179 research outputs found

    High Throughput Lattice-based Signatures on GPUs: Comparing Falcon and Mitaka

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    The US National Institute of Standards and Technology initiated a standardization process for post-quantum cryptography in 2017, with the aim of selecting key encapsulation mechanisms and signature schemes that can withstand the threat from emerging quantum computers. In 2022, Falcon was selected as one of the standard signature schemes, eventually attracting effort to optimize the implementation of Falcon on various hardware architectures for practical applications. Recently, Mitaka was proposed as an alternative to Falcon, allowing parallel execution of most of its operations. These recent advancements motivate us to develop high throughput implementations of Falcon and Mitaka signature schemes on Graphics Processing Units (GPUs), a massively parallel architecture widely available on cloud service platforms. In this paper, we propose the first parallel implementation of Falcon on various GPUs. An iterative version of the sampling process in Falcon, which is also the most time-consuming Falcon operation, was developed. This allows us to implement Falcon signature generation without relying on expensive recursive function calls on GPUs. In addition, we propose a parallel random samples generation approach to accelerate the performance of Mitaka on GPUs. We evaluate our implementation techniques on state-of-the-art GPU architectures (RTX 3080, A100, T4 and V100). Experimental results show that our Falcon-512 implementation achieves 58, 595 signatures/second and 2, 721, 562 verifications/second on an A100 GPU, which is 20.03× and 29.51× faster than the highly optimized AVX2 implementation on CPU. Our Mitaka implementation achieves 161, 985 signatures/second and 1, 421, 046 verifications/second on the same GPU. Due to the adoption of a parallelizable sampling process, Mitaka signature generation enjoys ≈ 2 – 20× higher throughput than Falcon on various GPUs. The high throughput signature generation and verification achieved by this work can be very useful in various emerging applications, including the Internet of Things

    The inherent overlapping in the parallel calculation of the Laplacian

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    Producción CientíficaA new approach for the parallel computation of the Laplacian in the Fourier domain is presented. This numerical problem inherits the intrinsic sequencing involved in the calculation of any multidimensional Fast Fourier Transform (FFT) where blocking communications assure that its computation is strictly carried out dimension by dimension. Such data dependency vanishes when one considers the Laplacian as the sum of n independent one-dimensional kernels, so that computation and communication can be naturally overlapped with nonblocking communications. Overlapping is demonstrated to be responsible for the speedup figures we obtain when our approach is compared to state-of-the-art parallel multidimensional FFTs.Junta de Castilla León (grant number VA296P18

    Computational Methods for Protein Inference in Shotgun Proteomics Experiments

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    In den letzten Jahrzehnten kam es zu einem signifikanten Anstiegs des Einsatzes von Hochdurchsatzmethoden in verschiedensten Bereichen der Naturwissenschaften, welche zu einem regelrechten Paradigmenwechsel führte. Eine große Anzahl an neuen Technologien wurde entwickelt um die Quantifizierung von Molekülen, die in verschiedenste biologische Prozesse involviert sind, voranzutreiben und zu beschleunigen. Damit einhergehend konnte eine beträchtliche Steigerung an Daten festgestellt werden, die durch diese verbesserten Methoden generiert wurden. Durch die Bereitstellung von computergestützten Verfahren zur Analyse eben dieser Masse an Rohdaten, spielt der Forschungsbereich der Bioinformatik eine immer größere Rolle bei der Extraktion biologischer Erkenntnisse. Im Speziellen hilft die computergestützte Massenspektrometrie bei der Prozessierung, Analyse und Visualisierung von Daten aus massenspektrometrischen Hochdursatzexperimenten. Bei der Erforschung der Gesamtheit aller Proteine einer Zelle oder einer anderweitigen Probe biologischen Materials, kommen selbst neueste Methoden an ihre Grenzen. Deswegen greifen viele Labore zu einer, dem Massenspektrometer vorgeschalteten, Verdauung der Probe um die Komplexität der zu messenden Moleküle zu verringern. Diese sogenannten "Bottom-up"-Proteomikexperimente mit Massenspektrometern führen allerdings zu einer erhöhten Schwierigkeit bei der anschließenden computergestützen Analyse. Durch die Verdauung von Proteinen zu Peptiden müssen komplexe Mehrdeutigkeiten während Proteininferenz, Proteingruppierung und Proteinquantifizierung berücksichtigt und/oder aufgelöst werden. Im Rahmen dieser Dissertation stellen wir mehrere Entwicklungen vor, die dabei helfen sollen eine effiziente und vollständig automatisierte Analyse von komplexen und umfangreichen \glqq Bottom-up\grqq{}-Proteomikexperimenten zu ermöglichen. Um die hinderliche Komplexität diskreter, Bayes'scher Proteininferenzmethoden zu verringern, wird neuerdings von sogenannten Faltungsbäumen (engl. "convolution trees") Gebrauch gemacht. Diese bieten bis jetzt jedoch keine genaue und gleichzeitig numerisch stabile Möglichkeit um "max-product"-Inferenz zu betreiben. Deswegen wird in dieser Dissertation zunächst eine neue Methode beschrieben die das mithilfe eines stückweisen bzw. extrapolierendem Verfahren ermöglicht. Basierend auf der Integration dieser Methode in eine mitentwickelte Bibliothek für Bayes'sche Inferenz, wird dann ein OpenMS-Tool für Proteininferenz präsentiert. Dieses Tool ermöglicht effiziente Proteininferenz auf Basis eines diskreten Bayes'schen Netzwerks mithilfe eines "loopy belief propagation" Algorithmus'. Trotz der streng probabilistischen Formulierung des Problems übertrifft unser Verfahren die meisten etablierten Methoden in Recheneffizienz. Das Interface des Algorithmus' bietet außerdem einzigartige Eingabe- und Ausgabeoptionen, wie z.B. das Regularisieren der Anzahl von Proteinen in einer Gruppe, proteinspezifische "Priors", oder rekalibrierte "Posteriors" der Peptide. Schließlich zeigt diese Arbeit einen kompletten, einfach zu benutzenden, aber trotzdem skalierenden Workflow für Proteininferenz und -quantifizierung, welcher um das neue Tool entwickelt wurde. Die Pipeline wurde in nextflow implementiert und ist Teil einer Gruppe von standardisierten, regelmäßig getesteten und von einer Community gepflegten Standardworkflows gebündelt unter dem Projekt nf-core. Unser Workflow ist in der Lage selbst große Datensätze mit komplizierten experimentellen Designs zu prozessieren. Mit einem einzigen Befehl erlaubt er eine (Re-)Analyse von lokalen oder öffentlich verfügbaren Datensätzen mit kompetetiver Genauigkeit und ausgezeichneter Performance auf verschiedensten Hochleistungsrechenumgebungen oder der Cloud.Since the beginning of this millennium, the advent of high-throughput methods in numerous fields of the life sciences led to a shift in paradigms. A broad variety of technologies emerged that allow comprehensive quantification of molecules involved in biological processes. Simultaneously, a major increase in data volume has been recorded with these techniques through enhanced instrumentation and other technical advances. By supplying computational methods that automatically process raw data to obtain biological information, the field of bioinformatics plays an increasingly important role in the analysis of the ever-growing mass of data. Computational mass spectrometry in particular, is a bioinformatics field of research which provides means to gather, analyze and visualize data from high-throughput mass spectrometric experiments. For the study of the entirety of proteins in a cell or an environmental sample, even current techniques reach limitations that need to be circumvented by simplifying the samples subjected to the mass spectrometer. These pre-digested (so-called bottom-up) proteomics experiments then pose an even bigger computational burden during analysis since complex ambiguities need to be resolved during protein inference, grouping and quantification. In this thesis, we present several developments in the pursuit of our goal to provide means for a fully automated analysis of complex and large-scale bottom-up proteomics experiments. Firstly, due to prohibitive computational complexities in state-of-the-art Bayesian protein inference techniques, a refined, more stable technique for performing inference on sums of random variables was developed to enable a variation of standard Bayesian inference for the problem. nextflow and part of a set of standardized, well-tested, and community-maintained workflows by the nf-core collective. Our workflow runs on large-scale data with complex experimental designs and allows a one-command analysis of local and publicly available data sets with state-of-the-art accuracy on various high-performance computing environments or the cloud

    A Modular Platform for Adaptive Heterogeneous Many-Core Architectures

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    Multi-/many-core heterogeneous architectures are shaping current and upcoming generations of compute-centric platforms which are widely used starting from mobile and wearable devices to high-performance cloud computing servers. Heterogeneous many-core architectures sought to achieve an order of magnitude higher energy efficiency as well as computing performance scaling by replacing homogeneous and power-hungry general-purpose processors with multiple heterogeneous compute units supporting multiple core types and domain-specific accelerators. Drifting from homogeneous architectures to complex heterogeneous systems is heavily adopted by chip designers and the silicon industry for more than a decade. Recent silicon chips are based on a heterogeneous SoC which combines a scalable number of heterogeneous processing units from different types (e.g. CPU, GPU, custom accelerator). This shifting in computing paradigm is associated with several system-level design challenges related to the integration and communication between a highly scalable number of heterogeneous compute units as well as SoC peripherals and storage units. Moreover, the increasing design complexities make the production of heterogeneous SoC chips a monopoly for only big market players due to the increasing development and design costs. Accordingly, recent initiatives towards agile hardware development open-source tools and microarchitecture aim to democratize silicon chip production for academic and commercial usage. Agile hardware development aims to reduce development costs by providing an ecosystem for open-source hardware microarchitectures and hardware design processes. Therefore, heterogeneous many-core development and customization will be relatively less complex and less time-consuming than conventional design process methods. In order to provide a modular and agile many-core development approach, this dissertation proposes a development platform for heterogeneous and self-adaptive many-core architectures consisting of a scalable number of heterogeneous tiles that maintain design regularity features while supporting heterogeneity. The proposed platform hides the integration complexities by supporting modular tile architectures for general-purpose processing cores supporting multi-instruction set architectures (multi-ISAs) and custom hardware accelerators. By leveraging field-programmable-gate-arrays (FPGAs), the self-adaptive feature of the many-core platform can be achieved by using dynamic and partial reconfiguration (DPR) techniques. This dissertation realizes the proposed modular and adaptive heterogeneous many-core platform through three main contributions. The first contribution proposes and realizes a many-core architecture for heterogeneous ISAs. It provides a modular and reusable tilebased architecture for several heterogeneous ISAs based on open-source RISC-V ISA. The modular tile-based architecture features a configurable number of processing cores with different RISC-V ISAs and different memory hierarchies. To increase the level of heterogeneity to support the integration of custom hardware accelerators, a novel hybrid memory/accelerator tile architecture is developed and realized as the second contribution. The hybrid tile is a modular and reusable tile that can be configured at run-time to operate as a scratchpad shared memory between compute tiles or as an accelerator tile hosting a local hardware accelerator logic. The hybrid tile is designed and implemented to be seamlessly integrated into the proposed tile-based platform. The third contribution deals with the self-adaptation features by providing a reconfiguration management approach to internally control the DPR process through processing cores (RISC-V based). The internal reconfiguration process relies on a novel DPR controller targeting FPGA design flow for RISC-V-based SoC to change the types and functionalities of compute tiles at run-time

    Wafer-Scale Fast Fourier Transforms

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    We have implemented fast Fourier transforms for one, two, and three-dimensional arrays on the Cerebras CS-2, a system whose memory and processing elements reside on a single silicon wafer. The wafer-scale engine (WSE) encompasses a two-dimensional mesh of roughly 850,000 processing elements (PEs) with fast local memory and equally fast nearest-neighbor interconnections. Our wafer-scale FFT (wsFFT) parallelizes a n3n^3 problem with up to n2n^2 PEs. At this point a PE processes only a single vector of the 3D domain (known as a pencil) per superstep, where each of the three supersteps performs FFT along one of the three axes of the input array. Between supersteps, wsFFT redistributes (transposes) the data to bring all elements of each one-dimensional pencil being transformed into the memory of a single PE. Each redistribution causes an all-to-all communication along one of the mesh dimensions. Given the level of parallelism, the size of the messages transmitted between pairs of PEs can be as small as a single word. In theory, a mesh is not ideal for all-to-all communication due to its limited bisection bandwidth. However, the mesh interconnecting PEs on the WSE lies entirely on-wafer and achieves nearly peak bandwidth even with tiny messages. This high efficiency on fine-grain communication allow wsFFT to achieve unprecedented levels of parallelism and performance. We analyse in detail computation and communication time, as well as the weak and strong scaling, using both FP16 and FP32 precision. With 32-bit arithmetic on the CS-2, we achieve 959 microseconds for 3D FFT of a 5123512^3 complex input array using a 512x512 subgrid of the on-wafer PEs. This is the largest ever parallelization for this problem size and the first implementation that breaks the millisecond barrier

    Towards a Common Software/Hardware Methodology for Future Advanced Driver Assistance Systems

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    The European research project DESERVE (DEvelopment platform for Safe and Efficient dRiVE, 2012-2015) had the aim of designing and developing a platform tool to cope with the continuously increasing complexity and the simultaneous need to reduce cost for future embedded Advanced Driver Assistance Systems (ADAS). For this purpose, the DESERVE platform profits from cross-domain software reuse, standardization of automotive software component interfaces, and easy but safety-compliant integration of heterogeneous modules. This enables the development of a new generation of ADAS applications, which challengingly combine different functions, sensors, actuators, hardware platforms, and Human Machine Interfaces (HMI). This book presents the different results of the DESERVE project concerning the ADAS development platform, test case functions, and validation and evaluation of different approaches. The reader is invited to substantiate the content of this book with the deliverables published during the DESERVE project. Technical topics discussed in this book include:Modern ADAS development platforms;Design space exploration;Driving modelling;Video-based and Radar-based ADAS functions;HMI for ADAS;Vehicle-hardware-in-the-loop validation system

    Exploring the possibilities of obtaining CNN-quality classification models without using convolutional neural networks

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    In this thesis, we pursue the success of Convolutional Neural Networks for image classification tasks. We explore the possibilities of achieving state-of-the-art performance without explicitly using CNNs on 2D grayscale images. We propose a Binary Patch Convolution (BPC) framework based on binarized patches from each group of images in a supervised task, eliminating the kernel learning process of CNNs. The binarized patches act as activations of different shapes and are applied using convolution. One of the key aspects of the framework is that it maintains a direct relation between the convolution kernels and the original images. Therefore, we can present a method to measure information content in a feature map for observing relations between different groups. We discuss and test different strategies for selecting groups of images to extract patches from while evaluating their effect on classification accuracy. The practical implementation of the BPC framework allows for many convolution kernels to be evaluated, positively impacting the framework’s performance. Ultimately, the proposed framework can extract pertinent features for classification and can be combined with any classifier. The framework is tested on the MNIST and Fashion-MNIST datasets and achieves competitive accuracy, even outperforming related work. We also discuss challenges and future work applicable to the framework. Furthermore, we have attempted to capture trends in the error of images by proposing an iterative variant of singular value bases classification. The proposed method fails to capture a generalizable error trend; thus, we have recognized that it is a challenging task for images. The process has given valuable insight into how to approach image classification problems. On top of that, we have examined the effects of negative transfer inherent in an original problem. Our experiments show that models trained on all groups in the data (global) are outperformed by models trained on different combinations of subgroups (local). Our proposed approaches for minimizing negative transfer within a task effectively increase classification accuracy. However, they are infeasible to deploy in practical scenarios due to the computation time introduced. The results are meant to motivate research toward within-task minimization of negative transfer, primarily since the existing research is focused on doing so in transfer learning

    Efficient algorithms and data structures for compressive sensing

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    Wegen der kontinuierlich anwachsenden Anzahl von Sensoren, und den stetig wachsenden Datenmengen, die jene produzieren, stößt die konventielle Art Signale zu verarbeiten, beruhend auf dem Nyquist-Kriterium, auf immer mehr Hindernisse und Probleme. Die kürzlich entwickelte Theorie des Compressive Sensing (CS) formuliert das Versprechen einige dieser Hindernisse zu beseitigen, indem hier allgemeinere Signalaufnahme und -rekonstruktionsverfahren zum Einsatz kommen können. Dies erlaubt, dass hierbei einzelne Abtastwerte komplexer strukturierte Informationen über das Signal enthalten können als dies bei konventiellem Nyquistsampling der Fall ist. Gleichzeitig verändert sich die Signalrekonstruktion notwendigerweise zu einem nicht-linearen Vorgang und ebenso müssen viele Hardwarekonzepte für praktische Anwendungen neu überdacht werden. Das heißt, dass man zwischen der Menge an Information, die man über Signale gewinnen kann, und dem Aufwand für das Design und Betreiben eines Signalverarbeitungssystems abwägen kann und muss. Die hier vorgestellte Arbeit trägt dazu bei, dass bei diesem Abwägen CS mehr begünstigt werden kann, indem neue Resultate vorgestellt werden, die es erlauben, dass CS einfacher in der Praxis Anwendung finden kann, wobei die zu erwartende Leistungsfähigkeit des Systems theoretisch fundiert ist. Beispielsweise spielt das Konzept der Sparsity eine zentrale Rolle, weshalb diese Arbeit eine Methode präsentiert, womit der Grad der Sparsity eines Vektors mittels einer einzelnen Beobachtung geschätzt werden kann. Wir zeigen auf, dass dieser Ansatz für Sparsity Order Estimation zu einem niedrigeren Rekonstruktionsfehler führt, wenn man diesen mit einer Rekonstruktion vergleicht, welcher die Sparsity des Vektors unbekannt ist. Um die Modellierung von Signalen und deren Rekonstruktion effizienter zu gestalten, stellen wir das Konzept von der matrixfreien Darstellung linearer Operatoren vor. Für die einfachere Anwendung dieser Darstellung präsentieren wir eine freie Softwarearchitektur und demonstrieren deren Vorzüge, wenn sie für die Rekonstruktion in einem CS-System genutzt wird. Konkret wird der Nutzen dieser Bibliothek, einerseits für das Ermitteln von Defektpositionen in Prüfkörpern mittels Ultraschall, und andererseits für das Schätzen von Streuern in einem Funkkanal aus Ultrabreitbanddaten, demonstriert. Darüber hinaus stellen wir für die Verarbeitung der Ultraschalldaten eine Rekonstruktionspipeline vor, welche Daten verarbeitet, die im Frequenzbereich Unterabtastung erfahren haben. Wir beschreiben effiziente Algorithmen, die bei der Modellierung und der Rekonstruktion zum Einsatz kommen und wir leiten asymptotische Resultate für die benötigte Anzahl von Messwerten, sowie die zu erwartenden Lokalisierungsgenauigkeiten der Defekte her. Wir zeigen auf, dass das vorgestellte System starke Kompression zulässt, ohne die Bildgebung und Defektlokalisierung maßgeblich zu beeinträchtigen. Für die Lokalisierung von Streuern mittels Ultrabreitbandradaren stellen wir ein CS-System vor, welches auf einem Random Demodulators basiert. Im Vergleich zu existierenden Messverfahren ist die hieraus resultierende Schätzung der Kanalimpulsantwort robuster gegen die Effekte von zeitvarianten Funkkanälen. Um den inhärenten Modellfehler, den gitterbasiertes CS begehen muss, zu beseitigen, zeigen wir auf wie Atomic Norm Minimierung es erlaubt ohne die Einschränkung auf ein endliches und diskretes Gitter R-dimensionale spektrale Komponenten aus komprimierten Beobachtungen zu schätzen. Hierzu leiten wir eine R-dimensionale Variante des ADMM her, welcher dazu in der Lage ist die Signalkovarianz in diesem allgemeinen Szenario zu schätzen. Weiterhin zeigen wir, wie dieser Ansatz zur Richtungsschätzung mit realistischen Antennenarraygeometrien genutzt werden kann. In diesem Zusammenhang präsentieren wir auch eine Methode, welche mittels Stochastic gradient descent Messmatrizen ermitteln kann, die sich gut für Parameterschätzung eignen. Die hieraus resultierenden Kompressionsverfahren haben die Eigenschaft, dass die Schätzgenauigkeit über den gesamten Parameterraum ein möglichst uniformes Verhalten zeigt. Zuletzt zeigen wir auf, dass die Kombination des ADMM und des Stochastic Gradient descent das Design eines CS-Systems ermöglicht, welches in diesem gitterfreien Szenario wünschenswerte Eigenschaften hat.Along with the ever increasing number of sensors, which are also generating rapidly growing amounts of data, the traditional paradigm of sampling adhering the Nyquist criterion is facing an equally increasing number of obstacles. The rather recent theory of Compressive Sensing (CS) promises to alleviate some of these drawbacks by proposing to generalize the sampling and reconstruction schemes such that the acquired samples can contain more complex information about the signal than Nyquist samples. The proposed measurement process is more complex and the reconstruction algorithms necessarily need to be nonlinear. Additionally, the hardware design process needs to be revisited as well in order to account for this new acquisition scheme. Hence, one can identify a trade-off between information that is contained in individual samples of a signal and effort during development and operation of the sensing system. This thesis addresses the necessary steps to shift the mentioned trade-off more to the favor of CS. We do so by providing new results that make CS easier to deploy in practice while also maintaining the performance indicated by theoretical results. The sparsity order of a signal plays a central role in any CS system. Hence, we present a method to estimate this crucial quantity prior to recovery from a single snapshot. As we show, this proposed Sparsity Order Estimation method allows to improve the reconstruction error compared to an unguided reconstruction. During the development of the theory we notice that the matrix-free view on the involved linear mappings offers a lot of possibilities to render the reconstruction and modeling stage much more efficient. Hence, we present an open source software architecture to construct these matrix-free representations and showcase its ease of use and performance when used for sparse recovery to detect defects from ultrasound data as well as estimating scatterers in a radio channel using ultra-wideband impulse responses. For the former of these two applications, we present a complete reconstruction pipeline when the ultrasound data is compressed by means of sub-sampling in the frequency domain. Here, we present the algorithms for the forward model, the reconstruction stage and we give asymptotic bounds for the number of measurements and the expected reconstruction error. We show that our proposed system allows significant compression levels without substantially deteriorating the imaging quality. For the second application, we develop a sampling scheme to acquire the channel Impulse Response (IR) based on a Random Demodulator that allows to capture enough information in the recorded samples to reliably estimate the IR when exploiting sparsity. Compared to the state of the art, this in turn allows to improve the robustness to the effects of time-variant radar channels while also outperforming state of the art methods based on Nyquist sampling in terms of reconstruction error. In order to circumvent the inherent model mismatch of early grid-based compressive sensing theory, we make use of the Atomic Norm Minimization framework and show how it can be used for the estimation of the signal covariance with R-dimensional parameters from multiple compressive snapshots. To this end, we derive a variant of the ADMM that can estimate this covariance in a very general setting and we show how to use this for direction finding with realistic antenna geometries. In this context we also present a method based on a Stochastic gradient descent iteration scheme to find compression schemes that are well suited for parameter estimation, since the resulting sub-sampling has a uniform effect on the whole parameter space. Finally, we show numerically that the combination of these two approaches yields a well performing grid-free CS pipeline
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