Journal
JOURNAL OF STRUCTURAL BIOLOGY
Volume 189, Issue 2, Pages 147-152Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jsb.2014.11.009
Keywords
Electron tomography; Reconstruction algorithms; SIRT; Parallel processing; Vectorization; AVX; Cache optimization
Funding
- European Reg. Dev. Funds (ERDF) [Mineco-TIN2012-37483, JA-P10-TIC-6002, JA-P11-TIC-7176]
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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. (C) 2014 Elsevier Inc. All rights reserved.
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