How to increase RAM for R scripts run in computer cluster

Question

[alhafidzhamdan]

Hi all, This is probably not specific to facets but i am struggling to run facets.R in an HPC (linux).

My command:

Rscript --vanilla facets.R -i $PATIENT_ID -f $INPUT -o $OUTPUT -c $CVAL

Loading required package: pctGCdata
Taking input= as a system command ('gunzip -c /exports/igmm/eddie/WGS/variants/cnv/facets/pileups/E13.csv.gz') and a variable has been used in the expression passed to input=. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Error: cannot allocate vector of size 2.3 Gb
Execution halted
  

I've give the job 32Gb of ram through the cluster setting but it keeps giving off this error. Is there a way around it? How do you increase RAM use for R scripts run through Rscript?

I've tried ulimit but the same error was obtained.

A

[ATpoint]

Please show what you are running, so the code of that script.

[alhafidzhamdan]

Essentially this -> https://github.com/mskcc/facets/blob/master/inst/extRfns/readSnpMatrixDT.R

[bruce.moran]

https://stackoverflow.com/questions/12582793/limiting-memory-usage-in-r-under-linux

Apologies, copy/pasted wrong link from bookmarks; TLDR set ulimit globally

[alhafidzhamdan]

That's for windows- i'm using linux ie computer cluster.