GPUs are used in many settings to accelerate large-scale scientific computation, including simulation, computational biology, and molecular dynamics. However, optimizing codes to run efficiently on GPUs requires developers to have both detailed understanding of the application logic and significant knowledge of parallel programming and GPU architectures. This paper shows that an automated GPU program optimization tool, GEVO, can leverage evolutionary computation to find code edits that reduce the runtime of three important applications, multiple sequence alignment, agent-based simulation and molecular dynamics codes, by 28.9%, 29%, and 17.8% respectively. The paper presents an in-depth analysis of the discovered optimizations, revealing that (1) several of the most important optimizations involve significant epistasis, (2) the primary sources of improvement are application-specific, and (3) many of the optimizations generalize across GPU architectures. In general, the discovered optimizations are not straightforward even for a GPU human expert, showcasing the potential of automated program optimization tools to both reduce the optimization burden for human domain experts and provide new insights for GPU experts.

GPUs are a key enabler of the revolution in machine learning and high-performance computing, functioning as de facto co-processors to accelerate large-scale computation. As the programming stack and tool support have matured, GPUs have also become accessible to programmers, who may lack detailed knowledge of the underlying architecture and fail to fully leverage the GPU’s computation power. GEVO (Gpu optimization using EVOlutionary computation) is a tool for automatically discovering optimization opportunities and tuning the performance of GPU kernels in the LLVM representation. GEVO uses population-based search to find edits to GPU code compiled to LLVM-IR and improves performance on desired criteria while retaining required functionality. We demonstrate that GEVO improves the execution time of general-purpose GPU programs and machine learning (ML) models on NVIDIA Tesla P100. For the Rodinia benchmarks, GEVO improves GPU kernel runtime performance by an average of 49.48% and by as much as 412% over the fully compiler-optimized baseline. If kernel output accuracy is relaxed to tolerate up to 1% error, GEVO can find kernel variants that outperform the baseline by an average of 51.08%. For the ML workloads, GEVO achieves kernel performance improvement for SVM on the MNIST handwriting recognition (3.24×) and the a9a income prediction (2.93×) datasets with no loss of model accuracy. GEVO achieves 1.79× kernel performance improvement on image classification using ResNet18/CIFAR-10, with less than 1% model accuracy reduction.

Designs of flow-based microfluidic biochips have emerged as a popular alternative for laboratory experiments because they replace conventional biochemical paradigms on a chip. As the applications become more complicated, a flow-based microfluidic biochip requires more valves to manipulate the sample flow for the large-scale and concurrent experiments. Despite the design complexity is increased very quickly, current synthesis methodologies still use full custom and bottom-up procedures to synthesize a biochip. These manual steps are time consuming and would lead to dispensable valve-switching. According to recent studies, frequently switching the valves may reduce the reliability. To minimize the valve-switching activities, we propose a top down synthesis methodology for flow-based microfluidic biochip. We develop a set-based minimum cost maximum flow (SMCMF) resource binding algorithm and an incremental cluster expansion (ICE) placement algorithm in architecture-level and physical-level synthesis, respectively. The experimental results show that our methodology not only makes significant reduction of valve-switching amount but also diminishes the application completion time for both real-life applications and a set of synthetic benchmarks.