Use of multicore parallelization with scran causes shinyapps.io memory errors

camlab-bioml / cytomarker

Interactive design and validation of antibody panels using single-cell atlases

https://camlab.shinyapps.io/cytomarker/

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Use of multicore parallelization with scran causes shinyapps.io memory errors #109

Closed matt-sd-watson closed 1 year ago

matt-sd-watson commented 1 year ago

Using the following parameter with scran's findMarkers function:

BPPARAM = MulticoreParam()

causes a memory kill error oom- container out of memory on shinyapps.io deployments.

Additional ideas for memory restriction on linux systems: https://stackoverflow.com/questions/12582793/limiting-memory-usage-in-r-under-linux

matt-sd-watson commented 1 year ago

removal of the MulticoreParam() specification for any relevant functions in scran was necessary in order to operate properly on shinyapps. Closing the issue but may need to find additional methods to speed up analysis in the future.