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. 2015 Feb;189(2):147-52.
doi: 10.1016/j.jsb.2014.11.009. Epub 2014 Dec 17.

Tomo3D 2.0--exploitation of advanced vector extensions (AVX) for 3D reconstruction

Jose-Ignacio Agulleiro  1 , Jose-Jesus Fernandez  2
Affiliations

Tomo3D 2.0--exploitation of advanced vector extensions (AVX) for 3D reconstruction

Jose-Ignacio Agulleiro et al. J Struct Biol. 2015 Feb.

Abstract

Tomo3D is a program for fast tomographic reconstruction on multicore computers. Its high speed stems from code optimization, vectorization with Streaming SIMD Extensions (SSE), multithreading and optimization of disk access. Recently, Advanced Vector eXtensions (AVX) have been introduced in the x86 processor architecture. Compared to SSE, AVX double the number of simultaneous operations, thus pointing to a potential twofold gain in speed. However, in practice, achieving this potential is extremely difficult. Here, we provide a technical description and an assessment of the optimizations included in Tomo3D to take advantage of AVX instructions. Tomo3D 2.0 allows huge reconstructions to be calculated in standard computers in a matter of minutes. Thus, it will be a valuable tool for electron tomography studies with increasing resolution needs.

Keywords: AVX; Cache optimization; Electron tomography; Parallel processing; Reconstruction algorithms; SIRT; Vectorization.

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