SpaCET.deconvolution function takes an unusually long time and was often suspended at some degree

[zhangzj0]

SpaCET.deconvolution function takes an unusually long time and was often suspended at 15%. However, the memory use was not really so high.

[beibeiru]

Hi, @zhangzj0 ,

This is weird. How long does it take to run the following example on your PC?

library(SpaCET)

visiumPath <- file.path(system.file(package = "SpaCET"), "extdata/Visium_BC")
SpaCET_obj <- create.SpaCET.object.10X(visiumPath = visiumPath)
SpaCET_obj <- SpaCET.deconvolution(SpaCET_obj, cancerType="BRCA", coreNo=1)

Best,
Beibei

[zhangzj0]

Hi, @beibeiru,
Thanks for your in-time reply.
As you can see in the following picture, I was encountered the same suspension when I run the code you provided in my linux server(visiumPath <- file.path(system.file(package = "SpaCET"), "extdata/Visium_BC")
SpaCET_obj <- create.SpaCET.object.10X(visiumPath = visiumPath)
SpaCET_obj <- SpaCET.deconvolution(SpaCET_obj, cancerType="BRCA", coreNo=1))

Best,
Zhijun

[zhangzj0]

Thanks for your clue! When I ran this code on my personal PC rather than Linux Server, it only needed 15 minutes!

[beibeiru]

For this BRCA ST sample,
it takes 10 mins (coreNo=6) and 35 mins (coreNo=1) on my MacBook, respectively;
or it takes 2 mins (coreNo=6) and 8 mins (coreNo=1) on our HPC, respectively.

Best,
Beibei