Efficient implementation of sparse matrix-sparse vector multiplication for large scale graph analytics

Author(s):  
Mauricio J. Serrano
2022 ◽  
Vol 15 (2) ◽  
pp. 1-33
Author(s):  
Mikhail Asiatici ◽  
Paolo Ienne

Applications such as large-scale sparse linear algebra and graph analytics are challenging to accelerate on FPGAs due to the short irregular memory accesses, resulting in low cache hit rates. Nonblocking caches reduce the bandwidth required by misses by requesting each cache line only once, even when there are multiple misses corresponding to it. However, such reuse mechanism is traditionally implemented using an associative lookup. This limits the number of misses that are considered for reuse to a few tens, at most. In this article, we present an efficient pipeline that can process and store thousands of outstanding misses in cuckoo hash tables in on-chip SRAM with minimal stalls. This brings the same bandwidth advantage as a larger cache for a fraction of the area budget, because outstanding misses do not need a data array, which can significantly speed up irregular memory-bound latency-insensitive applications. In addition, we extend nonblocking caches to generate variable-length bursts to memory, which increases the bandwidth delivered by DRAMs and their controllers. The resulting miss-optimized memory system provides up to 25% speedup with 24× area reduction on 15 large sparse matrix-vector multiplication benchmarks evaluated on an embedded and a datacenter FPGA system.


1987 ◽  
Vol 18 (6) ◽  
pp. 89-99 ◽  
Author(s):  
Hideki Asai ◽  
Mitsuo Asai ◽  
Mamoru Tanaka

Author(s):  
Bo Li ◽  
Ruihong Qiao ◽  
Zhizhi Wang ◽  
Weihong Zhou ◽  
Xin Li ◽  
...  

Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and a fragment of TNKS1 covering the second and third ankyrin-repeat clusters (ARC2-3) is presented at 2.2 Å resolution. The TNKS1–TRF1 complex crystals were optimized using an `oriented rescreening' strategy, in which the initial crystallization condition was used as a guide for a second round of large-scale sparse-matrix screening. This crystallographic and biochemical analysis provides a better understanding of the TRF1–TNKS1 interaction and the three-dimensional structure of the ankyrin-repeat domain of TNKS.


Author(s):  
Karel Kovářík ◽  
Juraj Mužík

This work focuses on the derivation of the local variant of the singular boundary method (SBM) for solving the advection-diffusion equation of tracer transport. Localization is based on the combination of SBM and finite collocation. Unlike the global variant, local SBM leads to a sparse matrix of the resulting system of equations, making it much more efficient to solve large-scale tasks. It also allows solving velocity vector variable tasks, which is a problem with global SBM. This paper compares the results on several examples for the steady and unsteady variant of the advection-diffusion equation and also examines the dependence of the accuracy of the solution on the density of the nodal grid and the size of the subdomain.


2021 ◽  
Author(s):  
Zhihui Du ◽  
Oliver Alvarado Rodriguez ◽  
David A. Bader
Keyword(s):  

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