Performance analysis and improvement of InfiniBand networks. Modelling and effective Quality-of-Service mechanisms for interconnection networks in cluster computing systems.

The InfiniBand Architecture (IBA) network has been proposed as a new industrial standard with high-bandwidth and low-latency suitable for constructing high-performance interconnected cluster computing systems. This architecture replaces the traditional bus-based interconnection with a switch-based network for the server Input-Output (I/O) and inter-processor communications. The efficient Quality-of-Service (QoS) mechanism is fundamental to ensure the import at QoS metrics, such as maximum throughput and minimum latency, leaving aside other aspects like guarantee to reduce the delay, blocking probability, and mean queue length, etc. Performance modelling and analysis has been and continues to be of great theoretical and practical importance in the design and development of communication networks. This thesis aims to investigate efficient and cost-effective QoS mechanisms for performance analysis and improvement of InfiniBand networks in cluster-based computing systems. Firstly, a rate-based source-response link-by-link admission and congestion control function with improved Explicit Congestion Notification (ECN) packet marking scheme is developed. This function adopts the rate control to reduce congestion of multiple-class traffic. Secondly, a credit-based flow control scheme is presented to reduce the mean queue length, throughput and response time of the system. In order to evaluate the performance of this scheme, a new queueing network model is developed. Theoretical analysis and simulation experiments show that these two schemes are quite effective and suitable for InfiniBand networks. Finally, to obtain a thorough and deep understanding of the performance attributes of InfiniBand Architecture network, two efficient threshold function flow control mechanisms are proposed to enhance the QoS of InfiniBand networks; one is Entry Threshold that sets the threshold for each entry in the arbitration table, and other is Arrival Job Threshold that sets the threshold based on the number of jobs in each Virtual Lane. Furthermore, the principle of Maximum Entropy is adopted to analyse these two new mechanisms with the Generalized Exponential (GE)-Type distribution for modelling the inter-arrival times and service times of the input traffic. Extensive simulation experiments are conducted to validate the accuracy of the analytical models

Optimizing Communication for Massively Parallel Processing

The current trends in high performance computing show that large machines with tens of thousands of processors will soon be readily available. The IBM Bluegene-L machine with 128k processors (which is currently being deployed) is an important step in this direction. In this scenario, it is going to be a significant burden for the programmer to manually scale his applications. This task of scaling involves addressing issues like load-imbalance and communication overhead. In this thesis, we explore several communication optimizations to help parallel applications to easily scale on a large number of processors. We also present automatic runtime techniques to relieve the programmer from the burden of optimizing communication in his applications. This thesis explores processor virtualization to improve communication performance in applications. With processor virtualization, the computation is mapped to virtual processors (VPs). After one VP has finished computation and is waiting for responses to its messages, another VP can compute, thus overlapping communication with computation. This overlap is only effective if the processor overhead of the communication operation is a small fraction of the total communication time. Fortunately, with network interfaces having co-processors, this happens to be true and processor virtualization has a natural advantage on such interconnects. The communication optimizations we present in this thesis, are motivated by applications such as NAMD (a classical molecular dynamics application) and CPAIMD (a quantum chemistry application). Applications like NAMD and CPAIMD consume a fair share of the time available on supercomputers. So, improving their performance would be of great value. We have successfully scaled NAMD to 1TF of peak performance on 3000 processors of PSC Lemieux, using the techniques presented in this thesis. We study both point-to-point communication and collective communication (specifically all-to-all communication). On a large number of processors all-to-all communication can take several milli-seconds to finish. With synchronous collectives defined in MPI, the processor idles while the collective messages are in flight. Therefore, we demonstrate an asynchronous collective communication framework, to let the CPU compute while the all-to-all messages are in flight. We also show that the best strategy for all-to-all communication depends on the message size, number of processors and other dynamic parameters. This suggests that these parameters can be observed at runtime and used to choose the optimal strategy for all-to-all communication. In this thesis, we demonstrate adaptive strategy switching for all-to-all communication. The communication optimization framework presented in this thesis, has been designed to optimize communication in the context of processor virtualization and dynamic migrating objects. We present the streaming strategy to optimize fine grained object-to-object communication. In this thesis, we motivate the need for hardware collectives, as processor based collectives can be delayed by intermediate that processors busy with computation. We explore a next generation interconnect that supports collectives in the switching hardware. We show the performance gains of hardware collectives through synthetic benchmarks

Efficient mechanisms to provide fault tolerance in interconnection networks for pc clusters

Actualmente, los clusters de PC son un alternativa rentable a los computadores paralelos. En estos sistemas, miles de componentes (procesadores y/o discos duros) se conectan a través de redes de interconexión de altas prestaciones. Entre las tecnologías de red actualmente disponibles para construir clusters, InfiniBand (IBA) ha emergido como un nuevo estándar de interconexión para clusters. De hecho, ha sido adoptado por muchos de los sistemas más potentes construidos actualmente (lista top500). A medida que el número de nodos aumenta en estos sistemas, la red de interconexión también crece. Junto con el aumento del número de componentes la probabilidad de averías aumenta dramáticamente, y así, la tolerancia a fallos en el sistema en general, y de la red de interconexión en particular, se convierte en una necesidad. Desafortunadamente, la mayor parte de las estrategias de encaminamiento tolerantes a fallos propuestas para los computadores masivamente paralelos no pueden ser aplicadas porque el encaminamiento y las transiciones de canal virtual son deterministas en IBA, lo que impide que los paquetes eviten los fallos. Por lo tanto, son necesarias nuevas estrategias para tolerar fallos. Por ello, esta tesis se centra en proporcionar los niveles adecuados de tolerancia a fallos a los clusters de PC, y en particular a las redes IBA. En esta tesis proponemos y evaluamos varios mecanismos adecuados para las redes de interconexión para clusters. El primer mecanismo para proporcionar tolerancia a fallos en IBA (al que nos referimos como encaminamiento tolerante a fallos basado en transiciones; TFTR) consiste en usar varias rutas disjuntas entre cada par de nodos origen-destino y seleccionar la ruta apropiada en el nodo fuente usando el mecanismo APM proporcionado por IBA. Consiste en migrar las rutas afectadas por el fallo a las rutas alternativas sin fallos. Sin embargo, con este fin, es necesario un algoritmo eficiente de encaminamiento capaz de proporcionar suficientesMontañana Aliaga, JM. (2008). Efficient mechanisms to provide fault tolerance in interconnection networks for pc clusters [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/2603Palanci

Routing on the Channel Dependency Graph:: A New Approach to Deadlock-Free, Destination-Based, High-Performance Routing for Lossless Interconnection Networks

In the pursuit for ever-increasing compute power, and with Moore's law slowly coming to an end, high-performance computing started to scale-out to larger systems. Alongside the increasing system size, the interconnection network is growing to accommodate and connect tens of thousands of compute nodes. These networks have a large influence on total cost, application performance, energy consumption, and overall system efficiency of the supercomputer. Unfortunately, state-of-the-art routing algorithms, which define the packet paths through the network, do not utilize this important resource efficiently. Topology-aware routing algorithms become increasingly inapplicable, due to irregular topologies, which either are irregular by design, or most often a result of hardware failures. Exchanging faulty network components potentially requires whole system downtime further increasing the cost of the failure. This management approach becomes more and more impractical due to the scale of today's networks and the accompanying steady decrease of the mean time between failures. Alternative methods of operating and maintaining these high-performance interconnects, both in terms of hardware- and software-management, are necessary to mitigate negative effects experienced by scientific applications executed on the supercomputer. However, existing topology-agnostic routing algorithms either suffer from poor load balancing or are not bounded in the number of virtual channels needed to resolve deadlocks in the routing tables. Using the fail-in-place strategy, a well-established method for storage systems to repair only critical component failures, is a feasible solution for current and future HPC interconnects as well as other large-scale installations such as data center networks. Although, an appropriate combination of topology and routing algorithm is required to minimize the throughput degradation for the entire system. This thesis contributes a network simulation toolchain to facilitate the process of finding a suitable combination, either during system design or while it is in operation. On top of this foundation, a key contribution is a novel scheduling-aware routing, which reduces fault-induced throughput degradation while improving overall network utilization. The scheduling-aware routing performs frequent property preserving routing updates to optimize the path balancing for simultaneously running batch jobs. The increased deployment of lossless interconnection networks, in conjunction with fail-in-place modes of operation and topology-agnostic, scheduling-aware routing algorithms, necessitates new solutions to solve the routing-deadlock problem. Therefore, this thesis further advances the state-of-the-art by introducing a novel concept of routing on the channel dependency graph, which allows the design of an universally applicable destination-based routing capable of optimizing the path balancing without exceeding a given number of virtual channels, which are a common hardware limitation. This disruptive innovation enables implicit deadlock-avoidance during path calculation, instead of solving both problems separately as all previous solutions

Non-minimal adaptive routing for efficient interconnection networks

RESUMEN: La red de interconexión es un concepto clave de los sistemas de computación paralelos. El primer aspecto que define una red de interconexión es su topología. Habitualmente, las redes escalables y eficientes en términos de coste y consumo energético tienen bajo diámetro y se basan en topologías que encaran el límite de Moore y en las que no hay diversidad de caminos mínimos. Una vez definida la topología, quedando implícitamente definidos los límites de rendimiento de la red, es necesario diseñar un algoritmo de enrutamiento que se acerque lo máximo posible a esos límites y debido a la ausencia de caminos mínimos, este además debe explotar los caminos no mínimos cuando el tráfico es adverso. Estos algoritmos de enrutamiento habitualmente seleccionan entre rutas mínimas y no mínimas en base a las condiciones de la red. Las rutas no mínimas habitualmente se basan en el algoritmo de balanceo de carga propuesto por Valiant, esto implica que doblan la longitud de las rutas mínimas y por lo tanto, la latencia soportada por los paquetes se incrementa. En cuanto a la tecnología, desde su introducción en entornos HPC a principios de los años 2000, Ethernet ha sido usado en un porcentaje representativo de los sistemas. Esta tesis introduce una implementación realista y competitiva de una red escalable y sin pérdidas basada en dispositivos de red Ethernet commodity, considerando topologías de bajo diámetro y bajo consumo energético y logrando un ahorro energético de hasta un 54%. Además, propone un enrutamiento sobre la citada arquitectura, en adelante QCN-Switch, el cual selecciona entre rutas mínimas y no mínimas basado en notificaciones de congestión explícitas. Una vez implementada la decisión de enrutar siguiendo rutas no mínimas, se introduce un enrutamiento adaptativo en fuente capaz de adaptar el número de saltos en las rutas no mínimas. Este enrutamiento, en adelante ACOR, es agnóstico de la topología y mejora la latencia en hasta un 28%. Finalmente, se introduce un enrutamiento dependiente de la topología, en adelante LIAN, que optimiza el número de saltos de las rutas no mínimas basado en las condiciones de la red. Los resultados de su evaluación muestran que obtiene una latencia cuasi óptima y mejora el rendimiento de algoritmos de enrutamiento actuales reduciendo la latencia en hasta un 30% y obteniendo un rendimiento estable y equitativo.ABSTRACT: Interconnection network is a key concept of any parallel computing system. The first aspect to define an interconnection network is its topology. Typically, power and cost-efficient scalable networks with low diameter rely on topologies that approach the Moore bound in which there is no minimal path diversity. Once the topology is defined, the performance bounds of the network are determined consequently, so a suitable routing algorithm should be designed to accomplish as much as possible of those limits and, due to the lack of minimal path diversity, it must exploit non-minimal paths when the traffic pattern is adversarial. These routing algorithms usually select between minimal and non-minimal paths based on the network conditions, where the non-minimal paths are built according to Valiant load-balancing algorithm. This implies that these paths double the length of minimal ones and then the latency supported by packets increases. Regarding the technology, from its introduction in HPC systems in the early 2000s, Ethernet has been used in a significant fraction of the systems. This dissertation introduces a realistic and competitive implementation of a scalable lossless Ethernet network for HPC environments considering low-diameter and low-power topologies. This allows for up to 54% power savings. Furthermore, it proposes a routing upon the cited architecture, hereon QCN-Switch, which selects between minimal and non-minimal paths per packet based on explicit congestion notifications instead of credits. Once the miss-routing decision is implemented, it introduces two mechanisms regarding the selection of the intermediate switch to develop a source adaptive routing algorithm capable of adapting the number of hops in the non-minimal paths. This routing, hereon ACOR, is topology-agnostic and improves average latency in all cases up to 28%. Finally, a topology-dependent routing, hereon LIAN, is introduced to optimize the number of hops in the non-minimal paths based on the network live conditions. Evaluations show that LIAN obtains almost-optimal latency and outperforms state-of-the-art adaptive routing algorithms, reducing latency by up to 30.0% and providing stable throughput and fairness.This work has been supported by the Spanish Ministry of Education, Culture and Sports under grant FPU14/02253, the Spanish Ministry of Economy, Industry and Competitiveness under contracts TIN2010-21291-C02-02, TIN2013-46957-C2-2-P, and TIN2013-46957-C2-2-P (AEI/FEDER, UE), the Spanish Research Agency under contract PID2019-105660RBC22/AEI/10.13039/501100011033, the European Union under agreements FP7-ICT-2011- 7-288777 (Mont-Blanc 1) and FP7-ICT-2013-10-610402 (Mont-Blanc 2), the University of Cantabria under project PAR.30.P072.64004, and by the European HiPEAC Network of Excellence through an internship grant supported by the European Union’s Horizon 2020 research and innovation program under grant agreement No. H2020-ICT-2015-687689

Improving the Scalability of High Performance Computer Systems

Improving the performance of future computing systems will be based upon the ability of increasing the scalability of current technology. New paths need to be explored, as operating principles that were applied up to now are becoming irrelevant for upcoming computer architectures. It appears that scaling the number of cores, processors and nodes within an system represents the only feasible alternative to achieve Exascale performance. To accomplish this goal, we propose three novel techniques addressing different layers of computer systems. The Tightly Coupled Cluster technique significantly improves the communication for inter node communication within compute clusters. By improving the latency by an order of magnitude over existing solutions the cost of communication is considerably reduced. This enables to exploit fine grain parallelism within applications, thereby, extending the scalability considerably. The mechanism virtually moves the network interconnect into the processor, bypassing the latency of the I/O interface and rendering protocol conversions unnecessary. The technique is implemented entirely through firmware and kernel layer software utilizing off-the-shelf AMD processors. We present a proof-of-concept implementation and real world benchmarks to demonstrate the superior performance of our technique. In particular, our approach achieves a software-to-software communication latency of 240 ns between two remote compute nodes. The second part of the dissertation introduces a new framework for scalable Networks-on-Chip. A novel rapid prototyping methodology is proposed, that accelerates the design and implementation substantially. Due to its flexibility and modularity a large application space is covered ranging from Systems-on-chip, to high performance many-core processors. The Network-on-Chip compiler enables to generate complex networks in the form of synthesizable register transfer level code from an abstract design description. Our engine supports different target technologies including Field Programmable Gate Arrays and Application Specific Integrated Circuits. The framework enables to build large designs while minimizing development and verification efforts. Many topologies and routing algorithms are supported by partitioning the tasks into several layers and by the introduction of a protocol agnostic architecture. We provide a thorough evaluation of the design that shows excellent results regarding performance and scalability. The third part of the dissertation addresses the Processor-Memory Interface within computer architectures. The increasing compute power of many-core processors, leads to an equally growing demand for more memory bandwidth and capacity. Current processor designs exhibit physical limitations that restrict the scalability of main memory. To address this issue we propose a memory extension technique that attaches large amounts of DRAM memory to the processor via a low pin count interface using high speed serial transceivers. Our technique transparently integrates the extension memory into the system architecture by providing full cache coherency. Therefore, applications can utilize the memory extension by applying regular shared memory programming techniques. By supporting daisy chained memory extension devices and by introducing the asymmetric probing approach, the proposed mechanism ensures high scalability. We furthermore propose a DMA offloading technique to improve the performance of the processor memory interface. The design has been implemented in a Field Programmable Gate Array based prototype. Driver software and firmware modifications have been developed to bring up the prototype in a Linux based system. We show microbenchmarks that prove the feasibility of our design

Study of the data acquisition network for the triggerless data acquisition of the LHCb experiment and new particle track reconstruction strategies for the LHCb upgrade

The LHCb experiment will receive a major upgrade by the end of February 2021. This upgrade will allow the recording of proton-proton collision data at $\sqrt{s} = 14\ \text{TeV}$ with an instantaneous luminosity of $2 \cdot 10^{33}\ \text{cm}^{-2}\text{s}^{-1}$, making possible measurements of unprecedented precision in the $b$ and $c$-quark flavour sectors. For taking advantage of the increased luminosity provided, the data acquisition system will receive a substantial upgrade. The upgraded system will be capable of processing the full collision rate of $30\ \text{MHz}$, without any low-level hardware preselection. This new design constraint poses a non-trivial technological challenge, both from a networking and computing point of view. A possible design of a $32\ \text{Tb/s}$ data acquisition network is presented, and low-level network simulations are used to validate the design. Those simulations use an accurate behavioural model developed and optimised for this specific purpose. It is mandatory to optimise the reconstruction algorithms using a computing and physics approach, to perform the online reconstruction of the full $30\ \text{MHz}$ $pp$ collisions rate. A new parametrisation of the charged particles' bending generated by the dipole of the LHCb experiment is presented. The accuracy of the model is tested against Monte Carlo data. This strategy can reduce by a factor four the size of the search windows needed in the SciFi sub-detector. The LookingForward algorithm in the Allen framework uses this model