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Sahand Kashani

Publications and source records attributed to Sahand Kashani.

2 recordsLinked to original sources

Manticore: Hardware-Accelerated RTL Simulation with Static Bulk-Synchronous Parallelism

The demise of Moore's Law and Dennard Scaling has revived interest in specialized computer architectures and accelerators. Verification and testing of this hardware depend heavily upon cycle-accurate simulation of register-transfer-level (RTL) designs. The fastest software RTL simulators can simulate designs at 1--1000 kHz, i.e., more than three orders of magnitude slower than hardware. Improved simulators can increase designers' productivity by speeding design iterations and permitting more exhaustive exploration. One possibility is to exploit low-level parallelism, as RTL expresses considerable fine-grain concurrency. Unfortunately, state-of-the-art RTL simulators often perform best on a single core since modern processors cannot effectively exploit fine-grain parallelism. This work presents Manticore: a parallel computer designed to accelerate RTL simulation. Manticore uses a static bulk-synchronous parallel (BSP) execution model to eliminate fine-grain synchronization overhead. It relies entirely on a compiler to schedule resources and communication, which is feasible since RTL code contains few divergent execution paths. With static scheduling, communication and synchronization no longer incur runtime overhead, making fine-grain parallelism practical. Moreover, static scheduling dramatically simplifies processor implementation, significantly increasing the number of cores that fit on a chip. Our 225-core FPGA implementation running at 475 MHz outperforms a state-of-the-art RTL simulator running on desktop and server computers in 8 out of 9 benchmarks.

cs.AR

IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback

Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis pipelines. This paper analyzes the feasibility of applying Darwins algorithms to the problem of protein sequence alignment. In addition to a behavioral analysis of Darwin when aligning proteins, we propose an algorithmic improvement to Darwins alignment algorithm, GACT, in the form of a multi-pass variant that increases its accuracy on protein sequence alignment. Concretely, our proposed multi-pass variant of GACT achieves on average 14\% better alignment scores.

q-bio.QM