Increase the memory and core usage of R

Question

[QX]

Hi All,

I am running R on a slurm interactive mode. Is there any command or library that allow R to fullly use the resources of the node? and to check the efficiency?

Best,

[ATpoint]

Your question is to broad to be answered. Most processes in R are single-threaded so one core is most of the time what will be used. Some multicore processes can be specified, for example via the parallel, future or BiocParallel packages, and in these you can tell it how many cores to use. Can you give a more specific example?

[QX]

Hi, I actually just want to run interactive section for general analysis using full resources of requested HPC node. For e.g.

> rlimit_all()
$cur
     as    core     cpu    data   fsize memlock  nofile   nproc   stack 
    Inf       0     Inf     Inf     Inf     Inf   65536  513727 8388608 

$max
      as     core      cpu     data    fsize  memlock   nofile    nproc    stack 
     Inf      Inf      Inf      Inf      Inf      Inf   131072 16512766      Inf 

Answer 1

[pinheirofabiano]

to expand your virtual memory, go to the terminal and write:

cd ~

touch .Renviron

open .Renviron

R_MAX_VSIZE=50Gb

[Mensur Dlakic]

The whole thing could be condensed into a single line:

cd ; echo "R_MAX_VSIZE=50Gb" >> .Renviron