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I would like to set my temporary directory using the scratch space of the cluster. I have tried various methods and this one: How to change directory for temporary files - problems with huge temporary raster files but nothing works.

I have to read a large file (12 GB) in R and run some code using it. I would like to read the file in this way:

library(data.table)
mydata<-fread("path/file")

But first I believe it is necessary to set the temporary directory as scratch/ otherwise the job has been killed. Feel free to suggest any other approach.

vgenepi
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  • You can just create a folder on /scratch then copy data & R script and run from there. Then delete everything after you get the results. These should be done in your job submission scripts (`qsub`, `slurm`, etc.) – Tung Aug 08 '18 at 22:39
  • Unfortunatelly it does not work... – vgenepi Aug 09 '18 at 09:44

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