Adaptive runtime-assisted block prefetching on chip-multiprocessors

Memory stalls are a significant source of performance degradation in modern processors. Data prefetching is a widely adopted and well studied technique used to alleviate this problem. Prefetching can be performed by the hardware, or be initiated and controlled by software. Among software controlled prefetching we find a wide variety of schemes, including runtime-directed prefetching and more specifically runtime-directed block prefetching. This paper proposes a hybrid prefetching mechanism that integrates a software driven block prefetcher with existing hardware prefetching techniques. Our runtime-assisted software prefetcher brings large blocks of data on-chip with the support of a low cost hardware engine, and synergizes with existing hardware prefetchers that manage locality at a finer granularity. The runtime system that drives the prefetch engine dynamically selects which cache to prefetch to. Our evaluation on a set of scientific benchmarks obtains a maximum speed up of 32 and 10 % on average compared to a baseline with hardware prefetching only. As a result, we also achieve a reduction of up to 18 and 3 % on average in energy-to-solution.Peer ReviewedPostprint (author's final draft

SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors

The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm computationally demanding for big databases. In this paper, we present SWAPHI, the first parallelized algorithm employing Xeon Phi coprocessors to accelerate SW protein database search. SWAPHI is designed based on the scale-and-vectorize approach, i.e. it boosts alignment speed by effectively utilizing both the coarse-grained parallelism from the many co-processing cores (scale) and the fine-grained parallelism from the 512-bit wide single instruction, multiple data (SIMD) vectors within each core (vectorize). By searching against the large UniProtKB/TrEMBL protein database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on one coprocessor and up to 228.4 GCUPS on four coprocessors. Furthermore, it demonstrates good parallel scalability on varying number of coprocessors, and is also superior to both SWIPE on 16 high-end CPU cores and BLAST+ on 8 cores when using four coprocessors, with the maximum speedup of 1.52 and 1.86, respectively. SWAPHI is written in C++ language (with a set of SIMD intrinsics), and is freely available at http://swaphi.sourceforge.net.Comment: A short version of this paper has been accepted by the IEEE ASAP 2014 conferenc

PRETZEL: Opening the Black Box of Machine Learning Prediction Serving Systems

Machine Learning models are often composed of pipelines of transformations. While this design allows to efficiently execute single model components at training time, prediction serving has different requirements such as low latency, high throughput and graceful performance degradation under heavy load. Current prediction serving systems consider models as black boxes, whereby prediction-time-specific optimizations are ignored in favor of ease of deployment. In this paper, we present PRETZEL, a prediction serving system introducing a novel white box architecture enabling both end-to-end and multi-model optimizations. Using production-like model pipelines, our experiments show that PRETZEL is able to introduce performance improvements over different dimensions; compared to state-of-the-art approaches PRETZEL is on average able to reduce 99th percentile latency by 5.5x while reducing memory footprint by 25x, and increasing throughput by 4.7x.Comment: 16 pages, 14 figures, 13th USENIX Symposium on Operating Systems Design and Implementation (OSDI), 201

A Survey of Techniques for Improving Security of GPUs

Graphics processing unit (GPU), although a powerful performance-booster, also has many security vulnerabilities. Due to these, the GPU can act as a safe-haven for stealthy malware and the weakest `link' in the security `chain'. In this paper, we present a survey of techniques for analyzing and improving GPU security. We classify the works on key attributes to highlight their similarities and differences. More than informing users and researchers about GPU security techniques, this survey aims to increase their awareness about GPU security vulnerabilities and potential countermeasures