monitor.py

It is a Python wrapper to system command calls that recursively checks memory usage at specified intervals (default every 1 second) and report the peak usage at the end of execution:

$ ./monitor.py R --slave -e "x = runif(1E2)"

time elapsed: 0.40s
peak first occurred: 0.29s
peak last occurred: 0.29s
max vms_memory: 0.33GB
max rss_memory: 0.05GB
memory check interval: 0.1s
return code: 0

$ ./monitor.py R --slave -e "x = runif(1E4)"

time elapsed: 0.42s
peak first occurred: 0.31s
peak last occurred: 0.31s
max vms_memory: 0.34GB
max rss_memory: 0.05GB
memory check interval: 0.1s
return code: 0

$ ./monitor.py R --slave -e "x = runif(1E8)"

time elapsed: 4.42s
peak first occurred: 0.45s
peak last occurred: 4.32s
max vms_memory: 1.27GB
max rss_memory: 0.91GB
memory check interval: 0.1s
return code: 0

$ ./monitor.py R --slave -e "x = runif(1E9)"

time elapsed: 39.09s
peak first occurred: 0.45s
peak last occurred: 38.68s
max vms_memory: 8.98GB
max rss_memory: 8.61GB
memory check interval: 0.1s
return code: 0

The check interval can be changed via:

$ export MEM_CHECK_INTERVAL=2
$ ./monitor.py R --slave -e "x = runif(1E9)"

time elapsed: 40.21s
peak first occurred: 2.05s
peak last occurred: 39.15s
max vms_memory: 8.98GB
max rss_memory: 8.61GB
memory check interval: 2.0s
return code: 0

To use on Uchicago RCC, you need to module load python/3.5.2. If the test command above does not work with error message psutil not found you then need to install that module:

pip install --user psutil

Overhead

The time it takes to run a command directly from shell is:

$ time R --slave -e "x = runif(1E9)"

real	0m38.996s
user	0m35.692s
sys	0m3.236s

which is 38.99s compared to the elapsed 39.09s when memory check is performed at every 0.1s interval. So the overhead of this program should be minimal.