R 1TB bug

R_1TB_bug.R

## allocate <1TB first, stuff works
> x <- 1:1.2e11
> gc()
               used     (Mb)  gc trigger      (Mb)     max used     (Mb)
Ncells       214403     11.5 4.60000e+05      24.6       350000     18.7
Vcells 120000397293 915530.4 1.72801e+11 1318366.9 120000398080 915530.4
> system("echo 1")
1


## allocate more, so >1TB allocated (total RAM ~2TB)
> y <- 1:0.2e11
> gc()
               used      (Mb)   gc trigger      (Mb)     max used      (Mb)
Ncells       214670      11.5       460000      24.6       350000      18.7
Vcells 140000397805 1068118.3 207361249221 1582040.8 140000400143 1068118.3

## this breaks:
> system("echo 1")
Warning message:
In system("echo 1") : system call failed: Cannot allocate memory
> sessionInfo()
Error in system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE) : 
  cannot popen '/usr/bin/which 'uname' 2>/dev/null', probable reason 'Cannot allocate memory'
> library()
Warning messages:
1: In library() : library ‘/usr/lib/R/site-library’ contains no packages
2: In file.show(outFile, delete.file = TRUE, title = gettext("R packages available")) :
  system call failed: Cannot allocate memory
  
## allocation in general still works:
> system.time(z <- 1:1e8)
   user  system elapsed 
  0.053   0.088   0.140 
  

## deallocate some (<1TB allocated now)
> y <- NULL
> gc()
               used     (Mb)   gc trigger      (Mb)     max used      (Mb)
Ncells       224057     12.0       460000      24.6       404441      21.6
Vcells 120000414088 915530.6 207361249221 1582040.8 140000676821 1068120.4

## stuff works again
> system("echo 1")
1
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS
[...]
> library()
Packages in library ‘/usr/local/lib/R/site-library’:
[...]