Efficient Algorithms And Optimizations For Scientific Computing On Many-Core Processors

Designing efficient algorithms for many-core and multicore architectures requires using different strategies to allow for the best exploitation of the hardware resources on those architectures. Researchers have ported many scientific applications to modern many-core and multicore parallel architectures, and by doing so they have achieved significant speedups over running on single CPU cores. While many applications have achieved significant speedups, some applications still require more effort to accelerate due to their inherently serial behavior. One class of applications that has this serial behavior is the Monte Carlo simulations. Monte Carlo simulations have been used to simulate many problems in statistical physics and statistical mechanics that were not possible to simulate using Molecular Dynamics. While there are a fair number of well-known and recognized GPU Molecular Dynamics codes, the existing Monte Carlo ensemble simulations have not been ported to the GPU, so they are relatively slow and could not run large systems in a reasonable amount of time. Due to the previously mentioned shortcomings of existing Monte Carlo ensemble codes and due to the interest of researchers to have a fast Monte Carlo simulation framework that can simulate large systems, a new GPU framework called GOMC is implemented to simulate different particle and molecular-based force fields and ensembles. GOMC simulates different Monte Carlo ensembles such as the canonical, grand canonical, and Gibbs ensembles. This work describes many challenges in developing a GPU Monte Carlo code for such ensembles and how I addressed these challenges. This work also describes efficient many-core and multicore large-scale energy calculations for Monte Carlo Gibbs ensemble using cell lists. Designing Monte Carlo molecular simulations is challenging as they have less computation and parallelism when compared to similar molecular dynamics applications. The modified cell list allows for more speedup gains for energy calculations on both many-core and multicore architectures when compared to other implementations without using the conventional cell lists. The work presents results and analysis of the cell list algorithms for each one of the parallel architectures using top of the line GPUs, CPUs, and Intel’s Phi coprocessors. In addition, the work evaluates the performance of the cell list algorithms for different problem sizes and different radial cutoffs. In addition, this work evaluates two cell list approaches, a hybrid MPI+OpenMP approach and a hybrid MPI+CUDA approach. The cell list methods are evaluated on a small cluster of multicore CPUs, Intel Phi coprocessors, and GPUs. The performance results are evaluated using different combinations of MPI processes, threads, and problem sizes. Another application presented in this dissertation involves the understanding of the properties of crystalline materials, and their design and control. Recent developments include the introduction of new models to simulate system behavior and properties that are of large experimental and theoretical interest. One of those models is the Phase-Field Crystal (PFC) model. The PFC model has enabled researchers to simulate 2D and 3D crystal structures and study defects such as dislocations and grain boundaries. In this work, GPUs are used to accelerate various dynamic properties of polycrystals in the 2D PFC model. Some properties require very intensive computation that may involve hundreds of thousands of atoms. The GPU implementation has achieved significant speedups of more than 46 times for some large systems simulations

Exploring Computational Chemistry on Emerging Architectures

Emerging architectures, such as next generation microprocessors, graphics processing units, and Intel MIC cards, are being used with increased popularity in high performance computing. Each of these architectures has advantages over previous generations of architectures including performance, programmability, and power efficiency. With the ever-increasing performance of these architectures, scientific computing applications are able to attack larger, more complicated problems. However, since applications perform differently on each of the architectures, it is difficult to determine the best tool for the job. This dissertation makes the following contributions to computer engineering and computational science. First, this work implements the computational chemistry variational path integral application, QSATS, on various architectures, ranging from microprocessors to GPUs to Intel MICs. Second, this work explores the use of analytical performance modeling to predict the runtime and scalability of the application on the architectures. This allows for a comparison of the architectures when determining which to use for a set of program input parameters. The models presented in this dissertation are accurate within 6%. This work combines novel approaches to this algorithm and exploration of the various architectural features to develop the application to perform at its peak. In addition, this expands the understanding of computational science applications and their implementation on emerging architectures while providing insight into the performance, scalability, and programmer productivity

Mechanistic Regimes of Vibronic Transport in a Heterodimer and the Design Principle of Incoherent Vibronic Transport in Phycobiliproteins

Following the observation of coherent oscillations in non-linear spectra of photosynthetic pigment protein complexes, particularly phycobilliprotein such as PC645, coherent vibronic transport has been suggested as a design principle for novel light harvesting materials operating at room temperature. Vibronic transport between energetically remote pigments is coherent when the presence of a resonant vibration supports transient delocalization between the pair of electronic excited states. Here, we establish the mechanism of vibronic transport for a model heterodimer across a wide range of molecular parameter values. The resulting mechanistic map demonstrates that the molecular parameters of phycobiliproteins in fact support incoherent vibronic transport. This result points to an important design principle: incoherent vibronic transport is more efficient than a coherent mechanism when energetic disorder exceeds the coupling between the donor and vibrationally excited acceptor states. Finally, our results suggest that the role of coherent vibronic transport in pigment protein complexes should be reevaluated

On the Enhancement of Remote GPU Virtualization in High Performance Clusters

Graphics Processing Units (GPUs) are being adopted in many computing facilities given their extraordinary computing power, which makes it possible to accelerate many general purpose applications from different domains. However, GPUs also present several side effects, such as increased acquisition costs as well as larger space requirements. They also require more powerful energy supplies. Furthermore, GPUs still consume some amount of energy while idle and their utilization is usually low for most workloads. In a similar way to virtual machines, the use of virtual GPUs may address the aforementioned concerns. In this regard, the remote GPU virtualization mechanism allows an application being executed in a node of the cluster to transparently use the GPUs installed at other nodes. Moreover, this technique allows to share the GPUs present in the computing facility among the applications being executed in the cluster. In this way, several applications being executed in different (or the same) cluster nodes can share one or more GPUs located in other nodes of the cluster. Sharing GPUs should increase overall GPU utilization, thus reducing the negative impact of the side effects mentioned before. Reducing the total amount of GPUs installed in the cluster may also be possible. In this dissertation we enhance one framework offering remote GPU virtualization capabilities, referred to as rCUDA, for its use in high-performance clusters. While the initial prototype version of rCUDA demonstrated its functionality, it also revealed concerns with respect to usability, performance, and support for new GPU features, which prevented its used in production environments. These issues motivated this thesis, in which all the research is primarily conducted with the aim of turning rCUDA into a production-ready solution for eventually transferring it to industry. The new version of rCUDA resulting from this work presents a reduction of up to 35% in execution time of the applications analyzed with respect to the initial version. Compared to the use of local GPUs, the overhead of this new version of rCUDA is below 5% for the applications studied when using the latest high-performance computing networks available.Las unidades de procesamiento gráfico (Graphics Processing Units, GPUs) están siendo utilizadas en muchas instalaciones de computación dada su extraordinaria capacidad de cálculo, la cual hace posible acelerar muchas aplicaciones de propósito general de diferentes dominios. Sin embargo, las GPUs también presentan algunas desventajas, como el aumento de los costos de adquisición, así como mayores requerimientos de espacio. Asimismo, también requieren un suministro de energía más potente. Además, las GPUs consumen una cierta cantidad de energía aún estando inactivas, y su utilización suele ser baja para la mayoría de las cargas de trabajo. De manera similar a las máquinas virtuales, el uso de GPUs virtuales podría hacer frente a los inconvenientes mencionados. En este sentido, el mecanismo de virtualización remota de GPUs permite que una aplicación que se ejecuta en un nodo de un clúster utilice de forma transparente las GPUs instaladas en otros nodos de dicho clúster. Además, esta técnica permite compartir las GPUs presentes en el clúster entre las aplicaciones que se ejecutan en el mismo. De esta manera, varias aplicaciones que se ejecutan en diferentes nodos de clúster (o los mismos) pueden compartir una o más GPUs ubicadas en otros nodos del clúster. Compartir GPUs aumenta la utilización general de la GPU, reduciendo así el impacto negativo de las desventajas anteriormente mencionadas. De igual forma, este mecanismo también permite reducir la cantidad total de GPUs instaladas en el clúster. En esta tesis mejoramos un entorno de trabajo llamado rCUDA, el cual ofrece funcionalidades de virtualización remota de GPUs para su uso en clusters de altas prestaciones. Si bien la versión inicial del prototipo de rCUDA demostró su funcionalidad, también reveló dificultades con respecto a la usabilidad, el rendimiento y el soporte para nuevas características de las GPUs, lo cual impedía su uso en entornos de producción. Estas consideraciones motivaron la presente tesis, en la que toda la investigación llevada a cabo tiene como objetivo principal convertir rCUDA en una solución lista para su uso entornos de producción, con la finalidad de transferirla eventualmente a la industria. La nueva versión de rCUDA resultante de este trabajo presenta una reducción de hasta el 35% en el tiempo de ejecución de las aplicaciones analizadas con respecto a la versión inicial. En comparación con el uso de GPUs locales, la sobrecarga de esta nueva versión de rCUDA es inferior al 5% para las aplicaciones estudiadas cuando se utilizan las últimas redes de computación de altas prestaciones disponibles.Les unitats de processament gràfic (Graphics Processing Units, GPUs) estan sent utilitzades en moltes instal·lacions de computació donada la seva extraordinària capacitat de càlcul, la qual fa possible accelerar moltes aplicacions de propòsit general de diferents dominis. No obstant això, les GPUs també presenten alguns desavantatges, com l'augment dels costos d'adquisició, així com major requeriment d'espai. Així mateix, també requereixen un subministrament d'energia més potent. A més, les GPUs consumeixen una certa quantitat d'energia encara estant inactives, i la seua utilització sol ser baixa per a la majoria de les càrregues de treball. D'una manera semblant a les màquines virtuals, l'ús de GPUs virtuals podria fer front als inconvenients esmentats. En aquest sentit, el mecanisme de virtualització remota de GPUs permet que una aplicació que s'executa en un node d'un clúster utilitze de forma transparent les GPUs instal·lades en altres nodes d'aquest clúster. A més, aquesta tècnica permet compartir les GPUs presents al clúster entre les aplicacions que s'executen en el mateix. D'aquesta manera, diverses aplicacions que s'executen en diferents nodes de clúster (o els mateixos) poden compartir una o més GPUs ubicades en altres nodes del clúster. Compartir GPUs augmenta la utilització general de la GPU, reduint així l'impacte negatiu dels desavantatges anteriorment esmentades. A més a més, aquest mecanisme també permet reduir la quantitat total de GPUs instal·lades al clúster. En aquesta tesi millorem un entorn de treball anomenat rCUDA, el qual ofereix funcionalitats de virtualització remota de GPUs per al seu ús en clústers d'altes prestacions. Si bé la versió inicial del prototip de rCUDA va demostrar la seua funcionalitat, també va revelar dificultats pel que fa a la usabilitat, el rendiment i el suport per a noves característiques de les GPUs, la qual cosa impedia el seu ús en entorns de producció. Aquestes consideracions van motivar la present tesi, en què tota la investigació duta a terme té com a objectiu principal convertir rCUDA en una solució preparada per al seu ús entorns de producció, amb la finalitat de transferir-la eventualment a la indústria. La nova versió de rCUDA resultant d'aquest treball presenta una reducció de fins al 35% en el temps d'execució de les aplicacions analitzades respecte a la versió inicial. En comparació amb l'ús de GPUs locals, la sobrecàrrega d'aquesta nova versió de rCUDA és inferior al 5% per a les aplicacions estudiades quan s'utilitzen les últimes xarxes de computació d'altes prestacions disponibles.Reaño González, C. (2017). On the Enhancement of Remote GPU Virtualization in High Performance Clusters [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86219TESISPremios Extraordinarios de tesis doctorale

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.Comment: 64 pages, 11 figure