1,572 research outputs found

    Lifting Code Generation of Cardiac Physiology Simulation to Novel Compiler Technology

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    International audienceThe study of numerical models for the human body has become a major focus of the research community in biology and medicine. For instance, numerical ionic models of a complex organ, such as the heart, must be able to represent individual cells and their interconnections through ionic channels, forming a system with billions of cells, and requiring efficient code to handle such a large system. The modeling of the electrical system of the heart combines a compute-intensive kernel that calculates the intensity of current flowing through cell membranes, and feeds a linear solver for computing the electrical potential of each cell. Considering this context, we propose limpetMLIR, a code generator and compiler transformer to accelerate the kernel phase of ionic models and bridge the gap between compiler technology and electrophysiology simulation. LimpetMLIR makes use of the MLIR infrastructure, its dialects, and transformations to drive forward the study of ionic models, and accelerate the execution of multi-cell systems. Experiments conducted in 43 ionic models show that our limpetMLIR based code generation greatly outperforms current state-ofthe-art simulation systems by an average of 2.9Ă—, reaching peak speedups of more than 15Ă— in some cases. To our knowledge, this is the first work that deeply connects an optimizing compiler infrastructure to electrophysiology models of the human body, showing the potential benefits of using compiler technology in the simulation of human cell interactions

    SonicJoin: fast, robust and worst-case optimal

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    The establishment of the AGM bound on the size of intermediate results of natural join queries has led to the development of several so-called worst-case join algorithms. These algorithms provably produce intermediate results that are (asymptotically) no larger than the final result of the join. The most notable ones are the Recursive Join, its successor, the Generic Join and the Leapfrog-Trie-Join. While algorithmically efficient, however, all of these algorithms require the availability of index structures that allow tuple lookups using the prefix of a key. Key-prefix-lookups in relational database systems are commonly supported by tree-based index structures since hash-based indices only support full-key lookups. In this paper, we study a wide variety of main-memory-oriented index structures that support key-prefix-lookups with a specific focus on supporting the Generic Join. Based on that study, we develop a novel, best-of-breed index structure called Sonic that combines the fast build and point lookup properties of hashtables with the prefix-lookups capabilities of trees and tries. To evaluate the performance of a variety of indices for worst-case optimal joins in a modern code-generating DBMS, we leveraged flexible, compile-time metaprogramming features to build a framework that creates highly efficient code, interweaving (at a microarchitectural level) a generic join implementation with any appropriate index structure. We demonstrate experimentally that in that framework, Sonic outperforms the fastest existing approaches by up to 2.5 times when supporting the Generic Join algorithm

    Using the IBM Analog In-Memory Hardware Acceleration Kit for Neural Network Training and Inference

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    Analog In-Memory Computing (AIMC) is a promising approach to reduce the latency and energy consumption of Deep Neural Network (DNN) inference and training. However, the noisy and non-linear device characteristics, and the non-ideal peripheral circuitry in AIMC chips, require adapting DNNs to be deployed on such hardware to achieve equivalent accuracy to digital computing. In this tutorial, we provide a deep dive into how such adaptations can be achieved and evaluated using the recently released IBM Analog Hardware Acceleration Kit (AIHWKit), freely available at https://github.com/IBM/aihwkit. The AIHWKit is a Python library that simulates inference and training of DNNs using AIMC. We present an in-depth description of the AIHWKit design, functionality, and best practices to properly perform inference and training. We also present an overview of the Analog AI Cloud Composer, that provides the benefits of using the AIHWKit simulation platform in a fully managed cloud setting. Finally, we show examples on how users can expand and customize AIHWKit for their own needs. This tutorial is accompanied by comprehensive Jupyter Notebook code examples that can be run using AIHWKit, which can be downloaded from https://github.com/IBM/aihwkit/tree/master/notebooks/tutorial

    Resilient and Scalable Forwarding for Software-Defined Networks with P4-Programmable Switches

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    Traditional networking devices support only fixed features and limited configurability. Network softwarization leverages programmable software and hardware platforms to remove those limitations. In this context the concept of programmable data planes allows directly to program the packet processing pipeline of networking devices and create custom control plane algorithms. This flexibility enables the design of novel networking mechanisms where the status quo struggles to meet high demands of next-generation networks like 5G, Internet of Things, cloud computing, and industry 4.0. P4 is the most popular technology to implement programmable data planes. However, programmable data planes, and in particular, the P4 technology, emerged only recently. Thus, P4 support for some well-established networking concepts is still lacking and several issues remain unsolved due to the different characteristics of programmable data planes in comparison to traditional networking. The research of this thesis focuses on two open issues of programmable data planes. First, it develops resilient and efficient forwarding mechanisms for the P4 data plane as there are no satisfying state of the art best practices yet. Second, it enables BIER in high-performance P4 data planes. BIER is a novel, scalable, and efficient transport mechanism for IP multicast traffic which has only very limited support of high-performance forwarding platforms yet. The main results of this thesis are published as 8 peer-reviewed and one post-publication peer-reviewed publication. The results cover the development of suitable resilience mechanisms for P4 data planes, the development and implementation of resilient BIER forwarding in P4, and the extensive evaluations of all developed and implemented mechanisms. Furthermore, the results contain a comprehensive P4 literature study. Two more peer-reviewed papers contain additional content that is not directly related to the main results. They implement congestion avoidance mechanisms in P4 and develop a scheduling concept to find cost-optimized load schedules based on day-ahead forecasts

    Tackling the Matrix Multiplication Micro-kernel Generation with Exo

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    The optimization of the matrix multiplication (or GEMM) has been a need during the last decades. This operation is considered the flagship of current linear algebra libraries such as BLIS, OpenBLAS, or Intel OneAPI because of its widespread use in a large variety of scientific applications. The GEMM is usually implemented following the GotoBLAS philosophy, which tiles the GEMM operands and uses a series of nested loops for performance improvement. These approaches extract the maximum computational power of the architectures through small pieces of hardware-oriented, high-performance code called micro-kernel. However, this approach forces developers to generate, with a non-negligible effort, a dedicated micro-kernel for each new hardware. In this work, we present a step-by-step procedure for generating micro-kernels with the Exo compiler that performs close to (or even better than) manually developed microkernels written with intrinsic functions or assembly language. Our solution also improves the portability of the generated code, since a hardware target is fully specified by a concise library-based description of its instructions.Comment: 11 pages, 18 figures. Presented at CGO 2024. It includes a software artifact step-by-step executio

    BitGNN: Unleashing the Performance Potential of Binary Graph Neural Networks on GPUs

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    Recent studies have shown that Binary Graph Neural Networks (GNNs) are promising for saving computations of GNNs through binarized tensors. Prior work, however, mainly focused on algorithm designs or training techniques, leaving it open to how to materialize the performance potential on accelerator hardware fully. This work redesigns the binary GNN inference backend from the efficiency perspective. It fills the gap by proposing a series of abstractions and techniques to map binary GNNs and their computations best to fit the nature of bit manipulations on GPUs. Results on real-world graphs with GCNs, GraphSAGE, and GraphSAINT show that the proposed techniques outperform state-of-the-art binary GNN implementations by 8-22X with the same accuracy maintained. BitGNN code is publicly available.Comment: To appear in the International Conference on Supercomputing (ICS'23

    Behavior quantification as the missing link between fields: Tools for digital psychiatry and their role in the future of neurobiology

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    The great behavioral heterogeneity observed between individuals with the same psychiatric disorder and even within one individual over time complicates both clinical practice and biomedical research. However, modern technologies are an exciting opportunity to improve behavioral characterization. Existing psychiatry methods that are qualitative or unscalable, such as patient surveys or clinical interviews, can now be collected at a greater capacity and analyzed to produce new quantitative measures. Furthermore, recent capabilities for continuous collection of passive sensor streams, such as phone GPS or smartwatch accelerometer, open avenues of novel questioning that were previously entirely unrealistic. Their temporally dense nature enables a cohesive study of real-time neural and behavioral signals. To develop comprehensive neurobiological models of psychiatric disease, it will be critical to first develop strong methods for behavioral quantification. There is huge potential in what can theoretically be captured by current technologies, but this in itself presents a large computational challenge -- one that will necessitate new data processing tools, new machine learning techniques, and ultimately a shift in how interdisciplinary work is conducted. In my thesis, I detail research projects that take different perspectives on digital psychiatry, subsequently tying ideas together with a concluding discussion on the future of the field. I also provide software infrastructure where relevant, with extensive documentation. Major contributions include scientific arguments and proof of concept results for daily free-form audio journals as an underappreciated psychiatry research datatype, as well as novel stability theorems and pilot empirical success for a proposed multi-area recurrent neural network architecture.Comment: PhD thesis cop

    Parallel and Flow-Based High Quality Hypergraph Partitioning

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    Balanced hypergraph partitioning is a classic NP-hard optimization problem that is a fundamental tool in such diverse disciplines as VLSI circuit design, route planning, sharding distributed databases, optimizing communication volume in parallel computing, and accelerating the simulation of quantum circuits. Given a hypergraph and an integer kk, the task is to divide the vertices into kk disjoint blocks with bounded size, while minimizing an objective function on the hyperedges that span multiple blocks. In this dissertation we consider the most commonly used objective, the connectivity metric, where we aim to minimize the number of different blocks connected by each hyperedge. The most successful heuristic for balanced partitioning is the multilevel approach, which consists of three phases. In the coarsening phase, vertex clusters are contracted to obtain a sequence of structurally similar but successively smaller hypergraphs. Once sufficiently small, an initial partition is computed. Lastly, the contractions are successively undone in reverse order, and an iterative improvement algorithm is employed to refine the projected partition on each level. An important aspect in designing practical heuristics for optimization problems is the trade-off between solution quality and running time. The appropriate trade-off depends on the specific application, the size of the data sets, and the computational resources available to solve the problem. Existing algorithms are either slow, sequential and offer high solution quality, or are simple, fast, easy to parallelize, and offer low quality. While this trade-off cannot be avoided entirely, our goal is to close the gaps as much as possible. We achieve this by improving the state of the art in all non-trivial areas of the trade-off landscape with only a few techniques, but employed in two different ways. Furthermore, most research on parallelization has focused on distributed memory, which neglects the greater flexibility of shared-memory algorithms and the wide availability of commodity multi-core machines. In this thesis, we therefore design and revisit fundamental techniques for each phase of the multilevel approach, and develop highly efficient shared-memory parallel implementations thereof. We consider two iterative improvement algorithms, one based on the Fiduccia-Mattheyses (FM) heuristic, and one based on label propagation. For these, we propose a variety of techniques to improve the accuracy of gains when moving vertices in parallel, as well as low-level algorithmic improvements. For coarsening, we present a parallel variant of greedy agglomerative clustering with a novel method to resolve cluster join conflicts on-the-fly. Combined with a preprocessing phase for coarsening based on community detection, a portfolio of from-scratch partitioning algorithms, as well as recursive partitioning with work-stealing, we obtain our first parallel multilevel framework. It is the fastest partitioner known, and achieves medium-high quality, beating all parallel partitioners, and is close to the highest quality sequential partitioner. Our second contribution is a parallelization of an n-level approach, where only one vertex is contracted and uncontracted on each level. This extreme approach aims at high solution quality via very fine-grained, localized refinement, but seems inherently sequential. We devise an asynchronous n-level coarsening scheme based on a hierarchical decomposition of the contractions, as well as a batch-synchronous uncoarsening, and later fully asynchronous uncoarsening. In addition, we adapt our refinement algorithms, and also use the preprocessing and portfolio. This scheme is highly scalable, and achieves the same quality as the highest quality sequential partitioner (which is based on the same components), but is of course slower than our first framework due to fine-grained uncoarsening. The last ingredient for high quality is an iterative improvement algorithm based on maximum flows. In the sequential setting, we first improve an existing idea by solving incremental maximum flow problems, which leads to smaller cuts and is faster due to engineering efforts. Subsequently, we parallelize the maximum flow algorithm and schedule refinements in parallel. Beyond the strive for highest quality, we present a deterministically parallel partitioning framework. We develop deterministic versions of the preprocessing, coarsening, and label propagation refinement. Experimentally, we demonstrate that the penalties for determinism in terms of partition quality and running time are very small. All of our claims are validated through extensive experiments, comparing our algorithms with state-of-the-art solvers on large and diverse benchmark sets. To foster further research, we make our contributions available in our open-source framework Mt-KaHyPar. While it seems inevitable, that with ever increasing problem sizes, we must transition to distributed memory algorithms, the study of shared-memory techniques is not in vain. With the multilevel approach, even the inherently slow techniques have a role to play in fast systems, as they can be employed to boost quality on coarse levels at little expense. Similarly, techniques for shared-memory parallelism are important, both as soon as a coarse graph fits into memory, and as local building blocks in the distributed algorithm

    Automated tailoring of system software stacks

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    In many industrial sectors, device manufacturers are moving away from expensive special-purpose hardware units and consolidate their systems on commodity hardware. As part of this change, developers are enabled to run their applications on general-purpose operating systems like Linux, which already supports thousands of different devices out of the box and can be used in a wide range of target scenarios. Furthermore, the Linux ecosystem allows them to integrate existing implementations of standard functionality in the form of shared libraries. However, as the libraries and the Linux kernel are designed as generic building blocks in order to support as many applications as possible, they cannot make assumptions about specific use cases for a single-purpose device. This generality leads to unnecessary overheads in narrowly defined target scenarios, as unneeded components do not only take up space on the target system but have to be maintained over the lifetime of the device as well. While the Linux kernel provides a configuration system to disable unneeded functionality like device drivers, determining the required features from over 16000 options is an infeasible task. Even worse, most shared libraries cannot be customized even though only around 10 percent of their functions are ever used by applications. In this thesis, I present my approaches for the automated identification and removal of unnecessary components in all layers of the software stack. As the configuration system is an integral part of the Linux kernel, we embrace its presence and automatically generate custom-fitted configurations for observed target scenarios with the help of an extracted variability model. For the much more diverse realm of shared libraries, with different programming languages, build systems, and a lack of configurability, I demonstrate a different approach. By identifying individual functions as logically distinct units, we construct a symbol-level dependency graph across the applications and all their required libraries. We then remove unneeded code at the binary level and rearrange the remaining parts to take up minimal space in the binary file by formulating their placement as an optimization problem. To lower the number of unnecessary updates to unused components in a deployed system, I lastly present an automated method to determine the impact of software changes on a target scenario and provide guidance for developers on whether they need to update their systems. Applying these techniques to different target systems, I demonstrate that we can disable up to 87 percent of configuration options in a Debian Linux kernel, shrink the size of an embedded OpenWrt kernel by 59 percent, and speed up the boot process of the embedded system by 21 percent. As part of the shared library tailoring process, we can remove 13060 functions from all libraries in OpenWrt and reduce their total size by 31 percent. In the memcached Docker container, we identify 381 entirely unneeded shared libraries and shrink the container image size by 82 percent. An analysis of the development history of two large library projects over the course of more than two years further shows that between 68 and 82 percent of all changes are not required for an OpenWrt appliance, reducing the number of patch days by up to 69 percent. These results demonstrate the broad applicability of our automated methods for both the Linux kernel and shared libraries to a wide range of scenarios. From embedded systems to server applications, custom-tailored system software stacks contribute to the reduction of overheads in space and time

    Natural Fracture Evolution: Investigations into the Middle Devonian Marcellus Shale, Appalachian Basin, USA

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    Optimizing recovery from unconventional shale reservoirs has generated considerable research into optimal recovery methods through hydraulic fracturing design and shale reservoir characterization in the development of long-term hydrocarbon producers. Permeability at multiple scales from nanometer-scale pore sizes and nano-darcy permeability to completion-induced fractures defining a 100’s of meter stimulated reservoir volume plays a significant role in hydrocarbon flow during production in shale reservoirs. Preexisting cemented fractures in unconventional shale reservoirs are abundant and preferentially reactivate during induced hydraulic fracturing treatment to create necessary large-scale permeability. While previous investigations have significantly improved our knowledge of shale reservoirs, it has also highlighted the need for increased understanding of the geologic evolution and effect on hydraulic stimulation of pre-existing cemented fractures. This three-part dissertation examines natural fractures from four middle Devonian Marcellus Shale wells across the Appalachian basin through integration of visual core observation, thin section petrography, spectral gamma ray logs, borehole image logs, petrophysical logs, elemental data, and X-ray computed tomography cores. The research goals are: (1) to establish clues to assess natural fracture development in source rocks from kerogen maturation, relative timing, and hydrocarbon migration; (2) to investigate the relationship of natural fractures in wells of varying thermal maturity levels, and preferential fracture distribution in various clay types and redox environments; and (3) to characterize mineralized natural fractures in 3D using a medical CT-scan core to quantify volume and assess connectivity. This research indicates that overpressure from kerogen expulsion of hydrocarbon creates numerous cemented fractures filled with calcite and bitumen that achieve orientations related to the geologic burial stresses during their evolution, predominant in clay-rich units of certain redox conditions, cluster at geomechanical boundaries, and have inconsistent 3D volume changes within the core
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