Survey of storage systems for high-performance computing

In current supercomputers, storage is typically provided by parallel distributed file systems for hot data and tape archives for cold data. These file systems are often compatible with local file systems due to their use of the POSIX interface and semantics, which eases development and debugging because applications can easily run both on workstations and supercomputers. There is a wide variety of file systems to choose from, each tuned for different use cases and implementing different optimizations. However, the overall application performance is often held back by I/O bottlenecks due to insufficient performance of file systems or I/O libraries for highly parallel workloads. Performance problems are dealt with using novel storage hardware technologies as well as alternative I/O semantics and interfaces. These approaches have to be integrated into the storage stack seamlessly to make them convenient to use. Upcoming storage systems abandon the traditional POSIX interface and semantics in favor of alternative concepts such as object and key-value storage; moreover, they heavily rely on technologies such as NVM and burst buffers to improve performance. Additional tiers of storage hardware will increase the importance of hierarchical storage management. Many of these changes will be disruptive and require application developers to rethink their approaches to data management and I/O. A thorough understanding of today's storage infrastructures, including their strengths and weaknesses, is crucially important for designing and implementing scalable storage systems suitable for demands of exascale computing

Freezing time emulating new and faster devices with virtual machines

Recent proposals of emerging data storage devices make it necessary to reevaluate all levels of the storage hierarchy to optimize the software stack performance. However, these new devices are not always widely available and therefore early experiments may be impossible. Emulators aim at mimicking as close as possible the behavior of a component, nonetheless, emulating new and fast storage devices is a challenging task due to time perception. In this work, we propose an approach to emulate storage devices using virtual machines (VMs) allowing the evaluation of a new device within a real system. We use a technique called freezing time, which pauses a VM to manipulate its clock and hide the real I/O completion time. Our approach is implemented at the hypervisor level and it is transparent to the guest operating system or application. We evaluate the technique under a real system using regular magnetic disks to emulate faster storage devices. Our method presented a latency error of 6.5% compared to a real device. Moreover, decoupled experiment between two laboratories, at the Barcelona Super Computing Center (BSC) in Spain, and the Center of Computer Science and Free Software (C3SL) in Brazil, demonstrated that our approach is reproducible and promising to allow the virtual evaluation of next-gen storage devices.This work was partially supported by the Spanish Ministry of Science and Innovation under the TIN2015-65316 Grant, the Generalitat de Catalunya under contract 2014-SGR-1051, the Serrapilheira Institute (Grant number Serra-1709-16621), as well as the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement no. 671951 (NEXTGenIO) for the extensions added after the MASCOTS paper.Peer ReviewedPostprint (author's final draft

A Survey on the Integration of NAND Flash Storage in the Design of File Systems and the Host Storage Software Stack

With the ever-increasing amount of data generate in the world, estimated to reach over 200 Zettabytes by 2025, pressure on efficient data storage systems is intensifying. The shift from HDD to flash-based SSD provides one of the most fundamental shifts in storage technology, increasing performance capabilities significantly. However, flash storage comes with different characteristics than prior HDD storage technology. Therefore, storage software was unsuitable for leveraging the capabilities of flash storage. As a result, a plethora of storage applications have been design to better integrate with flash storage and align with flash characteristics. In this literature study we evaluate the effect the introduction of flash storage has had on the design of file systems, which providing one of the most essential mechanisms for managing persistent storage. We analyze the mechanisms for effectively managing flash storage, managing overheads of introduced design requirements, and leverage the capabilities of flash storage. Numerous methods have been adopted in file systems, however prominently revolve around similar design decisions, adhering to the flash hardware constrains, and limiting software intervention. Future design of storage software remains prominent with the constant growth in flash-based storage devices and interfaces, providing an increasing possibility to enhance flash integration in the host storage software stack

A Survey on the Integration of NAND Flash Storage in the Design of File Systems and the Host Storage Software Stack

With the ever-increasing amount of data generate in the world, estimated to reach over 200 Zettabytes by 2025, pressure on efficient data storage systems is intensifying. The shift from HDD to flash-based SSD provides one of the most fundamental shifts in storage technology, increasing performance capabilities significantly. However, flash storage comes with different characteristics than prior HDD storage technology. Therefore, storage software was unsuitable for leveraging the capabilities of flash storage. As a result, a plethora of storage applications have been design to better integrate with flash storage and align with flash characteristics. In this literature study we evaluate the effect the introduction of flash storage has had on the design of file systems, which providing one of the most essential mechanisms for managing persistent storage. We analyze the mechanisms for effectively managing flash storage, managing overheads of introduced design requirements, and leverage the capabilities of flash storage. Numerous methods have been adopted in file systems, however prominently revolve around similar design decisions, adhering to the flash hardware constrains, and limiting software intervention. Future design of storage software remains prominent with the constant growth in flash-based storage devices and interfaces, providing an increasing possibility to enhance flash integration in the host storage software stack

A differentiated proposal of three dimension i/o performance characterization model focusing on storage environments

The I/O bottleneck remains a central issue in high-performance environments. Cloud computing, high-performance computing (HPC) and big data environments share many underneath difficulties to deliver data at a desirable time rate requested by high-performance applications. This increases the possibility of creating bottlenecks throughout the application feeding process by bottom hardware devices located in the storage system layer. In the last years, many researchers have been proposed solutions to improve the I/O architecture considering different approaches. Some of them take advantage of hardware devices while others focus on a sophisticated software approach. However, due to the complexity of dealing with high-performance environments, creating solutions to improve I/O performance in both software and hardware is challenging and gives researchers many opportunities. Classifying these improvements in different dimensions allows researchers to understand how these improvements have been built over the years and how it progresses. In addition, it also allows future efforts to be directed to research topics that have developed at a lower rate, balancing the general development process. This research present a three-dimension characterization model for classifying research works on I/O performance improvements for large scale storage computing facilities. This classification model can also be used as a guideline framework to summarize researches providing an overview of the actual scenario. We also used the proposed model to perform a systematic literature mapping that covered ten years of research on I/O performance improvements in storage environments. This study classified hundreds of distinct researches identifying which were the hardware, software, and storage systems that received more attention over the years, which were the most researches proposals elements and where these elements were evaluated. In order to justify the importance of this model and the development of solutions that targets I/O performance improvements, we evaluated a subset of these improvements using a a real and complete experimentation environment, the Grid5000. Analysis over different scenarios using a synthetic I/O benchmark demonstrates how the throughput and latency parameters behaves when performing different I/O operations using distinct storage technologies and approaches.O gargalo de E/S continua sendo um problema central em ambientes de alto desempenho. Os ambientes de computação em nuvem, computação de alto desempenho (HPC) e big data compartilham muitas dificuldades para fornecer dados em uma taxa de tempo desejável solicitada por aplicações de alto desempenho. Isso aumenta a possibilidade de criar gargalos em todo o processo de alimentação de aplicativos pelos dispositivos de hardware inferiores localizados na camada do sistema de armazenamento. Nos últimos anos, muitos pesquisadores propuseram soluções para melhorar a arquitetura de E/S considerando diferentes abordagens. Alguns deles aproveitam os dispositivos de hardware, enquanto outros se concentram em uma abordagem sofisticada de software. No entanto, devido à complexidade de lidar com ambientes de alto desempenho, criar soluções para melhorar o desempenho de E/S em software e hardware é um desafio e oferece aos pesquisadores muitas oportunidades. A classificação dessas melhorias em diferentes dimensões permite que os pesquisadores entendam como essas melhorias foram construídas ao longo dos anos e como elas progridem. Além disso, também permite que futuros esforços sejam direcionados para tópicos de pesquisa que se desenvolveram em menor proporção, equilibrando o processo geral de desenvolvimento. Esta pesquisa apresenta um modelo de caracterização tridimensional para classificar trabalhos de pesquisa sobre melhorias de desempenho de E/S para instalações de computação de armazenamento em larga escala. Esse modelo de classificação também pode ser usado como uma estrutura de diretrizes para resumir as pesquisas, fornecendo uma visão geral do cenário real. Também usamos o modelo proposto para realizar um mapeamento sistemático da literatura que abrangeu dez anos de pesquisa sobre melhorias no desempenho de E/S em ambientes de armazenamento. Este estudo classificou centenas de pesquisas distintas, identificando quais eram os dispositivos de hardware, software e sistemas de armazenamento que receberam mais atenção ao longo dos anos, quais foram os elementos de proposta mais pesquisados e onde esses elementos foram avaliados. Para justificar a importância desse modelo e o desenvolvimento de soluções que visam melhorias no desempenho de E/S, avaliamos um subconjunto dessas melhorias usando um ambiente de experimentação real e completo, o Grid5000. Análises em cenários diferentes usando um benchmark de E/S sintética demonstra como os parâmetros de vazão e latência se comportam ao executar diferentes operações de E/S usando tecnologias e abordagens distintas de armazenamento

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

A framework for multidimensional indexes on distributed and highly-available data stores

Spatial Big Data is considered an essential trend in future scientific and business applications. Indeed, research instruments, medical devices, and social networks generate hundreds of peta bytes of spatial data per year. However, as many authors have pointed out, the lack of specialized frameworks dealing with such kind of data is limiting possible applications and probably precluding many scientific breakthroughs. In this thesis, we describe three HPC scientific applications, ranging from molecular dynamics, neuroscience analysis, and physics simulations, where we experience first hand the limits of the existing technologies. Thanks to our experience, we define the desirable missing functionalities, and we focus on two features that when combined significantly improve the way scientific data is analyzed. On one side, scientific simulations generate complex datasets where multiple correlated characteristics describe each item. For instance, a particle might have a space position (x,y,z) at a given time (t). If we want to find all elements within the same area and period, we either have to scan the whole dataset, or we must organize the data so that all items in the same space and time are stored together. The second approach is called Multidimensional Indexing (MI), and it uses different techniques to cluster and to organize similar data together. On the other side, approximate analytics has been often indicated as a smart and flexible way to explore large datasets in a short period. Approximate analytics includes a broad family of algorithms which aims to speed up analytical workloads by relaxing the precision of the results within a specific interval of confidence. For instance, if we want to know the average age in a group with 1-year precision, we can consider just a random fraction of all the people, thus reducing the amount of calculation. But if we also want less I/O operations, we need efficient data sampling, which means organizing data in a way that we do not need to scan the whole data set to generate a random sample of it. According to our analysis, combining Multidimensional Indexing with efficient data Sampling (MIS) is a vital missing feature not available in the current distributed data management solutions. This thesis aims to solve such a shortcoming and it provides novel scalable solutions. At first, we describe the existing data management alternatives; then we motivate our preference for NoSQL key-value databases. Secondly, we propose an analytical model to study the influence of data models on the scalability and performance of this kind of distributed database. Thirdly, we use the analytical model to design two novel multidimensional indexes with efficient data sampling: the D8tree and the AOTree. Our first solution, the D8tree, improves state of the art for approximate spatial queries on static and mostly read dataset. Later, we enhanced the data ingestion capability or our approach by introducing the AOTree, an algorithm that enables the query performance of the D8tree even for HPC write-intensive applications. We compared our solution with PostgreSQL and plain storage, and we demonstrate that our proposal has better performance and scalability. Finally, we describe Qbeast, the novel distributed system that implements the D8tree and the AOTree using NoSQL technologies, and we illustrate how Qbeast simplifies the workflow of scientists in various HPC applications providing a scalable and integrated solution for data analysis and management.La gestión de BigData con información espacial está considerada como una tendencia esencial en el futuro de las aplicaciones científicas y de negocio. De hecho, se generan cientos de petabytes de datos espaciales por año mediante instrumentos de investigación, dispositivos médicos y redes sociales. Sin embargo, tal y como muchos autores han señalado, la falta de entornos especializados en manejar este tipo de datos está limitando sus posibles aplicaciones y está impidiendo muchos avances científicos. En esta tesis, describimos 3 aplicaciones científicas HPC, que cubren los ámbitos de dinámica molecular, análisis neurocientífico y simulaciones físicas, donde hemos experimentado en primera mano las limitaciones de las tecnologías existentes. Gracias a nuestras experiencias, hemos podido definir qué funcionalidades serían deseables y no existen, y nos hemos centrado en dos características que, al combinarlas, mejoran significativamente la manera en la que se analizan los datos científicos. Por un lado, las simulaciones científicas generan conjuntos de datos complejos, en los que cada elemento es descrito por múltiples características correlacionadas. Por ejemplo, una partícula puede tener una posición espacial (x, y, z) en un momento dado (t). Si queremos encontrar todos los elementos dentro de la misma área y periodo, o bien recorremos y analizamos todo el conjunto de datos, o bien organizamos los datos de manera que se almacenen juntos todos los elementos que comparten área en un momento dado. Esta segunda opción se conoce como Indexación Multidimensional (IM) y usa diferentes técnicas para agrupar y organizar datos similares. Por otro lado, se suele señalar que las analíticas aproximadas son una manera inteligente y flexible de explorar grandes conjuntos de datos en poco tiempo. Este tipo de analíticas incluyen una amplia familia de algoritmos que acelera el tiempo de procesado, relajando la precisión de los resultados dentro de un determinado intervalo de confianza. Por ejemplo, si queremos saber la edad media de un grupo con precisión de un año, podemos considerar sólo un subconjunto aleatorio de todas las personas, reduciendo así la cantidad de cálculo. Pero si además queremos menos operaciones de entrada/salida, necesitamos un muestreo eficiente de datos, que implica organizar los datos de manera que no necesitemos recorrerlos todos para generar una muestra aleatoria. De acuerdo con nuestros análisis, la combinación de Indexación Multidimensional con Muestreo eficiente de datos (IMM) es una característica vital que no está disponible en las soluciones actuales de gestión distribuida de datos. Esta tesis pretende resolver esta limitación y proporciona unas soluciones novedosas que son escalables. En primer lugar, describimos las alternativas de gestión de datos que existen y motivamos nuestra preferencia por las bases de datos NoSQL basadas en clave-valor. En segundo lugar, proponemos un modelo analítico para estudiar la influencia que tienen los modelos de datos sobre la escalabilidad y el rendimiento de este tipo de bases de datos distribuidas. En tercer lugar, usamos el modelo analítico para diseñar dos novedosos algoritmos IMM: el D8tree y el AOTree. Nuestra primera solución, el D8tree, mejora el estado del arte actual para consultas espaciales aproximadas, cuando el conjunto de datos es estático y mayoritariamente de lectura. Después, mejoramos la capacidad de ingestión introduciendo el AOTree, un algoritmo que conserva el rendimiento del D8tree incluso para aplicaciones HPC intensivas en escritura. Hemos comparado nuestra solución con PostgreSQL y almacenamiento plano demostrando que nuestra propuesta mejora tanto el rendimiento como la escalabilidad. Finalmente, describimos Qbeast, el sistema que implementa los algoritmos D8tree y AOTree, e ilustramos cómo Qbeast simplifica el flujo de trabajo de los científicos ofreciendo una solución escalable e integraPostprint (published version

A framework for multidimensional indexes on distributed and highly-available data stores

Spatial Big Data is considered an essential trend in future scientific and business applications. Indeed, research instruments, medical devices, and social networks generate hundreds of peta bytes of spatial data per year. However, as many authors have pointed out, the lack of specialized frameworks dealing with such kind of data is limiting possible applications and probably precluding many scientific breakthroughs. In this thesis, we describe three HPC scientific applications, ranging from molecular dynamics, neuroscience analysis, and physics simulations, where we experience first hand the limits of the existing technologies. Thanks to our experience, we define the desirable missing functionalities, and we focus on two features that when combined significantly improve the way scientific data is analyzed. On one side, scientific simulations generate complex datasets where multiple correlated characteristics describe each item. For instance, a particle might have a space position (x,y,z) at a given time (t). If we want to find all elements within the same area and period, we either have to scan the whole dataset, or we must organize the data so that all items in the same space and time are stored together. The second approach is called Multidimensional Indexing (MI), and it uses different techniques to cluster and to organize similar data together. On the other side, approximate analytics has been often indicated as a smart and flexible way to explore large datasets in a short period. Approximate analytics includes a broad family of algorithms which aims to speed up analytical workloads by relaxing the precision of the results within a specific interval of confidence. For instance, if we want to know the average age in a group with 1-year precision, we can consider just a random fraction of all the people, thus reducing the amount of calculation. But if we also want less I/O operations, we need efficient data sampling, which means organizing data in a way that we do not need to scan the whole data set to generate a random sample of it. According to our analysis, combining Multidimensional Indexing with efficient data Sampling (MIS) is a vital missing feature not available in the current distributed data management solutions. This thesis aims to solve such a shortcoming and it provides novel scalable solutions. At first, we describe the existing data management alternatives; then we motivate our preference for NoSQL key-value databases. Secondly, we propose an analytical model to study the influence of data models on the scalability and performance of this kind of distributed database. Thirdly, we use the analytical model to design two novel multidimensional indexes with efficient data sampling: the D8tree and the AOTree. Our first solution, the D8tree, improves state of the art for approximate spatial queries on static and mostly read dataset. Later, we enhanced the data ingestion capability or our approach by introducing the AOTree, an algorithm that enables the query performance of the D8tree even for HPC write-intensive applications. We compared our solution with PostgreSQL and plain storage, and we demonstrate that our proposal has better performance and scalability. Finally, we describe Qbeast, the novel distributed system that implements the D8tree and the AOTree using NoSQL technologies, and we illustrate how Qbeast simplifies the workflow of scientists in various HPC applications providing a scalable and integrated solution for data analysis and management.La gestión de BigData con información espacial está considerada como una tendencia esencial en el futuro de las aplicaciones científicas y de negocio. De hecho, se generan cientos de petabytes de datos espaciales por año mediante instrumentos de investigación, dispositivos médicos y redes sociales. Sin embargo, tal y como muchos autores han señalado, la falta de entornos especializados en manejar este tipo de datos está limitando sus posibles aplicaciones y está impidiendo muchos avances científicos. En esta tesis, describimos 3 aplicaciones científicas HPC, que cubren los ámbitos de dinámica molecular, análisis neurocientífico y simulaciones físicas, donde hemos experimentado en primera mano las limitaciones de las tecnologías existentes. Gracias a nuestras experiencias, hemos podido definir qué funcionalidades serían deseables y no existen, y nos hemos centrado en dos características que, al combinarlas, mejoran significativamente la manera en la que se analizan los datos científicos. Por un lado, las simulaciones científicas generan conjuntos de datos complejos, en los que cada elemento es descrito por múltiples características correlacionadas. Por ejemplo, una partícula puede tener una posición espacial (x, y, z) en un momento dado (t). Si queremos encontrar todos los elementos dentro de la misma área y periodo, o bien recorremos y analizamos todo el conjunto de datos, o bien organizamos los datos de manera que se almacenen juntos todos los elementos que comparten área en un momento dado. Esta segunda opción se conoce como Indexación Multidimensional (IM) y usa diferentes técnicas para agrupar y organizar datos similares. Por otro lado, se suele señalar que las analíticas aproximadas son una manera inteligente y flexible de explorar grandes conjuntos de datos en poco tiempo. Este tipo de analíticas incluyen una amplia familia de algoritmos que acelera el tiempo de procesado, relajando la precisión de los resultados dentro de un determinado intervalo de confianza. Por ejemplo, si queremos saber la edad media de un grupo con precisión de un año, podemos considerar sólo un subconjunto aleatorio de todas las personas, reduciendo así la cantidad de cálculo. Pero si además queremos menos operaciones de entrada/salida, necesitamos un muestreo eficiente de datos, que implica organizar los datos de manera que no necesitemos recorrerlos todos para generar una muestra aleatoria. De acuerdo con nuestros análisis, la combinación de Indexación Multidimensional con Muestreo eficiente de datos (IMM) es una característica vital que no está disponible en las soluciones actuales de gestión distribuida de datos. Esta tesis pretende resolver esta limitación y proporciona unas soluciones novedosas que son escalables. En primer lugar, describimos las alternativas de gestión de datos que existen y motivamos nuestra preferencia por las bases de datos NoSQL basadas en clave-valor. En segundo lugar, proponemos un modelo analítico para estudiar la influencia que tienen los modelos de datos sobre la escalabilidad y el rendimiento de este tipo de bases de datos distribuidas. En tercer lugar, usamos el modelo analítico para diseñar dos novedosos algoritmos IMM: el D8tree y el AOTree. Nuestra primera solución, el D8tree, mejora el estado del arte actual para consultas espaciales aproximadas, cuando el conjunto de datos es estático y mayoritariamente de lectura. Después, mejoramos la capacidad de ingestión introduciendo el AOTree, un algoritmo que conserva el rendimiento del D8tree incluso para aplicaciones HPC intensivas en escritura. Hemos comparado nuestra solución con PostgreSQL y almacenamiento plano demostrando que nuestra propuesta mejora tanto el rendimiento como la escalabilidad. Finalmente, describimos Qbeast, el sistema que implementa los algoritmos D8tree y AOTree, e ilustramos cómo Qbeast simplifica el flujo de trabajo de los científicos ofreciendo una solución escalable e integr