R system() process always uses same CPU, not multi-threaded/multi-core

Question

In R 3.0.2 on Linux 3.12.0, I am using the system() function to execute a number of tasks. The desired effect is for each of these tasks to run as they would i

Answer 1

I tested running:

system("dd if=/dev/urandom bs=32k count=2000 | bzip2 -9 >> /dev/null", ignore.stdout=TRUE,ignore.stderr=TRUE,wait=FALSE)
system("dd if=/dev/urandom bs=32k count=2000 | bzip2 -9 >> /dev/null", ignore.stdout=TRUE,ignore.stderr=TRUE,wait=FALSE)
system("dd if=/dev/urandom bs=32k count=2000 | bzip2 -9 >> /dev/null", ignore.stdout=TRUE,ignore.stderr=TRUE,wait=FALSE)
system("dd if=/dev/urandom bs=32k count=2000 | bzip2 -9 >> /dev/null", ignore.stdout=TRUE,ignore.stderr=TRUE,wait=FALSE)

on Linux 2.6.32 with R 3.0.2 and on Linux 3.8.0 with R 2.15.2. In both cases it takes up 4 CPU cores (as you would expect).

-- Edit --

I installed Linux 3.12 on a Virtual Box machine, and here R 3.0.2 also does what I expect: Takes up 4 CPUs. It even slowly wanders between the CPUs - so each process does not stick to the same CPU but changes every second or so.

This leads me to believe your system as some local modifications that forces R to use only one CPU.

From your description I would guess the local modifications are in R and not system wide (since your Python has no problems spawning more processes).

The modifications could be on your user alone, so create a new user and try with that. If it works for the new user, we need to figure out what your userid has installed.

If it does not work for the new user, it could be globally installed R libraries that causes the problem. Install an older R version and try that out. If the older version works, your R 3.0.2 installation is probably broken. Remove it and re-install it.