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Furthermore, the register-to-register nature of SIMD instructions causes current SIMD engines to have limitations in handling memory alignment, data reorganization, and control flow.
Our new algorithm uses a particular data structure that takes into account memory alignment constraints and avoids gather/scatter instructions that can significantly affect vectorization performances on current CPUs.
(b) Contiguous memory alignment.
(a) Non-contiguous memory alignment in the ghost zone (red arrows).
In the multi-GPU case with three-dimensional domain decomposition, the non-contiguous memory alignment in the ghost zones was found to impose quite long time in data transfer between GPU and the host node.
At this stage, we load and operate on four consecutive pixels of the image, unrolling the corresponding loop by a factor 4. Special caution must be taken in order to meet the memory alignment restrictions of the load/store vector instructions; to meet them, we apply zero-padding to the input image when necessary, according to its specific dimensions. 5.
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Forcing the memory address alignment for a mapping to be the same as the alignment within the memory object.
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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