A framework for FPGA functional units in high performance computing

FPGAs make it practical to speed up a program by defining hardware functional units that perform calculations faster than can be achieved in software. Specialised digital circuits avoid the overhead of executing sequences of instructions, and they make available the massive parallelism of the components. The FPGA operates as a coprocessor controlled by a conventional computer. An application that combines software with hardware in this way needs an interface between a communications port to the processor and the signals connected to the functional units. We present a framework that supports the design of such systems. The framework consists of a generic controller circuit defined in VHDL that can be configured by the user according to the needs of the functional units and the I/O channel. The controller contains a register file and a pipelined programmable register transfer machine, and it supports the design of both stateless and stateful functional units. Two examples are described: the implementation of a set of basic stateless arithmetic functional units, and the implementation of a stateful algorithm that exploits circuit parallelism

Exploiting tightly-coupled cores

This is the published manuscript. It was first published by Springer in the Journal of Signal Processing Systems here: http://link.springer.com/article/10.1007%2Fs11265-014-0944-6.The individual processors of a chip-multiprocessor traditionally have rigid boundaries. Inter-core communication is only possible via memory and control over a core’s resources is localised. Specialisation necessary to meet today’s challenging energy targets is typically provided through the provision of a range of processor types and accelerators. An alternative approach is to permit specialisation by tailoring the way a large number of homogeneous cores are used. The approach here is to relax processor boundaries, create a richer mix of intercore communication mechanisms and provide finer-grain control over, and access to, the resources of each core. We evaluate one such design, called Loki, that aims to support specialisation in software on a homogeneous many-core architecture. We focus on the design of a single 8-core tile, conceived as the building block for a larger many-core system. We explore the tile’s ability to support a range of parallelisation opportunities and detail the control and communication mechanisms needed to exploit each core’s resources in a flexible manner. Performance and a detailed breakdown of energy usage is provided for a range of benchmarks and configurations.This work was supported by EPSRC grant EP/G033110/1

Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae)

Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which (i) local adaptation and the early stages of speciation can be clearly identified and distinguished, (ii) the amount of genetic divergence driven by the two processes is similar, and (iii) comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly colored reef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome-wide levels of divergence that are comparable among allopatric populations (Fst estimate = 0.0042) and sympatric species (Fst estimate = 0.0038). Population genetic, clustering, and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fraction of the genome undifferentiated (Fst estimate ≈ 0), a very small proportion of Fst outlier loci (0.05–0.07%), and remarkably few repeated outliers (1–3). Nevertheless, different loci appear to be involved in the two processes in Hypoplectrus, with only 7% of the most differentiated SNPs and outliers shared between populations and species comparisons. In particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa) locus emerge as candidate loci (repeated outliers) for local adaptation and speciation, respectively. We conclude that marine populations may be locally adapted notwithstanding shallow levels of genetic divergence, and that from a population genomic perspective, this process does not appear to differ fundamentally from the early stages of speciation

Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

Citation: Koltes, J. E., Fritz-Waters, E., Eisley, C. J., Choi, I., Bao, H., Kommadath, A., . . . Reecy, J. M. (2015). Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection. Bmc Genomics, 16, 13. doi:10.1186/s12864-015-1635-9Background: Previously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4). Results: Within this QTL, guanylate binding protein 5 (GBP5) was differentially expressed (DE) (p < 0.05) in blood from AA versus AB rs80800372 genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs80800372 exhibited allele specific expression (ASE) in AB individuals (p < 0.0001). A transcript re-assembly revealed three alternatively spliced transcripts for GBP5. An intronic SNP in GBP5, rs340943904, introduces a splice acceptor site that inserts five nucleotides into the transcript. Individuals homozygous for the unfavorable AA genotype predominantly produced this transcript, with a shifted reading frame and early stop codon that truncates the 88 C-terminal amino acids of the protein. RNA-seq analysis confirmed this SNP was associated with differential splicing by QTL genotype (p < 0.0001) and this was validated by quantitative capillary electrophoresis (p < 0.0001). The wild-type transcript was expressed at a higher level in AB versus AA individuals, whereas the five-nucleotide insertion transcript was the dominant form in AA individuals. Splicing and ASE results are consistent with the observed dominant nature of the favorable QTL allele. The rs340943904 SNP was also 100 % concordant with rs80800372 in a validation population that possessed an alternate form of the favorable B QTL haplotype. Conclusions: GBP5 is known to play a role in inflammasome assembly during immune response. However, the role of GBP5 host genetic variation in viral immunity is novel. These findings demonstrate that rs340943904 is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV.Additional Authors: Lunney, J. K.;Liu, P.;Carpenter, S.;Rowland, R. R. R.;Dekkers, J. C. M.;Reecy, J. M