Updates to vmbox and bootstrap

(1) Updated the VM box.  With the latest virtual box (4.31.4) the old
vm box does not work.  Finding a VM box that works with chef proved time
consuming.
So updated to a VM box without chef and commented out the chef script
(2) Pip now needs to be updated.  But the new pip could have some
issues. So there are some workarounds for that in the script.
(3) The database is now created with updated options.