Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Scalability of broadcast performance in wireless network-on-chip

Networks-on-Chip (NoCs) are currently the paradigm of choice to interconnect the cores of a chip multiprocessor. However, conventional NoCs may not suffice to fulfill the on-chip communication requirements of processors with hundreds or thousands of cores. The main reason is that the performance of such networks drops as the number of cores grows, especially in the presence of multicast and broadcast traffic. This not only limits the scalability of current multiprocessor architectures, but also sets a performance wall that prevents the development of architectures that generate moderate-to-high levels of multicast. In this paper, a Wireless Network-on-Chip (WNoC) where all cores share a single broadband channel is presented. Such design is conceived to provide low latency and ordered delivery for multicast/broadcast traffic, in an attempt to complement a wireline NoC that will transport the rest of communication flows. To assess the feasibility of this approach, the network performance of WNoC is analyzed as a function of the system size and the channel capacity, and then compared to that of wireline NoCs with embedded multicast support. Based on this evaluation, preliminary results on the potential performance of the proposed hybrid scheme are provided, together with guidelines for the design of MAC protocols for WNoC.Peer ReviewedPostprint (published version

Safe and Secure Support for Public Safety Networks

International audienceAs explained by Tanzi et al. in the first volume of this book, communicating and autonomous devices will surely have a role to play in the future Public Safety Networks. The “communicating” feature comes from the fact that the information should be delivered in a fast way to rescuers. The “autonomous” characteristic comes from the fact that rescuers should not have to concern themselves about these objects: they should perform their mission autonomously so as not to delay the intervention of the rescuers, but rather to assist them efficiently and reliably.</p

Exploration of intercell wireless millimeter-wave communication in the landscape of intelligent metasurfaces

Software-defined metasurfaces are electromagnetically ultra-thin, artificial components thatcan provide engineered and externally controllable functionalities. The control over these functionalities isenabled by the metasurface tunability, which is implemented by embedded electronic circuits that modifylocally the surface resistance and reactance. Integrating controllers within the metasurface able them tointercommunicate and adaptively reconfigure, thus imparting a desired electromagnetic operation, opens thepath towards the creation of an artificially intelligent (AI) fabric where each unit cell can have its own sensing,programmable computing, and actuation facilities. In this work we take a crucial step towards bringing theAI metasurface technology to emerging applications, in particular exploring the wireless mm-wave intercellcommunication capabilities in a software-defined HyperSurface designed for operation in the microwaveregime. We examine three different wireless communication channels within the landscape of the reflectivemetasurface: Firstly, in the layer where the control electronics of the HyperSurface lie, secondly inside adedicated layer enclosed between two metallic plates, and, thirdly, inside the metasurface itself. For each casewe examine the physical implementation of the mm-wave transceiver nodes, we quantify communicationchannel metrics, and we identify complexity vs. performance trade-offs.Peer ReviewedPostprint (published version

Performance Implications of NoCs on 3D-Stacked Memories: Insights from the Hybrid Memory Cube

Memories that exploit three-dimensional (3D)-stacking technology, which integrate memory and logic dies in a single stack, are becoming popular. These memories, such as Hybrid Memory Cube (HMC), utilize a network-on-chip (NoC) design for connecting their internal structural organizations. This novel usage of NoC, in addition to aiding processing-in-memory capabilities, enables numerous benefits such as high bandwidth and memory-level parallelism. However, the implications of NoCs on the characteristics of 3D-stacked memories in terms of memory access latency and bandwidth have not been fully explored. This paper addresses this knowledge gap by (i) characterizing an HMC prototype on the AC-510 accelerator board and revealing its access latency behaviors, and (ii) by investigating the implications of such behaviors on system and software designs

성능과 용량 향상을 위한 적층형 메모리 구조

학위논문 (박사)-- 서울대학교 대학원 : 융합과학기술대학원 융합과학부(지능형융합시스템전공), 2019. 2. 안정호.The advance of DRAM manufacturing technology slows down, whereas the density and performance needs of DRAM continue to increase. This desire has motivated the industry to explore emerging Non-Volatile Memory (e.g., 3D XPoint) and the high-density DRAM (e.g., Managed DRAM Solution). Since such memory technologies increase the density at the cost of longer latency, lower bandwidth, or both, it is essential to use them with fast memory (e.g., conventional DRAM) to which hot pages are transferred at runtime. Nonetheless, we observe that page transfers to fast memory often block memory channels from servicing memory requests from applications for a long period. This in turn significantly increases the high-percentile response time of latency-sensitive applications. In this thesis, we propose a high-density managed DRAM architecture, dubbed 3D-XPath for applications demanding both low latency and high capacity for memory. 3D-XPath DRAM stacks conventional DRAM dies with high-density DRAM dies explored in this thesis and connects these DRAM dies with 3D-XPath. Especially, 3D-XPath allows unused memory channels to service memory requests from applications when primary channels supposed to handle the memory requests are blocked by page transfers at given moments, considerably increasing the high-percentile response time. This can also improve the throughput of applications frequently copying memory blocks between kernel and user memory spaces. Our evaluation shows that 3D-XPath DRAM decreases high-percentile response time of latency-sensitive applications by ∼30% while improving the throughput of an I/O-intensive applications by ∼39%, compared with DRAM without 3D-XPath. Recent computer systems are evolving toward the integration of more CPU cores into a single socket, which require higher memory bandwidth and capacity. Increasing the number of channels per socket is a common solution to the bandwidth demand and to better utilize these increased channels, data bus width is reduced and burst length is increased. However, this longer burst length brings increased DRAM access latency. On the memory capacity side, process scaling has been the answer for decades, but cell capacitance now limits how small a cell could be. 3D stacked memory solves this problem by stacking dies on top of other dies. We made a key observation in real multicore machine that multiple memory controllers are always not fully utilized on SPEC CPU 2006 rate benchmark. To bring these idle channels into play, we proposed memory channel sharing architecture to boost peak bandwidth of one memory channel and reduce the burst latency on 3D stacked memory. By channel sharing, the total performance on multi-programmed workloads and multi-threaded workloads improved up to respectively 4.3% and 3.6% and the average read latency reduced up to 8.22% and 10.18%.DRAM 제조 기술의 발전은 속도가 느려지는 반면 DRAM의 밀도 및 성능 요구는 계속 증가하고 있다. 이러한 요구로 인해 새로운 비 휘발성 메모리(예: 3D-XPoint) 및 고밀도 DRAM(예: Managed asymmetric latency DRAM Solution)이 등장하였다. 이러한 고밀도 메모리 기술은 긴 레이턴시, 낮은 대역폭 또는 두 가지 모두를 사용하는 방식으로 밀도를 증가시키기 때문에 성능이 좋지 않아, 핫 페이지를 고속 메모리(예: 일반 DRAM)로 스왑되는 저용량의 고속 메모리가 동시에 사용되는 것이 일반적이다. 이러한 스왑 과정에서 빠른 메모리로의 페이지 전송이 일반적인 응용프로그램의 메모리 요청을 오랫동안 처리하지 못하도록 하기 때문에, 대기 시간에 민감한 응용 프로그램의 백분위 응답 시간을 크게 증가시켜, 응답 시간의 표준 편차를 증가시킨다. 이러한 문제를 해결하기 위해 본 학위 논문에서는 저 지연시간 및 고용량 메모리를 요구하는 애플리케이션을 위해 3D-XPath, 즉 고밀도 관리 DRAM 아키텍처를 제안한다. 이러한 3D-톔소를 집적한 DRAM은 저속의 고밀도 DRAM 다이를 기존의 일반적인 DRAM 다이와 동시에 한 칩에 적층하고, DRAM 다이끼리는 제안하는 3D-XPath 하드웨어를 통해 연결된다. 이러한 3D-XPath는 핫 페이지 스왑이 일어나는 동안 응용프로그램의 메모리 요청을 차단하지 않고 사용량이 적은 메모리 채널로 핫 페이지 스왑을 처리 할 수 있도록 하여, 데이터 집중 응용 프로그램의 백분위 응답 시간을 개선시킨다. 또한 제안하는 하드웨어 구조를 사용하여, 추가적으로 O/S 커널과 유저 스페이스 간의 메모리 블록을 자주 복사하는 응용 프로그램의 처리량을 향상시킬 수 있다. 이러한 3D-XPath DRAM은 3D-XPath가 없는 DRAM에 비해 I/O 집약적인 응용프로그램의 처리량을 최대 39 % 향상시키면서 레이턴시에 민감한 응용 프로그램의 높은 백분위 응답 시간을 최대 30 %까지 감소시킬 수 있다. 또한 최근의 컴퓨터 시스템은 보다 많은 메모리 대역폭과 용량을 필요로하는 더 많은 CPU 코어를 단일 소켓으로 통합하는 방향으로 진화하고 있다. 이러한 소켓 당 채널 수를 늘리는 것은 대역폭 요구에 대한 일반적인 해결책이며, 최신의 DRAM 인터페이스의 발전 양상은 증가한 채널을 보다 잘 활용하기 위해 데이터 버스 폭이 감소되고 버스트 길이가 증가한다. 그러나 길어진 버스트 길이는 DRAM 액세스 대기 시간을 증가시킨다. 추가적으로 최신의 응용프로그램은 더 많은 메모리 용량을 요구하며, 미세 공정으로 메모리 용량을 증가시키는 방법론은 수십 년 동안 사용되었지만, 20 nm 이하의 미세공정에서는 더 이상 공정 미세화를 통해 메모리 밀도를 증가시키기가 어려운 상황이며, 적층형 메모리를 사용하여 용량을 증가시키는 방법을 사용한다. 이러한 상황에서, 실제 최신의 멀티코어 머신에서 SPEC CPU 2006 응용프로그램을 멀티코어에서 실행하였을 때, 항상 시스템의 모든 메모리 컨트롤러가 완전히 활용되지 않는다는 사실을 관찰했다. 이러한 유휴 채널을 사용하기 위해 하나의 메모리 채널의 피크 대역폭을 높이고 3D 스택 메모리의 버스트 대기 시간을 줄이기 위해 본 학위 논문에서는 메모리 채널 공유 아키텍처를 제안하였으며, 하드웨어 블록을 제안하였다. 이러한 채널 공유를 통해 멀티 프로그램 된 응용프로그램 및 다중 스레드 응용프로그램 성능이 각각 4.3 % 및 3.6 %로 향상되었으며 평균 읽기 대기 시간은 8.22 % 및 10.18 %로 감소하였다.Contents Abstract i Contents iv List of Figures vi List of Tables viii Introduction 1 1.1 3D-XPath: High-Density Managed DRAM Architecture with Cost-effective Alternative Paths for Memory Transactions 5 1.2 Boosting Bandwidth – Dynamic Channel Sharing on 3D Stacked Memory 9 1.3 Research contribution 13 1.4 Outline 14 3D-stacked Heterogeneous Memory Architecture with Cost-effective Extra Block Transfer Paths 17 2.1 Background 17 2.1.1 Heterogeneous Main Memory Systems 17 2.1.2 Specialized DRAM 19 2.1.3 3D-stacked Memory 22 2.2 HIGH-DENSITY DRAM ARCHITECTURE 27 2.2.1 Key Design Challenges 29 2.2.2 Plausible High-density DRAM Designs 33 2.3 3D-STACKED DRAM WITH ALTERNATIVE PATHS FOR MEMORY TRANSACTIONS 37 2.3.1 3D-XPath Architecture 41 2.3.2 3D-XPath Management 46 2.4 EXPERIMENTAL METHODOLOGY 52 2.5 EVALUATION 56 2.5.1 OLDI Workloads 56 2.5.2 Non-OLDI Workloads 61 2.5.3 Sensitivity Analysis 66 2.6 RELATED WORK 70 Boosting bandwidth –Dynamic Channel Sharing on 3D Stacked Memory 72 3.1 Background: Memory Operations 72 3.1.1. Memory Controller 72 3.1.2 DRAM column access sequence 73 3.2 Related Work 74 3.3. CHANNEL SHARING ENABLED MEMORY SYSTEM 76 3.3.1 Hardware Requirements 78 3.3.2 Operation Sequence 81 3.4 Analysis 87 3.4.1 Experiment Environment 87 3.4.2 Performance 88 3.4.3 Overhead 90 CONCLUSION 92 REFERENCES 94 국문초록 107Docto

Computational methods and software for the design of inertial microfluidic flow sculpting devices

The ability to sculpt inertially flowing fluid via bluff body obstacles has enormous promise for applications in bioengineering, chemistry, and manufacturing within microfluidic devices. However, the computational difficulty inherent to full scale 3-dimensional fluid flow simulations makes designing and optimizing such systems tedious, costly, and generally tasked to computational experts with access to high performance resources. The goal of this work is to construct efficient models for the design of inertial microfluidic flow sculpting devices, and implement these models in freely available, user-friendly software for the broader microfluidics community. Two software packages were developed to accomplish this: uFlow and FlowSculpt . uFlow solves the forward problem in flow sculpting, that of predicting the net deformation from an arbitrary sequence of obstacles (pillars), and includes estimations of transverse mass diffusion and particles formed by optical lithography. FlowSculpt solves the more difficult inverse problem in flow sculpting, which is to design a flow sculpting device which produces a target flow shape. Each piece of software uses efficient, experimentally validated forward models developed within this work, which are applied to deep learning techniques to explore other routes to solving the inverse problem. The models are also highly modular, capable of incorporating new microfluidic components and flow physics to the design process. It is anticipated that the microfluidics community will integrate the tools developed here into their own research, and bring new designs, components, and applications to the inertial flow sculpting platform

Parallel architectures and runtime systems co-design for task-based programming models

The increasing parallelism levels in modern computing systems has extolled the need for a holistic vision when designing multiprocessor architectures taking in account the needs of the programming models and applications. Nowadays, system design consists of several layers on top of each other from the architecture up to the application software. Although this design allows to do a separation of concerns where it is possible to independently change layers due to a well-known interface between them, it is hampering future systems design as the Law of Moore reaches to an end. Current performance improvements on computer architecture are driven by the shrinkage of the transistor channel width, allowing faster and more power efficient chips to be made. However, technology is reaching physical limitations were the transistor size will not be able to be reduced furthermore and requires a change of paradigm in systems design. This thesis proposes to break this layered design, and advocates for a system where the architecture and the programming model runtime system are able to exchange information towards a common goal, improve performance and reduce power consumption. By making the architecture aware of runtime information such as a Task Dependency Graph (TDG) in the case of dataflow task-based programming models, it is possible to improve power consumption by exploiting the critical path of the graph. Moreover, the architecture can provide hardware support to create such a graph in order to reduce the runtime overheads and making possible the execution of fine-grained tasks to increase the available parallelism. Finally, the current status of inter-node communication primitives can be exposed to the runtime system in order to perform a more efficient communication scheduling, and also creates new opportunities of computation and communication overlap that were not possible before. An evaluation of the proposals introduced in this thesis is provided and a methodology to simulate and characterize the application behavior is also presented.El aumento del paralelismo proporcionado por los sistemas de cómputo modernos ha provocado la necesidad de una visión holística en el diseño de arquitecturas multiprocesador que tome en cuenta las necesidades de los modelos de programación y las aplicaciones. Hoy en día el diseño de los computadores consiste en diferentes capas de abstracción con una interfaz bien definida entre ellas. Las limitaciones de esta aproximación junto con el fin de la ley de Moore limitan el potencial de los futuros computadores. La mayoría de las mejoras actuales en el diseño de los computadores provienen fundamentalmente de la reducción del tamaño del canal del transistor, lo cual permite chips más rápidos y con un consumo eficiente sin apenas cambios fundamentales en el diseño de la arquitectura. Sin embargo, la tecnología actual está alcanzando limitaciones físicas donde no será posible reducir el tamaño de los transistores motivando así un cambio de paradigma en la construcción de los computadores. Esta tesis propone romper este diseño en capas y abogar por un sistema donde la arquitectura y el sistema de tiempo de ejecución del modelo de programación sean capaces de intercambiar información para alcanzar una meta común: La mejora del rendimiento y la reducción del consumo energético. Haciendo que la arquitectura sea consciente de la información disponible en el modelo de programación, como puede ser el grafo de dependencias entre tareas en los modelos de programación dataflow, es posible reducir el consumo energético explotando el camino critico del grafo. Además, la arquitectura puede proveer de soporte hardware para crear este grafo con el objetivo de reducir el overhead de construir este grado cuando la granularidad de las tareas es demasiado fina. Finalmente, el estado de las comunicaciones entre nodos puede ser expuesto al sistema de tiempo de ejecución para realizar una mejor planificación de las comunicaciones y creando nuevas oportunidades de solapamiento entre cómputo y comunicación que no eran posibles anteriormente. Esta tesis aporta una evaluación de todas estas propuestas, así como una metodología para simular y caracterizar el comportamiento de las aplicacionesPostprint (published version