. To address this problem we use a preconditioned, inexact, Gauss-Newton- Krylov solver. Our algorithm integrates several components: a spectral discretization in space, a semi-Lagrangian formulation in time, analytic adjoints, different regularization functionals (including volume-preserving ones), a spectral preconditioner, a highly optimized distributed Fast Fourier Transform, and a cubic interpolation scheme for the semi-Lagrangian time-stepping. We demonstrate the scalability of our algorithm on images with resolution of up to $1024^3$ on the "Maverick" and "Stampede" systems at the Texas Advanced Computing Center (TACC). The critical problem in the medical imaging application domain is strong scaling, that is, solving registration problems of a moderate size of $256^3$---a typical resolution for medical images. We are able to solve the registration problem for images of this size in less than five seconds on 64 x86 nodes of TACC's "Maverick" system.Comment: accepted for publication at SC16 in Salt Lake City, Utah, USA; November 201

Propagation and Decay of Injected One-Off Delays on Clusters: A Case Study

Analytic, first-principles performance modeling of distributed-memory applications is difficult due to a wide spectrum of random disturbances caused by the application and the system. These disturbances (commonly called "noise") destroy the assumptions of regularity that one usually employs when constructing simple analytic models. Despite numerous efforts to quantify, categorize, and reduce such effects, a comprehensive quantitative understanding of their performance impact is not available, especially for long delays that have global consequences for the parallel application. In this work, we investigate various traces collected from synthetic benchmarks that mimic real applications on simulated and real message-passing systems in order to pinpoint the mechanisms behind delay propagation. We analyze the dependence of the propagation speed of idle waves emanating from injected delays with respect to the execution and communication properties of the application, study how such delays decay under increased noise levels, and how they interact with each other. We also show how fine-grained noise can make a system immune against the adverse effects of propagating idle waves. Our results contribute to a better understanding of the collective phenomena that manifest themselves in distributed-memory parallel applications.Comment: 10 pages, 9 figures; title change

A Lazy Bailout Approach for Dual-Criticality Systems on Uniprocessor Platforms

© 2019 by the authors. Licensee MDPI, Basel, Switzerland.A challenge in the design of cyber-physical systems is to integrate the scheduling of tasks of different criticality, while still providing service guarantees for the higher critical tasks in case of resource-shortages caused by faults. While standard real-time scheduling is agnostic to the criticality of tasks, the scheduling of tasks with different criticalities is called mixed-criticality scheduling. In this paper we present the Lazy Bailout Protocol (LBP), a mixed-criticality scheduling method where low-criticality jobs overrunning their time budget cannot threaten the timeliness of high-criticality jobs while at the same time the method tries to complete as many low-criticality jobs as possible. The key principle of LBP is instead of immediately abandoning low-criticality jobs when a high-criticality job overruns its optimistic WCET estimate, to put them in a low-priority queue for later execution. To compare mixed-criticality scheduling methods we introduce a formal quality criterion for mixed-criticality scheduling, which, above all else, compares schedulability of high-criticality jobs and only afterwards the schedulability of low-criticality jobs. Based on this criterion we prove that LBP behaves better than the original {\em Bailout Protocol} (BP). We show that LBP can be further improved by slack time exploitation and by gain time collection at runtime, resulting in LBPSG. We also show that these improvements of LBP perform better than the analogous improvements based on BP.Peer reviewedFinal Published versio

Sub-Nyquist Sampling: Bridging Theory and Practice

Sampling theory encompasses all aspects related to the conversion of continuous-time signals to discrete streams of numbers. The famous Shannon-Nyquist theorem has become a landmark in the development of digital signal processing. In modern applications, an increasingly number of functions is being pushed forward to sophisticated software algorithms, leaving only those delicate finely-tuned tasks for the circuit level. In this paper, we review sampling strategies which target reduction of the ADC rate below Nyquist. Our survey covers classic works from the early 50's of the previous century through recent publications from the past several years. The prime focus is bridging theory and practice, that is to pinpoint the potential of sub-Nyquist strategies to emerge from the math to the hardware. In that spirit, we integrate contemporary theoretical viewpoints, which study signal modeling in a union of subspaces, together with a taste of practical aspects, namely how the avant-garde modalities boil down to concrete signal processing systems. Our hope is that this presentation style will attract the interest of both researchers and engineers in the hope of promoting the sub-Nyquist premise into practical applications, and encouraging further research into this exciting new frontier.Comment: 48 pages, 18 figures, to appear in IEEE Signal Processing Magazin

Adaptive Mid-term and Short-term Scheduling of Mixed-criticality Systems

A mixed-criticality real-time system is a real-time system having multiple tasks classified according to their criticality. Research on mixed-criticality systems started to provide an effective and cost efficient a priori verification process for safety critical systems. The higher the criticality of a task within a system and the more the system should guarantee the required level of service for it. However, such model poses new challenges with respect to scheduling and fault tolerance within real-time systems. Currently, mixed-criticality scheduling protocols severely degrade lower criticality tasks in case of resource shortage to provide the required level of service for the most critical ones. The actual research challenge in this field is to devise robust scheduling protocols to minimise the impact on less critical tasks. This dissertation introduces two approaches, one short-term and the other medium-term, to appropriately allocate computing resources to tasks within mixed-criticality systems both on uniprocessor and multiprocessor systems. The short-term strategy consists of a protocol named Lazy Bailout Protocol (LBP) to schedule mixed-criticality task sets on single core architectures. Scheduling decisions are made about tasks that are active in the ready queue and that have to be dispatched to the CPU. LBP minimises the service degradation for lower criticality tasks by providing to them a background execution during the system idle time. After, I refined LBP with variants that aim to further increase the service level provided for lower criticality tasks. However, this is achieved at an increased cost of either system offline analysis or complexity at runtime. The second approach, named Adaptive Tolerance-based Mixed-criticality Protocol (ATMP), decides at runtime which task has to be allocated to the active cores according to the available resources. ATMP permits to optimise the overall system utility by tuning the system workload in case of shortage of computing capacity at runtime. Unlike the majority of current mixed-criticality approaches, ATMP allows to smoothly degrade also higher criticality tasks to keep allocated lower criticality ones

Holistic resource allocation for multicore real-time systems

This paper presents CaM, a holistic cache and memory bandwidth resource allocation strategy for multicore real-time systems. CaM is designed for partitioned scheduling, where tasks are mapped onto cores, and the shared cache and memory bandwidth resources are partitioned among cores to reduce resource interferences due to concurrent accesses. Based on our extension of LITMUSRT with Intel’s Cache Allocation Technology and MemGuard, we present an experimental evaluation of the relationship between the allocation of cache and memory bandwidth resources and a task’s WCET. Our resource allocation strategy exploits this relationship to map tasks onto cores, and to compute the resource allocation for each core. By grouping tasks with similar characteristics (in terms of resource demands) to the same core, it enables tasks on each core to fully utilize the assigned resources. In addition, based on the tasks’ execution time behaviors with respect to their assigned resources, we can determine a desirable allocation that maximizes schedulability under resource constraints. Extensive evaluations using real-world benchmarks show that CaM offers near optimal schedulability performance while being highly efficient, and that it substantially outperforms existing solutions