Sparse Matrix-Based HPC Tomography

Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster frame rates, larger fields of view or higher resolution, so high performance solutions are currently widely used for analysis. Tomographic instruments can vary significantly from one to another, including the hardware employed for reconstruction: from single CPU workstations to large scale hybrid CPU/GPU supercomputers. Flexibility on the software interfaces and reconstruction engines are also highly valued to allow for easy development and prototyping. This paper presents a novel software framework for tomographic analysis that tackles all aforementioned requirements. The proposed solution capitalizes on the increased performance of sparse matrix-vector multiplication and exploits multi-CPU and GPU reconstruction over MPI. The solution is implemented in Python and relies on CuPy for fast GPU operators and CUDA kernel integration, and on SciPy for CPU sparse matrix computation. As opposed to previous tomography solutions that are tailor-made for specific use cases or hardware, the proposed software is designed to provide flexible, portable and high-performance operators that can be used for continuous integration at different production environments, but also for prototyping new experimental settings or for algorithmic development. The experimental results demonstrate how our implementation can even outperform state-of-the-art software packages used at advanced X-ray sources worldwide

Devonian pearls and ammonoid-endoparasite co-evolution

Raised shell projections on the inner shell walls that form pits on the internal moulds of Devonian ammonoids have been known for several decades. New specimens from Morocco reveal novel details of these structures; most, if not all, of which consist of a capsule of ammonoid shell that covers tiny tubes attached to the outer (=lateral or ventral) shell wall from the inside. In accordance with comparable Recent occurrences of similar structures in molluscs, we use the term “pearls” for these structures and the pits they form on the internal moulds. The nature of these encapsulated tubes is described and discussed. Because of the presence of these tubes inside the pearls, pearl arrangement, and their similarity to Recent mollusc occurrences, the tubes are interpreted as traces of parasitoses. The pearls and pits were grouped into five types based on differences in morphology, size, and arrangement. Then, having used these traits to perform a simple cladistic analysis, the resulting cladogram was compared to the phylogeny of ammonoids. Based on this comparison, it appears likely that the parasites underwent a co-evolution with the ammonoids, which lasted 10 to 15 Ma. Patterns of evolutionary events include co-speciation, “drowning on arrival” (end of parasite lineage near base of a new host clade), and “missing the boat” (parasite lineage does not adapt to a new host clade, thus not evolving a new parasite clade). Because of the lack of fossilised soft tissue, only speculations can be made about the systematic affiliation of the parasites, their life-cycle, infection strategy, and ecological framework. Some co-occurring bivalves also have pits reminiscent to structures caused by trematodes in Recent forms. Based on the available information, the tubes are interpreted as artefacts of trematode infestations, which, if correct, would extend the fossil record of parasitic trematodes into the Early Devonian