Electromagnetic Waves

This volume is based on the contributions of several authors in electromagnetic waves propagations. Several issues are considered. The contents of most of the chapters are highlighting non classic presentation of wave propagation and interaction with matters. This volume bridges the gap between physics and engineering in these issues. Each chapter keeps the author notation that the reader should be aware of as he reads from chapter to the other

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

Cloud-efficient modelling and simulation of magnetic nano materials

Scientific simulations are rarely attempted in a cloud due to the substantial performance costs of virtualization. Considerable communication overheads, intolerable latencies, and inefficient hardware emulation are the main reasons why this emerging technology has not been fully exploited. On the other hand, the progress of computing infrastructure nowadays is strongly dependent on perspective storage medium development, where efficient micromagnetic simulations play a vital role in future memory design. This thesis addresses both these topics by merging micromagnetic simulations with the latest OpenStack cloud implementation while providing a time and costeffective alternative to expensive computing centers. However, many challenges have to be addressed before a high-performance cloud platform emerges as a solution for problems in micromagnetic research communities. First, the best solver candidate has to be selected and further improved, particularly in the parallelization and process communication domain. Second, a 3-level cloud communication hierarchy needs to be recognized and each segment adequately addressed. The required steps include breaking the VMisolation for the host’s shared memory activation, cloud network-stack tuning, optimization, and efficient communication hardware integration. The project work concludes with practical measurements and confirmation of successfully implemented simulation into an open-source cloud environment. It is achieved that the renewed Magpar solver runs for the first time in the OpenStack cloud by using ivshmem for shared memory communication. Also, extensive measurements proved the effectiveness of our solutions, yielding from sixty percent to over ten times better results than those achieved in the standard cloud.Aufgrund der erheblichen Leistungskosten der Virtualisierung werden wissenschaftliche Simulationen in einer Cloud selten versucht. Beträchtlicher Kommunikationsaufwand, erhebliche Latenzen und ineffiziente Hardwareemulation sind die Hauptgründe, warum diese aufkommende Technologie nicht vollständig genutzt wurde. Andererseits hängt der Fortschritt der Computertechnologie heutzutage stark von der Entwicklung perspektivischer Speichermedien ab, bei denen effiziente mikromagnetische Simulationen eine wichtige Rolle für die zukünftige Speichertechnologie spielen. Diese Arbeit befasst sich mit diesen beiden Themen, indem mikromagnetische Simulationen mit der neuesten OpenStack Cloud-Implementierung zusammengeführt werden, um eine zeit- und kostengünstige Alternative zu teuren Rechenzentren bereitzustellen. Viele Herausforderungen müssen jedoch angegangen werden, bevor eine leistungsstarke Cloud-Plattform als Lösung für Probleme in mikromagnetischen Forschungsgemeinschaften entsteht. Zunächst muss der beste Kandidat für die Lösung ausgewählt und weiter verbessert werden, insbesondere im Bereich der Parallelisierung und Prozesskommunikation. Zweitens muss eine 3-stufige CloudKommunikationshierarchie erkannt und jedes Segment angemessen adressiert werden. Die erforderlichen Schritte umfassen das Aufheben der VM-Isolation, um den gemeinsam genutzten Speicher zwischen Cloud-Instanzen zu aktivieren, die Optimierung des Cloud-Netzwerkstapels und die effiziente Integration von Kommunikationshardware. Die praktische Arbeit endet mit Messungen und der Bestätigung einer erfolgreich implementierten Simulation in einer Open-Source Cloud-Umgebung. Als Ergebnis haben wir erreicht, dass der neu erstellte Magpar-Solver zum ersten Mal in der OpenStack Cloud ausgeführt wird, indem ivshmem für die Shared-Memory Kommunikation verwendet wird. Umfangreiche Messungen haben auch die Wirksamkeit unserer Lösungen bewiesen und von sechzig Prozent bis zu zehnmal besseren Ergebnissen als in der Standard Cloud geführt

Architectural Support for Hypervisor-Level Intrusion Tolerance in MPSoCs

Increasingly, more aspects of our lives rely on the correctness and safety of computing systems, namely in the embedded and cyber-physical (CPS) domains, which directly affect the physical world. While systems have been pushed to their limits of functionality and efficiency, security threats and generic hardware quality have challenged their safety. Leveraging the enormous modular power, diversity and flexibility of these systems, often deployed in multi-processor systems-on-chip (MPSoC), requires careful orchestration of complex and heterogeneous resources, a task left to low-level software, e.g., hypervisors. In current architectures, this software forms a single point of failure (SPoF) and a worthwhile target for attacks: once compromised, adversaries can gain access to all information and full control over the platform and the environment it controls, for instance by means of privilege escalation and resource allocation. Currently, solutions to protect low-level software often rely on a simpler, underlying trusted layer which is often a SPoF itself and/or exhibits downgraded performance. Architectural hybridization allows for the introduction of trusted-trustworthy components, which combined with fault and intrusion tolerance (FIT) techniques leveraging replication, are capable of safely handling critical operations, thus eliminating SPoFs. Performing quorum-based consensus on all critical operations, in particular privilege management, ensures no compromised low-level software can single handedly manipulate privilege escalation or resource allocation to negatively affect other system resources by propagating faults or further extend an adversary’s control. However, the performance impact of traditional Byzantine fault tolerant state-machine replication (BFT-SMR) protocols is prohibitive in the context of MPSoCs due to the high costs of cryptographic operations and the quantity of messages exchanged. Furthermore, fault isolation, one of the key prerequisites in FIT, presents a complicated challenge to tackle, given the whole system resides within one chip in such platforms. There is so far no solution completely and efficiently addressing the SPoF issue in critical low-level management software. It is our aim, then, to devise such a solution that, additionally, reaps benefit of the tight-coupled nature of such manycore systems. In this thesis we present two architectures, using trusted-trustworthy mechanisms and consensus protocols, capable of protecting all software layers, specifically at low level, by performing critical operations only when a majority of correct replicas agree to their execution: iBFT and Midir. Moreover, we discuss ways in which these can be used at application level on the example of replicated applications sharing critical data structures. It then becomes possible to confine software-level faults and some hardware faults to the individual tiles of an MPSoC, converting tiles into fault containment domains, thus, enabling fault isolation and, consequently, making way to high-performance FIT at the lowest level

Architectural Support for Hypervisor-Level Intrusion Tolerance in MPSoCs

Increasingly, more aspects of our lives rely on the correctness and safety of computing systems, namely in the embedded and cyber-physical (CPS) domains, which directly affect the physical world. While systems have been pushed to their limits of functionality and efficiency, security threats and generic hardware quality have challenged their safety. Leveraging the enormous modular power, diversity and flexibility of these systems, often deployed in multi-processor systems-on-chip (MPSoC), requires careful orchestration of complex and heterogeneous resources, a task left to low-level software, e.g., hypervisors. In current architectures, this software forms a single point of failure (SPoF) and a worthwhile target for attacks: once compromised, adversaries can gain access to all information and full control over the platform and the environment it controls, for instance by means of privilege escalation and resource allocation. Currently, solutions to protect low-level software often rely on a simpler, underlying trusted layer which is often a SPoF itself and/or exhibits downgraded performance. Architectural hybridization allows for the introduction of trusted-trustworthy components, which combined with fault and intrusion tolerance (FIT) techniques leveraging replication, are capable of safely handling critical operations, thus eliminating SPoFs. Performing quorum-based consensus on all critical operations, in particular privilege management, ensures no compromised low-level software can single handedly manipulate privilege escalation or resource allocation to negatively affect other system resources by propagating faults or further extend an adversary’s control. However, the performance impact of traditional Byzantine fault tolerant state-machine replication (BFT-SMR) protocols is prohibitive in the context of MPSoCs due to the high costs of cryptographic operations and the quantity of messages exchanged. Furthermore, fault isolation, one of the key prerequisites in FIT, presents a complicated challenge to tackle, given the whole system resides within one chip in such platforms. There is so far no solution completely and efficiently addressing the SPoF issue in critical low-level management software. It is our aim, then, to devise such a solution that, additionally, reaps benefit of the tight-coupled nature of such manycore systems. In this thesis we present two architectures, using trusted-trustworthy mechanisms and consensus protocols, capable of protecting all software layers, specifically at low level, by performing critical operations only when a majority of correct replicas agree to their execution: iBFT and Midir. Moreover, we discuss ways in which these can be used at application level on the example of replicated applications sharing critical data structures. It then becomes possible to confine software-level faults and some hardware faults to the individual tiles of an MPSoC, converting tiles into fault containment domains, thus, enabling fault isolation and, consequently, making way to high-performance FIT at the lowest level

A shared-disk parallel cluster file system

Dissertação apresentada para obtenção do Grau de Doutor em Informática Pela Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaToday, clusters are the de facto cost effective platform both for high performance computing (HPC) as well as IT environments. HPC and IT are quite different environments and differences include, among others, their choices on file systems and storage: HPC favours parallel file systems geared towards maximum I/O bandwidth, but which are not fully POSIX-compliant and were devised to run on top of (fault prone) partitioned storage; conversely, IT data centres favour both external disk arrays (to provide highly available storage) and POSIX compliant file systems, (either general purpose or shared-disk cluster file systems, CFSs). These specialised file systems do perform very well in their target environments provided that applications do not require some lateral features, e.g., no file locking on parallel file systems, and no high performance writes over cluster-wide shared files on CFSs. In brief, we can say that none of the above approaches solves the problem of providing high levels of reliability and performance to both worlds. Our pCFS proposal makes a contribution to change this situation: the rationale is to take advantage on the best of both – the reliability of cluster file systems and the high performance of parallel file systems. We don’t claim to provide the absolute best of each, but we aim at full POSIX compliance, a rich feature set, and levels of reliability and performance good enough for broad usage – e.g., traditional as well as HPC applications, support of clustered DBMS engines that may run over regular files, and video streaming. pCFS’ main ideas include: · Cooperative caching, a technique that has been used in file systems for distributed disks but, as far as we know, was never used either in SAN based cluster file systems or in parallel file systems. As a result, pCFS may use all infrastructures (LAN and SAN) to move data. · Fine-grain locking, whereby processes running across distinct nodes may define nonoverlapping byte-range regions in a file (instead of the whole file) and access them in parallel, reading and writing over those regions at the infrastructure’s full speed (provided that no major metadata changes are required). A prototype was built on top of GFS (a Red Hat shared disk CFS): GFS’ kernel code was slightly modified, and two kernel modules and a user-level daemon were added. In the prototype, fine grain locking is fully implemented and a cluster-wide coherent cache is maintained through data (page fragments) movement over the LAN. Our benchmarks for non-overlapping writers over a single file shared among processes running on different nodes show that pCFS’ bandwidth is 2 times greater than NFS’ while being comparable to that of the Parallel Virtual File System (PVFS), both requiring about 10 times more CPU. And pCFS’ bandwidth also surpasses GFS’ (600 times for small record sizes, e.g., 4 KB, decreasing down to 2 times for large record sizes, e.g., 4 MB), at about the same CPU usage.Lusitania, Companhia de Seguros S.A, Programa IBM Shared University Research (SUR

Software for Exascale Computing - SPPEXA 2016-2019

This open access book summarizes the research done and results obtained in the second funding phase of the Priority Program 1648 "Software for Exascale Computing" (SPPEXA) of the German Research Foundation (DFG) presented at the SPPEXA Symposium in Dresden during October 21-23, 2019. In that respect, it both represents a continuation of Vol. 113 in Springer’s series Lecture Notes in Computational Science and Engineering, the corresponding report of SPPEXA’s first funding phase, and provides an overview of SPPEXA’s contributions towards exascale computing in today's sumpercomputer technology. The individual chapters address one or more of the research directions (1) computational algorithms, (2) system software, (3) application software, (4) data management and exploration, (5) programming, and (6) software tools. The book has an interdisciplinary appeal: scholars from computational sub-fields in computer science, mathematics, physics, or engineering will find it of particular interest