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SydneyBioX / CiteFuse

CiteFuse:
https://sydneybiox.github.io/CiteFuse/index.html
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CiteFuse SNF function runtime #3

Open shivarice opened 4 years ago

shivarice commented 4 years ago

Is there anyway to optimize the runtime on CiteFuse()? I'm currently running into issues where it's eating a lot of my RAM and not using any of my cores.

sorjuela commented 4 years ago

Hi @YingxinLin,

I also have this problem with CiteFuse(), it took almost 200 GB of memory on my SCE of size: 33694 genes 37 surface markers 37292 cells. The object on disk is only 184.7 MB.

Also might be worth implementing some BiocParallel methods to speed it up.

Best, Stephany

xiachenrui commented 2 years ago

Yes, I find the same problem and I find reducedDimSNF() can not work on 160,000 cells even I have 1500Gb memory