Added --pick-devices command line arg

-supply --pick-devices followed by a series of integers indicating
which gpu devices are to be used by the simulation

e.g. "python run_script.py j 1 1 -n --pick-devices 0 2 3" will use
devices 0 2 3.
Small fixes for bootstrap.py

*read_bootstrap_file is now more defensive, checks that the file
actually contains at least one properly formatted bootstrap summary

*can now supply either an opened file to read or a string
Removed junk from merge