Browsing by Author "Greth, J."

Now showing 1 - 3 of 3

Open Access
Energy efficient architecture for graph analytics accelerators
(IEEE, 2016-06) Özdal, Muhammet Mustafa; Yeşil, Şerif; Kim, T.; Ayupov, A.; Greth, J.; Burns, S.; Öztürk, Özcan
Specialized hardware accelerators can significantly improve the performance and power efficiency of compute systems. In this paper, we focus on hardware accelerators for graph analytics applications and propose a configurable architecture template that is specifically optimized for iterative vertex-centric graph applications with irregular access patterns and asymmetric convergence. The proposed architecture addresses the limitations of the existing multi-core CPU and GPU architectures for these types of applications. The SystemC-based template we provide can be customized easily for different vertex-centric applications by inserting application-level data structures and functions. After that, a cycle-accurate simulator and RTL can be generated to model the target hardware accelerators. In our experiments, we study several graph-parallel applications, and show that the hardware accelerators generated by our template can outperform a 24 core high end server CPU system by up to 3x in terms of performance. We also estimate the area requirement and power consumption of these hardware accelerators through physical-aware logic synthesis, and show up to 65x better power consumption with significantly smaller area. © 2016 IEEE.
Open Access
Graph analytics accelerators for cognitive systems
(Institute of Electrical and Electronics Engineers, 2017) Ozdal, M. M.; Yesil, S.; Kim, T.; Ayupov, A.; Greth, J.; Burns, S.; Ozturk, O.
Hardware accelerators are known to be performance and power efficient. This article focuses on accelerator design for graph analytics applications, which are commonly used kernels for cognitive systems. The authors propose a templatized architecture that is specifically optimized for vertex-centric graph applications with irregular memory access patterns, asynchronous execution, and asymmetric convergence. The proposed architecture addresses the limitations of existing CPU and GPU systems while providing a customizable template. The authors' experiments show that the generated accelerators can outperform a high-end CPU system with up to 3 times better performance and 65 times better power efficiency. © 1981-2012 IEEE.
Open Access
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping
(Oxford University Press, 2015) Xin, H.; Greth, J.; Emmons, J.; Pekhimenko, G.; Kingsford, C.; Alkan C.; Mutlu, O.
Motivation: Calculating the edit-distance (i.e. minimum number of insertions, deletions and substitutions) between short DNA sequences is the primary task performed by seed-and-extend based mappers, which compare billions of sequences. In practice, only sequence pairs with a small edit-distance provide useful scientific data. However, the majority of sequence pairs analyzed by seed-and-extend based mappers differ by significantly more errors than what is typically allowed. Such error-abundant sequence pairs needlessly waste resources and severely hinder the performance of read mappers. Therefore, it is crucial to develop a fast and accurate filter that can rapidly and efficiently detect error-abundant string pairs and remove them from consideration before more computationally expensive methods are used. Results: We present a simple and efficient algorithm, Shifted Hamming Distance (SHD), which accelerates the alignment verification procedure in read mapping, by quickly filtering out error-abundant sequence pairs using bit-parallel and SIMD-parallel operations. SHD only filters string pairs that contain more errors than a user-defined threshold, making it fully comprehensive. It also maintains high accuracy with moderate error threshold (up to 5% of the string length) while achieving a 3-fold speedup over the best previous algorithm (Gene Myers's bit-vector algorithm). SHD is compatible with all mappers that perform sequence alignment for verification.