Parallelization in Seurat with future

[Motoufiq]

Hi,

I attempted to use the future framework for parallelization during the FindIntegrationAnchors step in Seurat while working in R Studio on my Mac, but it caused R Studio to freeze and close. I then moved the analysis to an HPC system of my institution, but the future framework still didn’t work.

library(future)
plan("multiprocess", workers = 4)
> plan("multiprocess", workers = 4)
Error: No such strategy for futures: ‘multiprocess’

On Mac, I switched to:

plan("multisession", workers = 4)

I also tried:

options(future.globals.maxSize = 50000 * 1024^2) # for 50 GB RAM

However, R Studio continues to close unexpectedly.

Best regards,
Toufiq

[LilingJiang]

Hi,

I attempted to use the future framework for parallelization during the FindIntegrationAnchors step in Seurat while working in R Studio on my Mac, but it caused R Studio to freeze and close. I then moved the analysis to an HPC system of my institution, but the future framework still didn’t work.

library(future)
plan("multiprocess", workers = 4)
> plan("multiprocess", workers = 4)
Error: No such strategy for futures: ‘multiprocess’

On Mac, I switched to:

plan("multisession", workers = 4)

I also tried:

options(future.globals.maxSize = 50000 * 1024^2) # for 50 GB RAM

However, R Studio continues to close unexpectedly.

Best regards, Toufiq

Hi there! I ran into the same issue and fixed it by using the multicore option on Linux. Starting from version 1.20.0 of the future package, the multiprocess strategy has been removed and replaced with multisession and multicore. Hope that helps.