Translation techniques for distributed-shared memory programming models

This thesis argues that a modular, source-to-source translation system for distributed-shared memory programming models would be beneficial to the high-performance computing community. It goes on to present a proof-of-concept example in detail, translating between Global Arrays (GA) and Unified Parallel C (UPC). Some useful extensions to UPC are discussed, along with how they are implemented in the proof-of-concept translator

Translation techniques for distributed-shared memory programming models

The high performance computing community has experienced an explosive improvement in distributed-shared memory hardware. Driven by increasing real-world problem complexity, this explosion has ushered in vast numbers of new systems. Each new system presents new challenges to programmers and application developers. Part of the challenge is adapting to new architectures with new performance characteristics. Different vendors release systems with widely varying architectures that perform differently in different situations. Furthermore, since vendors need only provide a single performance number (total MFLOPS, typically for a single benchmark), they only have strong incentive initially to optimize the API of their choice. Consequently, only a fraction of the available APIs are well optimized on most systems. This causes issues porting and writing maintainable software, let alone issues for programmers burdened with mastering each new API as it is released. Also, programmers wishing to use a certain machine must choose their API based on the underlying hardware instead of the application. This thesis argues that a flexible, extensible translator for distributed-shared memory APIs can help address some of these issues. For example, a translator might take as input code in one API and output an equivalent program in another. Such a translator could provide instant porting for applications to new systems that do not support the application's library or language natively. While open-source APIs are abundant, they do not perform optimally everywhere. A translator would also allow performance testing using a single base code translated to a number of different APIs. Most significantly, this type of translator frees programmers to select the most appropriate API for a given application based on the application (and developer) itself instead of the underlying hardware

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

Scalable Data Structure to Compress Next-Generation Sequencing Files and its Application to Compressive Genomics

It is now possible to compress and decompress large-scale Next-Generation Sequencing files taking advantage of high-performance computing techniques. To this end, we have recently introduced a scalable hybrid parallel algorithm, called phyNGSC, which allows fast compression as well as decompression of big FASTQ datasets using distributed and shared memory programming models via MPI and OpenMP. In this paper we present the design and implementation of a novel parallel data structure which lessens the dependency on decompression and facilitates the handling of DNA sequences in their compressed state using fine-grained decompression in a technique that is identified as in compresso data processing. Using our data structure compression and decompression throughputs of up to 8.71 GB/s and 10.12 GB/s were observed. Our proposed structure and methodology brings us one step closer to compressive genomics and sublinear analysis of big NGS datasets. The code for this implementation is available at https://github.com/pcdslab/PHYNGS

AllScale API

Effectively implementing scientific algorithms in distributed memory parallel applications is a difficult task for domain scientists, as evident by the large number of domain-specific languages and libraries available today attempting to facilitate the process. However, they usually provide a closed set of parallel patterns and are not open for extension without vast modifications to the underlying system. In this work, we present the AllScale API, a programming interface for developing distributed memory parallel applications with the ease of shared memory programming models. The AllScale API is closed for a modification but open for an extension, allowing new user-defined parallel patterns and data structures to be implemented based on existing core primitives and therefore fully supported in the AllScale framework. Focusing on high-level functionality directly offered to application developers, we present the design advantages of such an API design, detail some of its specifications and evaluate it using three real-world use cases. Our results show that AllScale decreases the complexity of implementing scientific applications for distributed memory while attaining comparable or higher performance compared to MPI reference implementations

On the conditions for efficient interoperability with threads: An experience with PGAS languages using Cray communication domains

Today's high performance systems are typically built from shared memory nodes connected by a high speed network. That architecture, combined with the trend towards less memory per core, encourages programmers to use a mixture of message passing and multithreaded programming. Unfortunately, the advantages of using threads for in-node programming are hindered by their inability to efficiently communicate between nodes. In this work, we identify some of the performance problems that arise in such hybrid programming environments and characterize conditions needed to achieve high communication performance for multiple threads: addressability of targets, separability of communication paths, and full direct reachability to targets. Using the GASNet communication layer on the Cray XC30 as our experimental platform, we show how to satisfy these conditions. We also discuss how satisfying these conditions is influenced by the communication abstraction, implementation constraints, and the interconnect messaging capabilities. To evaluate these ideas, we compare the communication performance of a thread-based node runtime to a process-based runtime. Without our GASNet extensions, thread communication is significantly slower than processes - up to 21x slower. Once the implementation is modified to address each of our conditions, the two runtimes have comparable communication performance. This allows programmers to more easily mix models like OpenMP, CILK, or pthreads with a GASNet-based model like UPC, with the associated performance, convenience and interoperability advantages that come from using threads within a node. © 2014 ACM

Worksharing tasks: An efficient way to exploit irregular and fine-grained loop parallelism

Shared memory programming models usually provide worksharing and task constructs. The former relies on the efficient fork-join execution model to exploit structured parallelism; while the latter relies on fine-grained synchronization among tasks and a flexible data-flow execution model to exploit dynamic, irregular, and nested parallelism. On applications that show both structured and unstructured parallelism, both worksharing and task constructs can be combined. However, it is difficult to mix both execution models without penalizing the data-flow execution model. Hence, on many applications structured parallelism is also exploited using tasks to leverage the full benefits of a pure data-flow execution model. However, task creation and management might introduce a non-negligible overhead that prevents the efficient exploitation of fine-grained structured parallelism, especially on many-core processors. In this work, we propose worksharing tasks. These are tasks that internally leverage worksharing techniques to exploit fine-grained structured loop-based parallelism. The evaluation shows promising results on several benchmarks and platforms.This work is supported by the Spanish Ministerio de Ciencia, Innovacion y Universidades (TIN2015-65316-P), by the Generalitat de Catalunya (2014-SGR-1051) and by the European Union’s Seventh Framework Programme (FP7/2007-2013) and the H2020 funding framework under grant agreement no. H2020-FETHPC-754304 (DEEP-EST).Peer ReviewedPostprint (author's final draft