BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

Sandboxed, Online Debugging of Production Bugs for SOA Systems

Short time-to-bug localization is extremely important for any 24x7 service-oriented application. To this end, we introduce a new debugging paradigm called live debugging. There are two goals that any live debugging infrastructure must meet: Firstly, it must offer real-time insight for bug diagnosis and localization, which is paramount when errors happen in user-facing applications. Secondly, live debugging should not impact user-facing performance for normal events. In large distributed applications, bugs which impact only a small percentage of users are common. In such scenarios, debugging a small part of the application should not impact the entire system. With the above-stated goals in mind, this thesis presents a framework called Parikshan, which leverages user-space containers (OpenVZ) to launch application instances for the express purpose of live debugging. Parikshan is driven by a live-cloning process, which generates a replica (called debug container) of production services, cloned from a production container which continues to provide the real output to the user. The debug container provides a sandbox environment, for safe execution of monitoring/debugging done by the users without any perturbation to the execution environment. As a part of this framework, we have designed customized-network proxies, which replicate inputs from clients to both the production and test-container, as well safely discard all outputs. Together the network duplicator, and the debug container ensure both compute and network isolation of the debugging environment. We believe that this piece of work provides the first of its kind practical real-time debugging of large multi-tier and cloud applications, without requiring any application downtime, and minimal performance impact

EMU: Rapid prototyping of networking services

Due to their performance and flexibility, FPGAs are an attractive platform for the execution of network functions. It has been a challenge for a long time though to make FPGA programming accessible to a large audience of developers. An appealing solution is to compile code from a general-purpose language to hardware using high-level synthesis. Unfortunately, current approaches to implement rich network functionality are insufficient because they lack: (i) libraries with abstractions for common network operations and data structures, (ii) bindings to the underlying “substrate” on the FPGA, and (iii) debugging and profiling support. This paper describes Emu, a new standard library for an FPGA hardware compiler that enables developers to rapidly create and deploy network functionality. Emu allows for high-performance designs without being bound to particular packet processing paradigms. Furthermore, it supports running the same programs on CPUs, in Mininet, and on FPGAs, providing a better development environment that includes advanced debugging capabilities. We demonstrate that network functions implemented using Emu have only negligible resource and performance overheads compared with natively-written hardware versions

Addressing concerns in performance prediction : the impact of data dependencies and denormal arithmetic in scientific codes

To meet the increasing computational requirements of the scientific community, the use of parallel programming has become commonplace, and in recent years distributed applications running on clusters of computers have become the norm. Both parallel and distributed applications face the problem of predictive uncertainty and variations in runtime. Modern scientific applications have varying I/O, cache, and memory profiles that have significant and difficult to predict effects on their runtimes. Data-dependent sensitivities such as the costs of denormal floating point calculations introduce more variations in runtime, further hindering predictability. Applications with unpredictable performance or which have highly variable runtimes can cause several problems. If the runtime of an application is unknown or varies widely, workflow schedulers cannot e�ciently allocate them to compute nodes, leading to the under-utilisation of expensive resources. Similarly, a lack of accurate knowledge of the performance of an application on new hardware can lead to misguided procurement decisions. In heavily parallel applications, minor variations in runtime on individual nodes can have disproportionate effects on the overall application runtime. Even on a smaller scale, a lack of certainty about an application's runtime can preclude its use in real-time or time-critical applications such as clinical diagnosis. This thesis investigates two sources of data-dependent performance variability. The first source is algorithmic and is seen in a state-of-the-art C++ biomedical imaging application. It identifies the cause of the variability in the application and develops a means of characterising the variability. This 'probe task' based model is adapted for use with a workflow scheduler, and the scheduling improvements it brings are examined. The second source of variability is more subtle as it is micro-architectural in nature. Depending on the input data, two runs of an application executing exactly the same sequence of instructions and with exactly the same memory access patterns can have large differences in runtime due to deficiencies in common hardware implementations of denormal arithmetic1. An exception-based profiler is written to detect occurrences of denormal arithmetic and it is shown how this is insufficient to isolate the sources of denormal arithmetic in an application. A novel tool based on theValgrind binary instrumentation framework is developed which can trace the origins of denormal values and the frequency of their occurrence in an application's data structures. This second tool is used to isolate and remove the cause of denormal arithmetic both from a simple numerical code, and then from a face recognition application

Design considerations for workflow management systems use in production genomics research and the clinic

Abstract The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance

Smart technologies for effective reconfiguration: the FASTER approach

Current and future computing systems increasingly require that their functionality stays flexible after the system is operational, in order to cope with changing user requirements and improvements in system features, i.e. changing protocols and data-coding standards, evolving demands for support of different user applications, and newly emerging applications in communication, computing and consumer electronics. Therefore, extending the functionality and the lifetime of products requires the addition of new functionality to track and satisfy the customers needs and market and technology trends. Many contemporary products along with the software part incorporate hardware accelerators for reasons of performance and power efficiency. While adaptivity of software is straightforward, adaptation of the hardware to changing requirements constitutes a challenging problem requiring delicate solutions. The FASTER (Facilitating Analysis and Synthesis Technologies for Effective Reconfiguration) project aims at introducing a complete methodology to allow designers to easily implement a system specification on a platform which includes a general purpose processor combined with multiple accelerators running on an FPGA, taking as input a high-level description and fully exploiting, both at design time and at run time, the capabilities of partial dynamic reconfiguration. The goal is that for selected application domains, the FASTER toolchain will be able to reduce the design and verification time of complex reconfigurable systems providing additional novel verification features that are not available in existing tool flows