Molecular Dynamic Simulation on High Performance Infrastrucutres

This thesis covers comparison between different computer platforms of high performance computing while performing molecular dynamics simulations, which falls under very complex problems and needs lots of processing power. Our goal was to critically evaluate different platforms while solving molecular dynamics, so we used 1 to 16 processor cores on a computer cluster and one and two graphics processing units (GPU) for simulations. The results will be used while planning on buying new computer hardware for biomolecular simulations. We used time needed for simulations and platform scalability as our benchmarks. For comparing speed in biomolecular simulations we used ns/day for comparison. Ns/day tells us how many nanoseconds is a system capable of simulating in one day. For this thesis we simulated a large hydrated MAO B protein with endogen phenylethylamine substrate. The simulated system is extremely important for neuroscience, since it regulates levels of biogenic amines, which have an essential part in neuro signal transmitting. The results have shown us that the use of GPUs is significantly faster than regular processors when it comes to molecular dynamics. Moreover it is also the most cost effective platform for classical molecular dynamics. From the perspective of scalability it makes sense to only use one GPU at the time, since the speed-up when using two GPUs is lower than expected

MOWER : A NEW DESIGN FOR NON-BLOCKING MISPREDICTION RECOVERY

Mower is a micro-architecture technique which targets branch misprediction penalties in superscalar processors. It speeds-up the misprediction recovery process by dynamically evicting stale instructions and fixing the RAT (Register Alias Table) using explicit branch dependency tracking. Tracking branch dependencies is accomplished by using simple bit matrices. This low-overhead technique allows overlapping of the recovery process with instruction fetching, renaming and scheduling from the correct path. Our evaluation of the mechanism indicates that it yields performance very close to ideal recovery and provides up to 5% speed-up and 2% reduction in power consumption compared to a traditional recovery mechanism using a reorder buffer and a walker. The simplicity of the mechanism should permit easy implementation of Mower in an actual processor

Multithreading opportunities for program optimizations

The introduction of Multiprocessor On Chip (CMP) led to a substantial reformulation of the Moore law stating that the number of cores in a single chip doubles every one year and a half. The tech boom related to CMP gave a strong impulse to parallel program design diminishing its ``gap'' with parallel architectures. Nowadays a leading trend related to high performance products is represented by CMP with multithreading CPU nodes. Basically the CPU multithreading feature tries to overcome the underutilization of superscalar processors, due to the lack of exploitable instruction level parallelism (ILP), allowing the simultaneous processing of different programs during the same time slot. In multithreading architectures a thread is a concurrent computational entity supported directly at firmware level (these threads are usually called hardware threads). Multithreading technology opens a broad range of possible optimizations that can be applied to improve the performance of sequential and parallel applications. This thesis treat four possible optimization targeted for multithreading architectures: Speculative Precomputation, Threaded Multipath Execution, Speculative Multithreading and Communication threads. L'introduzione dei Multiprocessor On Chip (CMP) ha portato ad una sostanziale riformulazione della legge di Moore la quale afferma che il numero di cores in un singolo chip raddoppia ogni anno e mezzo. Il boom tecnologico relativo ai CMP ha dato un grande impulso al design relativo alla programmazione parallela diminuendo il gap con le architetture parallele. Allo stato attuale delle cose, un trend prominente relativo ai prodotti di high performance computing è rappresentato da CMP con nodi caratterizzati da hardware multithreading. Questa tecnologia prova a risolvere il sottoutilizzo di processori superscalari, dovuto alla mancanza di ILP (instruction level parallelism), permettendo la computazione simultanea di diversi programmi durante lo stesso time slot La tecnologia multithreading ha aperto un ampio spettro di possibili ottimizzazioni che possono essere utilizzate al fine di migliorare le performance di applicazioni sequenziali e parallele. Questa tesi tratta quattro possibili ottimizzazioni indirizzate per architetture multithreading: Speculative Precomputation (Helper Thread), Threaded Multipath Execution, Speculative Multithreading and Communication Threads

Levo - A scalable processor with high IPC

The Levo high IPC microarchitecture is described and evaluated. Levo employs instruction time-tags and Active Stations to ensure correct operation in a rampantly speculative and out-of-order resource flow execution model. The Tomasulo-algorithm-like broadcast buses are segmented; their lengths are constant, that is, do not increase with machine size. This helps to make Levo scalable. Known high-ILP techniques such as Disjoint Eager Execution and Minimal Control Dependencies are implemented in novel ways. Examples of basic Levo operation are given. A chip floorplan of Levo is presented, demonstrating feasibility and little cycle-time impact. Levo is simulated, characterizing its basic geometry and its performance

Book of abstracts of the 10th International Chemical and Biological Engineering Conference: CHEMPOR 2008

This book contains the extended abstracts presented at the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008, held in Braga, Portugal, over 3 days, from the 4th to the 6th of September, 2008. Previous editions took place in Lisboa (1975, 1889, 1998), Braga (1978), Póvoa de Varzim (1981), Coimbra (1985, 2005), Porto (1993), and Aveiro (2001). The conference was jointly organized by the University of Minho, “Ordem dos Engenheiros”, and the IBB - Institute for Biotechnology and Bioengineering with the usual support of the “Sociedade Portuguesa de Química” and, by the first time, of the “Sociedade Portuguesa de Biotecnologia”. Thirty years elapsed since CHEMPOR was held at the University of Minho, organized by T.R. Bott, D. Allen, A. Bridgwater, J.J.B. Romero, L.J.S. Soares and J.D.R.S. Pinheiro. We are fortunate to have Profs. Bott, Soares and Pinheiro in the Honor Committee of this 10th edition, under the high Patronage of his Excellency the President of the Portuguese Republic, Prof. Aníbal Cavaco Silva. The opening ceremony will confer Prof. Bott with a “Long Term Achievement” award acknowledging the important contribution Prof. Bott brought along more than 30 years to the development of the Chemical Engineering science, to the launch of CHEMPOR series and specially to the University of Minho. Prof. Bott’s inaugural lecture will address the importance of effective energy management in processing operations, particularly in the effectiveness of heat recovery and the associated reduction in greenhouse gas emission from combustion processes. The CHEMPOR series traditionally brings together both young and established researchers and end users to discuss recent developments in different areas of Chemical Engineering. The scope of this edition is broadening out by including the Biological Engineering research. One of the major core areas of the conference program is life quality, due to the importance that Chemical and Biological Engineering plays in this area. “Integration of Life Sciences & Engineering” and “Sustainable Process-Product Development through Green Chemistry” are two of the leading themes with papers addressing such important issues. This is complemented with additional leading themes including “Advancing the Chemical and Biological Engineering Fundamentals”, “Multi-Scale and/or Multi-Disciplinary Approach to Process-Product Innovation”, “Systematic Methods and Tools for Managing the Complexity”, and “Educating Chemical and Biological Engineers for Coming Challenges” which define the extended abstracts arrangements along this book. A total of 516 extended abstracts are included in the book, consisting of 7 invited lecturers, 15 keynote, 105 short oral presentations given in 5 parallel sessions, along with 6 slots for viewing 389 poster presentations. Full papers are jointly included in the companion Proceedings in CD-ROM. All papers have been reviewed and we are grateful to the members of scientific and organizing committees for their evaluations. It was an intensive task since 610 submitted abstracts from 45 countries were received. It has been an honor for us to contribute to setting up CHEMPOR 2008 during almost two years. We wish to thank the authors who have contributed to yield a high scientific standard to the program. We are thankful to the sponsors who have contributed decisively to this event. We also extend our gratefulness to all those who, through their dedicated efforts, have assisted us in this task. On behalf of the Scientific and Organizing Committees we wish you that together with an interesting reading, the scientific program and the social moments organized will be memorable for all.Fundação para a Ciência e a Tecnologia (FCT