Issues with snowfall - parallel execution
albertop210 opened this issue · comments
Hi authors,
thanks for your excellent work and very useful deconvolution tool!
I tried to use your package (I updated it just yesterday after looking at other issues), following the tutorial analysis in the vignette; everything works well until I launch run.Ted function.
I paste here the output code:
[1] "removing non-numeric genes..."
[1] "removing outlier genes..."
Number of outlier genes filtered= 6
[1] "aligning reference and mixture"
[1] "run first sampling"
Start run... This may take a while
R Version: R version 4.1.2 (2021-11-01)
snowfall 1.84-6.1 initialized (using snow 0.4-4): parallel execution on 8 CPUs.
After this, the CPU is starting working, but with a strange "pattern" looking at the system monitor, then it remains like that (without showing any other output for hours); I'm wondering what does snowfall do inside run.Ted function and if there could be a compatibility problem with the parallelization function, the R version or the system. I'm working on Ubuntu 18.04.6 LTS, AMD Opteron 6344 18 CPU.
Thanks in advance for your kind reply,
Best,
Alberto
Thanks a lot for your reply, I will try to subset the X matrix as you suggested, just to give a try with your tutorial data, than go on with my lab's data.
For sure an estimated run time printed on screen would be very useful, so I will wait for next updates of the package.
Best,
Alberto