Dias, Ricardo, João Louren{\c c}o, and Nuno Pregui{\c c}a. "
Efficient and Correct Transactional Memory Programs Combining Snapshot Isolation and Static Analysis."
Proceedings of the 3nd USENIX conference on Hot topics in parallelism (HotPar’11). HotPar’11. Usenix Association, 2011.
AbstractConcurrent programs may suffer from concurrency anomalies that may lead to erroneous and unpredictable program behaviors. To ensure program correctness, these anomalies must be diagnosed and corrected. This paper addresses the detection of both low- and high-level anomalies in the Transactional Memory setting. We propose a static analysis procedure and a framework to address Transactional Memory anomalies. We start by dealing with the classic case of low-level dataraces, identifying concurrent accesses to shared memory cells that are not protected within the scope of a memory transaction. Then, we address the case of high-level dataraces, bringing the programmer’s attention to pairs of memory transactions that were misspecified and should have been combined into a single transaction. Our framework was applied to a set of programs, collected form different sources, containing well known low- and high-level anomalies. The framework demonstrated to be accurate, confirming the effectiveness of using static analysis techniques to precisely identify concurrency anomalies in Transactional Memory programs.
Caires, L., Jorge A. Perez, J. C. Seco, Hugo T. Vieira, and Lúcio Ferrão. "
Type-based Access Control in Data-Centric Systems."
Programming Languages and Systems, 20th European Symposium on Programming, ESOP 2011. Ed. Gilles Barthe. Lecture Notes in Computer Science. Springer-Verlag, 2011.
Oliveira, Luís Picciochi, and João M. Lourenço. "
Aceleração de Computações Científicas com Processadores Heterogéneos."
InForum 2011: Proceedings of InForum Simpósio de Informática. Coimbra: Universidade do Coimbra, 2011.
AbstractActualmente o mercado residencial de computadores inclui não só multiprocessadores com diversos núcleos (CPUs) como também placas gráficas (GPUs) cuja capacidade de processamento tem evoluído a um ritmo exponencial. Este poder computacional pode ser utilizado para outros fins para além do processamento gráfico, tal como o processamento de algoritmos comuns em computação científica. Neste artigo é apresentada, discutida e avaliada a framework Cheetah, uma framework que distribui programas computacionalmente exigentes sobre uma rede de CPUs e GPUs. Um programador que utilize a Cheetah apenas necessita de especificar o seu programa como um conjunto de kernels OpenCL, relegando para a framework a distribuição destes pelas unidades de processamento disponíveis. O programa pode assim escalar à medida que são adicionados novos recursos computacionais, sem quaisquer esforços adicionais de adaptação ou recompilação. Os testes realizados demonstraram a capacidade de a framework providenciar aceleracçõs até duas ordens de grandeza com um esforço de desenvolvimento reduzido, mesmo quando na presença de recursos computacionais limitados.
Viegas, Aldino, Joao Manso, Marta C. Corvo, Manuel M. B. Marques, and Eurico J. Cabrita. "
Binding of ibuprofen, ketorolac and diclofenac to COX-1 and COX-2 studied by saturation transfer difference NMR."
Journal of Medicinal Chemistry. 54.24 (2011): 8555-8562.
AbstractSaturation Transfer Difference-NMR (STD-NMR) spectroscopy has emerged as a powerful screening tool and a straightforward way to study the binding epitopes of active compounds in early stage lead discovery in pharmaceutical research. Here we report the application of STD NMR to characterize the binding of the anti-inflammatory drugs ibuprofen, diclofenac and ketorolac to COX-1 and COX-2. Using well-studied COX inhibitors and by comparing STD signals with crystallographic structures we show that there is a relation between the orientations of ibuprofen and diclofenac in the COX-2 active site and the relative STD responses detected in the NMR experiments. Based on this analysis we propose that ketorolac should bind to the COX-2 active site in similar orientation as that of diclofenac. We also show that the combination of STD NMR with competition experiments constitutes a valuable tool to address the recently proposed behavior of COX-2 as functional heterodimers and complement enzyme activity studies in the effort to rationalize COX inhibition mechanisms.