Workflow models for heterogeneous distributed systems

The role of data in modern scientific workflows becomes more and more crucial. The unprecedented amount of data available in the digital era, combined with the recent advancements in Machine Learning and High-Performance Computing (HPC), let computers surpass human performances in a wide range of fields, such as Computer Vision, Natural Language Processing and Bioinformatics. However, a solid data management strategy becomes crucial for key aspects like performance optimisation, privacy preservation and security. Most modern programming paradigms for Big Data analysis adhere to the principle of data locality: moving computation closer to the data to remove transfer-related overheads and risks. Still, there are scenarios in which it is worth, or even unavoidable, to transfer data between different steps of a complex workflow. The contribution of this dissertation is twofold. First, it defines a novel methodology for distributed modular applications, allowing topology-aware scheduling and data management while separating business logic, data dependencies, parallel patterns and execution environments. In addition, it introduces computational notebooks as a high-level and user-friendly interface to this new kind of workflow, aiming to flatten the learning curve and improve the adoption of such methodology. Each of these contributions is accompanied by a full-fledged, Open Source implementation, which has been used for evaluation purposes and allows the interested reader to experience the related methodology first-hand. The validity of the proposed approaches has been demonstrated on a total of five real scientific applications in the domains of Deep Learning, Bioinformatics and Molecular Dynamics Simulation, executing them on large-scale mixed cloud-High-Performance Computing (HPC) infrastructures

Design Guidelines for High-Performance SCM Hierarchies

With emerging storage-class memory (SCM) nearing commercialization, there is evidence that it will deliver the much-anticipated high density and access latencies within only a few factors of DRAM. Nevertheless, the latency-sensitive nature of memory-resident services makes seamless integration of SCM in servers questionable. In this paper, we ask the question of how best to introduce SCM for such servers to improve overall performance/cost over existing DRAM-only architectures. We first show that even with the most optimistic latency projections for SCM, the higher memory access latency results in prohibitive performance degradation. However, we find that deployment of a modestly sized high-bandwidth 3D stacked DRAM cache makes the performance of an SCM-mostly memory system competitive. The high degree of spatial locality that memory-resident services exhibit not only simplifies the DRAM cache's design as page-based, but also enables the amortization of increased SCM access latencies and the mitigation of SCM's read/write latency disparity. We identify the set of memory hierarchy design parameters that plays a key role in the performance and cost of a memory system combining an SCM technology and a 3D stacked DRAM cache. We then introduce a methodology to drive provisioning for each of these design parameters under a target performance/cost goal. Finally, we use our methodology to derive concrete results for specific SCM technologies. With PCM as a case study, we show that a two bits/cell technology hits the performance/cost sweet spot, reducing the memory subsystem cost by 40% while keeping performance within 3% of the best performing DRAM-only system, whereas single-level and triple-level cell organizations are impractical for use as memory replacements.Comment: Published at MEMSYS'1

Helmholtz Portfolio Theme Large-Scale Data Management and Analysis (LSDMA)

The Helmholtz Association funded the "Large-Scale Data Management and Analysis" portfolio theme from 2012-2016. Four Helmholtz centres, six universities and another research institution in Germany joined to enable data-intensive science by optimising data life cycles in selected scientific communities. In our Data Life cycle Labs, data experts performed joint R&D together with scientific communities. The Data Services Integration Team focused on generic solutions applied by several communities

EFFECTIVE GROUPING FOR ENERGY AND PERFORMANCE: CONSTRUCTION OF ADAPTIVE, SUSTAINABLE, AND MAINTAINABLE DATA STORAGE

The performance gap between processors and storage systems has been increasingly critical overthe years. Yet the performance disparity remains, and further, storage energy consumption israpidly becoming a new critical problem. While smarter caching and predictive techniques domuch to alleviate this disparity, the problem persists, and data storage remains a growing contributorto latency and energy consumption.Attempts have been made at data layout maintenance, or intelligent physical placement ofdata, yet in practice, basic heuristics remain predominant. Problems that early studies soughtto solve via layout strategies were proven to be NP-Hard, and data layout maintenance todayremains more art than science. With unknown potential and a domain inherently full of uncertainty,layout maintenance persists as an area largely untapped by modern systems. But uncertainty inworkloads does not imply randomness; access patterns have exhibited repeatable, stable behavior.Predictive information can be gathered, analyzed, and exploited to improve data layouts. Ourgoal is a dynamic, robust, sustainable predictive engine, aimed at improving existing layouts byreplicating data at the storage device level.We present a comprehensive discussion of the design and construction of such a predictive engine,including workload evaluation, where we present and evaluate classical workloads as well asour own highly detailed traces collected over an extended period. We demonstrate significant gainsthrough an initial static grouping mechanism, and compare against an optimal grouping method ofour own construction, and further show significant improvement over competing techniques. We also explore and illustrate the challenges faced when moving from static to dynamic (i.e. online)grouping, and provide motivation and solutions for addressing these challenges. These challengesinclude metadata storage, appropriate predictive collocation, online performance, and physicalplacement. We reduced the metadata needed by several orders of magnitude, reducing the requiredvolume from more than 14% of total storage down to less than 12%. We also demonstrate how ourcollocation strategies outperform competing techniques. Finally, we present our complete modeland evaluate a prototype implementation against real hardware. This model was demonstrated tobe capable of reducing device-level accesses by up to 65%

Systems Support for Trusted Execution Environments

Cloud computing has become a default choice for data processing by both large corporations and individuals due to its economy of scale and ease of system management. However, the question of trust and trustoworthy computing inside the Cloud environments has been long neglected in practice and further exacerbated by the proliferation of AI and its use for processing of sensitive user data. Attempts to implement the mechanisms for trustworthy computing in the cloud have previously remained theoretical due to lack of hardware primitives in the commodity CPUs, while a combination of Secure Boot, TPMs, and virtualization has seen only limited adoption. The situation has changed in 2016, when Intel introduced the Software Guard Extensions (SGX) and its enclaves to the x86 ISA CPUs: for the first time, it became possible to build trustworthy applications relying on a commonly available technology. However, Intel SGX posed challenges to the practitioners who discovered the limitations of this technology, from the limited support of legacy applications and integration of SGX enclaves into the existing system, to the performance bottlenecks on communication, startup, and memory utilization. In this thesis, our goal is enable trustworthy computing in the cloud by relying on the imperfect SGX promitives. To this end, we develop and evaluate solutions to issues stemming from limited systems support of Intel SGX: we investigate the mechanisms for runtime support of POSIX applications with SCONE, an efficient SGX runtime library developed with performance limitations of SGX in mind. We further develop this topic with FFQ, which is a concurrent queue for SCONE's asynchronous system call interface. ShieldBox is our study of interplay of kernel bypass and trusted execution technologies for NFV, which also tackles the problem of low-latency clocks inside enclave. The two last systems, Clemmys and T-Lease are built on a more recent SGXv2 ISA extension. In Clemmys, SGXv2 allows us to significantly reduce the startup time of SGX-enabled functions inside a Function-as-a-Service platform. Finally, in T-Lease we solve the problem of trusted time by introducing a trusted lease primitive for distributed systems. We perform evaluation of all of these systems and prove that they can be practically utilized in existing systems with minimal overhead, and can be combined with both legacy systems and other SGX-based solutions. In the course of the thesis, we enable trusted computing for individual applications, high-performance network functions, and distributed computing framework, making a <vision of trusted cloud computing a reality

Computational Methods for Medical and Cyber Security

Over the past decade, computational methods, including machine learning (ML) and deep learning (DL), have been exponentially growing in their development of solutions in various domains, especially medicine, cybersecurity, finance, and education. While these applications of machine learning algorithms have been proven beneficial in various fields, many shortcomings have also been highlighted, such as the lack of benchmark datasets, the inability to learn from small datasets, the cost of architecture, adversarial attacks, and imbalanced datasets. On the other hand, new and emerging algorithms, such as deep learning, one-shot learning, continuous learning, and generative adversarial networks, have successfully solved various tasks in these fields. Therefore, applying these new methods to life-critical missions is crucial, as is measuring these less-traditional algorithms' success when used in these fields