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optimise for memory for very large all by all NBLAST #40

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jefferis opened this issue Jun 18, 2020 · 0 comments
Open

optimise for memory for very large all by all NBLAST #40

jefferis opened this issue Jun 18, 2020 · 0 comments

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@jefferis
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  • Use a pattern of small (e.g. 100 x 100) blocks that might 10s of seconds / a few minutes to compute
  • this should work better than doing a whole row or column that might have 20-50k neurons.
  • need to implement an x by y nblast function instead of all by all NBLAST for each block (would current NBLAST be ok?)
  • inputs could be neuronlistfh and read in for each process. I suspect that read time will be trivial compared with search time so long as blocks take 10s of seconds to compute. This might work well for memory.
  • ideally we would parallelise across those blocks with progress
  • if doing mean scores, we might want to do forward and reverse scores at the same time since they use the same sets of neurons
  • we might wish to fill a sparse matrix with the results with a threshold
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