BackgroundOver the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts.ResultsIn this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure.ConclusionsTavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis.The system can be accessed either through a cloud-enabled web-interface or downloaded and installed to run within the user's local environment. All resources related to Tavaxy are available at http://www.tavaxy.org.

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Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

The performance and behavior of large-scale distributed applications is highly influenced by network properties such as latency, bandwidth, packet loss, and jitter. For instance, an engineer might need to answer questions such as: What is the impact of an increase in network latency in application response time? How does moving a cluster between geographical regions affect application throughput? How network dynamics affects application stability? Answering these questions in a systematic and reproducible way is very hard, given the variability and lack of control over the underlying network. Unfortunately, state-of-the-art network emulation or testbeds scale poorly (i.e., MiniNet), focus exclusively on the control-plane (i.e., CrystalNet) or ignore network dynamics (i.e., EmuLab).Kollaps is a fully distributed network emulator that address these limitations. Kollaps hinges on two key observations. First, from an application's perspective, what matters are the emergent end-to-end properties (e.g., latency, bandwidth, packet loss, and jitter) rather than the internal state of the routers and switches leading to those properties. This premise allows us to build a simpler, dynamically adaptable, emulation model that circumvent maintaining the full network state. Second, this simplified model is maintainable in a fully decentralized way, allowing the emulation to scale with the number of machines for the application.Kollaps is fully decentralized, agnostic of the application language and transport protocol, scales to thousands of processes and is accurate when compared against a bare-metal deployment or state-of-the-art approaches that emulate the full state of the network. We showcase how Kollaps can accurately reproduce results from the literature and predict * Corresponding author † Corresponding author the behaviour of a complex unmodified distributed key-value store (i.e., Cassandra) under different deployments.also arise in the reproducibility crisis currently plaguing the system's community [29,64]. Different results for the same system emerge not only because systems are evaluated in different uncontrollable conditions, but also because research testbeds such as Emulab [46], CloudLab [72], or PlanetLab [35] used to conduct experiments tend to get overloaded right before system conference deadlines [51]. We therefore need tools to systematically assess and reproduce the evaluation of large-scale applications. Notably, similar tools could be used to test and (otherwise) prevent costly incidents due to mis-configurations, as in recent events [4,20]. One approach to systematically evaluate a large-scale distributed system is to resort to simulation, which relies on models that capture the key properties of the target system and environment [25]. Simulation provides full control of the system and environment -achieving full reproducibility -and allows to study the model of the system in a variety of scenarios. However, simulations suffer from several well-known problems. In fact, there is a large gap between the...

Transactional memory (TM) aims at simplifying concurrent programming via the familiar abstraction of atomic transactions. Recently, Intel and IBM have integrated hardware based TM (HTM) implementations in commodity processors, paving the way for the mainstream adoption of the TM paradigm. Yet, existing HTM implementations suffer from a crucial limitation, which hampers the adoption of HTM as a general technique for regulating concurrent access to shared memory: the inability to execute transactions whose working sets exceed the capacity of CPU caches. In this paper we propose P8TM, a novel approach that mitigates this limitation on IBM's POWER8 architecture by leveraging a key combination of techniques: uninstrumented read-only transactions, Rollback Only Transaction-based update transactions, HTM-friendly (software-based) read-set tracking, and self-tuning. P8TM can dynamically switch between different execution modes to best adapt to the nature of the transactions and the experienced abort patterns. Indepth evaluation with several benchmarks indicates that P8TM can achieve striking performance gains in workloads that stress the capacity limitations of HTM, while achieving performance on par with HTM even in unfavourable workloads.

Range locks are a synchronization construct designed to provide concurrent access to multiple threads (or processes) to disjoint parts of a shared resource. Originally conceived in the file system context, range locks are gaining increasing interest in the Linux kernel community seeking to alleviate bottlenecks in the virtual memory management subsystem. The existing implementation of range locks in the kernel, however, uses an internal spin lock to protect the underlying tree structure that keeps track of acquired and requested ranges. This spin lock becomes a point of contention on its own when the range lock is frequently acquired. Furthermore, where and exactly how specific (refined) ranges can be locked remains an open question.In this paper, we make two independent, but related contributions. First, we propose an alternative approach for building range locks based on linked lists. The lists are easy to maintain in a lock-less fashion, and in fact, our range locks do not use any internal locks in the common case. Second, we show how the range of the lock can be refined in the mprotect operation through a speculative mechanism. This refinement, in turn, allows concurrent execution of mprotect operations on non-overlapping memory regions. We implement our new algorithms and demonstrate their effectiveness in user-space and kernel-space, achieving up to 9× speedup compared to the stock version of the Linux kernel. Beyond the virtual memory management subsystem, we discuss other applications of range locks in parallel software. As a concrete example, we show how range locks can be used to facilitate the design of scalable concurrent data structures, such as skip lists.

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The hardware transactional memory (HTM) implementations in commercially available processors are significantly hindered by their tight capacity constraints. In practice, this renders current HTMs unsuitable to many real-world workloads of in-memory databases.This paper proposes SI-HTM, which stretches the capacity bounds of the underlying HTM, thus opening HTM to a much broader class of applications. SI-HTM leverages the HTM implementation of the IBM POWER architecture with a software layer to offer a single-version implementation of Snapshot Isolation. When compared to HTM-and softwarebased concurrency control alternatives, SI-HTM exhibits improved scalability, achieving speedups of up to 300% relatively to HTM on in-memory database benchmarks.