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Following publication of the original article [1], the author requested changes to the figures 4, 7, 8, 9, 12 and 14 to align these with the text. The corrected figures are supplied below.
Background Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence alignment of high-throughput NGS data, but has limited performance. In this article we present GASAL2, a GPU library for aligning DNA and RNA sequences that outperforms existing CPU...
Sequence alignment is a core step in the processing of DNA and RNA sequencing data. In this paper, we present a high performance GPU accelerated set of APIs (GASAL) for pairwise sequence alignment of DNA and RNA sequences. The GASAL APIs provide accelerated kernels for local, global as well as semi-global alignment, allowing the computation of the alignment score, and optionally the start and end...
Fast progress in next generation sequencing has dramatically increased the throughout of DNA sequencing, resulting in the availability of large DNA data sets ready for analysis. However, post-sequencing DNA analysis has become the bottleneck in using these data sets, as it requires powerful and scalable tools to perform the needed analysis. A typical analysis pipeline consists of a number of steps,...
Safety critical real time systems need to meet strict timing deadlines. We use a model checking based approach to calculate the WCET, where we apply optimizations to reduce the number of states stored by the model checker. Furthermore, we used deterministic shared memory accesses to further reduce calculation time, memory and number of states needed for calculating WCET. By optimizing the model checking...
In this paper, we present DetLock, a runtime system to ensure deterministic execution of multithreaded programs running on multicore systems. DetLock does not rely on any hardware support or kernel modification to ensure determinism. For tracking the progress of the threads, logical clocks are used. Unlike previous approaches, which rely on non-portable hardware to update the logical clocks, DetLock...
Parallel systems were for a long time confined to high-performance computing. However, with the increasing popularity of multicore processors, parallelization has also become important for other computing domains, such as desktops and embedded systems. Mission-critical embedded software, like that used in avionics and automotive industry, also needs to guarantee real time behavior. For that purpose,...
This paper describes a software based fault tolerance approach for multithreaded programs running on multicore processors. Redundant multithreaded processes are used to detect soft errors and recover from them. Our scheme makes sure that the execution of the redundant processes is identical even in the presence of non-determinism due to shared memory accesses. This is done by making sure that the...
Multicore systems are not only hard to program but also hard to test, debug and maintain. This is because the traditional way of accessing shared memory in multithreaded applications is to use lock-based synchronization, which is inherently non-deterministic and can cause a multithreaded application to have many different possible execution paths for the same input. This problem can be avoided however...
The ever decreasing transistor size has made it possible to integrate multiple cores on a single die. On the downside, this has introduced reliability concerns as smaller transistors are more prone to both transient and permanent faults. However, the abundant extra processing resources of a multicore system can be exploited to provide fault tolerance by using redundant execution. We have designed...
With the advent of modern nano-scale technology, it has become possible to implement multiple processing cores on a single die. The shrinking transistor sizes however have made reliability a concern for such systems as smaller transistors are more prone to permanent as well as transient faults. To reduce the probability of failures of such systems, online fault tolerance techniques can be applied...
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