gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.Comment: 10 pages, 4 figures. To appear in the HealthGrid 2012 con

Computing at massive scale: Scalability and dependability challenges

Large-scale Cloud systems and big data analytics frameworks are now widely used for practical services and applications. However, with the increase of data volume, together with the heterogeneity of workloads and resources, and the dynamic nature of massive user requests, the uncertainties and complexity of resource management and service provisioning increase dramatically, often resulting in poor resource utilization, vulnerable system dependability, and user-perceived performance degradations. In this paper we report our latest understanding of the current and future challenges in this particular area, and discuss both existing and potential solutions to the problems, especially those concerned with system efficiency, scalability and dependability. We first introduce a data-driven analysis methodology for characterizing the resource and workload patterns and tracing performance bottlenecks in a massive-scale distributed computing environment. We then examine and analyze several fundamental challenges and the solutions we are developing to tackle them, including for example incremental but decentralized resource scheduling, incremental messaging communication, rapid system failover, and request handling parallelism. We integrate these solutions with our data analysis methodology in order to establish an engineering approach that facilitates the optimization, tuning and verification of massive-scale distributed systems. We aim to develop and offer innovative methods and mechanisms for future computing platforms that will provide strong support for new big data and IoE (Internet of Everything) applications

A proactive fault tolerance framework for high performance computing (HPC) systems in the cloud

High Performance Computing (HPC) systems have been widely used by scientists and researchers in both industry and university laboratories to solve advanced computation problems. Most advanced computation problems are either data-intensive or computation-intensive. They may take hours, days or even weeks to complete execution. For example, some of the traditional HPC systems computations run on 100,000 processors for weeks. Consequently traditional HPC systems often require huge capital investments. As a result, scientists and researchers sometimes have to wait in long queues to access shared, expensive HPC systems. Cloud computing, on the other hand, offers new computing paradigms, capacity, and flexible solutions for both business and HPC applications. Some of the computation-intensive applications that are usually executed in traditional HPC systems can now be executed in the cloud. Cloud computing price model eliminates huge capital investments. However, even for cloud-based HPC systems, fault tolerance is still an issue of growing concern. The large number of virtual machines and electronic components, as well as software complexity and overall system reliability, availability and serviceability (RAS), are factors with which HPC systems in the cloud must contend. The reactive fault tolerance approach of checkpoint/restart, which is commonly used in HPC systems, does not scale well in the cloud due to resource sharing and distributed systems networks. Hence, the need for reliable fault tolerant HPC systems is even greater in a cloud environment. In this thesis we present a proactive fault tolerance approach to HPC systems in the cloud to reduce the wall-clock execution time, as well as dollar cost, in the presence of hardware failure. We have developed a generic fault tolerance algorithm for HPC systems in the cloud. We have further developed a cost model for executing computation-intensive applications on HPC systems in the cloud. Our experimental results obtained from a real cloud execution environment show that the wall-clock execution time and cost of running computation-intensive applications in the cloud can be considerably reduced compared to checkpoint and redundancy techniques used in traditional HPC systems

What does fault tolerant Deep Learning need from MPI?

Deep Learning (DL) algorithms have become the de facto Machine Learning (ML) algorithm for large scale data analysis. DL algorithms are computationally expensive - even distributed DL implementations which use MPI require days of training (model learning) time on commonly studied datasets. Long running DL applications become susceptible to faults - requiring development of a fault tolerant system infrastructure, in addition to fault tolerant DL algorithms. This raises an important question: What is needed from MPI for de- signing fault tolerant DL implementations? In this paper, we address this problem for permanent faults. We motivate the need for a fault tolerant MPI specification by an in-depth consideration of recent innovations in DL algorithms and their properties, which drive the need for specific fault tolerance features. We present an in-depth discussion on the suitability of different parallelism types (model, data and hybrid); a need (or lack thereof) for check-pointing of any critical data structures; and most importantly, consideration for several fault tolerance proposals (user-level fault mitigation (ULFM), Reinit) in MPI and their applicability to fault tolerant DL implementations. We leverage a distributed memory implementation of Caffe, currently available under the Machine Learning Toolkit for Extreme Scale (MaTEx). We implement our approaches by ex- tending MaTEx-Caffe for using ULFM-based implementation. Our evaluation using the ImageNet dataset and AlexNet, and GoogLeNet neural network topologies demonstrates the effectiveness of the proposed fault tolerant DL implementation using OpenMPI based ULFM

Predictive Reliability and Fault Management in Exascale Systems: State of the Art and Perspectives

© ACM, 2020. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in ACM Computing Surveys, Vol. 53, No. 5, Article 95. Publication date: September 2020. https://doi.org/10.1145/3403956[EN] Performance and power constraints come together with Complementary Metal Oxide Semiconductor technology scaling in future Exascale systems. Technology scaling makes each individual transistor more prone to faults and, due to the exponential increase in the number of devices per chip, to higher system fault rates. Consequently, High-performance Computing (HPC) systems need to integrate prediction, detection, and recovery mechanisms to cope with faults efficiently. This article reviews fault detection, fault prediction, and recovery techniques in HPC systems, from electronics to system level. We analyze their strengths and limitations. Finally, we identify the promising paths to meet the reliability levels of Exascale systems.This work has received funding from the European Union's Horizon 2020 (H2020) research and innovation program under the FET-HPC Grant Agreement No. 801137 (RECIPE). Jaume Abella was also partially supported by the Ministry of Economy and Competitiveness of Spain under Contract No. TIN2015-65316-P and under Ramon y Cajal Postdoctoral Fellowship No. RYC-2013-14717, as well as by the HiPEAC Network of Excellence. Ramon Canal is partially supported by the Generalitat de Catalunya under Contract No. 2017SGR0962.Canal, R.; Hernández Luz, C.; Tornero-Gavilá, R.; Cilardo, A.; Massari, G.; Reghenzani, F.; Fornaciari, W.... (2020). Predictive Reliability and Fault Management in Exascale Systems: State of the Art and Perspectives. ACM Computing Surveys. 53(5):1-32. https://doi.org/10.1145/3403956S132535Abella, J., Hernandez, C., Quinones, E., Cazorla, F. J., Conmy, P. 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IEEE Internet Com

Operating System Support for Redundant Multithreading

Failing hardware is a fact and trends in microprocessor design indicate that the fraction of hardware suffering from permanent and transient faults will continue to increase in future chip generations. Researchers proposed various solutions to this issue with different downsides: Specialized hardware components make hardware more expensive in production and consume additional energy at runtime. Fault-tolerant algorithms and libraries enforce specific programming models on the developer. Compiler-based fault tolerance requires the source code for all applications to be available for recompilation. In this thesis I present ASTEROID, an operating system architecture that integrates applications with different reliability needs. ASTEROID is built on top of the L4/Fiasco.OC microkernel and extends the system with Romain, an operating system service that transparently replicates user applications. Romain supports single- and multi-threaded applications without requiring access to the application's source code. Romain replicates applications and their resources completely and thereby does not rely on hardware extensions, such as ECC-protected memory. In my thesis I describe how to efficiently implement replication as a form of redundant multithreading in software. I develop mechanisms to manage replica resources and to make multi-threaded programs behave deterministically for replication. I furthermore present an approach to handle applications that use shared-memory channels with other programs. My evaluation shows that Romain provides 100% error detection and more than 99.6% error correction for single-bit flips in memory and general-purpose registers. At the same time, Romain's execution time overhead is below 14% for single-threaded applications running in triple-modular redundant mode. The last part of my thesis acknowledges that software-implemented fault tolerance methods often rely on the correct functioning of a certain set of hardware and software components, the Reliable Computing Base (RCB). I introduce the concept of the RCB and discuss what constitutes the RCB of the ASTEROID system and other fault tolerance mechanisms. Thereafter I show three case studies that evaluate approaches to protecting RCB components and thereby aim to achieve a software stack that is fully protected against hardware errors

Reliability models for HPC applications and a Cloud economic model

With the enormous number of computing resources in HPC and Cloud systems, failures become a major concern. Therefore, failure behaviors such as reliability, failure rate, and mean time to failure need to be understood to manage such a large system efficiently. This dissertation makes three major contributions in HPC and Cloud studies. First, a reliability model with correlated failures in a k-node system for HPC applications is studied. This model is extended to improve accuracy by accounting for failure correlation. Marshall-Olkin Multivariate Weibull distribution is improved by excess life, conditional Weibull, to better estimate system reliability. Also, the univariate method is proposed for estimating Marshall-Olkin Multivariate Weibull parameters of a system composed of a large number of nodes. Then, failure rate, and mean time to failure are derived. The model is validated by using log data from Blue Gene/L system at LLNL. Results show that when failures of nodes in the system have correlation, the system becomes less reliable. Secondly, a reliability model of Cloud computing is proposed. The reliability model and mean time to failure and failure rate are estimated based on a system of k nodes and s virtual machines under four scenarios: 1) Hardware components fail independently, and software components fail independently; 2) software components fail independently, and hardware components are correlated in failure; 3) correlated software failure and independent hardware failure; and 4) dependent software and hardware failure. Results show that if the failure of the nodes and/or software in the system possesses a degree of dependency, the system becomes less reliable. Also, an increase in the number of computing components decreases the reliability of the system. Finally, an economic model for a Cloud service provider is proposed. This economic model aims at maximizing profit based on the right pricing and rightsizing in the Cloud data center. Total cost is a key element in the model and it is analyzed by considering the Total Cost of Ownership (TCO) of the Cloud

Reliable and energy efficient resource provisioning in cloud computing systems

Cloud Computing has revolutionized the Information Technology sector by giving computing a perspective of service. The services of cloud computing can be accessed by users not knowing about the underlying system with easy-to-use portals. To provide such an abstract view, cloud computing systems have to perform many complex operations besides managing a large underlying infrastructure. Such complex operations confront service providers with many challenges such as security, sustainability, reliability, energy consumption and resource management. Among all the challenges, reliability and energy consumption are two key challenges focused on in this thesis because of their conflicting nature. Current solutions either focused on reliability techniques or energy efficiency methods. But it has been observed that mechanisms providing reliability in cloud computing systems can deteriorate the energy consumption. Adding backup resources and running replicated systems provide strong fault tolerance but also increase energy consumption. Reducing energy consumption by running resources on low power scaling levels or by reducing the number of active but idle sitting resources such as backup resources reduces the system reliability. This creates a critical trade-off between these two metrics that are investigated in this thesis. To address this problem, this thesis presents novel resource management policies which target the provisioning of best resources in terms of reliability and energy efficiency and allocate them to suitable virtual machines. A mathematical framework showing interplay between reliability and energy consumption is also proposed in this thesis. A formal method to calculate the finishing time of tasks running in a cloud computing environment impacted with independent and correlated failures is also provided. The proposed policies adopted various fault tolerance mechanisms while satisfying the constraints such as task deadlines and utility values. This thesis also provides a novel failure-aware VM consolidation method, which takes the failure characteristics of resources into consideration before performing VM consolidation. All the proposed resource management methods are evaluated by using real failure traces collected from various distributed computing sites. In order to perform the evaluation, a cloud computing framework, 'ReliableCloudSim' capable of simulating failure-prone cloud computing systems is developed. The key research findings and contributions of this thesis are: 1. If the emphasis is given only to energy optimization without considering reliability in a failure prone cloud computing environment, the results can be contrary to the intuitive expectations. Rather than reducing energy consumption, a system ends up consuming more energy due to the energy losses incurred because of failure overheads. 2. While performing VM consolidation in a failure prone cloud computing environment, a significant improvement in terms of energy efficiency and reliability can be achieved by considering failure characteristics of physical resources. 3. By considering correlated occurrence of failures during resource provisioning and VM allocation, the service downtime or interruption is reduced significantly by 34% in comparison to the environments with the assumption of independent occurrence of failures. Moreover, measured by our mathematical model, the ratio of reliability and energy consumption is improved by 14%