High Performance Stencil Code Generation with LIFT

Stencil computations are widely used from physical simulations to machine-learning. They are embarrassingly parallel and perfectly fit modern hardware such as Graphic Processing Units. Although stencil computations have been extensively studied, optimizing them for increasingly diverse hardware remains challenging. Domain Specific Languages (DSLs) have raised the programming abstraction and offer good performance. However, this places the burden on DSL implementers who have to write almost full-fledged parallelizing compilers and optimizers. Lift has recently emerged as a promising approach to achieve performance portability and is based on a small set of reusable parallel primitives that DSL or library writers can build upon. Lift’s key novelty is in its encoding of optimizations as a system of extensible rewrite rules which are used to explore the optimization space. However, Lift has mostly focused on linear algebra operations and it remains to be seen whether this approach is applicable for other domains. This paper demonstrates how complex multidimensional stencil code and optimizations such as tiling are expressible using compositions of simple 1D Lift primitives. By leveraging existing Lift primitives and optimizations, we only require the addition of two primitives and one rewrite rule to do so. Our results show that this approach outperforms existing compiler approaches and hand-tuned codes

Tiling Optimizations for Stencil Computations Using Rewrite Rules in Lift

Stencil computations are a widely used type of algorithm, found in applications from physical simulations to machine learning. Stencils are embarrassingly parallel, therefore fit on modern hardware such as Graphic Processing Units perfectly. Although stencil computations have been extensively studied, optimizing them for increasingly diverse hardware remains challenging. Domain-specific Languages (DSLs) have raised the programming abstraction and offer good performance; however, this method places the burden on DSL implementers to write almost full-fledged parallelizing compilers and optimizers. Lift has recently emerged as a promising approach to achieve performance portability by using a small set of reusable parallel primitives that DSL or library writers utilize. Lift’s key novelty is in its encoding of optimizations as a system of extensible rewrite rules which are used to explore the optimization space. This article demonstrates how complex multi-dimensional stencil code and optimizations are expressed using compositions of simple 1D Lift primitives and rewrite rules. We introduce two optimizations that provide high performance for stencils in particular: classical overlapped tiling for multi-dimensional stencils and 2.5D tiling specifically for 3D stencils. We provide an in-depth analysis on how the tiling optimizations affects stencils of different shapes and sizes across different applications. Our experimental results show that our approach outperforms existing compiler approaches and hand-tuned codes

Two new species and a new subgenus of toothed brachyhypopomus electric knifefishes (Gymnotiformes, Hypopomidae) from the central amazon and considerations pertaining to the evolution of a monophasic electric organ discharge

We describe two new, closely related species of toothed Brachyhypopomus (Hypopomidae: Gymnotiformes: Teleostei) from the central Amazon basin and create a new subgenus for them. Odontohypopomus, new subgenus of Brachyhypopomus, is diagnosed by (1) small teeth present on premaxillae; (2) medialmost two branchiostegal rays thin with blades oriented more vertically than remaining three rays; (3) background color in life (and to lesser extent in preservation) distinctly yellowish with head and sides peppered with small, widely spaced, very dark brown stellate chromatophores that greatly contrast with light background coloration; (4) a dark blotch or bar of subcutaneous pigment below the eye; (5) electric organ discharge waveform of very long duration (head-positive phase approx. 2 milliseconds or longer, head-negative phase shorter or absent) and slow pulse repetition rate (3-16 Hz). The type species of the new subgenus, Brachyhypopomus (Odontohypopomus) walteri sp. n., is diagnosed by the following additional character states: (1) subcutaneous dark pigment at base of orbit particularly prominent, (2) body semi-translucent and nearly bright yellow background coloration in life, (3) a biphasic electric organ discharge (EOD) waveform of very long duration (between 3.5 and 4 milliseconds at 25° C) with head-positive first phase significantly longer than second head-negative phase in both sexes. Brachyhypopomus (Odontohypopomus) bennetti sp. n. is diagnosed by two character states in addition to those used to diagnose the subgenus Odontohypopomus: (1) a deep electric organ, visible as large semi-transparent area, occupying approximately 14-17% body depth directly posterior to the abdominal cavity in combination with a short, but deep, caudal filament, and (2) a monophasic, head-positive EOD waveform, approximately 2.1 milliseconds in duration in both sexes. These are the only described rhamphichthyoid gymnotiforms with oral teeth, and B. bennetti is the first Brachyhypopomus reported to have a monophasic (head-positive) EOD waveform. Unlike biphasic species, the waveform of its EOD is largely unaffected by tail damage from predators. Such injuries are common among specimens in our collections. This species' preference for floating meadow habitat along the major channels of the Amazon River basin may put it at particularly high risk of predation and "tail grazing"

AN5D: Automated Stencil Framework for High-Degree Temporal Blocking on GPUs

Stencil computation is one of the most widely-used compute patterns in high performance computing applications. Spatial and temporal blocking have been proposed to overcome the memory-bound nature of this type of computation by moving memory pressure from external memory to on-chip memory on GPUs. However, correctly implementing those optimizations while considering the complexity of the architecture and memory hierarchy of GPUs to achieve high performance is difficult. We propose AN5D, an automated stencil framework which is capable of automatically transforming and optimizing stencil patterns in a given C source code, and generating corresponding CUDA code. Parameter tuning in our framework is guided by our performance model. Our novel optimization strategy reduces shared memory and register pressure in comparison to existing implementations, allowing performance scaling up to a temporal blocking degree of 10. We achieve the highest performance reported so far for all evaluated stencil benchmarks on the state-of-the-art Tesla V100 GPU

Light-Triggered Boost of Activity of Catalytic Bola-Type Surfactants by a Plasmonic Metal-Support Interaction Effect

The maximization of activity is a general aim in catalysis research. The possibility for light-triggered enhancement of a catalytic process, even if the process is not photochemical in nature, represents an intriguing concept. Here, we present a novel system for the exploration of the latter idea. A surfactant with a catalytically active head group, a protonated polyoxometalate (POM) cluster, is attached to the surface of a gold nanoparticle (Au NP) using thiol coupling chemistry. The distance of the catalytically active center to the gold surface could be adjusted precisely using surfactants containing hydrocarbon chains (Cn) of different lengths ( n = 4-10). Radiation with VIS-light has no effect on the catalytic activity of micellar aggregates of the surfactant. The situation changes, as soon as the surfactants have been attached to the Au NPs. The catalytic activity could almost be doubled. It was proven that the effect is caused by coupling the surface plasmon resonance of the Au NPs with the properties of the POM head group. The improvement of activity could only be observed if the excitation wavelength matches the absorption band of the used Au NPs. Furthermore, the shorter the distance between the POM group and the surface of the NP, the stronger is the effect. This phenomenon was explained by lowering the activation energy of the transition state relevant to the catalytic process by the strong electric fields in the vicinity of the surfaces of plasmonic nanoparticles. Because the catalytic enhancement is wavelength-selective, one can imagine the creation of complex systems in the future, a system of differently sized NPs, each responsible for a different catalytic step and activated by light of different colors.publishe

Communication behavior and sensory mechanisms in weakly electric fishes

Teleost freshwater fishes of the orders Mormyriformes (the elephantfishes plus Gymnarchus from Africa) and Gymnotiformes (the knifefishes from South America) are both electrogenic and electroreceptive. These fishes' electric system has a motor part, the electric organ, and a sensory part, the cutaneous electroreceptors that project to large, specialized brain areas. The electric systems of both groups of fishes, although evolved independently, are adapted to the same two functions, nocturnal electrolocation and communication. Weakly electric fishes discharge their electric organs in a pulselike or in a wavelike fashion ("buzzers" and "hummers," respectively). Whether a species is a hummer or a buzzer does not appear to be correlated with ecology but is strongly linked to phylogeny. There are representatives of both discharge types on both continents where these fishes are found. The elephantfishes (Mormyridae, about 200 species) are, apparently, all pulse fishes, whereas the related, monospecific Gymnarchus (Gymnarchidae) is the only known African wave fish. There are five families of South American knifefishes, with the majority of the 70 or so species being hummers, usually discharging at extremely constant frequencies (about 50- 1800 Hz). The sensory mechanisms of social communication, as studied by behavioral means, are reviewed in this chapter with the question of mechanisms of reproductive isolation in mind. The chapter focuses on the electric organ discharge as the basic communication unit, and on the frequency, repetition rate, or temporal patterns of discharges. In both wave and pulse fishes the frequencies or repetition rates of discharges are not usually species-specific but are species-characteristic, because of more or less broad overlap between two or more species (depending on the local community of species). Electrosensory discrimination thresholds for frequency and intensity are unusually low in a wave fish, lower by far than those for other acoustico-lateral senses of aquatic lower vertebrates, rivaling the discrimination thresholds for audition in the most sensitive mammals (e.g., the human). A similar conclusion applies for the pulse rate sensitivity of a mormyrid. Species specificity becomes apparent when more information about the discharge activity is considered. In the case of pulse fishes, especially mormyrids, this comprises temporal patterns of discharges, which also vary greatly according to behavioral context (like aggression, escape, courtship, feeding, etc.); these fishes have an interdischarge interval code of communication. In the case of wave fishes, various types of frequency modulations and brief, repetitive discharge stops occur. Also, wave fishes may engage in "phase coupling" and "jamming avoidance," maneuvers that involve precise interaction with another fish's discharges. The degree ' of species specificity of a fish's discharge activity is usually enhanced by features of the waveform of a single discharge; this is true in both pulse and wave fishes. Usually there is considerable intraspecific variability of discharge waveforms, and there are also examples of sexual dimorphism. At least a few species can discriminate the individually variable pulse or wave discharge waveforms of their species. In a wave fish, a sensory mechanism based on the temporal analysis of beat patterns can explain the observed results. This new sensory capacity detects the phase modulation within a beat, which always occurs when the wave discharges of two fish mix in the water. In pulse fishes, several hypothetical sensory mechanisms for the discrimination of intraspecific pulse waveforms have been proposed but it is not yet clear which is generally involved. In any case, the sensitivity of weakly electric fishes to the fine detail of their discharges shows that the electrosensory world is much more colorful than could be imagined until recently