AOmpLib: an aspect library for large-scale multi-core parallel programming

This paper introduces an aspect-oriented library aimed to support efficient execution of Java applications on multi-core systems. The library is coded in AspectJ and provides a set of parallel programming abstractions that mimics the OpenMP standard. The library supports the migration of sequential Java codes to multi-core machines with minor changes to the base code, intrinsically supports the sequential semantics of OpenMP and provides improved integration with object-oriented mechanisms. The aspect- oriented nature of library enables the encapsulation of parallelism-related code into well-defined modules. The approach makes the parallelisation and the maintenance of large-scale Java applications more manageable. Furthermore, the library can be used with plain Java annotations and can be easily extended with application- specific mechanisms in order to tune application performance. The library has a competitive performance, in comparison with traditional parallel programming in Java, and enhances programmability, since it allows an independent development of parallelism-related code.This work is funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within projects FCOMP-01-0124-FEDER- 011413 and FCOMP-01-0124-FEDER-010152

AOmpLib: An Aspect Library for Large-Scale Multi-Core Parallel Programming

Abstract-This paper introduces an aspect-oriented library aimed to support efficient execution of Java applications on multi-core systems. The library is coded in AspectJ and provides a set of parallel programming abstractions that mimics the OpenMP standard. The library supports the migration of sequential Java codes to multi-core machines with minor changes to the base code, intrinsically supports the sequential semantics of OpenMP and provides improved integration with object-oriented mechanisms. The aspectoriented nature of library enables the encapsulation of parallelism-related code into well-defined modules. The approach makes the parallelisation and the maintenance of large-scale Java applications more manageable. Furthermore, the library can be used with plain Java annotations and can be easily extended with applicationspecific mechanisms in order to tune application performance. The library has a competitive performance, in comparison with traditional parallel programming in Java, and enhances programmability, since it allows an independent development of parallelism-related code

A metadata-enhanced framework for high performance visual effects

This thesis is devoted to reducing the interactive latency of image processing computations in visual effects. Film and television graphic artists depend upon low-latency feedback to receive a visual response to changes in effect parameters. We tackle latency with a domain-specific optimising compiler which leverages high-level program metadata to guide key computational and memory hierarchy optimisations. This metadata encodes static and dynamic information about data dependence and patterns of memory access in the algorithms constituting a visual effect – features that are typically difficult to extract through program analysis – and presents it to the compiler in an explicit form. By using domain-specific information as a substitute for program analysis, our compiler is able to target a set of complex source-level optimisations that a vendor compiler does not attempt, before passing the optimised source to the vendor compiler for lower-level optimisation. Three key metadata-supported optimisations are presented. The first is an adaptation of space and schedule optimisation – based upon well-known compositions of the loop fusion and array contraction transformations – to the dynamic working sets and schedules of a runtimeparameterised visual effect. This adaptation sidesteps the costly solution of runtime code generation by specialising static parameters in an offline process and exploiting dynamic metadata to adapt the schedule and contracted working sets at runtime to user-tunable parameters. The second optimisation comprises a set of transformations to generate SIMD ISA-augmented source code. Our approach differs from autovectorisation by using static metadata to identify parallelism, in place of data dependence analysis, and runtime metadata to tune the data layout to user-tunable parameters for optimal aligned memory access. The third optimisation comprises a related set of transformations to generate code for SIMT architectures, such as GPUs. Static dependence metadata is exploited to guide large-scale parallelisation for tens of thousands of in-flight threads. Optimal use of the alignment-sensitive, explicitly managed memory hierarchy is achieved by identifying inter-thread and intra-core data sharing opportunities in memory access metadata. A detailed performance analysis of these optimisations is presented for two industrially developed visual effects. In our evaluation we demonstrate up to 8.1x speed-ups on Intel and AMD multicore CPUs and up to 6.6x speed-ups on NVIDIA GPUs over our best hand-written implementations of these two effects. Programmability is enhanced by automating the generation of SIMD and SIMT implementations from a single programmer-managed scalar representation

Pameran Reka Cipta, Penyelidikan dan Inovasi (PRPI) 2009

PRPI 2009 kini telah memasuki tahun penganjurannya yang ke-7. Pameran penyelidikan di UPM telah bermula sejak tahun 1997 semasa Exhibition & Seminar Harnessing for Industry Advantage. Pada tahun 2002, Pameran Reka Cipta dan Penyelidikan (PRP) buat pertama kali telah diadakan dengan menggunakan konsep pertandingan hasil projek penyelidikan yang telah dijalankan oleh para penyelidik UPM. Kejayaan penganjuran PRP 2002 telah merintis usaha untuk menjadikannya sebagai aktiviti tahunan UPM dan ianya terus berkembang sejajar dengan nama baharunya yang ditukar kepada Pameran Reka Cipta, Penyelidikan dan Inovasi yang bermula penganjurannya pada tahun 2005. Sebagai kesinambungan daripada kejayaan penganjuran PRPI 2006, 2007 dan 2008 yang lalu dan status UPM sebagai salah sebuah Universiti Penyelidikan, PRPI 2009 kali ini yang merupakan pameran penyelidikan yang terbesar di UPM terus dilaksanakan dengan aspirasi dan semangat yang lebih jitu. Pameran ini juga menjadi pelantar kepada para penyelidik untuk mengenengahkan hasil penyelidikan yang dijalankan dan penemuan baharu kepada umum. Di samping itu ianya juga menjadi penanda aras terhadap kualiti sesuatu projek penyelidikan bagi melayakkan para penyelidik UPM untuk menyertai pameran di peringkat kebangsaan dan seterusnya antarabangsa. Adalah diharapkan pelaksanaan PRPI 2009 ini akan dapat menyemarakkan budaya penyelidikan di kalangan staf dan juga pelajar UPM sekaligus menjadikan UPM sebagai Universiti Penyelidikan yang cemerlang di negara ini

Investigation into the effector repertoire of the H2 type VI secretion system of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen, causing both acute and chronic infections. This bacterium displays remarkable adaptability and potential for virulence, partly due to its arsenal of protein secretion systems. The type VI secretion system (T6SS) is a contractile injection apparatus, firing a spear-like structure into target cells to deliver its cargo of effector proteins. P. aeruginosa encodes three such systems, denoted H1-, H2- and H3-T6SS. This dissertation discloses work focused on progressing our understanding of the H2-T6SS in this pathogen. We reveal that the H2-T6SS is controlled by the Gac/Rsm pathway, a major regulatory network in this pathogen responsible for the lifestyle switch between motile and sessile bacteria. Quorum sensing, the sophisticated signalling network governing social behaviour, is responsible for the expression of this secretion system in a growth-phase dependent manner, while temperature also has an input in a strain-dependent fashion. We advance our understanding of the composition of the H2-T6SS nanomachine, identifying multiple components of the spear-like delivery device, comprising an Hcp tube capped with a spike structure composed of three VgrGs and one PAAR protein. Importantly, we begin to decipher the payload of this secretion system, describing several phospholipase family effectors which confer a significant advantage to P. aeruginosa during bacterial competition. Building upon this, we propose a hierarchy of effector delivery determined by the VgrG/PAAR composition of the spike. Finally, we characterise a specific H2-T6SS effector: the C-terminal extension of the VgrG2b spike protein. Although we initially investigate its reported role within eukaryotic cells, we determine that this metallopeptidase-like effector is part of a wider antibacterial T6SS toxin family. We describe its cognate periplasmic immunity determinant and progress the elucidation of the target of the effector. Overall, we advance our understanding of the H2-T6SS of P. aeruginosa in terms of its regulation, organisation and cargo.Open Acces