2,126 research outputs found
PyCUDA and PyOpenCL: A Scripting-Based Approach to GPU Run-Time Code Generation
High-performance computing has recently seen a surge of interest in
heterogeneous systems, with an emphasis on modern Graphics Processing Units
(GPUs). These devices offer tremendous potential for performance and efficiency
in important large-scale applications of computational science. However,
exploiting this potential can be challenging, as one must adapt to the
specialized and rapidly evolving computing environment currently exhibited by
GPUs. One way of addressing this challenge is to embrace better techniques and
develop tools tailored to their needs. This article presents one simple
technique, GPU run-time code generation (RTCG), along with PyCUDA and PyOpenCL,
two open-source toolkits that support this technique.
In introducing PyCUDA and PyOpenCL, this article proposes the combination of
a dynamic, high-level scripting language with the massive performance of a GPU
as a compelling two-tiered computing platform, potentially offering significant
performance and productivity advantages over conventional single-tier, static
systems. The concept of RTCG is simple and easily implemented using existing,
robust infrastructure. Nonetheless it is powerful enough to support (and
encourage) the creation of custom application-specific tools by its users. The
premise of the paper is illustrated by a wide range of examples where the
technique has been applied with considerable success.Comment: Submitted to Parallel Computing, Elsevie
Loo.py: From Fortran to performance via transformation and substitution rules
A large amount of numerically-oriented code is written and is being written
in legacy languages. Much of this code could, in principle, make good use of
data-parallel throughput-oriented computer architectures. Loo.py, a
transformation-based programming system targeted at GPUs and general
data-parallel architectures, provides a mechanism for user-controlled
transformation of array programs. This transformation capability is designed to
not just apply to programs written specifically for Loo.py, but also those
imported from other languages such as Fortran. It eases the trade-off between
achieving high performance, portability, and programmability by allowing the
user to apply a large and growing family of transformations to an input
program. These transformations are expressed in and used from Python and may be
applied from a variety of settings, including a pragma-like manner from other
languages.Comment: ARRAY 2015 - 2nd ACM SIGPLAN International Workshop on Libraries,
Languages and Compilers for Array Programming (ARRAY 2015
GSWO: A Programming Model for GPU-enabled Parallelization of Sliding Window Operations in Image Processing
Sliding Window Operations (SWOs) are widely used in image processing applications. They often have to be performed repeatedly across the target image, which can demand significant computing resources when processing large images with large windows. In applications in which real-time performance is essential, running these filters on a CPU often fails to deliver results within an acceptable timeframe. The emergence of sophisticated graphic processing units (GPUs) presents an opportunity to address this challenge. However, GPU programming requires a steep learning curve and is error-prone for novices, so the availability of a tool that can produce a GPU implementation automatically from the original CPU source code can provide an attractive means by which the GPU power can be harnessed effectively. This paper presents a GPUenabled programming model, called GSWO, which can assist GPU novices by converting their SWO-based image processing applications from the original C/C++ source code to CUDA code in a highly automated manner. This model includes a new set of simple SWO pragmas to generate GPU kernels and to support effective GPU memory management. We have implemented this programming model based on a CPU-to-GPU translator (C2GPU). Evaluations have been performed on a number of typical SWO image filters and applications. The experimental results show that the GSWO model is capable of efficiently accelerating these applications, with improved applicability and a speed-up of performance compared to several leading CPU-to- GPU source-to-source translators
Accelerating scientific applications on GPUs
We have analyzed and accelerated two large scientific applications used at the Barcelona Supercomputer Center (BSC). With this, we want to show how two complex applications can be efficiently ported to GPUs. In addition, we have developed a mechanism to manage the coherency of CPU/GPU memories
Locality Enhancement and Dynamic Optimizations on Multi-Core and GPU
Enhancing the match between software executions and hardware features is key to computing efficiency. The match is a continuously evolving and challenging problem. This dissertation focuses on the development of programming system support for exploiting two key features of modern hardware development: the massive parallelism of emerging computational accelerators such as Graphic Processing Units (GPU), and the non-uniformity of cache sharing in modern multicore processors. They are respectively driven by the important role of accelerators in today\u27s general-purpose computing and the ultimate importance of memory performance. This dissertation particularly concentrates on optimizing control flows and memory references, at both compilation and execution time, to tap into the full potential of pure software solutions in taking advantage of the two key hardware features.;Conditional branches cause divergences in program control flows, which may result in serious performance degradation on massively data-parallel GPU architectures with Single Instruction Multiple Data (SIMD) parallelism. On such an architecture, control divergence may force computing units to stay idle for a substantial time, throttling system throughput by orders of magnitude. This dissertation provides an extensive exploration of the solution to this problem and presents program level transformations based upon two fundamental techniques --- thread relocation and data relocation. These two optimizations provide fundamental support for swapping jobs among threads so that the control flow paths of threads converge within every SIMD thread group.;In memory performance, this dissertation concentrates on two aspects: the influence of nonuniform sharing on multithreading applications, and the optimization of irregular memory references on GPUs. In shared cache multicore chips, interactions among threads are complicated due to the interplay of cache contention and synergistic prefetching. This dissertation presents the first systematic study on the influence of non-uniform shared cache on contemporary parallel programs, reveals the mismatch between the software development and underlying cache sharing hierarchies, and further demonstrates it by proposing and applying cache-sharing-aware data transformations that bring significant performance improvement. For the second aspect, the efficiency of GPU accelerators is sensitive to irregular memory references, which refer to the memory references whose access patterns remain unknown until execution time (e.g., A[P[i]]). The root causes of the irregular memory reference problem are similar to that of the control flow problem, while in a more general and complex form. I developed a framework, named G-Streamline, as a unified software solution to dynamic irregularities in GPU computing. It treats both types of irregularities at the same time in a holistic fashion, maximizing the whole-program performance by resolving conflicts among optimizations
AceleraciĂłn de algoritmos de procesamiento de imĂĄgenes para el anĂĄlisis de partĂculas individuales con microscopia electrĂłnica
Tesis Doctoral inĂ©dita cotutelada por la Masaryk University (RepĂșblica Checa) y la Universidad AutĂłnoma de Madrid, Escuela PolitĂ©cnica Superior, Departamento de IngenierĂa InformĂĄtica. Fecha de Lectura: 24-10-2022Cryogenic Electron Microscopy (Cryo-EM) is a vital field in current structural biology. Unlike X-ray
crystallography and Nuclear Magnetic Resonance, it can be used to analyze membrane proteins and
other samples with overlapping spectral peaks. However, one of the significant limitations of Cryo-EM
is the computational complexity. Modern electron microscopes can produce terabytes of data per single
session, from which hundreds of thousands of particles must be extracted and processed to obtain a
near-atomic resolution of the original sample. Many existing software solutions use high-Performance
Computing (HPC) techniques to bring these computations to the realm of practical usability. The
common approach to acceleration is parallelization of the processing, but in praxis, we face many
complications, such as problem decomposition, data distribution, load scheduling, balancing, and
synchronization. Utilization of various accelerators further complicates the situation, as heterogeneous
hardware brings additional caveats, for example, limited portability, under-utilization due to synchronization,
and sub-optimal code performance due to missing specialization.
This dissertation, structured as a compendium of articles, aims to improve the algorithms used
in Cryo-EM, esp. the SPA (Single Particle Analysis). We focus on the single-node performance
optimizations, using the techniques either available or developed in the HPC field, such as heterogeneous
computing or autotuning, which potentially needs the formulation of novel algorithms. The
secondary goal of the dissertation is to identify the limitations of state-of-the-art HPC techniques. Since
the Cryo-EM pipeline consists of multiple distinct steps targetting different types of data, there is no
single bottleneck to be solved. As such, the presented articles show a holistic approach to performance
optimization.
First, we give details on the GPU acceleration of the specific programs. The achieved speedup is
due to the higher performance of the GPU, adjustments of the original algorithm to it, and application
of the novel algorithms. More specifically, we provide implementation details of programs for movie
alignment, 2D classification, and 3D reconstruction that have been sped up by order of magnitude
compared to their original multi-CPU implementation or sufficiently the be used on-the-fly. In addition
to these three programs, multiple other programs from an actively used, open-source software package
XMIPP have been accelerated and improved.
Second, we discuss our contribution to HPC in the form of autotuning. Autotuning is the ability of
software to adapt to a changing environment, i.e., input or executing hardware. Towards that goal, we
present cuFFTAdvisor, a tool that proposes and, through autotuning, finds the best configuration of the
cuFFT library for given constraints of input size and plan settings. We also introduce a benchmark set
of ten autotunable kernels for important computational problems implemented in OpenCL or CUDA,
together with the introduction of complex dynamic autotuning to the KTT tool.
Third, we propose an image processing framework Umpalumpa, which combines a task-based
runtime system, data-centric architecture, and dynamic autotuning. The proposed framework allows for
writing complex workflows which automatically use available HW resources and adjust to different HW
and data but at the same time are easy to maintainThe project that gave rise to these results received the support of a fellowship from the âla Caixaâ
Foundation (ID 100010434). The fellowship code is LCF/BQ/DI18/11660021.
This project has received funding from the European Unionâs Horizon 2020 research and innovation
programme under the Marie SkĆodowska-Curie grant agreement No. 71367
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