Specialized code generators

evoldoers / machineboss

Bioinformatics Open Source Sequence machine

BSD 3-Clause "New" or "Revised" License

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Specialized code generators #109

Closed ihh closed 4 years ago

ihh commented 4 years ago

GPUs: CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-117

FPGAs: Oliver et al Reconfigurable architectures for bio-sequence database scanning on FPGAs https://ieeexplore.ieee.org/document/1556805

http://dx.doi.org/10.1155/2012/752910 Benkrid et al High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

ihh commented 4 years ago

As was ever the case with DP acceleration... the question is whether the development time justifies the effort for specialized hardware.