FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Background Likelihood (ML)-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data. This method is used in applications such as RAxML, GARLI, MrBayes, PAML, and PAUP. The Phylogenetic Likelihood Function (PLF) is an important kernel computation for this method. The PLF consists of a loop with no conditional behavior or dependencies between iterations. As such it contains a high potential for exploiting parallelism using micro-architectural techniques. In this paper, we describe a technique for mapping the PLF and supporting logic onto a Field Programmable Gate Array (FPGA)-based co-processor. By leveraging the FPGA\u27s on-chip DSP modules and the high-bandwidth local memory attached to the FPGA, the resultant co-processor can accelerate ML-based methods and outperform state-of-the-art multi-core processors. Results We use the MrBayes 3 tool as a framework for designing our co-processor. For large datasets, we estimate that our accelerated MrBayes, if run on a current-generation FPGA, achieves a 10× speedup relative to software running on a state-of-the-art server-class microprocessor. The FPGA-based implementation achieves its performance by deeply pipelining the likelihood computations, performing multiple floating-point operations in parallel, and through a natural log approximation that is chosen specifically to leverage a deeply pipelined custom architecture. Conclusions Heterogeneous computing, which combines general-purpose processors with special-purpose co-processors such as FPGAs and GPUs, is a promising approach for high-performance phylogeny inference as shown by the growing body of literature in this field. FPGAs in particular are well-suited for this task because of their low power consumption as compared to many-core processors and Graphics Processor Units (GPUs)

Computation and storage of the bianisotropic scalar Green's function and its derivatives

A set of algorithms is proposed for the accurate and efficient computation and storage of the bianisotropic scalar Green's function. The computation is based on an expansion of the Green's function into Chebyshev polynomials. The analytical properties of these polynomials are exploited to allow the accurate computation of the derivatives of the Green's function as well as the Green's function itself. For lossy materials, the proposed computation strategy is provably robust. In addition, a multilevel storage scheme with a favorable complexity, based on the Chebyshev polynomial expansion, is proposed for the storage of the expansion coefficients. Numerical results showcase the accuracy and computational complexity of the proposed algorithms

Optimized linear, quadratic and cubic interpolators for elementary function hardware implementations

This paper presents a method for designing linear, quadratic and cubic interpolators that compute elementary functions using truncated multipliers, squarers and cubers. Initial coefficient values are obtained using a Chebyshev series approximation. A direct search algorithm is then used to optimize the quantized coefficient values to meet a user-specified error constraint. The algorithm minimizes coefficient lengths to reduce lookup table requirements, maximizes the number of truncated columns to reduce the area, delay and power of the arithmetic units, and minimizes the maximum absolute error of the interpolator output. The method can be used to design interpolators to approximate any function to a user-specified accuracy, up to and beyond 53-bits of precision (e.g., IEEE double precision significand). Linear, quadratic and cubic interpolator designs that approximate reciprocal, square root, reciprocal square root and sine are presented and analyzed. Area, delay and power estimates are given for 16, 24 and 32-bit interpolators that compute the reciprocal function, targeting a 65 nm CMOS technology from IBM. Results indicate the proposed method uses smaller arithmetic units and has reduced lookup table sizes compared to previously proposed methods. The method can be used to optimize coefficients in other systems while accounting for coefficient quantization as well as truncation and rounding effects of multiple arithmetic units.Peer reviewedElectrical and Computer Engineerin

Verifying a synthesized implementation of IEEE-754 floating-point exponential function using HOL

Deep datapath and algorithm complexity have made the verification of floating-point units a very hard task. Most simulation and reachability analysis verification tools fail to verify a circuit with a deep datapath like most industrial floating-point units. Theorem proving, however, offers a better solution to handle such verification. In this paper, we have hierarchically formalized and verified a hardware implementation of the IEEE-754 table-driven floating-point exponential function algorithm using the higher-order logic (HOL) theorem prover. The high ability of abstraction in the HOL verification system allows its use for the verification task over the whole design path of the circuit, starting from gate-level implementation of the circuit up to a high-level mathematical specification