Commodity many-core hardware is now mainstream, but parallel programming models are still lagging behind in efficiently utilizing the application parallelism. There are (at least) two principal reasons for this. First, real-world programs often take the form of a deeply nested composition of parallel operators, but mapping the available parallelism to the hardware requires a set of transformations that are tedious to do by hand and beyond the capability of the common user. Second, the best optimization strategy, such as what to parallelize and what to efficiently sequentialize, is often sensitive to the input dataset and therefore requires multiple code versions that are optimized differently, which also raises maintainability problems. This article presents three array-based applications from the financial domain that are suitable for gpgpu execution. Common benchmark-design practice has been to provide the same code for the sequential and parallel versions that are optimized for only one class of datasets. In comparison, we document (1) all available parallelism via nested map-reduce functional combinators, in a simple Haskell implementation that closely resembles the original code structure, (2) the invariants and code transformations that govern the main trade-offs of a data-sensitive optimization space, and (3) report target cpu and multiversion gpgpu code together with an evaluation that demonstrates optimization trade-offs and other difficulties. We believe that this work provides useful insight into the language constructs and compiler infrastructure capable of expressing and optimizing such applications, and we report in-progress work in this direction.

BACKGROUND: Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that this gap will disappear in the near future. Small angle X-ray scattering (SAXS) is an established low resolution method for routinely determining the structure of proteins in solution. The purpose of this study is to develop a method for the efficient calculation of accurate SAXS curves from coarse-grained protein models. Such a method can for example be used to construct a likelihood function, which is paramount for structure determination based on statistical inference. RESULTS: We present a method for the efficient calculation of accurate SAXS curves based on the Debye formula and a set of scattering form factors for dummy atom representations of amino acids. Such a method avoids the computationally costly iteration over all atoms. We estimated the form factors using generated data from a set of high quality protein structures. No ad hoc scaling or correction factors are applied in the calculation of the curves. Two coarse-grained representations of protein structure were investigated; two scattering bodies per amino acid led to significantly better results than a single scattering body. CONCLUSION: We show that the obtained point estimates allow the calculation of accurate SAXS curves from coarse-grained protein models. The resulting curves are on par with the current state-of-the-art program CRYSOL, which requires full atomic detail. Our method was also comparable to CRYSOL in recognizing native structures among native-like decoys. As a proof-of-concept, we combined the coarse-grained Debye calculation with a previously described probabilistic model of protein structure, TorusDBN. This resulted in a significant improvement in the decoy recognition performance. In conclusion, the presented method shows great promise for use in statistical inference of protein structures from SAXS data.