Transparent management of scratchpad memories in shared memory programming models

Cache-coherent shared memory has traditionally been the favorite memory organization for chip multiprocessors thanks to its high programmability. In this organization the cache hierarchy is in charge of moving the data and keeping it coherent between all the caches, enabling the usage of shared memory programming models where the programmer does not need to carry out any data management operation. Unfortunately, performing all the data management operations in hardware causes severe problems, being the primary concerns the power consumption originated in the caches and the amount of coherence traffic in the interconnection network. A good solution is to introduce ScratchPad Memories (SPMs) alongside the cache hierarchy, forming a hybrid memory hierarchy. SPMs are more power-efficient than caches and do not generate coherence traffic, but they degrade programmability. In particular, SPMs require the programmer to partition the data, to program data transfers, and to keep coherence between different copies of the data. A promising solution to exploit the benefits of the SPMs without harming programmability is to allow programmers to use shared memory programming models and to automatically generate code that manages the SPMs. Unfortunately, current compilers and runtime systems encounter serious limitations to automatically generate code for hybrid memory hierarchies from shared memory programming models. This thesis proposes to transparently manage the SPMs of hybrid memory hierarchies in shared memory programming models. In order to achieve this goal this thesis proposes a combination of hardware and compiler techniques to manage the SPMs in fork-join programming models and a set of runtime system techniques to manage the SPMs in task programming models. The proposed techniques allow to program hybrid memory hierarchies with these two well-known and easy-to-use forms of shared memory programming models, capitalizing on the benefits of hybrid memory hierarchies in power consumption and network traffic without harming programmability. The first contribution of this thesis is a hardware/software co-designed coherence protocol to transparently manage the SPMs of hybrid memory hierarchies in fork-join programming models. The solution allows the compiler to always generate code to manage the SPMs with tiling software caches, even in the presence of unknown memory aliasing hazards between memory references to the SPMs and to the cache hierarchy. On the software side, the compiler generates a special form of memory instruction for memory references with possible aliasing hazards. On the hardware side, the special memory instructions are diverted to the correct copy of the data using a set of directories that track what data is mapped to the SPMs. The second contribution of this thesis is a set of runtime system techniques to manage the SPMs of hybrid memory hierarchies in task programming models. The proposed runtime system techniques exploit the characteristics of these programming models to map the data specified in the task dependences to the SPMs. Different policies are proposed to mitigate the communication costs of the data transfers, overlapping them with other execution phases such as the task scheduling phase or the execution of the previous task. The runtime system can also reduce the number of data transfers by using a task scheduler that exploits data locality in the SPMs. In addition, the proposed techniques are combined with mechanisms that reduce the impact of fine-grained tasks, such as hardware runtime systems or large SPM sizes. The accomplishment of this thesis is that hybrid memory hierarchies can be programmed with fork-join and task programming models. Consequently, architectures with hybrid memory hierarchies can be exposed to the programmer as a shared memory multiprocessor, taking advantage of the benefits of the SPMs while maintaining the programming simplicity of shared memory programming models.La memoria compartida con coherencia de caches es la jerarquía de memoria más utilizada en multiprocesadores gracias a su programabilidad. En esta solución la jerarquía de caches se encarga de mover los datos y mantener la coherencia entre las caches, habilitando el uso de modelos de programación de memoria compartida donde el programador no tiene que realizar ninguna operación para gestionar las memorias. Desafortunadamente, realizar estas operaciones en la arquitectura causa problemas severos, siendo especialmente relevantes el consumo de energía de las caches y la cantidad de tráfico de coherencia en la red de interconexión. Una buena solución es añadir Memorias ScratchPad (SPMs) acompañando la jerarquía de caches, formando una jerarquía de memoria híbrida. Las SPMs son más eficientes en energía y tráfico de coherencia, pero dificultan la programabilidad ya que requieren que el programador particione los datos, programe transferencias de datos y mantenga la coherencia entre diferentes copias de datos. Una solución prometedora para beneficiarse de las ventajas de las SPMs sin dificultar la programabilidad es permitir que el programador use modelos de programación de memoria compartida y generar código para gestionar las SPMs automáticamente. El problema es que los compiladores y los entornos de ejecución actuales sufren graves limitaciones al gestionar automáticamente una jerarquía de memoria híbrida en modelos de programación de memoria compartida. Esta tesis propone gestionar automáticamente una jerarquía de memoria híbrida en modelos de programación de memoria compartida. Para conseguir este objetivo esta tesis propone una combinación de técnicas hardware y de compilador para gestionar las SPMs en modelos de programación fork-join, y técnicas en entornos de ejecución para gestionar las SPMs en modelos de programación basados en tareas. Las técnicas propuestas hacen que las jerarquías de memoria híbridas puedan programarse con estos dos modelos de programación de memoria compartida, de tal forma que las ventajas en energía y tráfico de coherencia se puedan explotar sin dificultar la programabilidad. La primera contribución de esta tesis en un protocolo de coherencia hardware/software para gestionar SPMs en modelos de programación fork-join. La propuesta consigue que el compilador siempre pueda generar código para gestionar las SPMs, incluso cuando hay posibles alias de memoria entre referencias a memoria a las SPMs y a la jerarquía de caches. En la solución el compilador genera instrucciones especiales para las referencias a memoria con posibles alias, y el hardware sirve las instrucciones especiales con la copia válida de los datos usando directorios que guardan información sobre qué datos están mapeados en las SPMs. La segunda contribución de esta tesis son una serie de técnicas para gestionar SPMs en modelos de programación basados en tareas. Las técnicas aprovechan las características de estos modelos de programación para mapear las dependencias de las tareas en las SPMs y se complementan con políticas para minimizar los costes de las transferencias de datos, como solaparlas con fases del entorno de ejecución o la ejecución de tareas anteriores. El número de transferencias también se puede reducir utilizando un planificador que tenga en cuenta la localidad de datos y, además, las técnicas se pueden combinar con mecanismos para reducir los efectos negativos de tener tareas pequeñas, como entornos de ejecución en hardware o SPMs de más capacidad. Las propuestas de esta tesis consiguen que las jerarquías de memoria híbridas se puedan programar con modelos de programación fork-join y basados en tareas. En consecuencia, las arquitecturas con jerarquías de memoria híbridas se pueden exponer al programador como multiprocesadores de memoria compartida, beneficiándose de las ventajas de las SPMs en energía y tráfico de coherencia y manteniendo la simplicidad de uso de los modelos de programación de memoria compartida

Teaching HPC systems and parallel programming with small-scale clusters

In the last decades, the continuous proliferation of High-Performance Computing (HPC) systems and data centers has augmented the demand for expert HPC system designers, administrators, and programmers. For this reason, most universities have introduced courses on HPC systems and parallel programming in their degrees. However, the laboratory assignments of these courses generally use clusters that are owned, managed and administrated by the university. This methodology has been shown effective to teach parallel programming, but using a remote cluster prevents the students from experimenting with the design, set up and administration of such systems. This paper presents a methodology and framework to teach HPC systems and parallel programming using a small-scale cluster of single-board computers. These boards are very cheap, their processors are fundamentally very similar to the ones found in HPC, and they are ready to execute Linux out of the box. So they represent a perfect laboratory playground for students experiencing how to assemble a cluster, setting it up, and configuring its system software. Also, we show that these small-scale clusters can be used as evaluation platforms for both, introductory and advanced parallel programming assignments.This work is partially supported by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology (contracts TIN2015-65316-P and FJCI-2016-30985), by the Generalitat de Catalunya (contract 2017-SGR-1414), and by the European Union’s Horizon 2020 research and innovation programme (grant agreements 671697 and 779877).Peer ReviewedPostprint (author's final draft

A review of CNN accelerators for embedded systems based on RISC-V

One of the great challenges of computing today is sustainable energy consumption. In the deployment of edge computing this challenge is particularly important considering the use of embedded equipment with limited energy and computation resources. In those systems, the energy consumption must be carefully managed to operate for long periods. Specifically, for embedded systems with machine learning capabilities in the Internet of Things (EMLIoT) era, the convolutional neural networks (CNN) model execution is energy challenging and requires massive data. Nowadays, high workload processing is designed separately into a host processor in charge of generic functions and an accelerator dedicated to executing the specific task. Open-hardware-based designs are pushing for new levels of energy efficiency. For achieving energy efficiency, open-source tools, such as the RISC-V ISA, have been introduced to optimize every internal stage of the system. This document aims to compare the EMLIoT accelerator designs based on RISC-V and highlights open topics for research.This work has been partially supported by the Mexican Government F-PROMEP-01/Rev-04 SEP-23-002-A; the Spanish Ministry of Science and Innovation (contract PID2019- 107255GB-C21/AEI/10.13039/501100011033) and by the Generalitat de Catalunya (contract 2017-SGR-1328); and DTS21/00089 del Instituto Carlos III.Peer ReviewedPostprint (author's final draft

TD-NUCA: runtime driven management of NUCA caches in task dataflow programming models

In high performance processors, the design of on-chip memory hierarchies is crucial for performance and energy efficiency. Current processors rely on large shared Non-Uniform Cache Architectures (NUCA) to improve performance and reduce data movement. Multiple solutions exploit information available at the microarchitecture level or in the operating system to optimize NUCA performance. However, existing methods have not taken advantage of the information captured by task dataflow programming models to guide the management of NUCA caches. In this paper we propose TD-NUCA, a hardware/software co-designed approach that leverages information present in the runtime system of task dataflow programming models to efficiently manage NUCA caches. TD-NUCA identifies the data access and reuse patterns of parallel applications in the runtime system and guides the operation of the NUCA caches in the hardware. As a result, TD-NUCA achieves a 1.18x average speedup over the baseline S-NUCA while requiring only 0.62x the data movement.This work has been supported by the Spanish Ministry of Science and Technology (contract PID2019-107255GB-C21) and the Generalitat de Catalunya (contract 2017-SGR-1414). M. Casas has been partially supported by the Grant RYC- 2017-23269 funded by MCIN/AEI/10.13039/501100011033 and ESF ‘Investing in your future’. M. Moreto has been partially supported by the Spanish Ministry of Economy, Industry and Competitiveness under Ramon y Cajal fellowship No. RYC-2016-21104.Peer ReviewedPostprint (published version

Runtime-assisted cache coherence deactivation in task parallel programs

With increasing core counts, the scalability of directory-based cache coherence has become a challenging problem. To reduce the area and power needs of the directory, recent proposals reduce its size by classifying data as private or shared, and disable coherence for private data. However, existing classification methods suffer from inaccuracies and require complex hardware support with limited scalability. This paper proposes a hardware/software co-designed approach: the runtime system identifies data that is guaranteed by the programming model semantics to not require coherence and notifies the microarchitecture. The microarchitecture deactivates coherence for this private data and powers off unused directory capacity. Our proposal reduces directory accesses to just 26% of the baseline system, and supports a 64x smaller directory with only 2.8% performance degradation. By dynamically calibrating the directory size our proposal saves 86% of dynamic energy consumption in the directory without harming performance.This work has been supported by the RoMoL ERC Advanced Grant (GA 321253), by the European HiPEAC Network of Excellence, by the Spanish Ministry of Economy and Competitiveness (contract TIN2015-65316-P), by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272) and by the European Unions Horizon 2020 research and innovation programme (grant agreements 671697 and 779877). M. Moreto has been partially supported by the Spanish Ministry of Economy, Industry and Competitiveness under Ramon y Cajal fellowship number RYC-2016-21104.Peer ReviewedPostprint (author's final draft

Architectural support for task dependence management with flexible software scheduling

The growing complexity of multi-core architectures has motivated a wide range of software mechanisms to improve the orchestration of parallel executions. Task parallelism has become a very attractive approach thanks to its programmability, portability and potential for optimizations. However, with the expected increase in core counts, finer-grained tasking will be required to exploit the available parallelism, which will increase the overheads introduced by the runtime system. This work presents Task Dependence Manager (TDM), a hardware/software co-designed mechanism to mitigate runtime system overheads. TDM introduces a hardware unit, denoted Dependence Management Unit (DMU), and minimal ISA extensions that allow the runtime system to offload costly dependence tracking operations to the DMU and to still perform task scheduling in software. With lower hardware cost, TDM outperforms hardware-based solutions and enhances the flexibility, adaptability and composability of the system. Results show that TDM improves performance by 12.3% and reduces EDP by 20.4% on average with respect to a software runtime system. Compared to a runtime system fully implemented in hardware, TDM achieves an average speedup of 4.2% with 7.3x less area requirements and significant EDP reductions. In addition, five different software schedulers are evaluated with TDM, illustrating its flexibility and performance gains.This work has been supported by the RoMoL ERC Advanced Grant (GA 321253), by the European HiPEAC Network of Excellence, by the Spanish Ministry of Science and Innovation (contracts TIN2015-65316-P, TIN2016-76635-C2-2-R and TIN2016-81840-REDT), by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272), and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 671697 and No. 671610. M. Moretó has been partially supported by the Ministry of Economy and Competitiveness under Juan de la Cierva postdoctoral fellowship number JCI-2012-15047.Peer ReviewedPostprint (author's final draft

An FPGA accelerator of the wavefront algorithm for genomics pairwise alignment

In the last years, advances in next-generation sequencing technologies have enabled the proliferation of genomic applications that guide personalized medicine. These applications have an enormous computational cost due to the large amount of genomic data they process. The first step in many of these applications consists in aligning reads against a reference genome. Very recently, the wavefront alignment algorithm has been introduced, significantly reducing the execution time of the read alignment process. This paper presents the first FPGA- based hardware/software co-designed accelerator of such relevant algorithm. Compared to the reference WFA CPU-only implementation, the proposed FPGA accelerator achieves performance speedups of up to 13.5× while consuming up to 14.6× less energy.ed medicine. These applications have an enormous computational cost due to the large amount of genomic data they process. The first step in many of these applications consists in aligning reads against a reference genome. Very recently, the wavefront alignment algorithm has been introduced, significantly reducing the execution time of the read alignment process. This paper presents the first FPGA- based hardware/software co-designed accelerator of such relevant algorithm. Compared to the reference WFA CPU-only imple- mentation, the proposed FPGA accelerator achieves performance speedups of up to 13.5× while consuming up to 14.6× less energy.This work has been supported by the European HiPEAC Network of Excellence, by the Spanish Ministry of Science and Innovation (contract PID2019-107255GB-C21/AEI/10.13039/501100011033), by the Generalitat de Catalunya (contracts 2017-SGR-1414 and 2017-SGR-1328), by the IBM/BSC Deep Learning Center initiative, and by the DRAC project, which is co-financed by the European Union Regional Development Fund within the framework of the ERDF Operational Program of Catalonia 2014-2020 with a grant of 50% of total eligible cost. Ll. Alvarez has been partially supported by the Spanish Ministry of Economy, Industry and Competitiveness under the Juan de la Cierva Formacion fellowship No. FJCI-2016-30984. M. Moreto has been partially supported by the Spanish Ministry of Economy, Industry and Competitiveness under Ramon y Cajal fellowship No. RYC-2016-21104.Peer ReviewedPostprint (author's final draft

Reducing cache coherence traffic with a NUMA-aware runtime approach

Cache Coherent NUMA (ccNUMA) architectures are a widespread paradigm due to the benefits they provide for scaling core count and memory capacity. Also, the flat memory address space they offer considerably improves programmability. However, ccNUMA architectures require sophisticated and expensive cache coherence protocols to enforce correctness during parallel executions, which trigger a significant amount of on- and off-chip traffic in the system. This paper analyses how coherence traffic may be best constrained in a large, real ccNUMA platform comprising 288 cores through the use of a joint hardware/software approach. For several benchmarks, we study coherence traffic in detail under the influence of an added hierarchical cache layer in the directory protocol combined with runtime managed NUMA-aware scheduling and data allocation techniques to make most efficient use of the added hardware. The effectiveness of this joint approach is demonstrated by speedups of 3.14× to 9.97× and coherence traffic reductions of up to 99% in comparison to NUMA-oblivious scheduling and data allocation.This work has been supported by the Spanish Government (Severo Ochoa grants SEV2015-0493), by the Spanish Ministry of Science and Innovation (contracts TIN2015-65316-P), by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272), by the RoMoL ERC Advanced Grant (GA 321253) and the European HiPEAC Network of Excellence. The Mont-Blanc project receives funding from the EU’s H2020 Framework Programme (H2020/2014-2020) under grant agreement no 671697. M. Moretó has been partially supported by the Ministry of Economy and Competitiveness under Juan de la Cierva postdoctoral fellowship number JCI-2012-15047. M. Casas is supported by the Secretary for Universities and Research of the Ministry of Economy and Knowledge of the Government of Catalonia and the Cofund programme of the Marie Curie Actions of the 7th R&D Framework Programme of the European Union (Contract 2013 BP B 00243).Peer ReviewedPostprint (author's final draft

Page size aware cache prefetching

The increase in working set sizes of contemporary applications outpaces the growth in cache sizes, resulting in frequent main memory accesses that deteriorate system per- formance due to the disparity between processor and memory speeds. Prefetching data blocks into the cache hierarchy ahead of demand accesses has proven successful at attenuating this bottleneck. However, spatial cache prefetchers operating in the physical address space leave significant performance on the table by limiting their pattern detection within 4KB physical page boundaries when modern systems use page sizes larger than 4KB to mitigate the address translation overheads. This paper exploits the high usage of large pages in modern systems to increase the effectiveness of spatial cache prefetch- ing. We design and propose the Page-size Propagation Module (PPM), a µarchitectural scheme that propagates the page size information to the lower-level cache prefetchers, enabling safe prefetching beyond 4KB physical page boundaries when the accessed blocks reside in large pages, at the cost of augmenting the first-level caches’ Miss Status Holding Register (MSHR) entries with one additional bit. PPM is compatible with any cache prefetcher without implying design modifications. We capitalize on PPM’s benefits by designing a module that consists of two page size aware prefetchers that inherently use different page sizes to drive prefetching. The composite module uses adaptive logic to dynamically enable the most appropriate page size aware prefetcher. Finally, we show that the proposed designs are transparent to which cache prefetcher is used. We apply the proposed page size exploitation techniques to four state-of-the-art spatial cache prefetchers. Our evalua- tion shows that our proposals improve single-core geomean performance by up to 8.1% (2.1% at minimum) over the original implementation of the considered prefetchers, across 80 memory-intensive workloads. In multi-core contexts, we report geomean speedups up to 7.7% across different cache prefetchers and core configurations.This work is supported by the Spanish Ministry of Science and Technology through the PID2019-107255GB project, the Generalitat de Catalunya (contract 2017-SGR-1414), the European Union Horizon 2020 research and innovation program under grant agreement No 955606 (DEEP-SEA EU project), the National Science Foundation through grants CNS-1938064 and CCF-1912617, and the Semiconductor Research Corporation project GRC 2936.001. Georgios Vavouliotis has been supported by the Spanish Ministry of Economy, Industry, and Competitiveness and the European Social Fund under the FPI fellowship No. PRE2018-087046. Marc Casas has been partially supported by the Grant RYC2017-23269 funded by MCIN/AEI/10.13039/501100011033 and ESF ‘Investing in your future’.Peer ReviewedPostprint (author's final draft

Accelerating edit-distance sequence alignment on GPU using the wavefront algorithm

Sequence alignment remains a fundamental problem with practical applications ranging from pattern recognition to computational biology. Traditional algorithms based on dynamic programming are hard to parallelize, require significant amounts of memory, and fail to scale for large inputs. This work presents eWFA-GPU, a GPU (graphics processing unit)-accelerated tool to compute the exact edit-distance sequence alignment based on the wavefront alignment algorithm (WFA). This approach exploits the similarities between the input sequences to accelerate the alignment process while requiring less memory than other algorithms. Our implementation takes full advantage of the massive parallel capabilities of modern GPUs to accelerate the alignment process. In addition, we propose a succinct representation of the alignment data that successfully reduces the overall amount of memory required, allowing the exploitation of the fast shared memory of a GPU. Our results show that our GPU implementation outperforms by 3- 9× the baseline edit-distance WFA implementation running on a 20 core machine. As a result, eWFA-GPU is up to 265 times faster than state-of-the-art CPU implementation, and up to 56 times faster than state-of-the-art GPU implementations.This work was supported in part by the European Unions’s Horizon 2020 Framework Program through the DeepHealth Project under Grant 825111; in part by the European Union Regional Development Fund within the Framework of the European Regional Development Fund (ERDF) Operational Program of Catalonia 2014–2020 with a Grant of 50% of Total Cost Eligible through the Designing RISC-V-based Accelerators for next-generation Computers Project under Grant 001-P-001723; in part by the Ministerio de Ciencia e Innovacion (MCIN) Agencia Estatal de Investigación (AEI)/10.13039/501100011033 under Contract PID2020-113614RB-C21 and Contract TIN2015-65316-P; and in part by the Generalitat de Catalunya (GenCat)-Departament de Recerca i Universitats (DIUiE) (GRR) under Contract 2017-SGR-313, Contract 2017-SGR-1328, and Contract 2017-SGR-1414. The work of Miquel Moreto was supported in part by the Spanish Ministry of Economy, Industry and Competitiveness under Ramon y Cajal Fellowship under Grant RYC-2016-21104.Peer ReviewedPostprint (published version