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Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled(More)
MOTIVATION One of the major challenges for contemporary bioinformatics is the analysis and accurate annotation of genomic datasets to enable extraction of useful information about the functional role of DNA sequences. This article describes a novel genome-wide statistical approach to the detection of specific DNA sequence motifs based on similarities(More)
A fault-tolerant version of Open Message Passing Interface (Open MPI), based on the draft User Level Failure Mitigation (ULFM) proposal of the MPI Forum's Fault Tolerance Working Group, is used to create fault-tolerant applications. This allows applications and libraries to design their own recovery methods and control them at the user level. However, only(More)
A key issue confronting petascale and exascale computing is the growth in probability of soft and hard faults with increasing system size. A promising approach to this problem is the use of algorithms that are inherently fault tolerant. We introduce such an algorithm for the solution of partial differential equations, based on the sparse grid approach.(More)
The increasing number of processing elements and decreasing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on massively parallel systems scientific software must evolve across the entire stack to exploit the multiple levels of(More)
Mesh smoothing is an important algorithm for the improvement of element quality in unstructured mesh finite element methods. A new optimisation based mesh smoothing algorithm is presented for anisotropic mesh adaptivity. It is shown that this smoothing kernel is very effective at raising the minimum local quality of the mesh. A number of strategies are(More)
Anisotropic mesh adaptation is a powerful way to directly minimise the computational cost of mesh based simulation. It is particularly important for multi-scale problems where the required number of floating-point operations can be reduced by orders of magnitude relative to more traditional static mesh approaches. Increasingly, finite element and finite(More)