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Posts

Dec, 15

JAX, M.D.: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python

A large fraction of computational science involves simulating the dynamics of particles that interact via pairwise or many-body interactions. These simulations, called Molecular Dynamics (MD), span a vast range of subjects from physics and materials science to biochemistry and drug discovery. Most MD software involves significant use of handwritten derivatives and code reuse across C++, […]
Dec, 15

libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications

There are many ways to represent a molecule as input to a machine learning model and each is associated with loss and retention of certain kinds of information. In the interest of preserving three-dimensional spatial information, including bond angles and torsions, we have developed libmolgrid, a general-purpose library for representing three-dimensional molecules using multidimensional arrays. […]
Dec, 15

Array Languages Make Neural Networks Fast

Modern machine learning frameworks are complex: they are typically organised in multiple layers each of which is written in a different language and they depend on a number of external libraries, but at their core they mainly consist of tensor operations. As array-oriented languages provide perfect abstractions to implement tensor operations, we consider a minimalistic […]
Dec, 8

The BondMachine toolkit: Enabling Machine Learning on FPGA

The BondMachine (BM) is an innovative prototype software ecosystem aimed at creating facilities where both hardware and software are co-designed, guaranteeing a full exploitation of fabric capabilities (both in terms of concurrency and heterogeneity) with the smallest possible power dissipation. In the present paper we will provide a technical overview of the key aspects of […]
Dec, 8

PyTorch: An Imperative Style, High-Performance Deep Learning Library

Deep learning frameworks have often focused on either usability or speed, but not both. PyTorch is a machine learning library that shows that these two goals are in fact compatible: it provides an imperative and Pythonic programming style that supports code as a model, makes debugging easy and is consistent with other popular scientific computing […]
Dec, 8

GGNN: Graph-based GPU Nearest Neighbor Search

Approximate nearest neighbor (ANN) search in high dimensions is an integral part of several computer vision systems and gains importance in deep learning with explicit memory representations. Since PQT and FAISS started to leverage the massive parallelism offered by GPUs, GPU-based implementations are a crucial resource for today’s state-of-the-art ANN methods. While most of these […]
Dec, 8

Masivo: Parallel Simulation Model Based on OpenCL for Massive Public Transportation Systems’ Routes

There is a large number of tools for the simulation of traffic and routes in public transport systems. These use different simulation models (macroscopic, microscopic, and mesoscopic). Unfortunately, these simulation tools are limited when simulating a complete public transport system, which includes all its buses and routes (up to 270 for the London Underground). The […]
Dec, 8

GPU Computing with Python: Performance, Energy Efficiency and Usability

In this work, we examine the performance, energy efficiency and usability when using Python for developing HPC codes running on the GPU. We investigate the portability of performance and energy efficiency between CUDA and OpenCL; between GPU generations; and between low-end, mid-range and high-end GPUs. Our findings show that the impact of using Python is […]
Dec, 1

FBLAS: Streaming Linear Algebra Kernels on FPGA

Reconfigurable hardware represents an attractive alternative to load-store architectures, as it allows eliminating expensive control and data movement overheads in computations. In practice, these devices are often not considered in the highperformance computing community, due to the steep learning curve and low productivity of hardware design, and the lack of available library support for fundamental […]
Dec, 1

Scalable Applications on Heterogeneous System Architectures: A Systematic Performance Analysis Framework

The efficient parallel execution of scientific applications is a key challenge in high-performance computing (HPC). With growing parallelism and heterogeneity of compute resources as well as increasingly complex software, performance analysis has become an indispensable tool in the development and optimization of parallel programs. It is a recurring task as HPC systems and their software […]
Dec, 1

FANN-on-MCU: An Open-Source Toolkit for Energy-Efficient Neural Network Inference at the Edge of the Internet of Things

The growing number of low-power smart devices in the Internet of Things is coupled with the concept of "Edge Computing", that is moving some of the intelligence, especially machine learning, towards the edge of the network. Enabling machine learning algorithms to run on resource-constrained hardware, typically on low-power smart devices, is challenging in terms of […]
Dec, 1

Titan: A Parallel Asynchronous Library for Multi-Agent and Soft-Body Robotics using NVIDIA CUDA

While most robotics simulation libraries are built for low-dimensional and intrinsically serial tasks, soft-body and multi-agent robotics have created a demand for simulation environments that can model many interacting bodies in parallel. Despite the increasing interest in these fields, no existing simulation library addresses the challenge of providing a unified, highly-parallelized, GPU-accelerated interface for simulating […]

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